From 0d10e57527651802d65b013e7bb7d37a74f6fe22 Mon Sep 17 00:00:00 2001 From: Stephen-Armstrong <58577114+Stephen-Armstrong@users.noreply.github.com> Date: Tue, 19 Jan 2021 19:30:24 -0600 Subject: [PATCH 01/14] Created a class to generate a Mesh2D This file creates a Mesh2D set of triangles. Converts more familiar user inputs to the specific type of inputs needed for RustBCA --- scripts/create_mesh2D.py | 254 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 254 insertions(+) create mode 100644 scripts/create_mesh2D.py diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py new file mode 100644 index 0000000..0f4b4d0 --- /dev/null +++ b/scripts/create_mesh2D.py @@ -0,0 +1,254 @@ +''' +Created on Jan 16, 2021 + +@author: Stephen +''' +import math +import numpy as np +import matplotlib.pyplot as plt +import matplotlib.tri +import scipy.spatial +import random +from shapely.geometry import Point +from shapely.geometry.polygon import Polygon +import string + +np.set_printoptions(formatter={'float': lambda x: "{0:0.10f}".format(x)}) + +class Mesh(): + """ + This is the class that contains all the stuff to create a mesh for RustBCA. currently the only default shapes are N-point polygons and random points within the simulation boundaries + """ + def __init__(self, length_unit, xmax, xmin, ymax, ymin, energy_barrier_thickness=1.7645653881793786e-4): + """ + The init functions requires the length units, x limits and y limits of the simulation. + The x and y limits are assumed to be on the points of a square. + """ + + self.trianglelist = [] + + if not type(xmax) == int: + print("xmax should be a int") + assert type(xmax) == int + if not type(xmin) == int: + print("xmin should be a int") + assert type(xmin) == int + if not type(ymax) == int: + print("ymax should be a int") + assert type(ymax) == int + if not type(ymin) == int: + print("ymin should be a int") + assert type(ymin) == int + + + self.Simulation_boundaries = [[xmax, ymax], [xmax, ymin], [xmin, ymax], [xmin, ymin]] + self.points = [] + self.shapes = [] + self.xmax, self.xmin, self.ymax, self.ymin = xmax, xmin, ymax,ymin + if not type(length_unit) == str: + print("length_units should be a string") + assert type(length_unit) == str + self.length_unit = length_unit + self.electronic_stopping_corrections = [] + self.energy_barrier_thickness = energy_barrier_thickness + + def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0.0, theta_offset = 0.0): + """ + This creates a polygon with n-points. + The x and y offset determine the center point + theta_offset is in radians + + easy shape examples: + circle: N_gon(5,100,1) + square: N_gon(2, 4, 2) + offset square: N_gon(5, 4, 2, 1, 1, np.pi/4) + """ + + n_points -= 0 + dtheta = np.pi*2/n_points + + temp_points = [] + for i in range(n_points): + temp_points.append( + Point(x_offset + radius*math.cos(dtheta*i + theta_offset), y_offset + radius*math.sin(dtheta*i + theta_offset)) + ) + + #print(temp_points) + poly = Polygon(temp_points) + #print(poly) + center = Point(x_offset,y_offset) + #print(zero.within(poly)) + #print(poly.covers(zero)) + if center.within(poly): + temp_points.append(center) + #poly = Polygon(temp_points) + #print(zero.within(poly)) + + self.points += temp_points + #temp_points = np.asarray(temp_points) + + self.shapes.append([poly, number_densities]) + + return True + + def add_Uniform_random(self, n_points): + """ + Adds uniformly random points to break up the triangles into fairly random triangles. + **Note** + Will cause some shapes to have parts of them be labeled the incorrect number density. + """ + temp_points = [] + for i in range(n_points): + temp_points.append( + Point(random.uniform(self.xmin, self.xmax), random.uniform(self.ymin, self.ymax)) + ) + #self.shapes.append(Polygon(temp_points)) + self.points += temp_points + return True + + def get_Points(self): + """ + Deprecated - Don't use + returns all of the individual points in the simulation. + """ + temp = [] + for point in self.points: + temp.append([point.x,point.y]) + + return np.asarray(temp) + + def generate_Triangles(self): + """ + Generates triangles via the Delauny method: + see scipy.spatial.Delaunay + """ + return scipy.spatial.Delaunay(self.get_Points()) + + def return_Triangles(self): + """ + Creates and Correlates the triangles to their number densities. + """ + points = self.get_Points() + tri = self.generate_Triangles() + + point_output = [] + triangles = [] + + for i in range(len(tri.simplices)): + point_output.append([points[tri.simplices[i,0], 0], points[tri.simplices[i,1], 0], points[tri.simplices[i,2], 0], points[tri.simplices[i,0], 1], points[tri.simplices[i,1], 1], points[tri.simplices[i,2], 1]]) + triangles.append(Polygon([points[tri.simplices[i,0]], points[tri.simplices[i,1]], points[tri.simplices[i,2]]])) + + #print("Length of tri.simplices " + str(len(tri.simplices))) + #print("Length of triangles " + str(len(triangles))) + + temp_material_densities = [0]*(len(triangles)) + self.electronic_stopping_corrections = [1.0]*(len(triangles)) + #print("Len of triangles " + str(len(triangles))) + for i, triangle in enumerate(triangles): + for shape, number_densities in self.shapes: + if shape.contains(triangle): + temp_material_densities[i] = number_densities + + #print(point_output) + return point_output, temp_material_densities + + def print_Triangles(self): + """ + Use only as a check with number densities as integers from 0 to 3 + Plots the triangles with their colors based on their number densities + Number densities should be integers currently + """ + triangle_list, material_densities = self.return_Triangles() + + #print(len(triangle_list)) + + #print(len(material_densities)) + + self.color_dict = {0:"b", 1:"g", 2:"r", 3:"c", 4:"m"} + + triangles = [] + for t in triangle_list: + triangles.append( + matplotlib.tri.Triangulation(t[0:3], t[3:6]) + ) + + #print(len(triangles)) + #print(type(triangles[0])) + + #plt.triplot(points[:,0], points[:,1], tri.simplices) + plt.xlim(self.Simulation_boundaries[1][0], self.Simulation_boundaries[-1][0]) + plt.ylim(self.Simulation_boundaries[0:2][1]) + for i, triangle in enumerate(triangles): + plt.triplot(triangle, self.color_dict[material_densities[i]]+ "-", ) + plt.show() + return True + def write_to_file(self): + triangle_list, material_densities = self.return_Triangles() + Simulation_Boundaries = self.Simulation_boundaries + + material_boundary_points = [] + for shape, _ in self.shapes: + material_boundary_points += shape.exterior.coords + for i, point in reversed(list(enumerate(material_boundary_points))): + for shape, _ in self.shapes: + pointPoint = Point(point) + if pointPoint.within(shape): + material_boundary_points.pop(i) + + import itertools + material_boundary_points.sort() + material_boundary_points = list(material_boundary_points for material_boundary_points,_ in itertools.groupby(material_boundary_points)) + #print(len(material_boundary_points)) + + electronic_stopping_correction_factors = self.electronic_stopping_corrections + + file = open("Mesh2D.toml", "w") + file.seek(0) + + temp_dict = { + "[mesh_2d_input]" : { + "length_unit":self.length_unit, + "energy_barrier_thickness": self.energy_barrier_thickness, + "triangles": triangle_list, + "densities":material_densities, + "material_boundary_points":material_boundary_points, + "simulation_boundary_points":Simulation_Boundaries, + "electronic_stopping_correction_factors":electronic_stopping_correction_factors + } + } + + import toml + toml.dump(temp_dict, file) + + print(type(triangle_list)) + + return True +if __name__ == "__main__": + '''triangles = [ [ 0.0, 0.0, 0.0012558103905862675, 0.0, 0.02, 0.019960534568565433], [ 0.0, 0.0012558103905862675, 0.0025066646712860853, 0.0, 0.019960534568565433, 0.019842294026289557], [ 0.0, 0.0025066646712860853, 0.003747626291714493, 0.0, 0.019842294026289557, 0.019645745014573775], [ 0.0, 0.003747626291714493, 0.004973797743297096, 0.0, 0.019645745014573775, 0.01937166322257262], [ 0.0, 0.004973797743297096, 0.0061803398874989484, 0.0, 0.01937166322257262, 0.019021130325903073], [ 0.0, 0.0061803398874989484, 0.00736249105369356, 0.0, 0.019021130325903073, 0.018595529717765027], [ 0.0, 0.00736249105369356, 0.008515585831301454, 0.0, 0.018595529717765027, 0.01809654104932039], [ 0.0, 0.008515585831301454, 0.009635073482034308, 0.0, 0.01809654104932039, 0.01752613360087727], [ 0.0, 0.009635073482034308, 0.010716535899579934, 0.0, 0.01752613360087727, 0.0168865585100403], [ 0.0, 0.010716535899579934, 0.011755705045849463, 0.0, 0.0168865585100403, 0.016180339887498948], [ 0.0, 0.011755705045849463, 0.012748479794973795, 0.0, 0.016180339887498948, 0.015410264855515783], [ 0.0, 0.012748479794973795, 0.013690942118573775, 0.0, 0.015410264855515783, 0.014579372548428232], [ 0.0, 0.013690942118573775, 0.014579372548428232, 0.0, 0.014579372548428232, 0.013690942118573773], [ 0.0, 0.014579372548428232, 0.015410264855515785, 0.0, 0.013690942118573773, 0.012748479794973793], [ 0.0, 0.015410264855515785, 0.016180339887498948, 0.0, 0.012748479794973793, 0.011755705045849461], [ 0.0, 0.016180339887498948, 0.0168865585100403, 0.0, 0.011755705045849461, 0.01071653589957993], [ 0.0, 0.0168865585100403, 0.017526133600877274, 0.0, 0.01071653589957993, 0.009635073482034304], [ 0.0, 0.017526133600877274, 0.018096541049320392, 0.0, 0.009635073482034304, 0.008515585831301454], [ 0.0, 0.018096541049320392, 0.01859552971776503, 0.0, 0.008515585831301454, 0.007362491053693557], [ 0.0, 0.01859552971776503, 0.019021130325903073, 0.0, 0.007362491053693557, 0.006180339887498949], [ 0.0, 0.019021130325903073, 0.01937166322257262, 0.0, 0.006180339887498949, 0.004973797743297095], [ 0.0, 0.01937166322257262, 0.019645745014573775, 0.0, 0.004973797743297095, 0.0037476262917144902], [ 0.0, 0.019645745014573775, 0.019842294026289557, 0.0, 0.0037476262917144902, 0.0025066646712860853], [ 0.0, 0.019842294026289557, 0.019960534568565433, 0.0, 0.0025066646712860853, 0.001255810390586266], [ 0.0, 0.019960534568565433, 0.02, 0.0, 0.001255810390586266, -3.2162452993532734e-18], [ 0.0, 0.02, 0.019960534568565433, 0.0, -3.2162452993532734e-18, -0.001255810390586268], [ 0.0, 0.019960534568565433, 0.019842294026289557, 0.0, -0.001255810390586268, -0.0025066646712860875], [ 0.0, 0.019842294026289557, 0.019645745014573772, 0.0, -0.0025066646712860875, -0.0037476262917144967], [ 0.0, 0.019645745014573772, 0.01937166322257262, 0.0, -0.0037476262917144967, -0.004973797743297097], [ 0.0, 0.01937166322257262, 0.019021130325903073, 0.0, -0.004973797743297097, -0.006180339887498951], [ 0.0, 0.019021130325903073, 0.01859552971776503, 0.0, -0.006180339887498951, -0.00736249105369356], [ 0.0, 0.01859552971776503, 0.01809654104932039, 0.0, -0.00736249105369356, -0.008515585831301454], [ 0.0, 0.01809654104932039, 0.01752613360087727, 0.0, -0.008515585831301454, -0.00963507348203431], [ 0.0, 0.01752613360087727, 0.0168865585100403, 0.0, -0.00963507348203431, -0.010716535899579938], [ 0.0, 0.0168865585100403, 0.016180339887498948, 0.0, -0.010716535899579938, -0.011755705045849461], [ 0.0, 0.016180339887498948, 0.015410264855515785, 0.0, -0.011755705045849461, -0.012748479794973795], [ 0.0, 0.015410264855515785, 0.014579372548428228, 0.0, -0.012748479794973795, -0.013690942118573775], [ 0.0, 0.014579372548428228, 0.01369094211857377, 0.0, -0.013690942118573775, -0.014579372548428234], [ 0.0, 0.01369094211857377, 0.01274847979497379, 0.0, -0.014579372548428234, -0.015410264855515788], [ 0.0, 0.01274847979497379, 0.011755705045849465, 0.0, -0.015410264855515788, -0.016180339887498948], [ 0.0, 0.011755705045849465, 0.010716535899579934, 0.0, -0.016180339887498948, -0.0168865585100403], [ 0.0, 0.010716535899579934, 0.009635073482034304, 0.0, -0.0168865585100403, -0.01752613360087727], [ 0.0, 0.009635073482034304, 0.00851558583130145, 0.0, -0.01752613360087727, -0.018096541049320392], [ 0.0, 0.00851558583130145, 0.007362491053693555, 0.0, -0.018096541049320392, -0.01859552971776503], [ 0.0, 0.007362491053693555, 0.006180339887498942, 0.0, -0.01859552971776503, -0.019021130325903073], [ 0.0, 0.006180339887498942, 0.004973797743297097, 0.0, -0.019021130325903073, -0.01937166322257262], [ 0.0, 0.004973797743297097, 0.0037476262917144915, 0.0, -0.01937166322257262, -0.019645745014573775], [ 0.0, 0.0037476262917144915, 0.002506664671286082, 0.0, -0.019645745014573775, -0.019842294026289557], [ 0.0, 0.002506664671286082, 0.0012558103905862628, 0.0, -0.019842294026289557, -0.019960534568565433], [ 0.0, 0.0012558103905862628, -6.432490598706547e-18, 0.0, -0.019960534568565433, -0.02], [ 0.0, -6.432490598706547e-18, -0.0012558103905862669, 0.0, -0.02, -0.019960534568565433], [ 0.0, -0.0012558103905862669, -0.0025066646712860858, 0.0, -0.019960534568565433, -0.019842294026289557], [ 0.0, -0.0025066646712860858, -0.0037476262917144954, 0.0, -0.019842294026289557, -0.019645745014573772], [ 0.0, -0.0037476262917144954, -0.0049737977432971, 0.0, -0.019645745014573772, -0.01937166322257262], [ 0.0, -0.0049737977432971, -0.0061803398874989545, 0.0, -0.01937166322257262, -0.019021130325903073], [ 0.0, -0.0061803398874989545, -0.007362491053693567, 0.0, -0.019021130325903073, -0.018595529717765024], [ 0.0, -0.007362491053693567, -0.008515585831301454, 0.0, -0.018595529717765024, -0.01809654104932039], [ 0.0, -0.008515585831301454, -0.009635073482034308, 0.0, -0.01809654104932039, -0.01752613360087727], [ 0.0, -0.009635073482034308, -0.010716535899579936, 0.0, -0.01752613360087727, -0.0168865585100403], [ 0.0, -0.010716535899579936, -0.011755705045849468, 0.0, -0.0168865585100403, -0.016180339887498944], [ 0.0, -0.011755705045849468, -0.0127484797949738, 0.0, -0.016180339887498944, -0.015410264855515781], [ 0.0, -0.0127484797949738, -0.013690942118573775, 0.0, -0.015410264855515781, -0.014579372548428232], [ 0.0, -0.013690942118573775, -0.014579372548428232, 0.0, -0.014579372548428232, -0.013690942118573773], [ 0.0, -0.014579372548428232, -0.015410264855515788, 0.0, -0.013690942118573773, -0.01274847979497379], [ 0.0, -0.015410264855515788, -0.016180339887498948, 0.0, -0.01274847979497379, -0.011755705045849465], [ 0.0, -0.016180339887498948, -0.016886558510040308, 0.0, -0.011755705045849465, -0.010716535899579927], [ 0.0, -0.016886558510040308, -0.01752613360087727, 0.0, -0.010716535899579927, -0.009635073482034306], [ 0.0, -0.01752613360087727, -0.018096541049320396, 0.0, -0.009635073482034306, -0.008515585831301443], [ 0.0, -0.018096541049320396, -0.01859552971776503, 0.0, -0.008515585831301443, -0.007362491053693556], [ 0.0, -0.01859552971776503, -0.019021130325903073, 0.0, -0.007362491053693556, -0.006180339887498951], [ 0.0, -0.019021130325903073, -0.019371663222572624, 0.0, -0.006180339887498951, -0.004973797743297089], [ 0.0, -0.019371663222572624, -0.019645745014573775, 0.0, -0.004973797743297089, -0.003747626291714493], [ 0.0, -0.019645745014573775, -0.019842294026289557, 0.0, -0.003747626291714493, -0.0025066646712860745], [ 0.0, -0.019842294026289557, -0.019960534568565433, 0.0, -0.0025066646712860745, -0.001255810390586264], [ 0.0, -0.019960534568565433, -0.02, 0.0, -0.001255810390586264, -3.673940397442059e-18], [ 0.0, -0.02, -0.019960534568565433, 0.0, -3.673940397442059e-18, 0.0012558103905862745], [ 0.0, -0.019960534568565433, -0.019842294026289557, 0.0, 0.0012558103905862745, 0.0025066646712860845], [ 0.0, -0.019842294026289557, -0.019645745014573772, 0.0, 0.0025066646712860845, 0.003747626291714503], [ 0.0, -0.019645745014573772, -0.01937166322257262, 0.0, 0.003747626291714503, 0.004973797743297099], [ 0.0, -0.01937166322257262, -0.019021130325903073, 0.0, 0.004973797743297099, 0.006180339887498945], [ 0.0, -0.019021130325903073, -0.018595529717765024, 0.0, 0.006180339887498945, 0.007362491053693565], [ 0.0, -0.018595529717765024, -0.018096541049320392, 0.0, 0.007362491053693565, 0.008515585831301452], [ 0.0, -0.018096541049320392, -0.017526133600877267, 0.0, 0.008515585831301452, 0.009635073482034314], [ 0.0, -0.017526133600877267, -0.0168865585100403, 0.0, 0.009635073482034314, 0.010716535899579936], [ 0.0, -0.0168865585100403, -0.01618033988749894, 0.0, 0.010716535899579936, 0.011755705045849473], [ 0.0, -0.01618033988749894, -0.015410264855515781, 0.0, 0.011755705045849473, 0.0127484797949738], [ 0.0, -0.015410264855515781, -0.014579372548428232, 0.0, 0.0127484797949738, 0.013690942118573773], [ 0.0, -0.014579372548428232, -0.013690942118573766, 0.0, 0.013690942118573773, 0.014579372548428239], [ 0.0, -0.013690942118573766, -0.012748479794973793, 0.0, 0.014579372548428239, 0.015410264855515788], [ 0.0, -0.012748479794973793, -0.011755705045849453, 0.0, 0.015410264855515788, 0.016180339887498955], [ 0.0, -0.011755705045849453, -0.010716535899579927, 0.0, 0.016180339887498955, 0.016886558510040305], [ 0.0, -0.010716535899579927, -0.009635073482034308, 0.0, 0.016886558510040305, 0.01752613360087727], [ 0.0, -0.009635073482034308, -0.008515585831301445, 0.0, 0.01752613360087727, 0.018096541049320396], [ 0.0, -0.008515585831301445, -0.007362491053693557, 0.0, 0.018096541049320396, 