def visualize_3d(data_in, title=None, save_file=None):
data = data_in[:]
data[data < 0.5] = 0
non_zero_indices = data.nonzero()
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax, non_zero_indices[0], non_zero_indices[1],
non_zero_indices[2])
ax.set_xlabel("x")
ax.set_ylabel("y")
ax.set_zlabel("z")
if title is not None:
plt.title(title)
if save_file:
# fig.show()
# import IPython
# IPython.embed()
plt.savefig(save_file)
plt.close('all')
else:
fig.show()
def plot_cam_location(camera_list, n, fig=None, ax=None):
FigSz = (8, 8)
L = np.array([list(c.location[n]) for c in camera_list])
x = L[:, 0]
y = L[:, 1]
z = L[:, 2]
if not fig:
fig = plt.figure(figsize=FigSz)
#view1 = np.array([-85., 60.])
if not ax:
ax = Axes3D(fig) #, azim=view1[0], elev=view1[1])
Axes3D.scatter(ax, x, y, zs=z, color='k')
zer = np.array
Axes3D.scatter(ax, zer([0]), zer([0]), zs=zer([5]), color='r')
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
ax.set_ylim3d(-50, 50)
ax.set_xlim3d(-50, 50)
ax.set_zlim3d(0, 50)
#if Flag['ShowPositions']:
fig.show()
#else:
# fig.savefig(fName)
return ax, fig
def visualize_occupancygrid(data, title=None, save_file=None):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
occupied = data == 1
non_zero_indices = occupied.nonzero()
Axes3D.scatter(ax,
non_zero_indices[0],
non_zero_indices[1],
non_zero_indices[2],
c='b')
occluded = data == 2
non_zero_indices = occluded.nonzero()
Axes3D.scatter(ax,
non_zero_indices[0],
non_zero_indices[1],
non_zero_indices[2],
c='r')
if title is not None:
plt.title(title)
if save_file:
plt.savefig(save_file)
else:
fig.show()
def plot_system(system, parameters):
x = []
y = []
z = []
colours = []
for i in range(len(system.particles)):
x.append(system.particles[i].position[0])
y.append(system.particles[i].position[1])
z.append(system.particles[i].position[2])
if parameters.charges[i] == 1:
colours.append('b')
elif parameters.charges[i] == -1:
colours.append('g')
ax = plt.axes(projection='3d')
ax.set_xlim3d(0, system.neighbourlist.box_space[0])
ax.set_ylim3d(0, system.neighbourlist.box_space[1])
ax.set_zlim3d(0, system.neighbourlist.box_space[2])
Axes3D.scatter(ax, x, y, z, c=colours)
plt.title("System")
#ax.legend(['Sodium','Chloride'], loc='upper right')
plt.show()
def plot_cam_location(camera_list, n, fig=None, ax=None):
FigSz = (8, 8)
L = np.array([list(c.location[n]) for c in camera_list])
x = L[:, 0]
y = L[:, 1]
z = L[:, 2]
if not fig:
fig = plt.figure(figsize=FigSz)
#view1 = np.array([-85., 60.])
