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gs_sphere_transformer
Commit 143e0756 by songxinkai
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81973754.pdf 0 → 100755
File added
GaussianSphereGeneration.py 0 → 100755
#!/mnt/storagedata1/renjj/anaconda3/bin/python
# -*- coding:utf-8 -*-
'''
Copyright (C) 2019 CCLI GROUP, PKU
Copyright (C) 2019 Jingjing Ren
NAME
GaussianShapeGeneration.py
PURPOSE
PROGRAMMER(S)
Jingjing Ren
REVISION HISTORY
REFERENCES
----------------------------------------------------------
This script was created at 2021-06-04 16:36
If you have any question, please email: renjj@pku.edu.cn
----------------------------------------------------------
'''
import numpy as np
import random
import scipy
def dist3d(p1,p2):
return ((p1[0]-p2[0])**2 + (p1[1]-p2[1])**2 +(p1[2]-p2[2])**2)**0.5
def takeSecond(elem):
return elem[0],elem[1]
if __name__=='__main__':
f = open('./shapefile/shape_gaussiansphere.dat','w')
a1 = [1,0,0]
a2 = [0,1,0]
space = [1,1,1]
Ls = 10
AX = Ls
AY = Ls
AZ = Ls
off = [0,0,0]
ii = 0
fload= open('/mnt/storagedata1/renjj/Model/ShapeFormation/Siris/G-sphere/pics/vtk.out')
lines = fload.readlines()
ii = 0
surface = []
out = []
for line in lines[5:583]:
x = line.strip().split()[0]
y = line.strip().split()[1]
z = line.strip().split()[2]
x = int(float(x)*100.0)
y = int(float(y)*100.0)
z = int(float(z)*100.0)
surface.append((x,y,z))
surface.sort(key =takeSecond)
surface = np.array(surface)
print (surface.shape)
for i in range(surface.shape[0]-1):
x = surface[i,0]
y = surface[i,1]
if (surface[i,0] == surface[i+1,0]) and (surface[i,1] == surface[i+1,1]):
z1 = surface[i,2]
z2 = surface[i+1,2]
if z1 <z2:
z1 = z1
z2 = z2
else:
z3 = z1
z4 = z2
z1 = z4
z2 = z3
for iz in range(z1,z2+1):
ii = ii +1
out.append((ii,x,y,iz,1,1,1))
out = np.array(out)
print (out.shape)
f.write(' >TARREC gaussiansphere; AX,AY,AZ= %.4f %.4f %.4f\r\n'%(AX,AY,AZ))
f.write(' %d = NAT\r\n'%(out.shape[0]))
f.write(' %.6f %.6f %.6f = A_1 vector\r\n'%(a1[0],a1[1],a1[2]))
f.write(' %.6f %.6f %.6f = A_2 vector\r\n'%(a2[0],a2[1],a2[2]))
f.write(' %.6f %.6f %.6f = lattice spacing (d_x,d_y,d_z)/d\r\n'%(space[0],space[1],space[2]))
f.write(' %.5f %.5f %.5f = lattice offset x0(1-3) = (x_TF,y_TF,z_TF)/d for dipole 0 0 0\r\n'%(off[0],off[1],off[2]))
f.write(' JA IX IY IZ ICOMP(x,y,z)\r\n')
for i in range(out.shape[0]):
f.write('%7d %3d %3d %3d %1d %1d %1d\r\n'%(out[i,0],out[i,1],out[i,2],out[i,3],out[i,4],out[i,5],out[i,6]))
#f.write('%3d %3d %3d \r\n'%(out[i,0],out[i,1],out[i,2]))
f.close()
Siris.tar.gz 0 → 100755
File added
data.rar 0 → 100755
File added
draw.py 0 → 100644
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # 空间三维画图
# 数据
with open('vtk.out', 'r') as f:
lines = f.readlines()[5:583]
data1 = np.array([[float(s) for s in line.strip().split()] for line in lines])
with open("gs_sphere.txt", 'r') as f:
lines = f.readlines()
data2 = np.array([[int(s) for s in line.strip().split(",")] for line in lines])
x1 = data1[:, 0] # [ 0 3 6 9 12 15 18 21]
y1 = data1[:, 1] # [ 1 4 7 10 13 16 19 22]
z1 = data1[:, 2] # [ 2 5 8 11 14 17 20 23]
x2 = data2[:, 0] # [ 0 3 6 9 12 15 18 21]
y2 = data2[:, 1] # [ 1 4 7 10 13 16 19 22]
z2 = data2[:, 2] # [ 2 5 8 11 14 17 20 23]
# 绘制散点图
fig = plt.figure()
ax = Axes3D(fig)
ax.scatter(x1, y1, z1, c='r', label='real')
ax.scatter(x2, y2, z2, c='g', label='int')
# 绘制图例
ax.legend(loc='best')
# 添加坐标轴(顺序是Z, Y, X)
ax.set_zlabel('Z', fontdict={'size': 15, 'color': 'red'})
ax.set_ylabel('Y', fontdict={'size': 15, 'color': 'red'})
ax.set_xlabel('X', fontdict={'size': 15, 'color': 'red'})