0.01859552971776503], [ 0.0, -0.007362491053693557, -0.006180339887498935, 0.0, 0.01859552971776503, 0.019021130325903076], [ 0.0, -0.006180339887498935, -0.00497379774329709, 0.0, 0.019021130325903076, 0.019371663222572624], [ 0.0, -0.00497379774329709, -0.0037476262917144937, 0.0, 0.019371663222572624, 0.019645745014573775], [ 0.0, -0.0037476262917144937, -0.002506664671286076, 0.0, 0.019645745014573775, 0.019842294026289557], [ 0.0, -0.002506664671286076, -0.0012558103905862654, 0.0, 0.019842294026289557, 0.019960534568565433], [ 0.0, -0.0012558103905862654, -4.898587196589413e-18, 0.0, 0.019960534568565433, 0.02]] + triangles = np.asarray(triangles) + print(np.shape(triangles)) + + points = [] + + for i in range(len(triangles)): + points.append([triangles[i,0], triangles[i,3]]) + points.append([triangles[i,1], triangles[i,4]]) + points.append([triangles[i,2], triangles[i,5]]) + + + import itertools + points.sort() + points = list(points for points,_ in itertools.groupby(points)) + + points = np.asarray(points) + print(np.shape(points)) + plt.triplot(points[:,0], points[:,1]) + plt.show()''' + + mesh = Mesh("MICRON", 10,-10,10,-10) + + mesh.N_gon(5,100, [ 6.5E+10, 6.5E+10,]) + #mesh.N_gon(1.5, 4, 2, 5, 0, np.pi/4) + #mesh.add_Uniform_random(10) + #mesh.print_Triangles() + mesh.write_to_file() \ No newline at end of file From 0efcdfb238c01725ff173499ab1cf36f91a1b3db Mon Sep 17 00:00:00 2001 From: zerostarm Date: Tue, 19 Jan 2021 21:59:07 -0600 Subject: [PATCH 02/14] Update to create_mesh2D removed extraneous imports, made changing the number of floats displayed for numpy arrays easier --- scripts/Mesh2D.toml | 0 scripts/create_mesh2D.py | 16 ++++++++++------ 2 files changed, 10 insertions(+), 6 deletions(-) create mode 100644 scripts/Mesh2D.toml diff --git a/scripts/Mesh2D.toml b/scripts/Mesh2D.toml new file mode 100644 index 0000000..e69de29 diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index 0f4b4d0..bf7012b 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -11,9 +11,12 @@ import random from shapely.geometry import Point from shapely.geometry.polygon import Polygon -import string -np.set_printoptions(formatter={'float': lambda x: "{0:0.10f}".format(x)}) + +number_of_decimals = "10" +np.set_printoptions(formatter={'float': lambda x: "{0:0." + number_of_decimals + "f}".format(x)}) + +test_dump = False class Mesh(): """ @@ -217,12 +220,13 @@ def write_to_file(self): } } - import toml - toml.dump(temp_dict, file) + if test_dump: + import toml + toml.dump(temp_dict, file) - print(type(triangle_list)) + #print(type(triangle_list)) - return True + return temp_dict if __name__ == "__main__": '''triangles = [ [ 0.0, 0.0, 0.0012558103905862675, 0.0, 0.02, 0.019960534568565433], [ 0.0, 0.0012558103905862675, 0.0025066646712860853, 0.0, 0.019960534568565433, 0.019842294026289557], [ 0.0, 0.0025066646712860853, 0.003747626291714493, 0.0, 0.019842294026289557, 0.019645745014573775], [ 0.0, 0.003747626291714493, 0.004973797743297096, 0.0, 0.019645745014573775, 0.01937166322257262], [ 0.0, 0.004973797743297096, 0.0061803398874989484, 0.0, 0.01937166322257262, 0.019021130325903073], [ 0.0, 0.0061803398874989484, 0.00736249105369356, 0.0, 0.019021130325903073, 0.018595529717765027], [ 0.0, 0.00736249105369356, 0.008515585831301454, 0.0, 0.018595529717765027, 0.01809654104932039], [ 0.0, 0.008515585831301454, 0.009635073482034308, 0.0, 0.01809654104932039, 0.01752613360087727], [ 0.0, 0.009635073482034308, 0.010716535899579934, 0.0, 0.01752613360087727, 0.0168865585100403], [ 0.0, 0.010716535899579934, 0.011755705045849463, 0.0, 0.0168865585100403, 0.016180339887498948], [ 0.0, 0.011755705045849463, 0.012748479794973795, 0.0, 0.016180339887498948, 0.015410264855515783], [ 0.0, 0.012748479794973795, 0.013690942118573775, 0.0, 0.015410264855515783, 0.014579372548428232], [ 0.0, 0.013690942118573775, 0.014579372548428232, 0.0, 0.014579372548428232, 0.013690942118573773], [ 0.0, 0.014579372548428232, 0.015410264855515785, 0.0, 0.013690942118573773, 0.012748479794973793], [ 0.0, 0.015410264855515785, 0.016180339887498948, 0.0, 0.012748479794973793, 0.011755705045849461], [ 0.0, 0.016180339887498948, 0.0168865585100403, 0.0, 0.011755705045849461, 0.01071653589957993], [ 0.0, 0.0168865585100403, 0.017526133600877274, 0.0, 0.01071653589957993, 0.009635073482034304], [ 0.0, 0.017526133600877274, 0.018096541049320392, 0.0, 0.009635073482034304, 0.008515585831301454], [ 0.0, 0.018096541049320392, 0.01859552971776503, 0.0, 0.008515585831301454, 0.007362491053693557], [ 0.0, 0.01859552971776503, 0.019021130325903073, 0.0, 0.007362491053693557, 0.006180339887498949], [ 0.0, 0.019021130325903073, 0.01937166322257262, 0.0, 0.006180339887498949, 0.004973797743297095], [ 0.0, 0.01937166322257262, 0.019645745014573775, 0.0, 0.004973797743297095, 0.0037476262917144902], [ 0.0, 0.019645745014573775, 0.019842294026289557, 0.0, 0.0037476262917144902, 0.0025066646712860853], [ 0.0, 0.019842294026289557, 0.019960534568565433, 0.0, 0.0025066646712860853, 0.001255810390586266], [ 0.0, 0.019960534568565433, 0.02, 0.0, 0.001255810390586266, -3.2162452993532734e-18], [ 0.0, 0.02, 0.019960534568565433, 0.0, -3.2162452993532734e-18, -0.001255810390586268], [ 0.0, 0.019960534568565433, 0.019842294026289557, 0.0, -0.001255810390586268, -0.0025066646712860875], [ 0.0, 0.019842294026289557, 0.019645745014573772, 0.0, -0.0025066646712860875, -0.0037476262917144967], [ 0.0, 0.019645745014573772, 0.01937166322257262, 0.0, -0.0037476262917144967, -0.004973797743297097], [ 0.0, 0.01937166322257262, 0.019021130325903073, 0.0, -0.004973797743297097, -0.006180339887498951], [ 0.0, 0.019021130325903073, 0.01859552971776503, 0.0, -0.006180339887498951, -0.00736249105369356], [ 0.0, 0.01859552971776503, 0.01809654104932039, 0.0, -0.00736249105369356, -0.008515585831301454], [ 0.0, 0.01809654104932039, 0.01752613360087727, 0.0, -0.008515585831301454, -0.00963507348203431], [ 0.0, 0.01752613360087727, 0.0168865585100403, 0.0, -0.00963507348203431, -0.010716535899579938], [ 0.0, 0.0168865585100403, 0.016180339887498948, 0.0, -0.010716535899579938, -0.011755705045849461], [ 0.0, 0.016180339887498948, 0.015410264855515785, 0.0, -0.011755705045849461, -0.012748479794973795], [ 0.0, 0.015410264855515785, 0.014579372548428228, 0.0, -0.012748479794973795, -0.013690942118573775], [ 0.0, 0.014579372548428228, 0.01369094211857377, 0.0, -0.013690942118573775, -0.014579372548428234], [ 0.0, 0.01369094211857377, 0.01274847979497379, 0.0, -0.014579372548428234, -0.015410264855515788], [ 0.0, 0.01274847979497379, 0.011755705045849465, 0.0, -0.015410264855515788, -0.016180339887498948], [ 0.0, 0.011755705045849465, 0.010716535899579934, 0.0, -0.016180339887498948, -0.0168865585100403], [ 0.0, 0.010716535899579934, 0.009635073482034304, 0.0, -0.0168865585100403, -0.01752613360087727], [ 0.0, 0.009635073482034304, 0.00851558583130145, 0.0, -0.01752613360087727, -0.018096541049320392], [ 0.0, 0.00851558583130145, 0.007362491053693555, 0.0, -0.018096541049320392, -0.01859552971776503], [ 0.0, 0.007362491053693555, 0.006180339887498942, 0.0, -0.01859552971776503, -0.019021130325903073], [ 0.0, 0.006180339887498942, 0.004973797743297097, 0.0, -0.019021130325903073, -0.01937166322257262], [ 0.0, 0.004973797743297097, 0.0037476262917144915, 0.0, -0.01937166322257262, -0.019645745014573775], [ 0.0, 0.0037476262917144915, 0.002506664671286082, 0.0, -0.019645745014573775, -0.019842294026289557], [ 0.0, 0.002506664671286082, 0.0012558103905862628, 0.0, -0.019842294026289557, -0.019960534568565433], [ 0.0, 0.0012558103905862628, -6.432490598706547e-18, 0.0, -0.019960534568565433, -0.02], [ 0.0, -6.432490598706547e-18, -0.0012558103905862669, 0.0, -0.02, -0.019960534568565433], [ 0.0, -0.0012558103905862669, -0.0025066646712860858, 0.0, -0.019960534568565433, -0.019842294026289557], [ 0.0, -0.0025066646712860858, -0.0037476262917144954, 0.0, -0.019842294026289557, -0.019645745014573772], [ 0.0, -0.0037476262917144954, -0.0049737977432971, 0.0, -0.019645745014573772, -0.01937166322257262], [ 0.0, -0.0049737977432971, -0.0061803398874989545, 0.0, -0.01937166322257262, -0.019021130325903073], [ 0.0, -0.0061803398874989545, -0.007362491053693567, 0.0, -0.019021130325903073, -0.018595529717765024], [ 0.0, -0.007362491053693567, -0.008515585831301454, 0.0, -0.018595529717765024, -0.01809654104932039], [ 0.0, -0.008515585831301454, -0.009635073482034308, 0.0, -0.01809654104932039, -0.01752613360087727], [ 0.0, -0.009635073482034308, -0.010716535899579936, 0.0, -0.01752613360087727, -0.0168865585100403], [ 0.0, -0.010716535899579936, -0.011755705045849468, 0.0, -0.0168865585100403, -0.016180339887498944], [ 0.0, -0.011755705045849468, -0.0127484797949738, 0.0, -0.016180339887498944, -0.015410264855515781], [ 0.0, -0.0127484797949738, -0.013690942118573775, 0.0, -0.015410264855515781, -0.014579372548428232], [ 0.0, -0.013690942118573775, -0.014579372548428232, 0.0, -0.014579372548428232, -0.013690942118573773], [ 0.0, -0.014579372548428232, -0.015410264855515788, 0.0, -0.013690942118573773, -0.01274847979497379], [ 0.0, -0.015410264855515788, -0.016180339887498948, 0.0, -0.01274847979497379, -0.011755705045849465], [ 0.0, -0.016180339887498948, -0.016886558510040308, 0.0, -0.011755705045849465, -0.010716535899579927], [ 0.0, -0.016886558510040308, -0.01752613360087727, 0.0, -0.010716535899579927, -0.009635073482034306], [ 0.0, -0.01752613360087727, -0.018096541049320396, 0.0, -0.009635073482034306, -0.008515585831301443], [ 0.0, -0.018096541049320396, -0.01859552971776503, 0.0, -0.008515585831301443, -0.007362491053693556], [ 0.0, -0.01859552971776503, -0.019021130325903073, 0.0, -0.007362491053693556, -0.006180339887498951], [ 0.0, -0.019021130325903073, -0.019371663222572624, 0.0, -0.006180339887498951, -0.004973797743297089], [ 0.0, -0.019371663222572624, -0.019645745014573775, 0.0, -0.004973797743297089, -0.003747626291714493], [ 0.0, -0.019645745014573775, -0.019842294026289557, 0.0, -0.003747626291714493, -0.0025066646712860745], [ 0.0, -0.019842294026289557, -0.019960534568565433, 0.0, -0.0025066646712860745, -0.001255810390586264], [ 0.0, -0.019960534568565433, -0.02, 0.0, -0.001255810390586264, -3.673940397442059e-18], [ 0.0, -0.02, -0.019960534568565433, 0.0, -3.673940397442059e-18, 0.0012558103905862745], [ 0.0, -0.019960534568565433, -0.019842294026289557, 0.0, 0.0012558103905862745, 0.0025066646712860845], [ 0.0, -0.019842294026289557, -0.019645745014573772, 0.0, 0.0025066646712860845, 0.003747626291714503], [ 0.0, -0.019645745014573772, -0.01937166322257262, 0.0, 0.003747626291714503, 0.004973797743297099], [ 0.0, -0.01937166322257262, -0.019021130325903073, 0.0, 0.004973797743297099, 0.006180339887498945], [ 0.0, -0.019021130325903073, -0.018595529717765024, 0.0, 0.006180339887498945, 0.007362491053693565], [ 0.0, -0.018595529717765024, -0.018096541049320392, 0.0, 0.007362491053693565, 0.008515585831301452], [ 0.0, -0.018096541049320392, -0.017526133600877267, 0.0, 0.008515585831301452, 0.009635073482034314], [ 0.0, -0.017526133600877267, -0.0168865585100403, 0.0, 0.009635073482034314, 0.010716535899579936], [ 0.0, -0.0168865585100403, -0.01618033988749894, 0.0, 0.010716535899579936, 0.011755705045849473], [ 0.0, -0.01618033988749894, -0.015410264855515781, 0.0, 0.011755705045849473, 0.0127484797949738], [ 0.0, -0.015410264855515781, -0.014579372548428232, 0.0, 0.0127484797949738, 0.013690942118573773], [ 0.0, -0.014579372548428232, -0.013690942118573766, 0.0, 0.013690942118573773, 0.014579372548428239], [ 0.0, -0.013690942118573766, -0.012748479794973793, 0.0, 0.014579372548428239, 0.015410264855515788], [ 0.0, -0.012748479794973793, -0.011755705045849453, 0.0, 0.015410264855515788, 0.016180339887498955], [ 0.0, -0.011755705045849453, -0.010716535899579927, 0.0, 0.016180339887498955, 0.016886558510040305], [ 0.0, -0.010716535899579927, -0.009635073482034308, 0.0, 0.016886558510040305, 0.01752613360087727], [ 0.0, -0.009635073482034308, -0.008515585831301445, 0.0, 0.01752613360087727, 0.018096541049320396], [ 0.0, -0.008515585831301445, -0.007362491053693557, 0.0, 0.018096541049320396, 0.01859552971776503], [ 0.0, -0.007362491053693557, -0.006180339887498935, 0.0, 0.01859552971776503, 0.019021130325903076], [ 0.0, -0.006180339887498935, -0.00497379774329709, 0.0, 0.019021130325903076, 0.019371663222572624], [ 0.0, -0.00497379774329709, -0.0037476262917144937, 0.0, 0.019371663222572624, 0.019645745014573775], [ 0.0, -0.0037476262917144937, -0.002506664671286076, 0.0, 0.019645745014573775, 0.019842294026289557], [ 0.0, -0.002506664671286076, -0.0012558103905862654, 0.0, 0.019842294026289557, 0.019960534568565433], [ 0.0, -0.0012558103905862654, -4.898587196589413e-18, 0.0, 0.019960534568565433, 0.02]] triangles = np.asarray(triangles) From cfca5e85b50e4a6e2af85349c15f4343ad6d730d Mon Sep 17 00:00:00 2001 From: Stephen Date: Wed, 20 Jan 2021 14:06:00 -0600 Subject: [PATCH 03/14] Update create_mesh2D moved the commented out test code for seeing the example triangles to the bottom and wrote a description for it. Added what is returned to each of the function descriptions --- scripts/create_mesh2D.py | 42 ++++++++++++++++++++++++++-------------- 1 file changed, 28 insertions(+), 14 deletions(-) diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index bf7012b..d4d8532 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -16,7 +16,6 @@ number_of_decimals = "10" np.set_printoptions(formatter={'float': lambda x: "{0:0." + number_of_decimals + "f}".format(x)}) -test_dump = False class Mesh(): """ @@ -24,6 +23,7 @@ class Mesh(): """ def __init__(self, length_unit, xmax, xmin, ymax, ymin, energy_barrier_thickness=1.7645653881793786e-4): """ + returns none. The init functions requires the length units, x limits and y limits of the simulation. The x and y limits are assumed to be on the points of a square. """ @@ -57,6 +57,7 @@ def __init__(self, length_unit, xmax, xmin, ymax, ymin, energy_barrier_thickness def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0.0, theta_offset = 0.0): """ + returns true on completion This creates a polygon with n-points. The x and y offset determine the center point theta_offset is in radians @@ -96,12 +97,13 @@ def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0 def add_Uniform_random(self, n_points): """ + returns True on completion. Adds uniformly random points to break up the triangles into fairly random triangles. **Note** Will cause some shapes to have parts of them be labeled the incorrect number density. """ temp_points = [] - for i in range(n_points): + for _ in range(n_points): temp_points.append( Point(random.uniform(self.xmin, self.xmax), random.uniform(self.ymin, self.ymax)) ) @@ -112,7 +114,7 @@ def add_Uniform_random(self, n_points): def get_Points(self): """ Deprecated - Don't use - returns all of the individual points in the simulation. + returns all of the individual points in the simulation as a np array """ temp = [] for point in self.points: @@ -122,6 +124,7 @@ def get_Points(self): def generate_Triangles(self): """ + returns a scipy.spatial.Delauny object Generates triangles via the Delauny method: see scipy.spatial.Delaunay """ @@ -129,6 +132,7 @@ def generate_Triangles(self): def return_Triangles(self): """ + returns 2 lists : points, material densities Creates and Correlates the triangles to their number densities. """ points = self.get_Points() @@ -157,6 +161,7 @@ def return_Triangles(self): def print_Triangles(self): """ + returns True on completion Use only as a check with number densities as integers from 0 to 3 Plots the triangles with their colors based on their number densities Number densities should be integers currently @@ -185,7 +190,13 @@ def print_Triangles(self): plt.triplot(triangle, self.color_dict[material_densities[i]]+ "-", ) plt.show() return True - def write_to_file(self): + + def write_to_file(self, dump_to_file = False): + ''' + returns a dictionary. + Turn the required mesh2D stuff into a format that TOML and RustBCA like. + Optional to write to a .toml file instead of returning a dictionary + ''' triangle_list, material_densities = self.return_Triangles() Simulation_Boundaries = self.Simulation_boundaries @@ -220,7 +231,7 @@ def write_to_file(self): } } - if test_dump: + if dump_to_file: import toml toml.dump(temp_dict, file) @@ -228,6 +239,17 @@ def write_to_file(self): return temp_dict if __name__ == "__main__": + + mesh = Mesh("MICRON", 10,-10,10,-10) + + mesh.N_gon(5,100, [ 6.5E+10, 6.5E+10,]) + #mesh.N_gon(1.5, 4, 2, 5, 0, np.pi/4) + #mesh.add_Uniform_random(10) + #mesh.print_Triangles() + mesh.write_to_file() + + + #code to plot out the example triangles '''triangles = [ [ 0.0, 0.0, 0.0012558103905862675, 0.0, 0.02, 0.019960534568565433], [ 0.0, 0.0012558103905862675, 0.0025066646712860853, 0.0, 0.019960534568565433, 0.019842294026289557], [ 0.0, 0.0025066646712860853, 0.003747626291714493, 0.0, 0.019842294026289557, 0.019645745014573775], [ 0.0, 0.003747626291714493, 0.004973797743297096, 0.0, 0.019645745014573775, 0.01937166322257262], [ 0.0, 