if not ax:
ax = Axes3D(fig) #, azim=view1[0], elev=view1[1])
Axes3D.scatter(ax, x, y, zs=z, color='k')
zer = np.array
Axes3D.scatter(ax, zer([0]), zer([0]), zs=zer([5]), color='r')
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
ax.set_ylim3d(-50, 50)
ax.set_xlim3d(-50, 50)
ax.set_zlim3d(0, 50)
#if Flag['ShowPositions']:
fig.show()
#else:
# fig.savefig(fName)
return ax, fig
def main():
global rR
global v
#v = polynomial_surface2(rR)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
v = [
345.01147843, -731.53883648, 701.43498064, -333.41157482, 61.69405675,
434.95848754, -734.92037163, 468.45066799, -108.66899203, 197.05683428,
-229.38490931, 73.72852732, 38.62490216, -23.11704968, 2.79760705,
1112.02959271, -1850.90352232, 1243.44148281, -301.1366546,
1096.50133704, -1278.21349214, 419.17838208, 338.80540403,
-201.95899053, 33.68403733, 1333.97626976, -1566.15905716, 552.3302448,
922.09578713, -558.92492054, 145.7445413, 705.90344671, -442.88105472,
259.89354682, 138.22604583
]
#ax=implicit.plot_implicit(fn4,bbox=(-1.5,0,-3.5,-1.5,-2,1),rc=200,ns=30,colors='b', ax=ax)
v = [
2.18930311, 0.24260729, 57.46589779, 3.38543536, -9.56889825,
34.36258001, -36.2221404, 4.86597348, 12.89329227, 21.10709896,
-4.36372996, -5.89323474, 3.98227029, 0.9848254, 0.23593784,
-36.46890674, -25.34400559, 81.86028261, 14.43120124, 44.89510312,
-52.04801532, -9.90597384, 16.49023335, 2.29875215, 0.40597427,
-55.46318028, -39.9563639, 26.95078929, 35.15384941, -18.2399162,
5.13417155, -31.78519693, -14.89522473, 10.38829065, -6.66988281
]
#ax=implicit.plot_implicit(fn4,bbox=(-1.5,0,-3.5,-1.5,-2,1),rc=200,ns=30,colors='r', ax=ax)
#rR = tree_time.tree_time(rR,0.05)
rR = array(rR)
Axes3D.scatter(ax, rR[:, 0], rR[:, 1], rR[:, 2])
Axes3D.scatter(ax, -0.87676517, -2.5211104, -0.76908632, color='green')
plt.show()
def plotFiguresTemp(xSolid, ySolid, zSolid, xFFDDeform, yFFDDeform, zFFDDeform):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
#fig = plt.figure()
#ax = fig.gca(projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
#ax.plot_trisurf(zSolid, xSolid, ySolid, cmap=cm.jet, linewidth=0.2)
ax.plot_wireframe(zSolid, xSolid, ySolid, rstride = 1, cstride = 1, color="y")
#Axes3D.scatter(ax, zSolid, xSolid, ySolid, s=10, c='b')
Axes3D.scatter(ax, zFFDDeform, xFFDDeform, yFFDDeform, s=30, c='r')
# Axes3D.set_ylim(ax, [-0.5,4.5])
# Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.7, 0.7])
plt.show(block=True)
def visualize_multiple_3d(data0, data1, title=None, save_file=None):
data0[data0 < 0.5] = 0
data1[data1 < 0.5] = 0
non_zero_indices0 = np.array(data0.nonzero()) - 0.1
non_zero_indices1 = np.array(data1.nonzero())
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,
non_zero_indices0[0],
non_zero_indices0[1],
non_zero_indices0[2],
c='b')
Axes3D.scatter(ax,
non_zero_indices1[0],
non_zero_indices1[1],
non_zero_indices1[2],
c='r')
if title is not None:
plt.title(title)
if save_file:
plt.savefig(save_file)
else:
fig.show()
def volume_display(self, zstep = 3.00):
"""
This is a daring attempt for 3-D plots of all the blobs in the brain.
Prerequisites: self.blobs_archive are established.
The magnification of the microscope must be known.
"""
fig3 = plt.figure(figsize = (10,6))
ax_3d = fig3.add_subplot(111, projection = '3d')
for n_frame in self.valid_frames:
# below the coordinates of the cells are computed.
blobs_list = self.c_list[n_frame]
ys = blobs_list[:,0]*magni_lateral
xs = blobs_list[:,1]*magni_lateral
zs = np.ones(len(blobs_list))*n_frame*zstep
ss = (np.sqrt(2)*blobs_list[:,2]*magni_lateral)**2*np.pi
Axes3D.scatter(xs,ys, zs, zdir = 'z', s=ss, c='g')
ax_3d.set_xlabel('x (micron)', fontsize = 12)
ax_3d.set_xlabel('y (micron)', fontsize = 12)
return fig3
def plotFigures(xSolid,ySolid,zSolid,xFFDDeform,yFFDDeform,zFFDDeform, xsolidInitial,
ysolidInitial, zsolidInitial, xFFDInitial, yFFDInitial, zFFDInitial):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
#Axes3D.scatter(ax, zSolid, xSolid, ySolid, s=10, c='b')
#Axes3D.plot_wireframe(ax, zSolid, xSolid, ySolid, rstride = 1, cstride = 1, color="b")
#Axes3D.scatter(ax, zFFDDeform, xFFDDeform, yFFDDeform, s=30, c='r')
Axes3D.scatter(ax, zsolidInitial, xsolidInitial, ysolidInitial, s=10, c='b')
#Axes3D.plot_wireframe(ax, zsolidInitial, xsolidInitial, ysolidInitial,rstride = 1, cstride = 1, color="y")
Axes3D.scatter(ax, zFFDInitial, xFFDInitial, yFFDInitial, s=30, c='r')
if (CONST_BodyType == "halfFuselage"):
Axes3D.set_zlim(ax, [0, 4])
Axes3D.set_ylim(ax, [0, 4])
Axes3D.set_xlim(ax, [0, 12])
else:
#Axes3D.set_ylim(ax, [-0.5,4.5])
#Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-1.2, 1.2])
plt.show(block=True)
def plotData(tuplesArray):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
x = []
y = []
z = []
for point in tuplesArray:
x.append(point[0])
y.append(point[1])
z.append(point[2])
if (FILEInQuestion == "newsbp.fuselageZ.dat"):
Axes3D.scatter(ax, x,y,z, s=30, c ='b')
Axes3D.set_zlim(ax, [0, 1000])
Axes3D.set_ylim(ax, [0, 3000])
Axes3D.set_xlim(ax, [0, 3000])
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
else:
Axes3D.scatter(ax, z,x,y, s=30, c ='b')
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
plt.show(block=True)
def plotData2files(tuplesArray1, tuplesArray2):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
x1 = []
y1 = []
z1 = []
for point in tuplesArray1:
x1.append(point[0])
y1.append(point[1])
z1.append(point[2])
x2 = []
y2 = []
z2 = []
for point in tuplesArray2:
x2.append(point[0])
y2.append(point[1])
z2.append(point[2])
Axes3D.scatter(ax, x1,y1,z1, s=30, c ='b')
Axes3D.scatter(ax, x2,y2,z2, s=30, c ='r')
Axes3D.set_xlim(ax, [0, 2000])
Axes3D.set_ylim(ax, [0, 3000])
Axes3D.set_zlim(ax, [0, 1000])
plt.show(block=True)
def plotData2files(tuplesArray1, tuplesArray2):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
x1 = []
y1 = []
z1 = []
for point in tuplesArray1:
x1.append(point[0])
y1.append(point[1])
z1.append(point[2])
x2 = []
y2 = []
z2 = []
for point in tuplesArray2:
x2.append(point[0])
y2.append(point[1])
z2.append(point[2])
Axes3D.scatter(ax, x1, y1, z1, s=30, c='b')
Axes3D.scatter(ax, x2, y2, z2, s=30, c='r')
Axes3D.set_xlim(ax, [0, 2000])
Axes3D.set_ylim(ax, [0, 3000])
Axes3D.set_zlim(ax, [0, 1000])
plt.show(block=True)
def plotFigures(xSolid,ySolid,zSolid,xFFDDeform,yFFDDeform,zFFDDeform, xsolidInitial,
ysolidInitial, zsolidInitial, xFFDInitial, yFFDInitial, zFFDInitial):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
#Axes3D.scatter(ax, zSolid, xSolid, ySolid, s=10, c='b')
Axes3D.plot_wireframe(ax, zSolid, xSolid, ySolid, rstride = 1, cstride = 1, color="b")
Axes3D.scatter(ax, zFFDDeform, xFFDDeform, yFFDDeform, s=30, c='r')
#Axes3D.scatter(ax, zsolidInitial, xsolidInitial, ysolidInitial, s=10, c='y')