# 展示
plt.show()
gen_gs_sphere.py 0 → 100755
#!/workspace/S/songxinkai/anaconda3/bin/python
import numpy as np
import sys
import math as m
def cart2sph(x, y, z):
XsqPlusYsq = x**2 + y**2
r = m.sqrt(XsqPlusYsq + z**2) # r
elev = m.atan2(z,m.sqrt(XsqPlusYsq)) # theta
az = m.atan2(y,x) # phi
return r, elev, az
def hash_func(theta: float, phi: float, delta: float, theta_min:float=-1.57, theta_max:float=1.57, phi_min: float = -3.14, phi_max: float = 3.14):
theta_min = int(np.floor(theta_min / delta))
theta_max = int(np.floor(theta_max / delta))
phi_min = int(np.floor(phi_min / delta))
phi_max = int(np.floor(phi_max / delta))
theta_idx = np.floor(theta / delta)
phi_idx = np.floor(phi / delta)
theta_idx = theta_min if theta_idx == theta_max else theta_idx
phi_idx = phi_min if phi_idx == phi_max else phi_idx
return int(theta_idx), int(phi_idx)
# setting
scale = int(sys.argv[1])
hash_delta = float(sys.argv[1])
# load data
points = []
max_ = 0
with open('vtk.out', 'r') as f:
lines = f.readlines()
for line in lines[5:583]:
x = float(line.strip().split()[0]) / 1.41 *scale
y = float(line.strip().split()[1]) / 1.41 *scale
z = float(line.strip().split()[2]) / 1.41 *scale
if abs(max((x,y,z))) > max_:
max_ = abs(max((x,y,z)))
points.append(cart2sph(x, y, z))
print (max_)
# output
hash_size_x = int(np.floor(1.57 / hash_delta) - np.floor(-1.57 / hash_delta))
hash_size_y = int(np.floor(3.14 / hash_delta) - np.floor(-3.14 / hash_delta))
hash_table = [[[] for i in range(hash_size_y)] for j in range(hash_size_x)]
hash_table_num = [[0 for i in range(hash_size_y)] for j in range(hash_size_x)]
for p in points:
theta_idx, phi_idx = hash_func(p[1], p[2], hash_delta)
# print ("%d, %d ==== %.2f, %.2f"%(theta_idx, phi_idx, p[1], p[2]))
hash_table[theta_idx][phi_idx].append(p)
hash_table_num[theta_idx][phi_idx] += 1
print (hash_table_num)
thetas = [np.floor(p[1]/0.3) for p in points]
phis = [np.floor(p[2]/0.3) for p in points]
thetas = list(set(thetas))
phis = list(set(phis))
thetas = sorted(thetas)
phis = sorted(phis)
print (thetas)
print (phis)
print (max([p[0] for p in points]))
output_points = []
for x in range(-scale, scale):
for y in range(-scale, scale):
for z in range(-scale, scale):
output_points.append(cart2sph(x, y, z))
def get_neighbor_node(t, x, y):
id_x = [x]
id_y = [y]
if x > 0:
id_x.append(x-1)
if x < len(t) - 1:
id_x.append(x+1)
if y > 0:
id_y.append(y-1)
if y < len(t) - 1:
id_y.append(y+1)
tmp_t = []
for i in id_x:
for j in id_y:
tmp_t += t[i][j]
if len(tmp_t) == 0:
print ("Error: empty hash node")
return tmp_t
def dist(p1, p2):
x = p1[0] - p2[0]
y = p1[1] - p2[1]
return x**2 + y**2
res = []
res_xyz = []
for output_id, output_p in enumerate(output_points):
theta_idx, phi_idx = hash_func(p[1], p[2], hash_delta)
real_list = hash_table[theta_idx][phi_idx]
if len(real_list) == 0:
real_list = get_neighbor_node(hash_table, theta_idx, phi_idx)
nearest_id = np.argmin([dist(output_p[1:], p[1:]) for p in real_list])
if output_p[0] <= real_list[nearest_id][0]:
res.append(output_p)
res_xyz.append((int(output_id/((2*scale)**2))-scale, int(output_id%((2*scale)**2)/(2*scale))-scale, output_id % (2*scale)-scale))
print (len(res_xyz))
with open("gs_sphere.txt", 'w') as f:
for p in res_xyz:
x, y, z = p
f.write("%d,%d,%d\n"%(x, y, z))
gs_sphere.txt 0 → 100644
-7,-5,0
-7,-5,1
-7,-4,-1
-7,-4,0
-7,-4,1
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-2,2,1
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vtk.out 0 → 100755
# vtk DataFile Version 2.0
gsphere output
ASCII
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