0.004973797743297096, 0.0061803398874989484, 0.0, 0.01937166322257262, 0.019021130325903073], [ 0.0, 0.0061803398874989484, 0.00736249105369356, 0.0, 0.019021130325903073, 0.018595529717765027], [ 0.0, 0.00736249105369356, 0.008515585831301454, 0.0, 0.018595529717765027, 0.01809654104932039], [ 0.0, 0.008515585831301454, 0.009635073482034308, 0.0, 0.01809654104932039, 0.01752613360087727], [ 0.0, 0.009635073482034308, 0.010716535899579934, 0.0, 0.01752613360087727, 0.0168865585100403], [ 0.0, 0.010716535899579934, 0.011755705045849463, 0.0, 0.0168865585100403, 0.016180339887498948], [ 0.0, 0.011755705045849463, 0.012748479794973795, 0.0, 0.016180339887498948, 0.015410264855515783], [ 0.0, 0.012748479794973795, 0.013690942118573775, 0.0, 0.015410264855515783, 0.014579372548428232], [ 0.0, 0.013690942118573775, 0.014579372548428232, 0.0, 0.014579372548428232, 0.013690942118573773], [ 0.0, 0.014579372548428232, 0.015410264855515785, 0.0, 0.013690942118573773, 0.012748479794973793], [ 0.0, 0.015410264855515785, 0.016180339887498948, 0.0, 0.012748479794973793, 0.011755705045849461], [ 0.0, 0.016180339887498948, 0.0168865585100403, 0.0, 0.011755705045849461, 0.01071653589957993], [ 0.0, 0.0168865585100403, 0.017526133600877274, 0.0, 0.01071653589957993, 0.009635073482034304], [ 0.0, 0.017526133600877274, 0.018096541049320392, 0.0, 0.009635073482034304, 0.008515585831301454], [ 0.0, 0.018096541049320392, 0.01859552971776503, 0.0, 0.008515585831301454, 0.007362491053693557], [ 0.0, 0.01859552971776503, 0.019021130325903073, 0.0, 0.007362491053693557, 0.006180339887498949], [ 0.0, 0.019021130325903073, 0.01937166322257262, 0.0, 0.006180339887498949, 0.004973797743297095], [ 0.0, 0.01937166322257262, 0.019645745014573775, 0.0, 0.004973797743297095, 0.0037476262917144902], [ 0.0, 0.019645745014573775, 0.019842294026289557, 0.0, 0.0037476262917144902, 0.0025066646712860853], [ 0.0, 0.019842294026289557, 0.019960534568565433, 0.0, 0.0025066646712860853, 0.001255810390586266], [ 0.0, 0.019960534568565433, 0.02, 0.0, 0.001255810390586266, -3.2162452993532734e-18], [ 0.0, 0.02, 0.019960534568565433, 0.0, -3.2162452993532734e-18, -0.001255810390586268], [ 0.0, 0.019960534568565433, 0.019842294026289557, 0.0, -0.001255810390586268, -0.0025066646712860875], [ 0.0, 0.019842294026289557, 0.019645745014573772, 0.0, -0.0025066646712860875, -0.0037476262917144967], [ 0.0, 0.019645745014573772, 0.01937166322257262, 0.0, -0.0037476262917144967, -0.004973797743297097], [ 0.0, 0.01937166322257262, 0.019021130325903073, 0.0, -0.004973797743297097, -0.006180339887498951], [ 0.0, 0.019021130325903073, 0.01859552971776503, 0.0, -0.006180339887498951, -0.00736249105369356], [ 0.0, 0.01859552971776503, 0.01809654104932039, 0.0, -0.00736249105369356, -0.008515585831301454], [ 0.0, 0.01809654104932039, 0.01752613360087727, 0.0, -0.008515585831301454, -0.00963507348203431], [ 0.0, 0.01752613360087727, 0.0168865585100403, 0.0, -0.00963507348203431, -0.010716535899579938], [ 0.0, 0.0168865585100403, 0.016180339887498948, 0.0, -0.010716535899579938, -0.011755705045849461], [ 0.0, 0.016180339887498948, 0.015410264855515785, 0.0, -0.011755705045849461, -0.012748479794973795], [ 0.0, 0.015410264855515785, 0.014579372548428228, 0.0, -0.012748479794973795, -0.013690942118573775], [ 0.0, 0.014579372548428228, 0.01369094211857377, 0.0, -0.013690942118573775, -0.014579372548428234], [ 0.0, 0.01369094211857377, 0.01274847979497379, 0.0, -0.014579372548428234, -0.015410264855515788], [ 0.0, 0.01274847979497379, 0.011755705045849465, 0.0, -0.015410264855515788, -0.016180339887498948], [ 0.0, 0.011755705045849465, 0.010716535899579934, 0.0, -0.016180339887498948, -0.0168865585100403], [ 0.0, 0.010716535899579934, 0.009635073482034304, 0.0, -0.0168865585100403, -0.01752613360087727], [ 0.0, 0.009635073482034304, 0.00851558583130145, 0.0, -0.01752613360087727, -0.018096541049320392], [ 0.0, 0.00851558583130145, 0.007362491053693555, 0.0, -0.018096541049320392, -0.01859552971776503], [ 0.0, 0.007362491053693555, 0.006180339887498942, 0.0, -0.01859552971776503, -0.019021130325903073], [ 0.0, 0.006180339887498942, 0.004973797743297097, 0.0, -0.019021130325903073, -0.01937166322257262], [ 0.0, 0.004973797743297097, 0.0037476262917144915, 0.0, -0.01937166322257262, -0.019645745014573775], [ 0.0, 0.0037476262917144915, 0.002506664671286082, 0.0, -0.019645745014573775, -0.019842294026289557], [ 0.0, 0.002506664671286082, 0.0012558103905862628, 0.0, -0.019842294026289557, -0.019960534568565433], [ 0.0, 0.0012558103905862628, -6.432490598706547e-18, 0.0, -0.019960534568565433, -0.02], [ 0.0, -6.432490598706547e-18, -0.0012558103905862669, 0.0, -0.02, -0.019960534568565433], [ 0.0, -0.0012558103905862669, -0.0025066646712860858, 0.0, -0.019960534568565433, -0.019842294026289557], [ 0.0, -0.0025066646712860858, -0.0037476262917144954, 0.0, -0.019842294026289557, -0.019645745014573772], [ 0.0, -0.0037476262917144954, -0.0049737977432971, 0.0, -0.019645745014573772, -0.01937166322257262], [ 0.0, -0.0049737977432971, -0.0061803398874989545, 0.0, -0.01937166322257262, -0.019021130325903073], [ 0.0, -0.0061803398874989545, -0.007362491053693567, 0.0, -0.019021130325903073, -0.018595529717765024], [ 0.0, -0.007362491053693567, -0.008515585831301454, 0.0, -0.018595529717765024, -0.01809654104932039], [ 0.0, -0.008515585831301454, -0.009635073482034308, 0.0, -0.01809654104932039, -0.01752613360087727], [ 0.0, -0.009635073482034308, -0.010716535899579936, 0.0, -0.01752613360087727, -0.0168865585100403], [ 0.0, -0.010716535899579936, -0.011755705045849468, 0.0, -0.0168865585100403, -0.016180339887498944], [ 0.0, -0.011755705045849468, -0.0127484797949738, 0.0, -0.016180339887498944, -0.015410264855515781], [ 0.0, -0.0127484797949738, -0.013690942118573775, 0.0, -0.015410264855515781, -0.014579372548428232], [ 0.0, -0.013690942118573775, -0.014579372548428232, 0.0, -0.014579372548428232, -0.013690942118573773], [ 0.0, -0.014579372548428232, -0.015410264855515788, 0.0, -0.013690942118573773, -0.01274847979497379], [ 0.0, -0.015410264855515788, -0.016180339887498948, 0.0, -0.01274847979497379, -0.011755705045849465], [ 0.0, -0.016180339887498948, -0.016886558510040308, 0.0, -0.011755705045849465, -0.010716535899579927], [ 0.0, -0.016886558510040308, -0.01752613360087727, 0.0, -0.010716535899579927, -0.009635073482034306], [ 0.0, -0.01752613360087727, -0.018096541049320396, 0.0, -0.009635073482034306, -0.008515585831301443], [ 0.0, -0.018096541049320396, -0.01859552971776503, 0.0, -0.008515585831301443, -0.007362491053693556], [ 0.0, -0.01859552971776503, -0.019021130325903073, 0.0, -0.007362491053693556, -0.006180339887498951], [ 0.0, -0.019021130325903073, -0.019371663222572624, 0.0, -0.006180339887498951, -0.004973797743297089], [ 0.0, -0.019371663222572624, -0.019645745014573775, 0.0, -0.004973797743297089, -0.003747626291714493], [ 0.0, -0.019645745014573775, -0.019842294026289557, 0.0, -0.003747626291714493, -0.0025066646712860745], [ 0.0, -0.019842294026289557, -0.019960534568565433, 0.0, -0.0025066646712860745, -0.001255810390586264], [ 0.0, -0.019960534568565433, -0.02, 0.0, -0.001255810390586264, -3.673940397442059e-18], [ 0.0, -0.02, -0.019960534568565433, 0.0, -3.673940397442059e-18, 0.0012558103905862745], [ 0.0, -0.019960534568565433, -0.019842294026289557, 0.0, 0.0012558103905862745, 0.0025066646712860845], [ 0.0, -0.019842294026289557, -0.019645745014573772, 0.0, 0.0025066646712860845, 0.003747626291714503], [ 0.0, -0.019645745014573772, -0.01937166322257262, 0.0, 0.003747626291714503, 0.004973797743297099], [ 0.0, -0.01937166322257262, -0.019021130325903073, 0.0, 0.004973797743297099, 0.006180339887498945], [ 0.0, -0.019021130325903073, -0.018595529717765024, 0.0, 0.006180339887498945, 0.007362491053693565], [ 0.0, -0.018595529717765024, -0.018096541049320392, 0.0, 0.007362491053693565, 0.008515585831301452], [ 0.0, -0.018096541049320392, -0.017526133600877267, 0.0, 0.008515585831301452, 0.009635073482034314], [ 0.0, -0.017526133600877267, -0.0168865585100403, 0.0, 0.009635073482034314, 0.010716535899579936], [ 0.0, -0.0168865585100403, -0.01618033988749894, 0.0, 0.010716535899579936, 0.011755705045849473], [ 0.0, -0.01618033988749894, -0.015410264855515781, 0.0, 0.011755705045849473, 0.0127484797949738], [ 0.0, -0.015410264855515781, -0.014579372548428232, 0.0, 0.0127484797949738, 0.013690942118573773], [ 0.0, -0.014579372548428232, -0.013690942118573766, 0.0, 0.013690942118573773, 0.014579372548428239], [ 0.0, -0.013690942118573766, -0.012748479794973793, 0.0, 0.014579372548428239, 0.015410264855515788], [ 0.0, -0.012748479794973793, -0.011755705045849453, 0.0, 0.015410264855515788, 0.016180339887498955], [ 0.0, -0.011755705045849453, -0.010716535899579927, 0.0, 0.016180339887498955, 0.016886558510040305], [ 0.0, -0.010716535899579927, -0.009635073482034308, 0.0, 0.016886558510040305, 0.01752613360087727], [ 0.0, -0.009635073482034308, -0.008515585831301445, 0.0, 0.01752613360087727, 0.018096541049320396], [ 0.0, -0.008515585831301445, -0.007362491053693557, 0.0, 0.018096541049320396, 0.01859552971776503], [ 0.0, -0.007362491053693557, -0.006180339887498935, 0.0, 0.01859552971776503, 0.019021130325903076], [ 0.0, -0.006180339887498935, -0.00497379774329709, 0.0, 0.019021130325903076, 0.019371663222572624], [ 0.0, -0.00497379774329709, -0.0037476262917144937, 0.0, 0.019371663222572624, 0.019645745014573775], [ 0.0, -0.0037476262917144937, -0.002506664671286076, 0.0, 0.019645745014573775, 0.019842294026289557], [ 0.0, -0.002506664671286076, -0.0012558103905862654, 0.0, 0.019842294026289557, 0.019960534568565433], [ 0.0, -0.0012558103905862654, -4.898587196589413e-18, 0.0, 0.019960534568565433, 0.02]] triangles = np.asarray(triangles) print(np.shape(triangles)) @@ -247,12 +269,4 @@ def write_to_file(self): points = np.asarray(points) print(np.shape(points)) plt.triplot(points[:,0], points[:,1]) - plt.show()''' - - mesh = Mesh("MICRON", 10,-10,10,-10) - - mesh.N_gon(5,100, [ 6.5E+10, 6.5E+10,]) - #mesh.N_gon(1.5, 4, 2, 5, 0, np.pi/4) - #mesh.add_Uniform_random(10) - #mesh.print_Triangles() - mesh.write_to_file() \ No newline at end of file + plt.show()''' \ No newline at end of file From 453a4daf2592f3a2a9fba7abc0ab411d8ee8076f Mon Sep 17 00:00:00 2001 From: Stephen Date: Wed, 20 Jan 2021 16:36:17 -0600 Subject: [PATCH 04/14] Update create_mesh2D values are now output with ending zeros as RustBCA wants --- scripts/Mesh2D.toml | 8 ++++++ scripts/create_mesh2D.py | 62 ++++++++++++++++++++++++++++++---------- 2 files changed, 55 insertions(+), 15 deletions(-) diff --git a/scripts/Mesh2D.toml b/scripts/Mesh2D.toml index e69de29..cdfd4d7 100644 --- a/scripts/Mesh2D.toml +++ b/scripts/Mesh2D.toml @@ -0,0 +1,8 @@ +[mesh_2d_input] +length_unit = "MICRON" +energy_barrier_thickness = 0.000176456540 +triangles = [ [ -4.9114362536434432730, -4.96057350657238949050, 0.0000, 0.9369065729286228940, 0.6266661678215204030, 0.0000,], [ -4.6488824294412571800, -4.7552825814757682110, 0.0000, 1.8406227634233887080, 1.5450849718747354800, 0.0000,], [ -4.0450849718747363680, -4.2216396275100755990, 0.0000, 2.9389262614623663520, 2.679133974894983170, 0.0000,], [ -4.2216396275100755990, -4.3815334002193182530, 0.0000, 2.679133974894983170, 2.408768370508576060, 0.0000,], [ -0.62666616782152184670, -0.93690657292862411510, 0.0000, 4.960573506572388600, 4.911436253643443270, 0.0000,], [ -0.93690657292862411510, -1.24344943582427425180, 0.0000, 4.911436253643443270, 4.842915805643155380, 0.0000,], [ -2.9389262614623650190, -3.18711994874344872740, 0.0000, 4.045084971874737260, 3.852566213878946040, 0.0000,], [ 4.9605735065723894910, 4.911436253643443270, 0.0000, 0.6266661678215212920, 0.9369065729286231160, 0.0000,], [ 4.755282581475767320, 4.648882429441256290, 0.0000, 1.545084971874737030, 1.8406227634233898180, 0.0000,], [ 4.221639627510075600, 4.045084971874737260, 0.0000, 2.679133974894983170, 2.938926261462365910, 0.0000,], [ 4.648882429441256290, 4.524135262330097440, 0.0000, 1.8406227634233898180, 2.1288964578253635200, 0.0000,], [ 0.9369065729286225610, 0.6266661678215212920, 0.0000, 4.911436253643443270, 4.9605735065723894910, 0.0000,], [ 1.8406227634233893740, 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-4.8429158056431553800,], [ 1.5450849718747361460, -4.7552825814757682110,], [ 1.5450849718747372560, 4.755282581475767320,], [ 1.8406227634233893740, 4.648882429441257180,], [ 1.8406227634233913730, -4.6488824294412562920,], [ 2.128896457825363080, -4.5241352623300983280,], [ 2.1288964578253635200, 4.524135262330098330,], [ 2.4087683705085756180, 4.381533400219318250,], [ 2.4087683705085787270, -4.38153340021931647640,], [ 2.6791339748949827280, 4.221639627510075600,], [ 2.6791339748949836160, -4.2216396275100747100,], [ 2.938926261462365020, 4.045084971874737260,], [ 2.9389262614623685720, -4.0450849718747345920,], [ 3.1871199487434482830, 3.852566213878946040,], [ 3.18711994874345010, -3.8525662138789451560,], [ 3.422735529643443190, -3.6448431371070579840,], [ 3.422735529643443190, 3.644843137107057980,], [ 3.644843137107057980, 3.4227355296434436300,], [ 3.6448431371070593170, -3.42273552964344141000,], [ 3.8525662138789456000, 3.1871199487434487270,], [ 3.852566213878946930, -3.18711994874344828330,], [ 4.045084971874737260, 2.938926261462365910,], [ 4.045084971874739030, -2.9389262614623627990,], [ 4.221639627510075600, 2.679133974894983170,], [ 4.2216396275100764870, -2.6791339748949818400,], [ 4.381533400219318250, -2.40876837050857650620,], [ 4.381533400219318250, 2.4087683705085765060,], [ 4.524135262330097440, 2.1288964578253635200,], [ 4.524135262330098330, -2.1288964578253608550,], [ 4.648882429441256290, 1.8406227634233898180,], [ 4.648882429441257180, -1.84062276342338937420,], [ 4.755282581475767320, 1.545084971874737030,], [ 4.755282581475769100, -1.5450849718747339260,], [ 4.842915805643155380, 1.243449435824274030,], [ 4.842915805643156270, -1.24344943582427247540,], [ 4.911436253643443270, -0.93690657292862344900,], [ 4.911436253643443270, 0.9369065729286231160,], [ 4.9605735065723894910, -0.6266661678215189600,], [ 4.9605735065723894910, 0.6266661678215212920,], [ 4.990133642141358020, -0.31395259764656630040,], [ 4.990133642141358020, 0.31395259764656685550,], [ 5.0000, 0.0000,],] +simulation_boundary_points = [ [ 10.000, 10.000,], [ 10.000, -10.0000,], [ -10.0000, 10.000,], [ -10.0000, -10.0000,],] +electronic_stopping_correction_factors = [ 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000,] diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index d4d8532..c6b04eb 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -12,9 +12,10 @@ from shapely.geometry import Point from shapely.geometry.polygon import Polygon +from decimal import Decimal -number_of_decimals = "10" -np.set_printoptions(formatter={'float': lambda x: "{0:0." + number_of_decimals + "f}".format(x)}) +number_of_decimals = "11" +np.set_printoptions(formatter={'float': lambda x: "{0:0." + number_of_decimals + "f}".format(x)+"0"}) class Mesh(): @@ -148,13 +149,13 @@ def return_Triangles(self): #print("Length of tri.simplices " + str(len(tri.simplices))) #print("Length of triangles " + str(len(triangles))) - temp_material_densities = [0]*(len(triangles)) + temp_material_densities = [None]*(len(triangles)) self.electronic_stopping_corrections = [1.0]*(len(triangles)) #print("Len of triangles " + str(len(triangles))) for i, triangle in enumerate(triangles): for shape, number_densities in self.shapes: if shape.contains(triangle): - temp_material_densities[i] = number_densities + temp_material_densities[i] = list(number_densities) #print(point_output) return point_output, temp_material_densities @@ -215,19 +216,50 @@ def write_to_file(self, dump_to_file = False): #print(len(material_boundary_points)) electronic_stopping_correction_factors = self.electronic_stopping_corrections - + import decimal + decimal.getcontext().prec = int(number_of_decimals) + 2 + def have_ending_zeros(lis): + #lis = np.asarray(lis) + + if type(lis[0]) == tuple: + for i in range(len(lis)): + lis[i] = list(lis[i]) + + for i in range(len(lis)): + if type(lis[i]) == np.float64 or type(lis[i]) == np.float32 or type(lis[i]) == int or type(lis[i]) == float: + lis[i] = decimal.Decimal(("{0:0." + str(len(str(lis[i]))) + "f}").format(lis[i])+"0")#.quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + #lis[i] = decimal.Decimal(lis[i]).quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + else: + if type(lis[i]) == type(decimal.Decimal(1.0)): + pass + for j in range(len(lis[i])): + if type(lis[i][j]) == np.float64 or type(lis[i][j]) == np.float32 or type(lis[i][j]) == int or type(lis[i][j]) == float: + lis[i][j] = decimal.Decimal(("{0:0." + str(len(str(lis[i][j]))) + "f}").format(lis[i][j])+"0")#.quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + #lis[i][j] = decimal.Decimal(lis[i][j]).quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + else: + if type(lis[i][j]) == type(decimal.Decimal(1.0)): + pass + for k in range(len(lis[i][j])): + if type(lis[i][j][k]) == np.float64 