Axes3D.plot_wireframe(ax, zsolidInitial, xsolidInitial, ysolidInitial,rstride = 1, cstride = 1, color="y")
Axes3D.scatter(ax, zFFDInitial, xFFDInitial, yFFDInitial, s=30, c='g')
xZCross = []
yZCross = []
zZCross = []
#plot the points for the limits of each cross section
for zCrossSect in GLOBAL_zCrossSectionObjects:
zCrossSectionObject = GLOBAL_zCrossSectionObjects[zCrossSect]
#add to the arrays, for a fixed z, the following combinations
# (xmax, ymax) (xmax, ymin) (xmin, ymin) (xmin, ymax)
# (xmax, ymax)
xZCross.append(zCrossSectionObject.getXMax())
yZCross.append(zCrossSectionObject.getYMax())
zZCross.append(zCrossSect)
#(xmax, ymin)
xZCross.append(zCrossSectionObject.getXMax())
yZCross.append(zCrossSectionObject.getYMin())
zZCross.append(zCrossSect)
#(xmin, ymin)
xZCross.append(zCrossSectionObject.getXMin())
yZCross.append(zCrossSectionObject.getYMin())
zZCross.append(zCrossSect)
#(xmin, ymax)
xZCross.append(zCrossSectionObject.getXMin())
yZCross.append(zCrossSectionObject.getYMax())
zZCross.append(zCrossSect)
#Axes3D.plot_wireframe(ax, zZCross, xZCross, yZCross)
#Axes3D.set_ylim(ax, [-0.5,4.5])
#Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.7, 0.7])
plt.show(block=True)
def plotFigures(xSolid,ySolid,zSolid,xFFDDeform,yFFDDeform,zFFDDeform, xsolidInitial,
ysolidInitial, zsolidInitial, xFFDInitial, yFFDInitial, zFFDInitial):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
#Axes3D.scatter(ax, zSolid, xSolid, ySolid, s=10, c='b')
Axes3D.plot_wireframe(ax, zSolid, xSolid, ySolid, rstride = 1, cstride = 1, color="b")
Axes3D.scatter(ax, zFFDDeform, xFFDDeform, yFFDDeform, s=30, c='r')
#Axes3D.scatter(ax, zsolidInitial, xsolidInitial, ysolidInitial, s=10, c='y')
Axes3D.plot_wireframe(ax, zsolidInitial, xsolidInitial, ysolidInitial,rstride = 1, cstride = 1, color="y")
Axes3D.scatter(ax, zFFDInitial, xFFDInitial, yFFDInitial, s=30, c='g')
xZCross = []
yZCross = []
zZCross = []
#plot the points for the limits of each cross section
for zCrossSect in GLOBAL_zCrossSectionObjects:
zCrossSectionObject = GLOBAL_zCrossSectionObjects[zCrossSect]
#add to the arrays, for a fixed z, the following combinations
# (xmax, ymax) (xmax, ymin) (xmin, ymin) (xmin, ymax)
# (xmax, ymax)
xZCross.append(zCrossSectionObject.getXMax())
yZCross.append(zCrossSectionObject.getYMax())
zZCross.append(zCrossSect)
#(xmax, ymin)
xZCross.append(zCrossSectionObject.getXMax())
yZCross.append(zCrossSectionObject.getYMin())
zZCross.append(zCrossSect)
#(xmin, ymin)
xZCross.append(zCrossSectionObject.getXMin())
yZCross.append(zCrossSectionObject.getYMin())
zZCross.append(zCrossSect)
#(xmin, ymax)
xZCross.append(zCrossSectionObject.getXMin())
yZCross.append(zCrossSectionObject.getYMax())
zZCross.append(zCrossSect)
#Axes3D.plot_wireframe(ax, zZCross, xZCross, yZCross)
#Axes3D.set_ylim(ax, [-0.5,4.5])
#Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.7, 0.7])
plt.show(block=True)
def custom_plot(self, additional):
for k in additional:
if(k == Simulation.DISCRETIZE):
for i in range(self.examples.noutputs):
for j in range(self.nbr_epoch):
if(self.plots['discretize_div'][i][j] != 0):
self.plots['discretize'][i][j] /= (self.plots['discretize_div'][i][j] * (self.nbDiscre ** self.nbDiscre))
colors = [(0.2, 0.8, 0.88), 'b', 'g', 'r', 'c', 'm', 'y', 'k', (0.8, 0.1, 0.8), (0., 0.2, 0.5)]
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
for j in range(self.examples.noutputs):
ax.scatter([self.plots['discretize'][j][k] for k in self.plots['discretize_valid'][j]], [j] *
len(self.plots['discretize_valid'][j]), self.plots['discretize_valid'][j], color=colors[j], marker='x')
ax.set_xlabel('DISCRETIZED VALUE')
ax.set_ylabel('SHAPE')
ax.set_zlabel('EPOCH')
path = "/tmp/pyplot.%s.%s.png" % (sys.argv[0], time.strftime("%m-%d-%H-%M-%S", time.localtime()))
plt.savefig(path)
plt.show()
plt.title('Discretize hidden layer')
plt.ylabel('DISCRETIZED VALUE')
plt.xlabel("EPOCHS")
for j in range(self.examples.noutputs):
plt.plot(self.plots['discretize_valid'][j], [self.plots['discretize'][j][k]
for k in self.plots['discretize_valid'][j]], '.', color=colors[j])
path = "/tmp/pyplot.%s.%s.png" % (sys.argv[0], time.strftime("%m-%d-%H-%M-%S", time.localtime()))
try:
plt.savefig(path)
except ValueError:
print('Cannot save discretize_cloud')
try:
plt.show()
except ValueError:
print('Cannot display discretize_cloud')
elif(k == Simulation.PROTOTYPE):
lplot = [[0. for _ in range(self.examples.ninputs)] for _ in range(self.examples.noutputs)]
for network in self.networks:
for i in range(len(self.examples.inputs)):
network['FoN'].calc_output(self.examples.inputs[i])
network['SoN'].calc_output(network['FoN'].stateHiddenNeurons)
im = index_max(self.examples.outputs[i])
for j in range(self.examples.ninputs):
lplot[im][j] += network['SoN'].stateOutputNeurons[j]
fig = plt.figure()
plt.clf()
for i in range(self.examples.noutputs):
rpr.show_repr(lplot[i], self.width, fig, 250 + i, i)
path = "/tmp/pyplot.%s.%s.png" % (sys.argv[0], time.strftime("%m-%d-%H-%M-%S", time.localtime()))
plt.savefig(path)
plt.show()
def plot():
ax = implicit.plot_implicit(fn4,
bbox=(-5, 5, -5, 5, -5, 5),
rc=150,
ns=50,
colors='r')
Axes3D.scatter(ax, rays[:, 0], rays[:, 1], rays[:, 2])
plt.show()
def main():
# initialize ros node
rospy.init_node('compute_calibration')
# get path to folder containing recorded data
#filesPath = rospy.get_param('~files_path')
filesPath =os.environ['HOME']+"/catkin_ws/src/panda_hand_eye_calibrate/config/"
# load trajectories
marker2camera = np.loadtxt('%smarker2camera' % (filesPath), delimiter=',')
ee2base = np.loadtxt('%see2base' % (filesPath), delimiter=',')
# compute absolute orientation
kinectOut, rot, trans = absOrientation(marker2camera,ee2base)
########画出轨迹图###########
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# plot the data
Axes3D.scatter(ax, kinectOut[:,0], kinectOut[:,1], kinectOut[:,2], s=20, c='r')
Axes3D.scatter(ax, ee2base[:,0],ee2base[:,1], ee2base[:,2], s=20, c='b')
# add labels and title
ax.set_xticks([])
ax.set_yticks([])
ax.set_zticks([])
ax.set_xlabel('X-axis')
ax.set_ylabel('Y-axis')
ax.set_zlabel('Z-axis')
plt.title('Kinect-Panda Calibration')
plt.legend(['Kinect','Panda'])
plt.show()
# get rotation matrix as quaternion and euler angles
euler = tf.transformations.euler_from_matrix(rot)
quat = tf.transformations.quaternion_from_euler(*euler)
# save results to yaml file 写base与kinect之间的关系
f = open('%spanda2camera_calibration.yaml' % (filesPath), 'w')
lines = ['trans: [', 'rot: [', 'rot_euler: [']
for elem in trans: lines[0] += str(elem) + ', ' #trans
lines[0] += ']\n'
for elem in quat: lines[1] += str(elem) + ', ' #rot
lines[1] += ']\n'
for elem in euler: lines[2] += str(elem) + ', ' #rot_euler
lines[2] += ']\n'
lines.append('parent: /panda_link0\n')
lines.append('child: /kinect2_link\n')
f.writelines(lines)
f.close()
print ('Calibration Done !')