or type(lis[i][j][k]) == np.float32 or type(lis[i][j][k]) == int or type(lis[i][j][k]) == float: + lis[i][j][k] = decimal.Decimal(("{0:0." + str(len(str(lis[i][j][k]))) + "f}").format(lis[i][j][k])+"0")#.quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + #lis[i][j][k] = decimal.Decimal(lis[i][j][k]).quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + else: + pass + + return lis + file = open("Mesh2D.toml", "w") file.seek(0) temp_dict = { - "[mesh_2d_input]" : { + "mesh_2d_input" : { "length_unit":self.length_unit, - "energy_barrier_thickness": self.energy_barrier_thickness, - "triangles": triangle_list, - "densities":material_densities, - "material_boundary_points":material_boundary_points, - "simulation_boundary_points":Simulation_Boundaries, - "electronic_stopping_correction_factors":electronic_stopping_correction_factors + "energy_barrier_thickness": decimal.Decimal(("{0:0." + number_of_decimals + "f}").format(self.energy_barrier_thickness)+"0"), + "triangles": have_ending_zeros(triangle_list), + "densities":have_ending_zeros(material_densities), + "material_boundary_points": have_ending_zeros(material_boundary_points), + "simulation_boundary_points":have_ending_zeros(Simulation_Boundaries), + "electronic_stopping_correction_factors":have_ending_zeros(electronic_stopping_correction_factors) } } @@ -246,11 +278,11 @@ def write_to_file(self, dump_to_file = False): #mesh.N_gon(1.5, 4, 2, 5, 0, np.pi/4) #mesh.add_Uniform_random(10) #mesh.print_Triangles() - mesh.write_to_file() + mesh.write_to_file(True) #code to plot out the example triangles - '''triangles = [ [ 0.0, 0.0, 0.0012558103905862675, 0.0, 0.02, 0.019960534568565433], [ 0.0, 0.0012558103905862675, 0.0025066646712860853, 0.0, 0.019960534568565433, 0.019842294026289557], [ 0.0, 0.0025066646712860853, 0.003747626291714493, 0.0, 0.019842294026289557, 0.019645745014573775], [ 0.0, 0.003747626291714493, 0.004973797743297096, 0.0, 0.019645745014573775, 0.01937166322257262], [ 0.0, 0.004973797743297096, 0.0061803398874989484, 0.0, 0.01937166322257262, 0.019021130325903073], [ 0.0, 0.0061803398874989484, 0.00736249105369356, 0.0, 0.019021130325903073, 0.018595529717765027], [ 0.0, 0.00736249105369356, 0.008515585831301454, 0.0, 0.018595529717765027, 0.01809654104932039], [ 0.0, 0.008515585831301454, 0.009635073482034308, 0.0, 0.01809654104932039, 0.01752613360087727], [ 0.0, 0.009635073482034308, 0.010716535899579934, 0.0, 0.01752613360087727, 0.0168865585100403], [ 0.0, 0.010716535899579934, 0.011755705045849463, 0.0, 0.0168865585100403, 0.016180339887498948], [ 0.0, 0.011755705045849463, 0.012748479794973795, 0.0, 0.016180339887498948, 0.015410264855515783], [ 0.0, 0.012748479794973795, 0.013690942118573775, 0.0, 0.015410264855515783, 0.014579372548428232], [ 0.0, 0.013690942118573775, 0.014579372548428232, 0.0, 0.014579372548428232, 0.013690942118573773], [ 0.0, 0.014579372548428232, 0.015410264855515785, 0.0, 0.013690942118573773, 0.012748479794973793], [ 0.0, 0.015410264855515785, 0.016180339887498948, 0.0, 0.012748479794973793, 0.011755705045849461], [ 0.0, 0.016180339887498948, 0.0168865585100403, 0.0, 0.011755705045849461, 0.01071653589957993], [ 0.0, 0.0168865585100403, 0.017526133600877274, 0.0, 0.01071653589957993, 0.009635073482034304], [ 0.0, 0.017526133600877274, 0.018096541049320392, 0.0, 0.009635073482034304, 0.008515585831301454], [ 0.0, 0.018096541049320392, 0.01859552971776503, 0.0, 0.008515585831301454, 0.007362491053693557], [ 0.0, 0.01859552971776503, 0.019021130325903073, 0.0, 0.007362491053693557, 0.006180339887498949], [ 0.0, 0.019021130325903073, 0.01937166322257262, 0.0, 0.006180339887498949, 0.004973797743297095], [ 0.0, 0.01937166322257262, 0.019645745014573775, 0.0, 0.004973797743297095, 0.0037476262917144902], [ 0.0, 0.019645745014573775, 0.019842294026289557, 0.0, 0.0037476262917144902, 0.0025066646712860853], [ 0.0, 0.019842294026289557, 0.019960534568565433, 0.0, 0.0025066646712860853, 0.001255810390586266], [ 0.0, 0.019960534568565433, 0.02, 0.0, 0.001255810390586266, -3.2162452993532734e-18], [ 0.0, 0.02, 0.019960534568565433, 0.0, -3.2162452993532734e-18, -0.001255810390586268], [ 0.0, 0.019960534568565433, 0.019842294026289557, 0.0, -0.001255810390586268, -0.0025066646712860875], [ 0.0, 0.019842294026289557, 0.019645745014573772, 0.0, -0.0025066646712860875, -0.0037476262917144967], [ 0.0, 0.019645745014573772, 0.01937166322257262, 0.0, -0.0037476262917144967, -0.004973797743297097], [ 0.0, 0.01937166322257262, 0.019021130325903073, 0.0, -0.004973797743297097, -0.006180339887498951], [ 0.0, 0.019021130325903073, 0.01859552971776503, 0.0, -0.006180339887498951, -0.00736249105369356], [ 0.0, 0.01859552971776503, 0.01809654104932039, 0.0, -0.00736249105369356, -0.008515585831301454], [ 0.0, 0.01809654104932039, 0.01752613360087727, 0.0, -0.008515585831301454, -0.00963507348203431], [ 0.0, 0.01752613360087727, 0.0168865585100403, 0.0, -0.00963507348203431, -0.010716535899579938], [ 0.0, 0.0168865585100403, 0.016180339887498948, 0.0, -0.010716535899579938, -0.011755705045849461], [ 0.0, 0.016180339887498948, 0.015410264855515785, 0.0, -0.011755705045849461, -0.012748479794973795], [ 0.0, 0.015410264855515785, 0.014579372548428228, 0.0, -0.012748479794973795, -0.013690942118573775], [ 0.0, 0.014579372548428228, 0.01369094211857377, 0.0, -0.013690942118573775, -0.014579372548428234], [ 0.0, 0.01369094211857377, 0.01274847979497379, 0.0, -0.014579372548428234, -0.015410264855515788], [ 0.0, 0.01274847979497379, 0.011755705045849465, 0.0, -0.015410264855515788, -0.016180339887498948], [ 0.0, 0.011755705045849465, 0.010716535899579934, 0.0, -0.016180339887498948, -0.0168865585100403], [ 0.0, 0.010716535899579934, 0.009635073482034304, 0.0, -0.0168865585100403, -0.01752613360087727], [ 0.0, 0.009635073482034304, 0.00851558583130145, 0.0, -0.01752613360087727, -0.018096541049320392], [ 0.0, 0.00851558583130145, 0.007362491053693555, 0.0, -0.018096541049320392, -0.01859552971776503], [ 0.0, 0.007362491053693555, 0.006180339887498942, 0.0, -0.01859552971776503, -0.019021130325903073], [ 0.0, 0.006180339887498942, 0.004973797743297097, 0.0, -0.019021130325903073, -0.01937166322257262], [ 0.0, 0.004973797743297097, 0.0037476262917144915, 0.0, -0.01937166322257262, -0.019645745014573775], [ 0.0, 0.0037476262917144915, 0.002506664671286082, 0.0, -0.019645745014573775, -0.019842294026289557], [ 0.0, 0.002506664671286082, 0.0012558103905862628, 0.0, -0.019842294026289557, -0.019960534568565433], [ 0.0, 0.0012558103905862628, -6.432490598706547e-18, 0.0, -0.019960534568565433, -0.02], [ 0.0, -6.432490598706547e-18, -0.0012558103905862669, 0.0, -0.02, -0.019960534568565433], [ 0.0, -0.0012558103905862669, -0.0025066646712860858, 0.0, -0.019960534568565433, -0.019842294026289557], [ 0.0, -0.0025066646712860858, -0.0037476262917144954, 0.0, -0.019842294026289557, -0.019645745014573772], [ 0.0, -0.0037476262917144954, -0.0049737977432971, 0.0, -0.019645745014573772, -0.01937166322257262], [ 0.0, -0.0049737977432971, -0.0061803398874989545, 0.0, -0.01937166322257262, -0.019021130325903073], [ 0.0, -0.0061803398874989545, -0.007362491053693567, 0.0, -0.019021130325903073, -0.018595529717765024], [ 0.0, -0.007362491053693567, -0.008515585831301454, 0.0, -0.018595529717765024, -0.01809654104932039], [ 0.0, -0.008515585831301454, -0.009635073482034308, 0.0, -0.01809654104932039, -0.01752613360087727], [ 0.0, -0.009635073482034308, -0.010716535899579936, 0.0, -0.01752613360087727, -0.0168865585100403], [ 0.0, -0.010716535899579936, -0.011755705045849468, 0.0, -0.0168865585100403, -0.016180339887498944], [ 0.0, -0.011755705045849468, -0.0127484797949738, 0.0, -0.016180339887498944, -0.015410264855515781], [ 0.0, -0.0127484797949738, -0.013690942118573775, 0.0, -0.015410264855515781, -0.014579372548428232], [ 0.0, -0.013690942118573775, -0.014579372548428232, 0.0, -0.014579372548428232, -0.013690942118573773], [ 0.0, -0.014579372548428232, -0.015410264855515788, 0.0, -0.013690942118573773, -0.01274847979497379], [ 0.0, -0.015410264855515788, -0.016180339887498948, 0.0, -0.01274847979497379, -0.011755705045849465], [ 0.0, -0.016180339887498948, -0.016886558510040308, 0.0, -0.011755705045849465, -0.010716535899579927], [ 0.0, -0.016886558510040308, -0.01752613360087727, 0.0, -0.010716535899579927, -0.009635073482034306], [ 0.0, -0.01752613360087727, -0.018096541049320396, 0.0, -0.009635073482034306, -0.008515585831301443], [ 0.0, -0.018096541049320396, -0.01859552971776503, 0.0, -0.008515585831301443, -0.007362491053693556], [ 0.0, -0.01859552971776503, -0.019021130325903073, 0.0, -0.007362491053693556, -0.006180339887498951], [ 0.0, -0.019021130325903073, -0.019371663222572624, 0.0, -0.006180339887498951, -0.004973797743297089], [ 0.0, -0.019371663222572624, -0.019645745014573775, 0.0, -0.004973797743297089, -0.003747626291714493], [ 0.0, -0.019645745014573775, -0.019842294026289557, 0.0, -0.003747626291714493, -0.0025066646712860745], [ 0.0, -0.019842294026289557, -0.019960534568565433, 0.0, -0.0025066646712860745, -0.001255810390586264], [ 0.0, -0.019960534568565433, -0.02, 0.0, -0.001255810390586264, -3.673940397442059e-18], [ 0.0, -0.02, -0.019960534568565433, 0.0, -3.673940397442059e-18, 0.0012558103905862745], [ 0.0, 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0.0127484797949738], [ 0.0, -0.015410264855515781, -0.014579372548428232, 0.0, 0.0127484797949738, 0.013690942118573773], [ 0.0, -0.014579372548428232, -0.013690942118573766, 0.0, 0.013690942118573773, 0.014579372548428239], [ 0.0, -0.013690942118573766, -0.012748479794973793, 0.0, 0.014579372548428239, 0.015410264855515788], [ 0.0, -0.012748479794973793, -0.011755705045849453, 0.0, 0.015410264855515788, 0.016180339887498955], [ 0.0, -0.011755705045849453, -0.010716535899579927, 0.0, 0.016180339887498955, 0.016886558510040305], [ 0.0, -0.010716535899579927, -0.009635073482034308, 0.0, 0.016886558510040305, 0.01752613360087727], [ 0.0, -0.009635073482034308, -0.008515585831301445, 0.0, 0.01752613360087727, 0.018096541049320396], [ 0.0, -0.008515585831301445, -0.007362491053693557, 0.0, 0.018096541049320396, 0.01859552971776503], [ 0.0, -0.007362491053693557, -0.006180339887498935, 0.0, 0.01859552971776503, 0.019021130325903076], [ 0.0, -0.006180339887498935, -0.00497379774329709, 0.0, 0.019021130325903076, 0.019371663222572624], [ 0.0, -0.00497379774329709, -0.0037476262917144937, 0.0, 0.019371663222572624, 0.019645745014573775], [ 0.0, -0.0037476262917144937, -0.002506664671286076, 0.0, 0.019645745014573775, 0.019842294026289557], [ 0.0, -0.002506664671286076, -0.0012558103905862654, 0.0, 0.019842294026289557, 0.019960534568565433], [ 0.0, -0.0012558103905862654, -4.898587196589413e-18, 0.0, 0.019960534568565433, 0.02]] + triangles = [ [ 0.0, 0.01, 0.0, 0.5, 0.5, -0.5,], [ 0.0, 0.01, 0.01, -0.5, 0.5, -0.5,], [ 0.01, 0.01, 0.04, -0.5, 0.5, -0.5,], [ 0.01, 0.04, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.5, -0.5, 0.5, -0.5,],] triangles = np.asarray(triangles) print(np.shape(triangles)) @@ -269,4 +301,4 @@ def write_to_file(self, dump_to_file = False): points = np.asarray(points) print(np.shape(points)) plt.triplot(points[:,0], points[:,1]) - plt.show()''' \ No newline at end of file + plt.show() \ No newline at end of file From f0f4a4a32de6b51dbf8dc9ab435734ec7c699865 Mon Sep 17 00:00:00 2001 From: Stephen Date: Wed, 20 Jan 2021 17:06:15 -0600 Subject: [PATCH 05/14] updates to create_mesh2d added triangle and rectangle specific functions. removed unneeded type checks in __init__. --- scripts/Mesh2D.toml | 6 ++--- scripts/create_mesh2D.py | 47 +++++++++++++++++++++++++--------------- 2 files changed, 32 insertions(+), 21 deletions(-) diff --git a/scripts/Mesh2D.toml b/scripts/Mesh2D.toml index cdfd4d7..d8c5b88 100644 --- a/scripts/Mesh2D.toml +++ b/scripts/Mesh2D.toml @@ -1,8 +1,8 @@ [mesh_2d_input] length_unit = "MICRON" energy_barrier_thickness = 0.000176456540 -triangles = [ [ -4.9114362536434432730, -4.96057350657238949050, 0.0000, 0.9369065729286228940, 0.6266661678215204030, 0.0000,], [ -4.6488824294412571800, -4.7552825814757682110, 0.0000, 1.8406227634233887080, 1.5450849718747354800, 0.0000,], [ -4.0450849718747363680, -4.2216396275100755990, 0.0000, 2.9389262614623663520, 2.679133974894983170, 0.0000,], [ -4.2216396275100755990, -4.3815334002193182530, 0.0000, 2.679133974894983170, 2.408768370508576060, 0.0000,], [ -0.62666616782152184670, -0.93690657292862411510, 0.0000, 4.960573506572388600, 4.911436253643443270, 0.0000,], [ -0.93690657292862411510, -1.24344943582427425180, 0.0000, 4.911436253643443270, 4.842915805643155380, 0.0000,], [ -2.9389262614623650190, -3.18711994874344872740, 0.0000, 4.045084971874737260, 3.852566213878946040, 0.0000,], [ 4.9605735065723894910, 4.911436253643443270, 0.0000, 0.6266661678215212920, 0.9369065729286231160, 0.0000,], [ 4.755282581475767320, 4.648882429441256290, 0.0000, 1.545084971874737030, 1.8406227634233898180, 0.0000,], [ 4.221639627510075600, 4.045084971874737260, 0.0000, 2.679133974894983170, 2.938926261462365910, 0.0000,], [ 4.648882429441256290, 4.524135262330097440, 0.0000, 1.8406227634233898180, 2.1288964578253635200, 0.0000,], [ 0.9369065729286225610, 0.6266661678215212920, 0.0000, 4.911436253643443270, 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0.0012558103905862675380,], [ 0.02000, 0.0000,],] +simulation_boundary_points = [ [ 0.03000, 0.03000,], [ 0.03000, -0.030000,], [ -0.030000, 0.03000,], [ -0.030000, -0.030000,],] electronic_stopping_correction_factors = [ 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000,] diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index c6b04eb..87ff8e7 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -31,20 +31,6 @@ def __init__(self, length_unit, xmax, xmin, ymax, ymin, energy_barrier_thickness self.trianglelist = [] - if not type(xmax) == int: - print("xmax should be a int") - assert type(xmax) == int - if not type(xmin) == int: - print("xmin should be a int") - assert type(xmin) == int - if not type(ymax) == int: - print("ymax should be a int") - assert type(ymax) == int - if not type(ymin) == int: - print("ymin should be a int") - assert type(ymin) == int - - self.Simulation_boundaries = [[xmax, ymax], [xmax, ymin], [xmin, ymax], [xmin, ymin]] self.points = [] self.shapes = [] @@ -96,6 +82,27 @@ def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0 return True + def triangle(self, arm1, arm2, theta, number_densities, x_offset = 0, y_offset = 0, theta_offset = 0): + point1 = Point(x_offset + arm1*math.cos(theta_offset), y_offset + arm1*math.sin(theta_offset)) + point2 = Point(x_offset + arm2*math.cos(theta + theta_offset), y_offset + arm2*math.sin(theta + theta_offset)) + center_point = Point(x_offset, y_offset) + + temp_points = [point1,point2,center_point] + + self.points += temp_points + self.shapes.append(Polygon(temp_points), number_densities) + + + def rectangle(self, length1, length2,number_densities, x_offset = 0.0, y_offset = 0.0): + temp_points = [Point(x_offset, y_offset)] + for i in range(4): + temp_points.append(Point(x_offset + (-1)**i*length1/2.0, y_offset + (-1)**(math.floor(i/2))*length2/2.0)) + + self.points += temp_points + self.shapes.append(Polygon(temp_points), number_densities) + + return True + def add_Uniform_random(self, n_points): """ returns True on completion. @@ -254,7 +261,7 @@ def have_ending_zeros(lis): temp_dict = { "mesh_2d_input" : { "length_unit":self.length_unit, - "energy_barrier_thickness": decimal.Decimal(("{0:0." + number_of_decimals + "f}").format(self.energy_barrier_thickness)+"0"), + "energy_barrier_thickness": decimal.Decimal(("{0:0." + str(len(str(self.energ_barrier_thickness))) + "f}").format(self.energy_barrier_thickness)+"0"), "triangles": have_ending_zeros(triangle_list), "densities":have_ending_zeros(material_densities), "material_boundary_points": have_ending_zeros(material_boundary_points), @@ -272,16 +279,19 @@ def have_ending_zeros(lis): return temp_dict if __name__ == "__main__": - mesh = Mesh("MICRON", 10,-10,10,-10) + mesh = Mesh("MICRON", .03,-.03,.03,-.03) - mesh.N_gon(5,100, [ 6.5E+10, 6.5E+10,]) + mesh.N_gon(.02,100, [ 6.5E+10, 6.5E+10,]) #mesh.N_gon(1.5, 4, 2, 5, 0, np.pi/4) #mesh.add_Uniform_random(10) #mesh.print_Triangles() mesh.write_to_file(True) + + #code to plot out the example triangles + ''' triangles = [ [ 0.0, 0.01, 0.0, 0.5, 0.5, -0.5,], [ 0.0, 0.01, 0.01, -0.5, 0.5, -0.5,], [ 0.01, 0.01, 0.04, -0.5, 0.5, -0.5,], [ 0.01, 0.04, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.5, -0.5, 0.5, -0.5,],] triangles = np.asarray(triangles) print(np.shape(triangles)) @@ -301,4 +311,5 @@ def have_ending_zeros(lis): points = np.asarray(points) print(np.shape(points)) plt.triplot(points[:,0], points[:,1]) - plt.show() \ No newline at end of file + plt.show() + ''' \ No newline at end of file From 99268e663c0749ec266c4ca364feb7cdf96ef350 Mon Sep 17 00:00:00 2001 From: Stephen Date: Wed, 20 Jan 2021 17:12:33 -0600 Subject: [PATCH 06/14] Update create_mesh2D added descriptions to triangle and rectangle functions --- scripts/create_mesh2D.py | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index 87ff8e7..0b9f3c3 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -83,6 +83,12 @@ def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0 return True def triangle(self, arm1, arm2, theta, number_densities, x_offset = 0, y_offset = 0, theta_offset = 0): + ''' + returns True on completion + creates a single triangle with arm lengths arm2 and arm2 and major angle theta (radians) + The x and y offset determine the center point + theta_offset determines the rotation of the triangle + ''' point1 = Point(x_offset + arm1*math.cos(theta_offset), y_offset + arm1*math.sin(theta_offset)) point2 = Point(x_offset + arm2*math.cos(theta + theta_offset), y_offset + arm2*math.sin(theta + theta_offset)) center_point = Point(x_offset, y_offset) @@ -93,10 +99,16 @@ def triangle(self, arm1, arm2, theta, number_densities, x_offset = 0, y_offset = self.shapes.append(Polygon(temp_points), number_densities) - def rectangle(self, length1, length2,number_densities, x_offset = 0.0, y_offset = 0.0): + def rectangle(self, length1, length2, number_densities, x_offset = 0.0, y_offset = 0.0, theta_offset = 0.0): + ''' + returns True on completion + creates a single rectangle with center (x_offset, y_offset) and side lengths length1 and length2 + length1 is the x-axis + theta_offset rotates around the center point (radians) + ''' temp_points = [Point(x_offset, y_offset)] for i in range(4): - temp_points.append(Point(x_offset + (-1)**i*length1/2.0, y_offset + (-1)**(math.floor(i/2))*length2/2.0)) + temp_points.append(Point(x_offset + ((-1)**i*length1/2.0)*math.cos(theta_offset), y_offset + ((-1)**(math.floor(i/2))*length2/2.0)*math.sin(theta_offset) )) self.points += temp_points self.shapes.append(Polygon(temp_points), number_densities) From 5a42fb9c80a23796d161fe958b2223b9a32a8dbb Mon Sep 17 00:00:00 2001 From: Stephen Date: Wed, 20 Jan 2021 17:13:45 -0600 Subject: [PATCH 07/14] Update create_mesh2d clarified a description --- scripts/create_mesh2D.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index 0b9f3c3..97ef8b4 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -302,7 +302,7 @@ def have_ending_zeros(lis): - #code to plot out the example triangles + #code to plot out the example triangles for boron_nitride ''' triangles = [ [ 0.0, 0.01, 0.0, 0.5, 0.5, -0.5,], [ 0.0, 0.01, 0.01, -0.5, 0.5, -0.5,], [ 0.01, 0.01, 0.04, -0.5, 0.5, -0.5,], [ 0.01, 0.04, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.5, -0.5, 0.5, -0.5,],] triangles = np.asarray(triangles) From 2f0566d4da04494687be7f6c491f8fe507adbddd Mon Sep 17 00:00:00 2001 From: Stephen Date: Wed, 20 Jan 2021 17:16:15 -0600 Subject: [PATCH 08/14] Update create_mesh2D Added check that x and y min are less than x and y max --- scripts/create_mesh2D.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index 97ef8b4..713b4d2 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -13,6 +13,7 @@ from shapely.geometry.polygon import Polygon from decimal import Decimal +from pickle import FALSE number_of_decimals = "11" np.set_printoptions(formatter={'float': lambda x: "{0:0." + number_of_decimals + "f}".format(x)+"0"}) @@ -28,6 +29,12 @@ def __init__(self, length_unit, xmax, xmin, ymax, ymin, energy_barrier_thickness The init functions requires the length units, x limits and y limits of the simulation. The x and y limits are assumed to be on the points of a square. """ + if xmin >= xmax: + print("xmin should be less than xmax") + assert xmin < xmax + if ymin >= ymax: + print("ymin should be less than ymax") + assert ymin < ymax self.trianglelist = [] From 6853be207fcc168c27194580fbb1bcdcbb8cb001 Mon Sep 17 00:00:00 2001 From: Stephen Date: Wed, 20 Jan 2021 17:17:36 -0600 Subject: [PATCH 09/14] Update create_mesh2D removed unnneeded import statements. fixed misspelling of energy --- scripts/Mesh2D.toml | 2 +- scripts/create_mesh2D.py | 5 +---- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/scripts/Mesh2D.toml b/scripts/Mesh2D.toml index d8c5b88..f1229e3 100644 --- a/scripts/Mesh2D.toml +++ b/scripts/Mesh2D.toml @@ -1,6 +1,6 @@ [mesh_2d_input] length_unit = "MICRON" -energy_barrier_thickness = 0.000176456540 +energy_barrier_thickness = 0.00017645653881793785090 triangles = [ [ -0.0190211303259030725670, -0.019371663222572620830, 0.0000, 0.006180339887498942360, 0.004973797743297096900, 0.0000,], [ -0.0136909421185737751460, -0.0145793725484282335470, 0.0000, 0.014579372548428228340, 0.01369094211857376990, 0.0000,], [ -0.017526133600877270850, -0.0180965410493203922300, 0.0000, 0.009635073482034304040, 0.00851558583130145040, 0.0000,], [ -0.0012558103905862679720, 0.0000, -3.216250E-18, 0.019960534568565432840, 0.0000, 0.02000,], [ -0.00374762629171449673790, -0.0049737977432970969030, 0.0000, 0.019645745014573771920, 0.01937166322257262080, 0.0000,], [ -0.0107165358995799375740, -0.0117557050458494613540, 0.0000, 0.0168865585100403010, 0.016180339887498947780, 0.0000,], [ -0.007362491053693559670, -0.0085155858313014538840, 0.0000, 0.018595529717765027500, 0.01809654104932038880, 0.0000,], [ 0.019960534568565432840, 0.0000, 0.02000, 0.0012558103905862675380, 0.0000, 0.0000,], [ 0.019645745014573775390, 0.01937166322257262080, 0.0000, 0.003747626291714492830, 0.004973797743297096040, 0.0000,], [ 0.0168865585100403010, 0.016180339887498947780, 0.0000, 0.010716535899579934100, 0.011755705045849463090, 0.0000,], [ 0.018595529717765027500, 0.01809654104932038880, 0.0000, 0.00736249105369355970, 0.008515585831301453880, 0.0000,], [ 0.008515585831301453880, 0.007362491053693557070, 0.0000, 0.018096541049320392230, 0.01859552971776503100, 0.0000,], [ 0.012748479794973793450, 0.011755705045849461350, 0.0000, 0.015410264855515784860, 0.016180339887498947780, 0.0000,], [ 0.011755705045849461350, 0.01071653589957993060, 0.0000, 0.016180339887498947780, 0.0168865585100403010, 0.0000,], [ -0.0199605345685654328450, 0.0000, -0.020000, -0.00125581039058626688780, 0.0000, -6.43250E-18,], [ -0.0196457450145737719250, -0.019371663222572620830, 0.0000, -0.00374762629171449543690, -0.00497379774329710040, 0.0000,], [ -0.01688655851004030110, -0.0161803398874989443070, 0.0000, -0.0107165358995799358390, -0.0117557050458494682930, 0.0000,], [ -0.0185955297177650240300, -0.018096541049320388760, 0.0000, -0.0073624910536935666070, -0.0085155858313014538840, 0.0000,], [ -0.0037476262917144928350, -0.00250666467128607449790, 0.0000, -0.0196457450145737753940, -0.0198422940262895572410, 0.0000,], [ -0.0073624910536935561990, -0.0061803398874989510380, 0.0000, -0.018595529717765030970, -0.0190211303259030725670, 0.0000,], [ -0.012748479794973789980, -0.0117557050458494648240, 0.0000, -0.0154102648555157883260, -0.0161803398874989477760, 0.0000,], [ 0.018096541049320395700, 0.01859552971776503100, 0.0000, -0.0085155858313014452100, -0.0073624910536935570670, 0.0000,], [ 0.013690942118573773410, 0.014579372548428238750, 0.0000, -0.0145793725484282318120, -0.0136909421185737664730, 0.0000,], [ 0.016180339887498954720, 0.016886558510040308030, 0.0000, -0.0117557050458494526810, -0.0107165358995799271660, 0.0000,], [ -3.67390E-18, 0.0012558103905862744770, 0.0000, -0.020000, -0.0199605345685654328450, 0.0000,], [ 0.003747626291714502810, 0.004973797743297098640, 0.0000, -0.0196457450145737719250, -0.019371663222572620830, 0.0000,], [ 0.010716535899579935840, 0.011755705045849473500, 0.0000, -0.01688655851004030110, -0.016180339887498940840, 0.0000,], [ 0.009635073482034314450, 0.010716535899579935840, 0.0000, -0.0175261336008772673770, -0.01688655851004030110, 0.0000,], [ 0.0000, -0.0199605345685654328450, -0.020000, 0.0000, 0.0012558103905862627680, -6.43250E-18,], [ -0.0198422940262895572410, -0.0199605345685654328450, 0.0000, 0.002506664671286081870, 0.0012558103905862627680, 0.0000,], [ -0.019371663222572620830, -0.0196457450145737753940, 0.0000, 0.004973797743297096900, 0.0037476262917144915340, 0.0000,], [ -0.0196457450145737753940, -0.0198422940262895572410, 0.0000, 0.0037476262917144915340, 0.002506664671286081870, 0.0000,], [ -0.0180965410493203922300, -0.018595529717765030970, 0.0000, 0.00851558583130145040, 0.007362491053693555330, 0.0000,], [ -0.018595529717765030970, -0.0190211303259030725670, 0.0000, 0.007362491053693555330, 0.006180339887498942360, 0.0000,], [ -0.0154102648555157883260, -0.0161803398874989477760, 0.0000, 0.01274847979497379000, 0.011755705045849464820, 0.0000,], [ -0.0145793725484282335470, -0.0154102648555157883260, 0.0000, 0.01369094211857376990, 0.01274847979497379000, 0.0000,], [ -0.0161803398874989477760, -0.01688655851004030110, 0.0000, 0.011755705045849464820, 0.010716535899579934100, 0.0000,], [ -0.01688655851004030110, -0.017526133600877270850, 0.0000, 0.010716535899579934100, 0.009635073482034304040, 0.0000,], [ -0.00250666467128608750830, -0.00374762629171449673790, 0.0000, 0.019842294026289557240, 0.019645745014573771920, 0.0000,], [ -0.0012558103905862679720, -0.00250666467128608750830, 0.0000, 0.019960534568565432840, 0.019842294026289557240, 0.0000,], [ -0.0061803398874989510380, -0.007362491053693559670, 0.0000, 0.019021130325903072570, 0.018595529717765027500, 0.0000,], [ -0.0049737977432970969030, -0.0061803398874989510380, 0.0000, 0.01937166322257262080, 0.019021130325903072570, 0.0000,], [ -0.0127484797949737951870, -0.0136909421185737751460, 0.0000, 0.015410264855515784860, 0.014579372548428228340, 0.0000,], [ -0.0117557050458494613540, -0.0127484797949737951870, 0.0000, 0.016180339887498947780, 0.015410264855515784860, 0.0000,], [ -0.009635073482034309240, -0.0107165358995799375740, 0.0000, 0.01752613360087727080, 0.0168865585100403010, 0.0000,], [ -0.0085155858313014538840, -0.009635073482034309240, 0.0000, 0.01809654104932038880, 0.01752613360087727080, 0.0000,], [ 0.019842294026289557240, 0.019645745014573775390, 0.0000, 0.0025066646712860853400, 0.003747626291714492830, 0.0000,], [ 0.019960534568565432840, 0.019842294026289557240, 0.0000, 0.0012558103905862675380, 0.0025066646712860853400, 0.0000,], [ 0.019021130325903072570, 0.018595529717765027500, 0.0000, 0.0061803398874989484350, 0.00736249105369355970, 0.0000,], [ 0.01937166322257262080, 0.019021130325903072570, 0.0000, 0.004973797743297096040, 0.0061803398874989484350, 0.0000,], [ 0.015410264855515783120, 0.014579372548428231810, 0.0000, 0.012748479794973795190, 0.013690942118573775150, 0.0000,], [ 0.016180339887498947780, 0.015410264855515783120, 0.0000, 0.011755705045849463090, 0.012748479794973795190, 0.0000,], [ 0.01752613360087727080, 0.0168865585100403010, 0.0000, 0.009635073482034307510, 0.010716535899579934100, 0.0000,], [ 0.01809654104932038880, 0.01752613360087727080, 0.0000, 0.008515585831301453880, 0.009635073482034307510, 0.0000,], [ 0.0000, 0.001255810390586266020, -3.216250E-18, 0.0000, 0.019960534568565432840, 0.02000,], [ 0.0025066646712860853400, 0.001255810390586266020, 0.0000, 0.019842294026289557240, 0.019960534568565432840, 0.0000,], [ 0.004973797743297095170, 0.0037476262917144902330, 0.0000, 0.01937166322257262080, 0.019645745014573775390, 0.0000,], [ 0.0037476262917144902330, 0.0025066646712860853400, 0.0000, 0.019645745014573775390, 0.019842294026289557240, 0.0000,], [ 0.006180339887498949300, 0.004973797743297095170, 0.0000, 0.019021130325903072570, 0.01937166322257262080, 0.0000,], [ 0.007362491053693557070, 0.006180339887498949300, 0.0000, 0.01859552971776503100, 0.019021130325903072570, 0.0000,], [ 0.014579372548428231810, 0.013690942118573773410, 0.0000, 0.013690942118573775150, 0.014579372548428231810, 0.0000,], [ 0.013690942118573773410, 0.012748479794973793450, 0.0000, 0.014579372548428231810, 0.015410264855515784860, 0.0000,], [ 0.009635073482034304040, 0.008515585831301453880, 0.0000, 0.017526133600877274320, 0.018096541049320392230, 0.0000,], [ 0.01071653589957993060, 0.009635073482034304040, 0.0000, 0.0168865585100403010, 0.017526133600877274320, 0.0000,], [ -0.0198422940262895572410, -0.0196457450145737719250, 0.0000, -0.00250666467128608577360, -0.00374762629171449543690, 0.0000,], [ -0.0199605345685654328450, -0.0198422940262895572410, 0.0000, -0.00125581039058626688780, -0.00250666467128608577360, 0.0000,], [ -0.0190211303259030725670, -0.0185955297177650240300, 0.0000, -0.00618033988749895450700, -0.0073624910536935666070, 0.0000,], [ -0.019371663222572620830, -0.0190211303259030725670, 0.0000, 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-0.0085155858313014452100,], [ 0.018595529717765027500, 0.00736249105369355970,], [ 0.01859552971776503100, -0.0073624910536935570670,], [ 0.019021130325903072570, 0.0061803398874989484350,], [ 0.019021130325903076040, -0.0061803398874989354250,], [ 0.01937166322257262080, 0.004973797743297096040,], [ 0.019371663222572624300, -0.004973797743297089960,], [ 0.019645745014573775390, -0.00374762629171449370220,], [ 0.019645745014573775390, 0.003747626291714492830,], [ 0.019842294026289557240, -0.0025066646712860757990,], [ 0.019842294026289557240, 0.0025066646712860853400,], [ 0.019960534568565432840, -0.00125581039058626536990,], [ 0.019960534568565432840, 0.0012558103905862675380,], [ 0.02000, 0.0000,],] diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index 713b4d2..a6d67c0 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -12,9 +12,6 @@ from shapely.geometry import Point from shapely.geometry.polygon import Polygon -from decimal import Decimal -from pickle import FALSE - number_of_decimals = "11" np.set_printoptions(formatter={'float': lambda x: "{0:0." + number_of_decimals + "f}".format(x)+"0"}) @@ -280,7 +277,7 @@ def have_ending_zeros(lis): temp_dict = { "mesh_2d_input" : { "length_unit":self.length_unit, - "energy_barrier_thickness": decimal.Decimal(("{0:0." + str(len(str(self.energ_barrier_thickness))) + "f}").format(self.energy_barrier_thickness)+"0"), + "energy_barrier_thickness": decimal.Decimal(("{0:0." + str(len(str(self.energy_barrier_thickness))) + "f}").format(self.energy_barrier_thickness)+"0"), "triangles": have_ending_zeros(triangle_list), "densities":have_ending_zeros(material_densities), "material_boundary_points": have_ending_zeros(material_boundary_points), From c5e7970d2a32e69807740977972c2316b7a59927 Mon Sep 17 00:00:00 2001 From: Stephen Date: Wed, 20 Jan 2021 18:18:19 -0600 Subject: [PATCH 10/14] testing multipi-polygon shapes tested multiploygon shapes --- scripts/Mesh2D.toml | 6 +++--- scripts/create_mesh2D.py | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/Mesh2D.toml b/scripts/Mesh2D.toml index f1229e3..4d9848e 100644 --- a/scripts/Mesh2D.toml +++ b/scripts/Mesh2D.toml @@ -1,8 +1,8 @@ [mesh_2d_input] length_unit = "MICRON" energy_barrier_thickness = 0.00017645653881793785090 -triangles = [ [ -0.0190211303259030725670, -0.019371663222572620830, 0.0000, 0.006180339887498942360, 0.004973797743297096900, 0.0000,], [ -0.0136909421185737751460, -0.0145793725484282335470, 0.0000, 0.014579372548428228340, 0.01369094211857376990, 0.0000,], [ -0.017526133600877270850, -0.0180965410493203922300, 0.0000, 0.009635073482034304040, 0.00851558583130145040, 0.0000,], [ -0.0012558103905862679720, 0.0000, -3.216250E-18, 0.019960534568565432840, 0.0000, 0.02000,], [ -0.00374762629171449673790, -0.0049737977432970969030, 0.0000, 0.019645745014573771920, 0.01937166322257262080, 0.0000,], [ -0.0107165358995799375740, -0.0117557050458494613540, 0.0000, 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65000000000.00000000000000, 65000000000.00000000000000,], [ 65000000000.00000000000000, 65000000000.00000000000000,], [ 65000000000.00000000000000, 65000000000.00000000000000,],] material_boundary_points = [ [ -0.020000, -6.43250E-18,], [ -0.0199605345685654328450, -0.00125581039058626688780,], [ -0.0199605345685654328450, 0.0012558103905862627680,], [ -0.0198422940262895572410, -0.00250666467128608577360,], [ -0.0198422940262895572410, 0.002506664671286081870,], [ -0.0196457450145737753940, 0.0037476262917144915340,], [ -0.0196457450145737719250, -0.00374762629171449543690,], [ -0.019371663222572620830, -0.00497379774329710040,], [ -0.019371663222572620830, 0.004973797743297096900,], [ -0.0190211303259030725670, -0.00618033988749895450700,], [ -0.0190211303259030725670, 0.006180339887498942360,], [ -0.018595529717765030970, 0.007362491053693555330,], [ -0.0185955297177650240300, -0.0073624910536935666070,], [ -0.0180965410493203922300, 0.00851558583130145040,], [ 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0.010716535899579935840, -0.01688655851004030110,], [ 0.011755705045849461350, 0.016180339887498947780,], [ 0.011755705045849473500, -0.016180339887498940840,], [ 0.012748479794973793450, 0.015410264855515784860,], [ 0.0127484797949738000, -0.0154102648555157813880,], [ 0.013690942118573773410, -0.0145793725484282318120,], [ 0.013690942118573773410, 0.014579372548428231810,], [ 0.014579372548428231810, 0.013690942118573775150,], [ 0.014579372548428238750, -0.0136909421185737664730,], [ 0.015410264855515783120, 0.012748479794973795190,], [ 0.015410264855515788330, -0.0127484797949737934520,], [ 0.016180339887498947780, 0.011755705045849463090,], [ 