def plot3d(x, y, z, show=True, **kwds):
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax, xs=x, ys=y, zs=z)
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
if show:
plt.show()
def __draw_scatter_from_dict(ax: Axes3D, dict: Dict[Tuple[int, int], float],
color: str, marker: str, size: int):
id_pairs = dict.keys()
tested_ids = [id_pair[1] for id_pair in id_pairs]
test_ids = [id_pair[0] for id_pair in id_pairs]
predict_value = [value for value in dict.values()]
zs = np.array(predict_value)
xs = np.array(test_ids)
ys = np.array(tested_ids)
ax.scatter(xs, ys, zs, c=color, marker=marker, s=size)
def plot_skeleton_on_axes3d(skel,
skel_desc,
ax: Axes3D,
invert=True,
alpha=1.0):
ax.set_xlabel('x')
ax.set_ylabel('z')
ax.set_zlabel('y')
# NOTE: y and z axes are swapped
xs = skel.narrow(-1, 0, 1).numpy()
ys = skel.narrow(-1, 2, 1).numpy()
zs = skel.narrow(-1, 1, 1).numpy()
# Correct aspect ratio (https://stackoverflow.com/a/21765085)
max_range = np.array(
[xs.max() - xs.min(),
ys.max() - ys.min(),
zs.max() - zs.min()]).max() / 2.0
mid_x = (xs.max() + xs.min()) * 0.5
mid_y = (ys.max() + ys.min()) * 0.5
mid_z = (zs.max() + zs.min()) * 0.5
ax.set_xlim(mid_x - max_range, mid_x + max_range)
ax.set_ylim(mid_y - max_range, mid_y + max_range)
ax.set_zlim(mid_z - max_range, mid_z + max_range)
ax.set_aspect('equal')
if invert:
ax.invert_zaxis()
# Set starting view
ax.view_init(elev=20, azim=-100)
get_joint_metadata = _make_joint_metadata_fn(skel_desc)
for joint_id, joint in enumerate(skel):
meta = get_joint_metadata(joint_id)
color = 'magenta'
if meta['group'] == 'left':
color = 'blue'
if meta['group'] == 'right':
color = 'red'
parent = skel[meta['parent']]
offset = parent - joint
ax.quiver(
[joint[0]],
[joint[2]],
[joint[1]],
[offset[0]],
[offset[2]],
[offset[1]],
color=color,
alpha=alpha,
)
ax.scatter(xs, ys, zs, color='grey', alpha=alpha)
def plotAgentVel(self, agent_num):
vels = self.dataframe['velocity']
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,
getWithout(vels[agent_num][:, 0], -1),
getWithout(vels[agent_num][:, 1], -1),
zs=np.arange(len(
vels[agent_num]))[vels[agent_num][:, 0] != -1],
s=3)
plt.show()
def plotAgentPos(self, agent_num):
coords = self.dataframe['coordinates']
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,
getWithout(coords[agent_num][:, 0], 1),
getWithout(coords[agent_num][:, 1], 1),
zs=np.arange(len(
coords[agent_num]))[coords[agent_num][:, 0] != 1],
s=3)
plt.show()
def visualize_pointcloud(pc, subsample=False):
pc = np.copy(pc)
if subsample:
mask = np.random.rand(pc.shape[0])
pc = pc[mask < .1]
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax, pc[:, 0], pc[:, 1], pc[:, 2])
fig.show()
def main():
# initialize ros node
rospy.init_node('compute_calibration')
# get path to folder containing recorded data
filesPath = rospy.get_param('~files_path')
# load trajectories
kinectTraj = np.loadtxt('%skinect_trajectory' % (filesPath), delimiter=',')
baxterTraj = np.loadtxt('%sbaxter_trajectory' % (filesPath), delimiter=',')
# compute absolute orientation
kinectOut, rot, trans = absOrientation(kinectTraj,baxterTraj)
# plot both point sets together
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# plot the data
Axes3D.scatter(ax, kinectOut[:,0], kinectOut[:,1], kinectOut[:,2], s=20, c='r')
Axes3D.scatter(ax, baxterTraj[:,0],baxterTraj[:,1], baxterTraj[:,2], s=20, c='b')
# add labels and title
ax.set_xticks([])
ax.set_yticks([])
ax.set_zticks([])
ax.set_xlabel('X-axis')
ax.set_ylabel('Y-axis')
ax.set_zlabel('Z-axis')