0.016180339887498954720, -0.0117557050458494526810,], [ 0.0168865585100403010, 0.010716535899579934100,], [ 0.016886558510040308030, -0.0107165358995799271660,], [ 0.01752613360087727080, -0.0096350734820343075100,], [ 0.01752613360087727080, 0.009635073482034307510,], [ 0.01809654104932038880, 0.008515585831301453880,], [ 0.018096541049320395700, -0.0085155858313014452100,], [ 0.018595529717765027500, 0.00736249105369355970,], [ 0.01859552971776503100, -0.0073624910536935570670,], [ 0.019021130325903072570, 0.0061803398874989484350,], [ 0.019021130325903076040, -0.0061803398874989354250,], [ 0.01937166322257262080, 0.004973797743297096040,], [ 0.019371663222572624300, -0.004973797743297089960,], [ 0.019645745014573775390, -0.00374762629171449370220,], [ 0.019645745014573775390, 0.003747626291714492830,], [ 0.019842294026289557240, -0.0025066646712860757990,], [ 0.019842294026289557240, 0.0025066646712860853400,], [ 0.019960534568565432840, -0.00125581039058626536990,], [ 0.019960534568565432840, 0.0012558103905862675380,], [ 0.02000, 0.0000,],] simulation_boundary_points = [ [ 0.03000, 0.03000,], [ 0.03000, -0.030000,], [ -0.030000, 0.03000,], [ -0.030000, -0.030000,],] -electronic_stopping_correction_factors = [ 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000,] +electronic_stopping_correction_factors = [ 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000,] diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index a6d67c0..d8f828c 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -172,7 +172,7 @@ def return_Triangles(self): #print("Length of tri.simplices " + str(len(tri.simplices))) #print("Length of triangles " + str(len(triangles))) - temp_material_densities = [None]*(len(triangles)) + temp_material_densities = [0.0]*(len(triangles)) self.electronic_stopping_corrections = [1.0]*(len(triangles)) #print("Len of triangles " + str(len(triangles))) for i, triangle in enumerate(triangles): @@ -298,7 +298,7 @@ def have_ending_zeros(lis): mesh = Mesh("MICRON", .03,-.03,.03,-.03) mesh.N_gon(.02,100, [ 6.5E+10, 6.5E+10,]) - #mesh.N_gon(1.5, 4, 2, 5, 0, np.pi/4) + mesh.N_gon(.01, 4, [2*6.5E+10, 0.0,], 0, 0, np.pi/4) #mesh.add_Uniform_random(10) #mesh.print_Triangles() mesh.write_to_file(True) From c5b22a98b7cd4dc0da39cc2ddff3ead1a4b7e8b3 Mon Sep 17 00:00:00 2001 From: Stephen Date: Fri, 22 Jan 2021 16:39:52 -0600 Subject: [PATCH 11/14] Added Timeit Added timeit to see how long it takes to create mesh. --- scripts/Mesh2D.toml | 8 ++++---- scripts/create_mesh2D.py | 15 +++++++++++++-- 2 files changed, 17 insertions(+), 6 deletions(-) diff --git a/scripts/Mesh2D.toml b/scripts/Mesh2D.toml index 4d9848e..b229cd0 100644 --- a/scripts/Mesh2D.toml +++ b/scripts/Mesh2D.toml @@ -1,8 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-0.00175702393101486559720,], [ 0.01992267218286344900, 0.0017570239310148636460,], [ 0.019943178005212277430, -0.00150653611055865440520,], [ 0.019943178005212277430, 0.0015065361105586544050,], [ 0.019960534568565432840, -0.00125581039058626536990,], [ 0.019960534568565432840, 0.0012558103905862675380,], [ 0.01997473913212035120, -0.00100488636359538684520,], [ 0.01997473913212035120, 0.0010048863635953911820,], [ 0.019985789452811784930, -0.00075380365339868427190,], [ 0.019985789452811784930, 0.0007538036533986908860,], [ 0.019993683785666000, -0.0005026019088667409630,], [ 0.019993683785666000, 0.0005026019088667496360,], [ 0.019998420884076321960, -0.000251320797667041440600,], [ 0.019998420884076321960, 0.0002513207976670521740,], [ 0.02000, 0.0000,],] simulation_boundary_points = [ [ 0.03000, 0.03000,], [ 0.03000, -0.030000,], [ -0.030000, 0.03000,], [ -0.030000, -0.030000,],] -electronic_stopping_correction_factors = [ 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 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d8f828c..416df12 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -45,6 +45,7 @@ def __init__(self, length_unit, xmax, xmin, ymax, ymin, energy_barrier_thickness self.length_unit = length_unit self.electronic_stopping_corrections = [] self.energy_barrier_thickness = energy_barrier_thickness + self.pointnum = 0 def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0.0, theta_offset = 0.0): """ @@ -58,6 +59,8 @@ def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0 square: N_gon(2, 4, 2) offset square: N_gon(5, 4, 2, 1, 1, np.pi/4) """ + n_points = int(n_points) + self.pointnum += n_points n_points -= 0 dtheta = np.pi*2/n_points @@ -93,6 +96,7 @@ def triangle(self, arm1, arm2, theta, number_densities, x_offset = 0, y_offset = The x and y offset determine the center point theta_offset determines the rotation of the triangle ''' + self.pointnum += 3 point1 = Point(x_offset + arm1*math.cos(theta_offset), y_offset + arm1*math.sin(theta_offset)) point2 = Point(x_offset + arm2*math.cos(theta + theta_offset), y_offset + arm2*math.sin(theta + theta_offset)) center_point = Point(x_offset, y_offset) @@ -110,6 +114,7 @@ def rectangle(self, length1, length2, number_densities, x_offset = 0.0, y_offset length1 is the x-axis theta_offset rotates around the center point (radians) ''' + self.pointnum += 4 temp_points = [Point(x_offset, y_offset)] for i in range(4): temp_points.append(Point(x_offset + ((-1)**i*length1/2.0)*math.cos(theta_offset), y_offset + ((-1)**(math.floor(i/2))*length2/2.0)*math.sin(theta_offset) )) @@ -126,6 +131,7 @@ def add_Uniform_random(self, n_points): **Note** Will cause some shapes to have parts of them be labeled the incorrect number density. """ + self.pointnum += n_points temp_points = [] for _ in range(n_points): temp_points.append( @@ -295,16 +301,21 @@ def have_ending_zeros(lis): return temp_dict if __name__ == "__main__": + import timeit + start = timeit.default_timer() mesh = Mesh("MICRON", .03,-.03,.03,-.03) - mesh.N_gon(.02,100, [ 6.5E+10, 6.5E+10,]) + mesh.N_gon(.02,500, [ 6.5E+10, 6.5E+10,]) mesh.N_gon(.01, 4, [2*6.5E+10, 0.0,], 0, 0, np.pi/4) #mesh.add_Uniform_random(10) #mesh.print_Triangles() mesh.write_to_file(True) + end = timeit.default_timer() - + triangle_list, material_densities = mesh.return_Triangles() + + print(str(end-start) + "s to do " + str(len(triangle_list)) + " triangles" ) #code to plot out the example triangles for boron_nitride ''' From 9ea5e613dab1641f19ca602915220c003ff81430 Mon Sep 17 00:00:00 2001 From: Stephen Date: Tue, 2 Feb 2021 11:11:35 -0600 Subject: [PATCH 12/14] Added a Particle Generator Added a particle species creator for the input file in python. --- scripts/Mesh2D.toml | 10 +-- scripts/Particles.toml | 14 +++ scripts/create_mesh2D.py | 116 ++++++++++++++++++------- scripts/create_particle_parameters.py | 120 ++++++++++++++++++++++++++ 4 files changed, 224 insertions(+), 36 deletions(-) create mode 100644 scripts/Particles.toml create mode 100644 scripts/create_particle_parameters.py diff --git a/scripts/Mesh2D.toml b/scripts/Mesh2D.toml index b229cd0..348cd75 100644 --- a/scripts/Mesh2D.toml +++ b/scripts/Mesh2D.toml @@ -1,8 +1,8 @@ [mesh_2d_input] length_unit = "MICRON" energy_barrier_thickness = 0.00017645653881793785090 -triangles = [ [ 0.007071067811865473610, -0.0070710678118654770800, -3.67390E-18, -0.0070710678118654770800, -0.00707106781186547447840, -0.020000,], [ -0.0070710678118654770800, 0.007071067811865473610, 0.0000, -0.00707106781186547447840, -0.0070710678118654770800, 0.0000,], [ -0.0070710678118654770800, -0.00707106781186547447840, -0.020000, -0.00707106781186547447840, 0.007071067811865476210, 2.44930E-18,], [ 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500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,], [ 500000.000000000,],] +material_boundary_points = [ [ 0.0000, 0.0000,], [ 0.0000, 5.0000,], [ 0.0000, 10.00000,], [ 0.0000, 15.00000,], [ 0.0000, 20.00000,], [ 0.0000, 25.00000,], [ 0.0000, 30.00000,], [ 0.0000, 35.00000,], [ 0.0000, 40.00000,], [ 0.0000, 45.00000,], [ 0.0000, 50.00000,], [ 5.0000, 0.0000,], [ 5.0000, 5.0000,], [ 5.0000, 10.00000,], [ 5.0000, 15.00000,], [ 5.0000, 20.00000,], [ 5.0000, 25.00000,], [ 5.0000, 30.00000,], [ 5.0000, 35.00000,], [ 5.0000, 40.00000,], [ 5.0000, 45.00000,], [ 5.0000, 50.00000,], [ 10.00000, 0.0000,], [ 10.00000, 5.0000,], [ 10.00000, 10.00000,], [ 10.00000, 15.00000,], [ 10.00000, 20.00000,], [ 10.00000, 25.00000,], [ 10.00000, 30.00000,], [ 10.00000, 35.00000,], [ 10.00000, 40.00000,], [ 10.00000, 45.00000,], [ 10.00000, 50.00000,], [ 15.00000, 0.0000,], [ 15.00000, 5.0000,], [ 15.00000, 10.00000,], [ 15.00000, 15.00000,], [ 15.00000, 20.00000,], [ 15.00000, 25.00000,], [ 15.00000, 30.00000,], [ 15.00000, 35.00000,], [ 15.00000, 40.00000,], [ 15.00000, 45.00000,], [ 15.00000, 50.00000,], [ 20.00000, 0.0000,], [ 20.00000, 5.0000,], [ 20.00000, 10.00000,], [ 20.00000, 15.00000,], [ 20.00000, 20.00000,], [ 20.00000, 25.00000,], [ 20.00000, 30.00000,], [ 20.00000, 35.00000,], [ 20.00000, 40.00000,], [ 20.00000, 45.00000,], [ 20.00000, 50.00000,], [ 25.00000, 0.0000,], [ 25.00000, 5.0000,], [ 25.00000, 10.00000,], [ 25.00000, 15.00000,], [ 25.00000, 20.00000,], [ 25.00000, 25.00000,], [ 25.00000, 30.00000,], [ 25.00000, 35.00000,], [ 25.00000, 40.00000,], [ 25.00000, 45.00000,], [ 25.00000, 50.00000,], [ 30.00000, 0.0000,], [ 30.00000, 5.0000,], [ 30.00000, 10.00000,], [ 30.00000, 15.00000,], [ 30.00000, 20.00000,], [ 30.00000, 25.00000,], [ 30.00000, 30.00000,], [ 30.00000, 35.00000,], [ 30.00000, 40.00000,], [ 30.00000, 45.00000,], [ 30.00000, 50.00000,], [ 35.00000, 0.0000,], [ 35.00000, 5.0000,], [ 35.00000, 10.00000,], [ 35.00000, 15.00000,], [ 35.00000, 20.00000,], [ 35.00000, 25.00000,], [ 35.00000, 30.00000,], [ 35.00000, 35.00000,], [ 35.00000, 40.00000,], [ 35.00000, 45.00000,], [ 35.00000, 50.00000,], [ 40.00000, 0.0000,], [ 40.00000, 5.0000,], [ 40.00000, 10.00000,], [ 40.00000, 15.00000,], [ 40.00000, 20.00000,], [ 40.00000, 25.00000,], [ 40.00000, 30.00000,], [ 40.00000, 35.00000,], [ 40.00000, 40.00000,], [ 40.00000, 45.00000,], [ 40.00000, 50.00000,], [ 45.00000, 0.0000,], [ 45.00000, 5.0000,], [ 45.00000, 10.00000,], [ 45.00000, 15.00000,], [ 45.00000, 20.00000,], [ 45.00000, 25.00000,], [ 45.00000, 30.00000,], [ 45.00000, 35.00000,], [ 45.00000, 40.00000,], [ 45.00000, 45.00000,], [ 45.00000, 50.00000,], [ 50.00000, 0.0000,], [ 50.00000, 5.0000,], [ 50.00000, 10.00000,], [ 50.00000, 15.00000,], [ 50.00000, 20.00000,], [ 50.00000, 25.00000,], [ 50.00000, 30.00000,], [ 50.00000, 35.00000,], [ 50.00000, 40.00000,], [ 50.00000, 45.00000,], [ 50.00000, 50.00000,],] +simulation_boundary_points = [ [ 50.10000, 50.10000,], [ 50.10000, -0.10000,], [ -0.10000, -0.10000,], [ -0.10000, 50.10000,],] +electronic_stopping_correction_factors = [ 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 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1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000,] diff --git a/scripts/Particles.toml b/scripts/Particles.toml new file mode 100644 index 0000000..6ac8e61 --- /dev/null +++ b/scripts/Particles.toml @@ -0,0 +1,14 @@ +[particle_parameters] +length_unit = "MICRON" +energy_unit = "EV" +mass_unit = "AMU" +N = [ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,] +m = [ 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000,] +Z = [ 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00,] +E = [ 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000,] +Ec = [ 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000,] +Es = [ 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000,] +pos = [ [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,],] +dir = [ [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,],] +interaction_index = [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,] +particle_input_filename = "" diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index 416df12..ba3db54 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -9,6 +9,7 @@ import matplotlib.tri import scipy.spatial import random +import itertools from shapely.geometry import Point from shapely.geometry.polygon import Polygon @@ -35,7 +36,7 @@ def __init__(self, length_unit, xmax, xmin, ymax, ymin, energy_barrier_thickness self.trianglelist = [] - self.Simulation_boundaries = [[xmax, ymax], [xmax, ymin], [xmin, ymax], [xmin, ymin]] + self.Simulation_boundaries = [[xmax, ymax], [xmax, ymin], [xmin, ymin], [xmin, ymax]] self.points = [] self.shapes = [] self.xmax, self.xmin, self.ymax, self.ymin = xmax, xmin, ymax,ymin @@ -45,7 +46,7 @@ def __init__(self, length_unit, xmax, xmin, ymax, ymin, energy_barrier_thickness self.length_unit = length_unit self.electronic_stopping_corrections = [] self.energy_barrier_thickness = energy_barrier_thickness - self.pointnum = 0 + def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0.0, theta_offset = 0.0): """ @@ -60,7 +61,6 @@ def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0 offset square: N_gon(5, 4, 2, 1, 1, np.pi/4) """ n_points = int(n_points) - self.pointnum += n_points n_points -= 0 dtheta = np.pi*2/n_points @@ -71,19 +71,13 @@ def N_gon(self, radius, n_points, number_densities, x_offset = 0.0, y_offset = 0 Point(x_offset + radius*math.cos(dtheta*i + theta_offset), y_offset + radius*math.sin(dtheta*i + theta_offset)) ) - #print(temp_points) poly = Polygon(temp_points) - #print(poly) + center = Point(x_offset,y_offset) - #print(zero.within(poly)) - #print(poly.covers(zero)) if center.within(poly): temp_points.append(center) - #poly = Polygon(temp_points) - #print(zero.within(poly)) - + self.points += temp_points - #temp_points = np.asarray(temp_points) self.shapes.append([poly, number_densities]) @@ -96,7 +90,6 @@ def triangle(self, arm1, arm2, theta, number_densities, x_offset = 0, y_offset = The x and y offset determine the center point theta_offset determines the rotation of the triangle ''' - self.pointnum += 3 point1 = Point(x_offset + arm1*math.cos(theta_offset), y_offset + arm1*math.sin(theta_offset)) point2 = Point(x_offset + arm2*math.cos(theta + theta_offset), y_offset + arm2*math.sin(theta + theta_offset)) center_point = Point(x_offset, y_offset) @@ -104,26 +97,58 @@ def triangle(self, arm1, arm2, theta, number_densities, x_offset = 0, y_offset = temp_points = [point1,point2,center_point] self.points += temp_points - self.shapes.append(Polygon(temp_points), number_densities) + self.shapes.append([Polygon(temp_points), number_densities]) - def rectangle(self, length1, length2, number_densities, x_offset = 0.0, y_offset = 0.0, theta_offset = 0.0): + def rectangle(self, length_x, length_y, number_densities, x_offset = 0.0, y_offset = 0.0, theta_offset = 0.0): ''' returns True on completion creates a single rectangle with center (x_offset, y_offset) and side lengths length1 and length2 length1 is the x-axis - theta_offset rotates around the center point (radians) + theta_offset rotates around the center point (radians) <- NOT IMPLEMENTED CORRECTLY CURRENTLY ''' - self.pointnum += 4 - temp_points = [Point(x_offset, y_offset)] - for i in range(4): - temp_points.append(Point(x_offset + ((-1)**i*length1/2.0)*math.cos(theta_offset), y_offset + ((-1)**(math.floor(i/2))*length2/2.0)*math.sin(theta_offset) )) + temp_points = [] + for i in range(0,2): + for j in range(0,2): + temp_points.append( + Point(x_offset + (-1)**i * length_x/2.0, y_offset + (-1)**(i ^ j) * length_y/2.0) + ) + + #print(temp_points) + + + poly = Polygon(temp_points) + center = Point(x_offset,y_offset) + #print(center.within(poly)) + if center.within(poly): + temp_points.append(center) + + self.points += temp_points - self.shapes.append(Polygon(temp_points), number_densities) + self.shapes.append([poly, number_densities]) return True + + def rectangle_grid(self, n_x, n_y, total_length_x, total_length_y, number_densities, bottom_left_x = 0.0, bottom_left_y = 0.0): + ''' + returns True on completion + Uses the total length and number of rectangles per side to calculate how rectangles should be made + The anchor point is the bottom left most point of the grid of rectangles + Since rectangles are defined the way they are in the code below it has to divide the number of rectangles per side by 2 to get what people intuit as the number of rectangles made of two triangles per side + ''' + + n_x, n_y = n_x, n_y + length_x = total_length_x/n_x + length_y = total_length_y/n_y + + for j in range(n_y): + for i in range(n_x): + self.rectangle(length_x, length_y, number_densities, x_offset = (bottom_left_x + length_x/2 + i*length_x), y_offset = (bottom_left_y + length_y/2 + j*length_y)) + + return True + def add_Uniform_random(self, n_points): """ returns True on completion. @@ -131,7 +156,6 @@ def add_Uniform_random(self, n_points): **Note** Will cause some shapes to have parts of them be labeled the incorrect number density. """ - self.pointnum += n_points temp_points = [] for _ in range(n_points): temp_points.append( @@ -141,11 +165,27 @@ def add_Uniform_random(self, n_points): self.points += temp_points return True + def clean_points(self): + temp = [] + for point in self.points: + temp.append([point.x,point.y]) + + temp.sort() + temp = list(temp for temp,_ in itertools.groupby(temp)) + + for i in range(len(temp)): + temp[i] = Point(temp[i]) + + self.points = temp + + return True + def get_Points(self): """ Deprecated - Don't use returns all of the individual points in the simulation as a np array """ + #self.clean_points() temp = [] for point in self.points: temp.append([point.x,point.y]) @@ -158,13 +198,17 @@ def generate_Triangles(self): Generates triangles via the Delauny method: see scipy.spatial.Delaunay """ + #print(len(self.get_Points())) return scipy.spatial.Delaunay(self.get_Points()) def return_Triangles(self): """ returns 2 lists : points, material densities Creates and Correlates the triangles to their number densities. + + Will throw errors shapely errors if lines overlap """ + points = self.get_Points() tri = self.generate_Triangles() @@ -183,10 +227,14 @@ def return_Triangles(self): #print("Len of triangles " + str(len(triangles))) for i, triangle in enumerate(triangles): for shape, number_densities in self.shapes: - if shape.contains(triangle): + if shape.contains(triangle) or shape.relate_pattern(triangle, 'FF2FF1212') or shape.relate_pattern(triangle, '212101212'): + #print(shape.relate(triangle)) temp_material_densities[i] = list(number_densities) - + else: + #print(shape.relate(triangle)) + continue #print(point_output) + print(len(temp_material_densities)) return point_output, temp_material_densities def print_Triangles(self): @@ -214,10 +262,13 @@ def print_Triangles(self): #print(type(triangles[0])) #plt.triplot(points[:,0], points[:,1], tri.simplices) - plt.xlim(self.Simulation_boundaries[1][0], self.Simulation_boundaries[-1][0]) - plt.ylim(self.Simulation_boundaries[0:2][1]) + plt.xlim(self.Simulation_boundaries[-1][0], self.Simulation_boundaries[1][0]) + plt.ylim(self.Simulation_boundaries[1][1], self.Simulation_boundaries[0][1]) for i, triangle in enumerate(triangles): - plt.triplot(triangle, self.color_dict[material_densities[i]]+ "-", ) + if type(material_densities[i]) == list: + plt.triplot(triangle, self.color_dict[material_densities[i][0]]+ "-", ) + else: + plt.triplot(triangle, self.color_dict[material_densities[i]]+ "-", ) plt.show() return True @@ -239,7 +290,7 @@ def write_to_file(self, dump_to_file = False): if pointPoint.within(shape): material_boundary_points.pop(i) - import itertools + material_boundary_points.sort() material_boundary_points = list(material_boundary_points for material_boundary_points,_ in itertools.groupby(material_boundary_points)) #print(len(material_boundary_points)) @@ -303,14 +354,17 @@ def have_ending_zeros(lis): import timeit start = timeit.default_timer() - mesh = Mesh("MICRON", .03,-.03,.03,-.03) + mesh = Mesh("MICRON", 50.1, -0.1, 50.1, -0.1) + + #mesh.N_gon(2, 4, [1], 1, 1, -np.pi/4 ) + #mesh.rectangle(1, 1, [2], 1, 1) + mesh.rectangle_grid(10, 10, 50, 50, [5e5]) #Actual Number = 5.305e11 - mesh.N_gon(.02,500, [ 6.5E+10, 6.5E+10,]) - mesh.N_gon(.01, 4, [2*6.5E+10, 0.0,], 0, 0, np.pi/4) - #mesh.add_Uniform_random(10) #mesh.print_Triangles() mesh.write_to_file(True) + + end = timeit.default_timer() triangle_list, material_densities = mesh.return_Triangles() diff --git a/scripts/create_particle_parameters.py b/scripts/create_particle_parameters.py new file mode 100644 index 0000000..9f6b88f --- /dev/null +++ b/scripts/create_particle_parameters.py @@ -0,0 +1,120 @@ +''' +Created on Jan 28, 2021 + +@author: Stephen +''' +import numpy as np +from schedula.utils.cst import SELF + +number_of_decimals = "11" +np.set_printoptions(formatter={'float': lambda x: "{0:0." + number_of_decimals + "f}".format(x)+"0"}) + +zero = [0.9999999999984769, 1.7453292519934434e-6, 0.0] + +class Particles(): + def __init__(self): + + self.N = [] + self.masses = [] + self.Z = [] + self.E = [] + self.Ec = [] + self.Es = [] + self.positions = [] + self.directions = [] + self.interaction_index = [] + + + def add_particle_species(self, number_of_parts, N, mass, Z, E, Ec, Es, position = None, direction = None, interaction_index = None): + for _ in range(number_of_parts): + self.N.append(N) + self.masses.append(mass) + self.Z.append(Z) + self.E.append(E) + self.Ec.append(Ec) + self.Es.append(Es) + + + + if position != None: + if type(position) == list: + self.positions.append(position) + else: + self.positions.append([0.0, 0.0, 0.0]) + if direction != None: + if type(direction) == list: + self.directions.append(np.asarray(direction)) + else: + self.directions.append(zero) + + if interaction_index != None: + if type(interaction_index) == list: + self.interaction_index.append(interaction_index) + else: + self.interaction_index.append(0) + + + return True + + def write_to_file(self, dump_to_file = False): + + import decimal + decimal.getcontext().prec = int(number_of_decimals) + 2 + def have_ending_zeros(lis): + #lis = np.asarray(lis) + + if type(lis[0]) == tuple: + for i in range(len(lis)): + lis[i] = list(lis[i]) + + for i in range(len(lis)): + if type(lis[i]) == np.float64 or type(lis[i]) == np.float32 or type(lis[i]) == int or type(lis[i]) == float: + lis[i] = decimal.Decimal(("{0:0." + str(len(str(lis[i]))) + "f}").format(lis[i])+"0")#.quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + #lis[i] = decimal.Decimal(lis[i]).quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + else: + if type(lis[i]) == type(decimal.Decimal(1.0)): + pass + for j in range(len(lis[i])): + if type(lis[i][j]) == np.float64 or type(lis[i][j]) == np.float32 or type(lis[i][j]) == int or type(lis[i][j]) == float or True: + lis[i][j] = decimal.Decimal(("{0:0." + str(len(str(lis[i][j]))) + "f}").format(lis[i][j])+"0")#.quantize(decimal.Decimal("1." + "0"*(int(number_of_decimals)))) + #lis[i][j] = decimal.Decimal(lis[i][j]).quantize(decimal.Decimal("1." + "0"*(int(number_of_decimals)))) + else: + if type(lis[i][j]) == type(decimal.Decimal(1.0)): + pass + for k in range(len(lis[i][j])): + if type(lis[i][j][k]) == np.float64 or type(lis[i][j][k]) == np.float32 or type(lis[i][j][k]) == int or type(lis[i][j][k]) == float: + lis[i][j][k] = decimal.Decimal(("{0:0." + str(len(str(lis[i][j][k]))) + "f}").format(lis[i][j][k])+"0")#.quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + #lis[i][j][k] = decimal.Decimal(lis[i][j][k]).quantize(Decimal("1." + "0"*(int(number_of_decimals)))) + else: + pass + + return lis + + file = open("Particles.toml", "w") + file.seek(0) + temp_dict = { + "particle_parameters" :{ + "length_unit" : "MICRON", + "energy_unit" : "EV", + "mass_unit" : "AMU", + "N" : [int(i) for i in self.N], + "m" : have_ending_zeros(self.masses), + "Z" : have_ending_zeros(self.Z), + "E" : have_ending_zeros(self.E), + "Ec" : have_ending_zeros(self.Ec), + "Es" : have_ending_zeros(self.Es), + "pos" : have_ending_zeros(self.positions), + "dir" : have_ending_zeros(self.directions), + "interaction_index" : [int(i) for i in self.interaction_index], + "particle_input_filename" : "" + } + } + if dump_to_file: + import toml + toml.dump(temp_dict, file) + return temp_dict + +if __name__ == "__main__": + particle = Particles() + particle.add_particle_species(10, 1, 1.008, 1, 100000.0, .5, 10.0, position = [0.0,25.0,0.0]) + particle.write_to_file(True) \ No newline at end of file From 4a803a67faa6568366f479d87b1b6ec0279bdc9e Mon Sep 17 00:00:00 2001 From: Stephen Date: Tue, 2 Feb 2021 11:42:03 -0600 Subject: [PATCH 13/14] Testing Copper Space Ship Removed some print statements in create_mesh2D and ran tests for a copper 50x50 micron ship --- scripts/Mesh2D.toml | 2 +- scripts/Particles.toml | 2 +- scripts/create_mesh2D.py | 4 ++-- scripts/create_particle_parameters.py | 5 ++++- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/scripts/Mesh2D.toml b/scripts/Mesh2D.toml index 348cd75..4818f71 100644 --- a/scripts/Mesh2D.toml +++ b/scripts/Mesh2D.toml @@ -2,7 +2,7 @@ length_unit = "MICRON" energy_barrier_thickness = 0.00017645653881793785090 triangles = [ [ 5.0000, 2.5000, 0.0000, 0.0000, 2.5000, 0.0000,], [ 25.00000, 30.00000, 27.50000, 0.0000, 0.0000, 2.5000,], [ 2.5000, 0.0000, 0.0000, 2.5000, 5.0000, 0.0000,], [ 0.0000, 0.0000, 2.5000, 30.00000, 25.00000, 27.50000,], [ 20.00000, 22.50000, 25.00000, 50.00000, 47.50000, 50.00000,], [ 47.50000, 50.00000, 50.00000, 2.5000, 0.0000, 5.0000,], [ 0.0000, 2.5000, 5.0000, 50.00000, 47.50000, 50.00000,], [ 50.00000, 50.00000, 47.50000, 15.00000, 20.00000, 17.50000,], [ 47.50000, 50.00000, 50.00000, 22.50000, 20.00000, 25.00000,], [ 35.00000, 40.00000, 37.50000, 0.0000, 0.0000, 2.5000,], [ 47.50000, 45.00000, 50.00000, 2.5000, 0.0000, 0.0000,], [ 40.00000, 45.00000, 42.50000, 0.0000, 0.0000, 2.5000,], [ 0.0000, 2.5000, 0.0000, 45.00000, 47.50000, 50.00000,], [ 0.0000, 0.0000, 2.5000, 45.00000, 40.00000, 42.50000,], [ 2.5000, 0.0000, 0.0000, 32.50000, 35.00000, 30.00000,], [ 0.0000, 0.0000, 2.5000, 40.00000, 35.00000, 37.50000,], [ 0.0000, 0.0000, 2.5000, 10.00000, 5.0000, 7.5000,], [ 0.0000, 0.0000, 2.5000, 15.00000, 10.00000, 12.50000,], [ 0.0000, 2.5000, 0.0000, 20.00000, 22.50000, 25.00000,], [ 50.00000, 50.00000, 47.50000, 40.00000, 45.00000, 42.50000,], [ 50.00000, 47.50000, 50.00000, 30.00000, 27.50000, 25.00000,], [ 35.00000, 30.00000, 32.50000, 50.00000, 50.00000, 47.50000,], [ 27.50000, 30.00000, 25.00000, 47.50000, 50.00000, 50.00000,], [ 2.5000, 0.0000, 0.0000, 17.50000, 20.00000, 15.00000,], [ 50.00000, 47.50000, 50.00000, 10.00000, 7.5000, 5.0000,], [ 47.50000, 50.00000, 50.00000, 12.50000, 10.00000, 15.00000,], [ 50.00000, 47.50000, 50.00000, 40.00000, 37.50000, 35.00000,], [ 47.50000, 50.00000, 50.00000, 32.50000, 30.00000, 35.00000,], [ 35.00000, 37.50000, 40.00000, 50.00000, 47.50000, 50.00000,], [ 20.00000, 17.50000, 15.00000, 0.0000, 2.5000, 0.0000,], [ 22.50000, 20.00000, 25.00000, 2.5000, 0.0000, 0.0000,], [ 12.50000, 10.00000, 15.00000, 2.5000, 0.0000, 0.0000,], [ 47.50000, 50.00000, 50.00000, 47.50000, 45.00000, 50.00000,], [ 45.00000, 47.50000, 50.00000, 50.00000, 47.50000, 50.00000,], [ 42.50000, 45.00000, 40.00000, 47.50000, 50.00000, 50.00000,], [ 35.00000, 32.50000, 30.00000, 0.0000, 2.5000, 0.0000,], [ 15.00000, 17.50000, 20.00000, 50.00000, 47.50000, 50.00000,], [ 10.00000, 7.5000, 5.0000, 0.0000, 2.5000, 0.0000,], [ 7.5000, 10.00000, 5.0000, 47.50000, 50.00000, 50.00000,], [ 10.00000, 12.50000, 15.00000, 50.00000, 47.50000, 50.00000,], [ 5.0000, 0.0000, 2.5000, 5.0000, 5.0000, 2.5000,], [ 0.0000, 5.0000, 2.5000, 5.0000, 5.0000, 7.5000,], [ 22.50000, 27.50000, 25.00000, 47.50000, 47.50000, 50.00000,], [ 27.50000, 22.50000, 25.00000, 47.50000, 47.50000, 45.00000,], [ 0.0000, 5.0000, 2.5000, 10.00000, 10.00000, 12.50000,], [ 5.0000, 0.0000, 2.5000, 10.00000, 10.00000, 7.5000,], [ 45.00000, 45.00000, 42.50000, 0.0000, 5.0000, 2.5000,], [ 45.00000, 45.00000, 47.50000, 5.0000, 0.0000, 2.5000,], [ 47.50000, 47.50000, 50.00000, 27.50000, 22.50000, 25.00000,], [ 47.50000, 47.50000, 45.00000, 22.50000, 27.50000, 25.00000,], [ 47.50000, 42.50000, 45.00000, 27.50000, 27.50000, 25.00000,], [ 42.50000, 47.50000, 45.00000, 27.50000, 27.50000, 30.00000,], [ 30.00000, 27.50000, 25.00000, 5.0000, 7.5000, 5.0000,], [ 30.00000, 25.00000, 27.50000, 5.0000, 5.0000, 2.5000,], [ 0.0000, 5.0000, 2.5000, 40.00000, 40.00000, 42.50000,], [ 5.0000, 0.0000, 2.5000, 40.00000, 40.00000, 37.50000,], [ 0.0000, 5.0000, 2.5000, 45.00000, 45.00000, 47.50000,], [ 5.0000, 0.0000, 2.5000, 45.00000, 45.00000, 42.50000,], [ 5.0000, 5.0000, 2.5000, 40.00000, 45.00000, 42.50000,], [ 5.0000, 5.0000, 7.5000, 45.00000, 40.00000, 42.50000,], [ 2.5000, 5.0000, 0.0000, 22.50000, 25.00000, 25.00000,], [ 0.0000, 5.0000, 2.5000, 25.00000, 25.00000, 27.50000,], [ 12.50000, 12.50000, 10.00000, 22.50000, 27.50000, 25.00000,], [ 12.50000, 12.50000, 15.00000, 27.50000, 22.50000, 25.00000,], [ 17.50000, 12.50000, 15.00000, 27.50000, 27.50000, 25.00000,], [ 12.50000, 17.50000, 15.00000, 27.50000, 27.50000, 30.00000,], [ 17.50000, 17.50000, 15.00000, 22.50000, 27.50000, 25.00000,], [ 17.50000, 17.50000, 20.00000, 27.50000, 22.50000, 25.00000,], [ 17.50000, 20.00000, 22.50000, 22.50000, 20.00000, 22.50000,], [ 20.00000, 17.50000, 22.50000, 25.00000, 22.50000, 22.50000,], [ 5.0000, 7.5000, 2.5000, 5.0000, 7.5000, 7.5000,], [ 7.5000, 5.0000, 2.5000, 7.5000, 10.00000, 7.5000,], [ 7.5000, 7.5000, 5.0000, 7.5000, 12.50000, 10.00000,], [ 7.5000, 7.5000, 10.00000, 12.50000, 7.5000, 10.00000,], [ 5.0000, 7.5000, 2.5000, 10.00000, 12.50000, 12.50000,], [ 7.5000, 5.0000, 2.5000, 12.50000, 15.00000, 12.50000,], [ 2.5000, 7.5000, 5.0000, 17.50000, 17.50000, 20.00000,], [ 7.5000, 2.5000, 5.0000, 17.50000, 17.50000, 15.00000,], [ 5.0000, 2.5000, 2.5000, 15.00000, 17.50000, 12.50000,], [ 2.5000, 0.0000, 2.5000, 17.50000, 15.00000, 12.50000,], [ 2.5000, 2.5000, 5.0000, 22.50000, 17.50000, 20.00000,], [ 0.0000, 2.5000, 2.5000, 20.00000, 17.50000, 22.50000,], [ 40.00000, 40.00000, 42.50000, 5.0000, 0.0000, 2.5000,], [ 40.00000, 40.00000, 37.50000, 0.0000, 5.0000, 2.5000,], [ 47.50000, 45.00000, 47.50000, 7.5000, 5.0000, 2.5000,], [ 47.50000, 47.50000, 50.00000, 7.5000, 2.5000, 5.0000,], [ 45.00000, 50.00000, 47.50000, 20.00000, 20.00000, 22.50000,], [ 50.00000, 45.00000, 47.50000, 20.00000, 20.00000, 17.50000,], [ 45.00000, 47.50000, 45.00000, 20.00000, 22.50000, 25.00000,], [ 42.50000, 45.00000, 45.00000, 22.50000, 20.00000, 25.00000,], [ 47.50000, 47.50000, 50.00000, 12.50000, 7.5000, 10.00000,], [ 47.50000, 47.50000, 45.00000, 7.5000, 12.50000, 10.00000,], [ 45.00000, 47.50000, 47.50000, 15.00000, 12.50000, 17.50000,], [ 47.50000, 50.00000, 47.50000, 12.50000, 15.00000, 17.50000,], [ 47.50000, 47.50000, 45.00000, 27.50000, 32.50000, 30.00000,], [ 47.50000, 47.50000, 50.00000, 32.50000, 27.50000, 30.00000,], [ 47.50000, 47.50000, 45.00000, 32.50000, 37.50000, 35.00000,], [ 47.50000, 47.50000, 50.00000, 37.50000, 32.50000, 35.00000,], [ 42.50000, 47.50000, 45.00000, 32.50000, 32.50000, 35.00000,], [ 47.50000, 42.50000, 45.00000, 32.50000, 32.50000, 30.00000,], [ 40.00000, 35.00000, 37.50000, 25.00000, 25.00000, 22.50000,], [ 35.00000, 40.00000, 37.50000, 25.00000, 25.00000, 27.50000,], [ 42.50000, 40.00000, 45.00000, 27.50000, 25.00000, 25.00000,], [ 40.00000, 42.50000, 45.00000, 25.00000, 22.50000, 25.00000,], [ 35.00000, 37.50000, 32.50000, 45.00000, 47.50000, 47.50000,], [ 37.50000, 35.00000, 32.50000, 47.50000, 50.00000, 47.50000,], [ 30.00000, 30.00000, 27.50000, 45.00000, 50.00000, 47.50000,], [ 30.00000, 30.00000, 32.50000, 50.00000, 45.00000, 47.50000,], [ 30.00000, 32.50000, 35.00000, 45.00000, 42.50000, 45.00000,], [ 30.00000, 35.00000, 32.50000, 45.00000, 45.00000, 47.50000,], [ 25.00000, 25.00000, 27.50000, 25.00000, 20.00000, 22.50000,], [ 25.00000, 25.00000, 22.50000, 20.00000, 25.00000, 22.50000,], [ 17.50000, 15.00000, 17.50000, 17.50000, 15.00000, 12.50000,], [ 17.50000, 17.50000, 20.00000, 17.50000, 12.50000, 15.00000,], [ 30.00000, 32.50000, 27.50000, 5.0000, 7.5000, 7.5000,], [ 32.50000, 30.00000, 27.50000, 7.5000, 10.00000, 7.5000,], [ 22.50000, 22.50000, 25.00000, 47.50000, 42.50000, 45.00000,], [ 20.00000, 22.50000, 22.50000, 45.00000, 42.50000, 47.50000,], [ 30.00000, 30.00000, 32.50000, 35.00000, 30.00000, 32.50000,], [ 30.00000, 30.00000, 27.50000, 30.00000, 35.00000, 32.50000,], [ 35.00000, 35.00000, 37.50000, 40.00000, 35.00000, 37.50000,], [ 35.00000, 35.00000, 32.50000, 35.00000, 40.00000, 37.50000,], [ 35.00000, 30.00000, 32.50000, 35.00000, 35.00000, 32.50000,], [ 30.00000, 35.00000, 32.50000, 35.00000, 35.00000, 37.50000,], [ 7.5000, 5.0000, 2.5000, 22.50000, 25.00000, 22.50000,], [ 7.5000, 2.5000, 5.0000, 22.50000, 22.50000, 20.00000,], [ 7.5000, 7.5000, 5.0000, 22.50000, 27.50000, 25.00000,], [ 7.5000, 7.5000, 10.00000, 27.50000, 22.50000, 25.00000,], [ 17.50000, 20.00000, 15.00000, 27.50000, 30.00000, 30.00000,], [ 20.00000, 17.50000, 15.00000, 30.00000, 32.50000, 30.00000,], [ 25.00000, 22.50000, 27.50000, 5.0000, 2.5000, 2.5000,], [ 22.50000, 25.00000, 27.50000, 2.5000, 0.0000, 2.5000,], [ 17.50000, 22.50000, 20.00000, 2.5000, 2.5000, 5.0000,], [ 22.50000, 17.50000, 20.00000, 2.5000, 2.5000, 0.0000,], [ 22.50000, 22.50000, 25.00000, 7.5000, 2.5000, 5.0000,], [ 22.50000, 22.50000, 20.00000, 2.5000, 7.5000, 5.0000,], [ 15.00000, 10.00000, 12.50000, 15.00000, 15.00000, 12.50000,], [ 10.00000, 15.00000, 12.50000, 15.00000, 15.00000, 17.50000,], [ 7.5000, 10.00000, 5.0000, 12.50000, 15.00000, 15.00000,], [ 10.00000, 7.5000, 5.0000, 15.00000, 17.50000, 15.00000,], [ 12.50000, 10.00000, 10.00000, 12.50000, 15.00000, 10.00000,], [ 10.00000, 7.5000, 10.00000, 15.00000, 12.50000, 10.00000,], [ 47.50000, 42.50000, 45.00000, 12.50000, 12.50000, 10.00000,], [ 42.50000, 47.50000, 45.00000, 12.50000, 12.50000, 15.00000,], [ 45.00000, 42.50000, 40.00000, 40.00000, 42.50000, 40.00000,], [ 42.50000, 45.00000, 40.00000, 37.50000, 40.00000, 40.00000,], [ 45.00000, 45.00000, 47.50000, 45.00000, 40.00000, 42.50000,], [ 45.00000, 45.00000, 42.50000, 40.00000, 45.00000, 42.50000,], [ 47.50000, 45.00000, 45.00000, 37.50000, 40.00000, 35.00000,], [ 45.00000, 45.00000, 42.50000, 35.00000, 40.00000, 37.50000,], [ 45.00000, 50.00000, 47.50000, 40.00000, 40.00000, 42.50000,], [ 45.00000, 47.50000, 50.00000, 40.00000, 37.50000, 40.00000,], [ 