plt.title('Kinect-Baxter Calibration')
plt.legend(['Kinect','Baxter'])
plt.show()
# get rotation matrix as quaternion and euler angles
euler = tf.transformations.euler_from_matrix(rot)
quat = tf.transformations.quaternion_from_euler(*euler)
# save results to yaml file
f = open('%skinect_calibration.yaml' % (filesPath), 'w')
lines = ['trans: [', 'rot: [', 'rot_euler: [']
for elem in trans: lines[0] += str(elem) + ', '
lines[0] += ']\n'
for elem in quat: lines[1] += str(elem) + ', '
lines[1] += ']\n'
for elem in euler: lines[2] += str(elem) + ', '
lines[2] += ']\n'
lines.append('parent: /base\n')
lines.append('child: /kinect2_link\n')
f.writelines(lines)
f.close()
def plot(self, axes: Axes3D, **kwargs):
# Plot all sensors
sx = list(map(lambda s: s.x, self.sensors))
sy = list(map(lambda s: s.y, self.sensors))
sz = list(map(lambda s: -s.depth, self.sensors))
axes.scatter(sx, sy, sz, c='r', label='Sensors')
# Plot all relays
rx = list(map(lambda r: r.x, self.relays))
ry = list(map(lambda r: r.y, self.relays))
rz = list(map(lambda r: r.height, self.relays))
axes.scatter(rx, ry, rz, c='b', label='Relays')
def plotPCA(proj3D, X_r, PCs, ligs, colors, csvPath, save_flag):
"""
Plot the PCA data on 2D plot
"""
# Main figure
fig = plt.figure(figsize=(13, 12), dpi=100)
if proj3D:
ax = fig.add_subplot(111, projection="3d")
for label, col, x, y, z in zip(ligs, colors,
X_r[:, 0], X_r[:, 1], X_r[:, 2]):
newCol = makeColor(col)
Axes3D.scatter(ax, x, y, z, label=label, color=newCol,
marker="o", lw=1, s=800)
ax.set_xlabel("PC1 (" + '{0:g}'.format(PCs[0]) + " %)", fontsize=30)
ax.set_ylabel("PC2 (" + '{0:g}'.format(PCs[1]) + " %)", fontsize=30)
ax.set_zlabel("PC3 (" + '{0:g}'.format(PCs[2]) + " %)", fontsize=30)
ax.tick_params(axis="both", which="major", labelsize=20)
pngPath = csvPath.replace(".csv", "_3D.png")
else:
ax = fig.add_subplot(111)
for label, col, x, y in zip(ligs, colors, X_r[:, 0], X_r[:, 1]):
newCol = makeColor(col)
ax.scatter(x, y, label=label, color=newCol, marker="o", lw=1, s=800)
# ax.annotate(label, xy=(x, y - 0.05), fontsize=10,
# ha='center', va='top')
ax.set_xlabel("PC1 (" + '{0:g}'.format(PCs[0]) + " %)", fontsize=30)
ax.set_ylabel("PC2 (" + '{0:g}'.format(PCs[1]) + " %)", fontsize=30)
ax.tick_params(axis="both", which="major", labelsize=30)
pngPath = csvPath.replace(".csv", "_2D.png")
# figTitle = "PCA on " + csvPath + " (PC1=" + pcVals[0] + ", PC2=" +
# pcVals[1] + ")"
# ax.text(0.5, 1.04, figTitle, horizontalalignment="center", fontsize=30,
# transform=ax.transAxes)
# Legend figure
fig_legend = plt.figure(figsize=(13, 12), dpi=100)
plt.figlegend(*ax.get_legend_handles_labels(), scatterpoints=1,
loc="center", fancybox=True,
shadow=True, prop={"size": 30})
# Save figures if save flag was used
if save_flag:
print("\nSAVING figures\n")
fig.savefig(pngPath, bbox_inches="tight")
fig_legend.savefig(pngPath.replace(".png", "_legend.png"))
# Otherwise show the plots
else:
print("\nSHOWING figures\n")
plt.show()
def plot_system(system):
x = []
y = []
z = []
for i in range(len(system.particles)):
x.append(system.particles[i].position[0])
y.append(system.particles[i].position[1])
z.append(system.particles[i].position[2])
ax = plt.axes(projection='3d')
Axes3D.scatter(ax, x, y, z)
plt.show()
def plot_point_cloud(self, point_cloud):
height = point_cloud.shape[0]
point_cloud = point_cloud.reshape([height**2, 3])
px = point_cloud[:, 0]
py = point_cloud[:, 1]
pz = point_cloud[:, 2]
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax, px, py, pz)
plt.show()