47.50000, 45.00000, 47.50000, 47.50000, 45.00000, 42.50000,], [ 50.00000, 47.50000, 47.50000, 45.00000, 47.50000, 42.50000,], [ 42.50000, 37.50000, 40.00000, 47.50000, 47.50000, 45.00000,], [ 37.50000, 42.50000, 40.00000, 47.50000, 47.50000, 50.00000,], [ 47.50000, 42.50000, 45.00000, 47.50000, 47.50000, 45.00000,], [ 42.50000, 47.50000, 45.00000, 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30.00000,], [ 50.00000, 35.00000,], [ 50.00000, 40.00000,], [ 50.00000, 45.00000,], [ 50.00000, 50.00000,],] simulation_boundary_points = [ [ 50.10000, 50.10000,], [ 50.10000, -0.10000,], [ -0.10000, -0.10000,], [ -0.10000, 50.10000,],] electronic_stopping_correction_factors = [ 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 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1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000, 1.0000,] diff --git a/scripts/Particles.toml b/scripts/Particles.toml index 6ac8e61..308d60c 100644 --- a/scripts/Particles.toml +++ b/scripts/Particles.toml @@ -8,7 +8,7 @@ Z = [ 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00,] E = [ 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000,] Ec = [ 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000,] Es = [ 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000,] -pos = [ [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,], [ 0E-8, 25.00000000000000000000000000000000000000000, 0E-8,],] +pos = [ [ 0.0000, 35.000, 0.0000,], [ 0.0000, 7.00, 0.0000,], [ 0.0000, 11.000, 0.0000,], [ 0.0000, 19.000, 0.0000,], [ 0.0000, 10.000, 0.0000,], [ 0.0000, 40.000, 0.0000,], [ 0.0000, 50.000, 0.0000,], [ 0.0000, 39.000, 0.0000,], [ 0.0000, 1.00, 0.0000,], [ 0.0000, 16.000, 0.0000,],] dir = [ [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,],] interaction_index = [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,] particle_input_filename = "" diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index ba3db54..528d2f8 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -234,7 +234,7 @@ def return_Triangles(self): #print(shape.relate(triangle)) continue #print(point_output) - print(len(temp_material_densities)) + #print(len(temp_material_densities)) return point_output, temp_material_densities def print_Triangles(self): @@ -358,7 +358,7 @@ def have_ending_zeros(lis): #mesh.N_gon(2, 4, [1], 1, 1, -np.pi/4 ) #mesh.rectangle(1, 1, [2], 1, 1) - mesh.rectangle_grid(10, 10, 50, 50, [5e5]) #Actual Number = 5.305e11 + mesh.rectangle_grid(10, 10, 50, 50, [5.305e9]) #Actual Number = 5.305e11 #mesh.print_Triangles() mesh.write_to_file(True) diff --git a/scripts/create_particle_parameters.py b/scripts/create_particle_parameters.py index 9f6b88f..4766b43 100644 --- a/scripts/create_particle_parameters.py +++ b/scripts/create_particle_parameters.py @@ -115,6 +115,9 @@ def have_ending_zeros(lis): return temp_dict if __name__ == "__main__": + import random particle = Particles() - particle.add_particle_species(10, 1, 1.008, 1, 100000.0, .5, 10.0, position = [0.0,25.0,0.0]) + + for i in range(10): + particle.add_particle_species(1, 1, 1.008, 1, 100000.0, .5, 10.0, position = [0.0,random.randint(0,50.0),0.0]) particle.write_to_file(True) \ No newline at end of file From f742236eefa1bf0819b8390f9ee6356fc7698e94 Mon Sep 17 00:00:00 2001 From: Stephen Date: Wed, 17 Feb 2021 20:39:59 -0600 Subject: [PATCH 14/14] Made ending zeros simple Removed custom function to make everything have ending zeros for toml. Now uses the toml encoder keyword --- scripts/Mesh2D.toml | 12 ++++++------ scripts/Particles.toml | 14 -------------- scripts/create_mesh2D.py | 23 ++++++++++++++++++----- scripts/create_particle_parameters.py | 20 ++++++++++---------- 4 files changed, 34 insertions(+), 35 deletions(-) diff --git a/scripts/Mesh2D.toml b/scripts/Mesh2D.toml index 4818f71..91fcc89 100644 --- a/scripts/Mesh2D.toml +++ b/scripts/Mesh2D.toml @@ -1,8 +1,8 @@ [mesh_2d_input] length_unit = "MICRON" -energy_barrier_thickness = 0.00017645653881793785090 -triangles = [ [ 5.0000, 2.5000, 0.0000, 0.0000, 2.5000, 0.0000,], [ 25.00000, 30.00000, 27.50000, 0.0000, 0.0000, 2.5000,], [ 2.5000, 0.0000, 0.0000, 2.5000, 5.0000, 0.0000,], [ 0.0000, 0.0000, 2.5000, 30.00000, 25.00000, 27.50000,], [ 20.00000, 22.50000, 25.00000, 50.00000, 47.50000, 50.00000,], [ 47.50000, 50.00000, 50.00000, 2.5000, 0.0000, 5.0000,], [ 0.0000, 2.5000, 5.0000, 50.00000, 47.50000, 50.00000,], [ 50.00000, 50.00000, 47.50000, 15.00000, 20.00000, 17.50000,], [ 47.50000, 50.00000, 50.00000, 22.50000, 20.00000, 25.00000,], [ 35.00000, 40.00000, 37.50000, 0.0000, 0.0000, 2.5000,], [ 47.50000, 45.00000, 50.00000, 2.5000, 0.0000, 0.0000,], [ 40.00000, 45.00000, 42.50000, 0.0000, 0.0000, 2.5000,], [ 0.0000, 2.5000, 0.0000, 45.00000, 47.50000, 50.00000,], [ 0.0000, 0.0000, 2.5000, 45.00000, 40.00000, 42.50000,], [ 2.5000, 0.0000, 0.0000, 32.50000, 35.00000, 30.00000,], [ 0.0000, 0.0000, 2.5000, 40.00000, 35.00000, 37.50000,], [ 0.0000, 0.0000, 2.5000, 10.00000, 5.0000, 7.5000,], [ 0.0000, 0.0000, 2.5000, 15.00000, 10.00000, 12.50000,], [ 0.0000, 2.5000, 0.0000, 20.00000, 22.50000, 25.00000,], [ 50.00000, 50.00000, 47.50000, 40.00000, 45.00000, 42.50000,], [ 50.00000, 47.50000, 50.00000, 30.00000, 27.50000, 25.00000,], [ 35.00000, 30.00000, 32.50000, 50.00000, 50.00000, 47.50000,], [ 27.50000, 30.00000, 25.00000, 47.50000, 50.00000, 50.00000,], [ 2.5000, 0.0000, 0.0000, 17.50000, 20.00000, 15.00000,], [ 50.00000, 47.50000, 50.00000, 10.00000, 7.5000, 5.0000,], [ 47.50000, 50.00000, 50.00000, 12.50000, 10.00000, 15.00000,], [ 50.00000, 47.50000, 50.00000, 40.00000, 37.50000, 35.00000,], [ 47.50000, 50.00000, 50.00000, 32.50000, 30.00000, 35.00000,], [ 35.00000, 37.50000, 40.00000, 50.00000, 47.50000, 50.00000,], [ 20.00000, 17.50000, 15.00000, 0.0000, 2.5000, 0.0000,], [ 22.50000, 20.00000, 25.00000, 2.5000, 0.0000, 0.0000,], [ 12.50000, 10.00000, 15.00000, 2.5000, 0.0000, 0.0000,], [ 47.50000, 50.00000, 50.00000, 47.50000, 45.00000, 50.00000,], [ 45.00000, 47.50000, 50.00000, 50.00000, 47.50000, 50.00000,], [ 42.50000, 45.00000, 40.00000, 47.50000, 50.00000, 50.00000,], [ 35.00000, 32.50000, 30.00000, 0.0000, 2.5000, 0.0000,], [ 15.00000, 17.50000, 20.00000, 50.00000, 47.50000, 50.00000,], [ 10.00000, 7.5000, 5.0000, 0.0000, 2.5000, 0.0000,], [ 7.5000, 10.00000, 5.0000, 47.50000, 50.00000, 50.00000,], [ 10.00000, 12.50000, 15.00000, 50.00000, 47.50000, 50.00000,], [ 5.0000, 0.0000, 2.5000, 5.0000, 5.0000, 2.5000,], [ 0.0000, 5.0000, 2.5000, 5.0000, 5.0000, 7.5000,], [ 22.50000, 27.50000, 25.00000, 47.50000, 47.50000, 50.00000,], [ 27.50000, 22.50000, 25.00000, 47.50000, 47.50000, 45.00000,], [ 0.0000, 5.0000, 2.5000, 10.00000, 10.00000, 12.50000,], [ 5.0000, 0.0000, 2.5000, 10.00000, 10.00000, 7.5000,], [ 45.00000, 45.00000, 42.50000, 0.0000, 5.0000, 2.5000,], [ 45.00000, 45.00000, 47.50000, 5.0000, 0.0000, 2.5000,], [ 47.50000, 47.50000, 50.00000, 27.50000, 22.50000, 25.00000,], [ 47.50000, 47.50000, 45.00000, 22.50000, 27.50000, 25.00000,], [ 47.50000, 42.50000, 45.00000, 27.50000, 27.50000, 25.00000,], [ 42.50000, 47.50000, 45.00000, 27.50000, 27.50000, 30.00000,], [ 30.00000, 27.50000, 25.00000, 5.0000, 7.5000, 5.0000,], [ 30.00000, 25.00000, 27.50000, 5.0000, 5.0000, 2.5000,], [ 0.0000, 5.0000, 2.5000, 40.00000, 40.00000, 42.50000,], [ 5.0000, 0.0000, 2.5000, 40.00000, 40.00000, 37.50000,], [ 0.0000, 5.0000, 2.5000, 45.00000, 45.00000, 47.50000,], [ 5.0000, 0.0000, 2.5000, 45.00000, 45.00000, 42.50000,], [ 5.0000, 5.0000, 2.5000, 40.00000, 45.00000, 42.50000,], [ 5.0000, 5.0000, 7.5000, 45.00000, 40.00000, 42.50000,], [ 2.5000, 5.0000, 0.0000, 22.50000, 25.00000, 25.00000,], [ 0.0000, 5.0000, 2.5000, 25.00000, 25.00000, 27.50000,], [ 12.50000, 12.50000, 10.00000, 22.50000, 27.50000, 25.00000,], [ 12.50000, 12.50000, 15.00000, 27.50000, 22.50000, 25.00000,], [ 17.50000, 12.50000, 15.00000, 27.50000, 27.50000, 25.00000,], [ 12.50000, 17.50000, 15.00000, 27.50000, 27.50000, 30.00000,], [ 17.50000, 17.50000, 15.00000, 22.50000, 27.50000, 25.00000,], [ 17.50000, 17.50000, 20.00000, 27.50000, 22.50000, 25.00000,], [ 17.50000, 20.00000, 22.50000, 22.50000, 20.00000, 22.50000,], [ 20.00000, 17.50000, 22.50000, 25.00000, 22.50000, 22.50000,], [ 5.0000, 7.5000, 2.5000, 5.0000, 7.5000, 7.5000,], [ 7.5000, 5.0000, 2.5000, 7.5000, 10.00000, 7.5000,], [ 7.5000, 7.5000, 5.0000, 7.5000, 12.50000, 10.00000,], [ 7.5000, 7.5000, 10.00000, 12.50000, 7.5000, 10.00000,], [ 5.0000, 7.5000, 2.5000, 10.00000, 12.50000, 12.50000,], [ 7.5000, 5.0000, 2.5000, 12.50000, 15.00000, 12.50000,], [ 2.5000, 7.5000, 5.0000, 17.50000, 17.50000, 20.00000,], [ 7.5000, 2.5000, 5.0000, 17.50000, 17.50000, 15.00000,], [ 5.0000, 2.5000, 2.5000, 15.00000, 17.50000, 12.50000,], [ 2.5000, 0.0000, 2.5000, 17.50000, 15.00000, 12.50000,], [ 2.5000, 2.5000, 5.0000, 22.50000, 17.50000, 20.00000,], [ 0.0000, 2.5000, 2.5000, 20.00000, 17.50000, 22.50000,], [ 40.00000, 40.00000, 42.50000, 5.0000, 0.0000, 2.5000,], [ 40.00000, 40.00000, 37.50000, 0.0000, 5.0000, 2.5000,], [ 47.50000, 45.00000, 47.50000, 7.5000, 5.0000, 2.5000,], [ 47.50000, 47.50000, 50.00000, 7.5000, 2.5000, 5.0000,], [ 45.00000, 50.00000, 47.50000, 20.00000, 20.00000, 22.50000,], [ 50.00000, 45.00000, 47.50000, 20.00000, 20.00000, 17.50000,], [ 45.00000, 47.50000, 45.00000, 20.00000, 22.50000, 25.00000,], [ 42.50000, 45.00000, 45.00000, 22.50000, 20.00000, 25.00000,], [ 47.50000, 47.50000, 50.00000, 12.50000, 7.5000, 10.00000,], [ 47.50000, 47.50000, 45.00000, 7.5000, 12.50000, 10.00000,], [ 45.00000, 47.50000, 47.50000, 15.00000, 12.50000, 17.50000,], [ 47.50000, 50.00000, 47.50000, 12.50000, 15.00000, 17.50000,], [ 47.50000, 47.50000, 45.00000, 27.50000, 32.50000, 30.00000,], [ 47.50000, 47.50000, 50.00000, 32.50000, 27.50000, 30.00000,], [ 47.50000, 47.50000, 45.00000, 32.50000, 37.50000, 35.00000,], [ 47.50000, 47.50000, 50.00000, 37.50000, 32.50000, 35.00000,], [ 42.50000, 47.50000, 45.00000, 32.50000, 32.50000, 35.00000,], [ 47.50000, 42.50000, 45.00000, 32.50000, 32.50000, 30.00000,], [ 40.00000, 35.00000, 37.50000, 25.00000, 25.00000, 22.50000,], [ 35.00000, 40.00000, 37.50000, 25.00000, 25.00000, 27.50000,], [ 42.50000, 40.00000, 45.00000, 27.50000, 25.00000, 25.00000,], [ 40.00000, 42.50000, 45.00000, 25.00000, 22.50000, 25.00000,], [ 35.00000, 37.50000, 32.50000, 45.00000, 47.50000, 47.50000,], [ 37.50000, 35.00000, 32.50000, 47.50000, 50.00000, 47.50000,], [ 30.00000, 30.00000, 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530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,], [ 530500000000.0,],] +material_boundary_points = [ [ 0.0, 0.0,], [ 0.0, 5.0,], [ 0.0, 10.0,], [ 0.0, 15.0,], [ 0.0, 20.0,], [ 0.0, 25.0,], [ 0.0, 30.0,], [ 0.0, 35.0,], [ 0.0, 40.0,], [ 0.0, 45.0,], [ 0.0, 50.0,], [ 5.0, 0.0,], [ 5.0, 5.0,], [ 5.0, 10.0,], [ 5.0, 15.0,], [ 5.0, 20.0,], [ 5.0, 25.0,], [ 5.0, 30.0,], [ 5.0, 35.0,], [ 5.0, 40.0,], [ 5.0, 45.0,], [ 5.0, 50.0,], [ 10.0, 0.0,], [ 10.0, 5.0,], [ 10.0, 10.0,], [ 10.0, 15.0,], [ 10.0, 20.0,], [ 10.0, 25.0,], [ 10.0, 30.0,], [ 10.0, 35.0,], [ 10.0, 40.0,], [ 10.0, 45.0,], [ 10.0, 50.0,], [ 15.0, 0.0,], [ 15.0, 5.0,], [ 15.0, 10.0,], [ 15.0, 15.0,], [ 15.0, 20.0,], [ 15.0, 25.0,], [ 15.0, 30.0,], [ 15.0, 35.0,], [ 15.0, 40.0,], [ 15.0, 45.0,], [ 15.0, 50.0,], [ 20.0, 0.0,], [ 20.0, 5.0,], [ 20.0, 10.0,], [ 20.0, 15.0,], [ 20.0, 20.0,], [ 20.0, 25.0,], [ 20.0, 30.0,], [ 20.0, 35.0,], [ 20.0, 40.0,], [ 20.0, 45.0,], [ 20.0, 50.0,], [ 25.0, 0.0,], [ 25.0, 5.0,], [ 25.0, 10.0,], [ 25.0, 15.0,], [ 25.0, 20.0,], [ 25.0, 25.0,], [ 25.0, 30.0,], [ 25.0, 35.0,], [ 25.0, 40.0,], [ 25.0, 45.0,], [ 25.0, 50.0,], [ 30.0, 0.0,], [ 30.0, 5.0,], [ 30.0, 10.0,], [ 30.0, 15.0,], [ 30.0, 20.0,], [ 30.0, 25.0,], [ 30.0, 30.0,], [ 30.0, 35.0,], [ 30.0, 40.0,], [ 30.0, 45.0,], [ 30.0, 50.0,], [ 35.0, 0.0,], [ 35.0, 5.0,], [ 35.0, 10.0,], [ 35.0, 15.0,], [ 35.0, 20.0,], [ 35.0, 25.0,], [ 35.0, 30.0,], [ 35.0, 35.0,], [ 35.0, 40.0,], [ 35.0, 45.0,], [ 35.0, 50.0,], [ 40.0, 0.0,], [ 40.0, 5.0,], [ 40.0, 10.0,], [ 40.0, 15.0,], [ 40.0, 20.0,], [ 40.0, 25.0,], [ 40.0, 30.0,], [ 40.0, 35.0,], [ 40.0, 40.0,], [ 40.0, 45.0,], [ 40.0, 50.0,], [ 45.0, 0.0,], [ 45.0, 5.0,], [ 45.0, 10.0,], [ 45.0, 15.0,], [ 45.0, 20.0,], [ 45.0, 25.0,], [ 45.0, 30.0,], [ 45.0, 35.0,], [ 45.0, 40.0,], [ 45.0, 45.0,], [ 45.0, 50.0,], [ 50.0, 0.0,], [ 50.0, 5.0,], [ 50.0, 10.0,], [ 50.0, 15.0,], [ 50.0, 20.0,], [ 50.0, 25.0,], [ 50.0, 30.0,], [ 50.0, 35.0,], [ 50.0, 40.0,], [ 50.0, 45.0,], [ 50.0, 50.0,],] +simulation_boundary_points = [ [ 50.1, 50.1,], [ 50.1, -0.1,], [ -0.1, -0.1,], [ -0.1, 50.1,],] +electronic_stopping_correction_factors = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,] diff --git a/scripts/Particles.toml b/scripts/Particles.toml index 308d60c..e69de29 100644 --- a/scripts/Particles.toml +++ b/scripts/Particles.toml @@ -1,14 +0,0 @@ -[particle_parameters] -length_unit = "MICRON" -energy_unit = "EV" -mass_unit = "AMU" -N = [ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,] -m = [ 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000, 1.008000,] -Z = [ 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00,] -E = [ 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000, 100000.000000000,] -Ec = [ 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000, 0.5000,] -Es = [ 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000, 10.00000,] -pos = [ [ 0.0000, 35.000, 0.0000,], [ 0.0000, 7.00, 0.0000,], [ 0.0000, 11.000, 0.0000,], [ 0.0000, 19.000, 0.0000,], [ 0.0000, 10.000, 0.0000,], [ 0.0000, 40.000, 0.0000,], [ 0.0000, 50.000, 0.0000,], [ 0.0000, 39.000, 0.0000,], [ 0.0000, 1.00, 0.0000,], [ 0.0000, 16.000, 0.0000,],] -dir = [ [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,], [ 0.9999999999984768850000000000000000000000000000, 0.00000174532925199344340000000000000000000000000000, 0E-8,],] -interaction_index = [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,] -particle_input_filename = "" diff --git a/scripts/create_mesh2D.py b/scripts/create_mesh2D.py index 528d2f8..1b1cace 100644 --- a/scripts/create_mesh2D.py +++ b/scripts/create_mesh2D.py @@ -296,7 +296,8 @@ def write_to_file(self, dump_to_file = False): #print(len(material_boundary_points)) electronic_stopping_correction_factors = self.electronic_stopping_corrections - import decimal + + '''import decimal decimal.getcontext().prec = int(number_of_decimals) + 2 def have_ending_zeros(lis): #lis = np.asarray(lis) @@ -327,10 +328,12 @@ def have_ending_zeros(lis): pass return lis - + ''' + file = open("Mesh2D.toml", "w") file.seek(0) + ''' temp_dict = { "mesh_2d_input" : { "length_unit":self.length_unit, @@ -341,11 +344,21 @@ def have_ending_zeros(lis): "simulation_boundary_points":have_ending_zeros(Simulation_Boundaries), "electronic_stopping_correction_factors":have_ending_zeros(electronic_stopping_correction_factors) } + }''' + temp_dict = { + "mesh_2d_input" : { + "length_unit":self.length_unit, + "energy_barrier_thickness":self.energy_barrier_thickness, + "triangles": triangle_list, + "densities": material_densities, + "material_boundary_points": material_boundary_points, + "simulation_boundary_points": Simulation_Boundaries, + "electronic_stopping_correction_factors": electronic_stopping_correction_factors + } } - if dump_to_file: import toml - toml.dump(temp_dict, file) + toml.dump(temp_dict, file, encoder=toml.TomlNumpyEncoder()) #print(type(triangle_list)) @@ -358,7 +371,7 @@ def have_ending_zeros(lis): #mesh.N_gon(2, 4, [1], 1, 1, -np.pi/4 ) #mesh.rectangle(1, 1, [2], 1, 1) - mesh.rectangle_grid(10, 10, 50, 50, [5.305e9]) #Actual Number = 5.305e11 + mesh.rectangle_grid(10, 10, 50, 50, [5.305e11]) #Actual Number = 5.305e11 #mesh.print_Triangles() mesh.write_to_file(True) diff --git a/scripts/create_particle_parameters.py b/scripts/create_particle_parameters.py index 4766b43..3debf36 100644 --- a/scripts/create_particle_parameters.py +++ b/scripts/create_particle_parameters.py @@ -98,26 +98,26 @@ def have_ending_zeros(lis): "energy_unit" : "EV", "mass_unit" : "AMU", "N" : [int(i) for i in self.N], - "m" : have_ending_zeros(self.masses), - "Z" : have_ending_zeros(self.Z), - "E" : have_ending_zeros(self.E), - "Ec" : have_ending_zeros(self.Ec), - "Es" : have_ending_zeros(self.Es), - "pos" : have_ending_zeros(self.positions), - "dir" : have_ending_zeros(self.directions), + "m" : self.masses, + "Z" : self.Z, + "E" : self.E, + "Ec" : self.Ec, + "Es" : self.Es, + "pos" : self.positions, + "dir" : self.directions, "interaction_index" : [int(i) for i in self.interaction_index], "particle_input_filename" : "" } } if dump_to_file: import toml - toml.dump(temp_dict, file) + toml.dump(temp_dict, file, encoder=toml.TomlNumpyEncoder()) return temp_dict if __name__ == "__main__": import random particle = Particles() - for i in range(10): - particle.add_particle_species(1, 1, 1.008, 1, 100000.0, .5, 10.0, position = [0.0,random.randint(0,50.0),0.0]) + for i in range(100): + particle.add_particle_species(1, 1, 1.008, 1, 1.00e6, .5, 10.0, position = [0.0,random.randint(0,50.0),0.0]) particle.write_to_file(True) \ No newline at end of file