def show_pose(frame, highlight_marker=None):
"""
Create 3D plot of marker positions
:param frame: trajectory (1d numpy array: [markers])
:param highlight_marker: order number of marker to be highlighted
:return: True
"""
show_frame = frame.reshape(int(frame.shape[0]/3), 3)
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, projection='3d')
ax.set_xlim3d(-1000, 1000)
ax.set_ylim3d(-1000, 1000)
ax.set_zlim3d(-1000, 1000)
if highlight_marker is None:
Axes3D.scatter(ax, xs=show_frame[:, 0], ys=show_frame[:, 1], zs=show_frame[:, 2], c='b', marker='o')
else:
Axes3D.scatter(ax, xs=show_frame[:highlight_marker, 0], ys=show_frame[:highlight_marker, 1], zs=show_frame[:highlight_marker, 2], c='b', marker='o')
Axes3D.scatter(ax, xs=show_frame[highlight_marker+1:, 0], ys=show_frame[highlight_marker+1:, 1], zs=show_frame[highlight_marker+1:, 2], c='b', marker='o')
Axes3D.scatter(ax, xs=show_frame[highlight_marker, 0], ys=show_frame[highlight_marker, 1], zs=show_frame[highlight_marker, 2], c='r', marker='o', label='marker #{}'.format(highlight_marker))
ax.legend()
ax.set_xlabel('X Axis')
ax.set_ylabel('Y Axis')
ax.set_zlabel('Z Axis')
# Axes3D.plot(ax, xs=trajectory[:, 0], ys=trajectory[:, 1], zs=trajectory[:, 2], c='k', linestyle='dashed')
ax.view_init(90, -90)
plt.show()
return True
def add_bands_scatter_plot(axes3d: Axes3D,
kpoints: numpy.ndarray,
eigenvalues: numpy.ndarray,
axis: int,
layer: int,
band_indices: Union[List[int], range],
offset: Union[List[float], numpy.ndarray] = None):
x, y, zs = get_x_y_zs(kpoints, eigenvalues, axis, layer)
if offset is not None:
x += offset[0]
y += offset[1]
zs += offset[2]
for b in band_indices:
axes3d.scatter(x, y, zs[:, b])
def check_output():
fname = "data.txt"
m, x, vx, y, vy, z, vz = np.loadtxt(fname, unpack=True)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
maxsize = 30
plt3d.scatter(ax,
x,
y,
z,
c='k',
s=maxsize * m / np.max(m),
label="Before")
plt.show()
def point_cloud(df, columns=[0, 1, 2]):
"""3-D Point cloud for plotting things like mesh models of horses ;)"""
df = df if isinstance(df, pd.DataFrame) else pd.DataFrame(df)
if not all(c in df.columns for c in columns):
columns = list(df.columns)[:3]
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d') # noqa
Axes3D.scatter(*[df[columns[i]] for i in range(3)],
zdir='z',
s=20,
c=None,
depthshade=True)
return ax
def plotAgentVel(self, agent_num):
agent = self.dataframe[agent_num]['velocity']
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,
getWithout(agent[:, 0], -1),
getWithout(agent[:, 1], -1),
zs=np.arange(len(agent))[agent[:, 0] != -1],
s=3)
plt.title("Example Velocity of Agent")
plt.xlabel("x component")
plt.ylabel("y component")
plt.zlabel("Time")
plt.show()
def plotAgentPos(self, agent_num):
agent = self.dataframe[agent_num]['coordinates']
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,
getWithout(agent[:, 0], 1),
getWithout(agent[:, 1], 1),
zs=np.arange(len(agent))[agent[:, 0] != 1],
s=3)
plt.title("Example Trajectory of Agent")
plt.xlabel("x coordinate")
plt.ylabel("y coordinate")
plt.zlabel("Time")
plt.show()
def plot_results():
os.chdir("result")
all_data = []
maxt = -1
for f in sorted(os.listdir("./")):
all_data.append(np.loadtxt(f, unpack=True))
maxt += 1
d = np.array(all_data)
shape = d.shape
m = d[0, 0, :]
maxsize = 20
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
maxxyz = 0
minsep = 1e8
maxsep = 0
for t in range(shape[0]):
maxxyz = max(
maxxyz,
max(np.max(np.abs(d[t, 1, :])), np.max(np.abs(d[t, 2, :])),
np.max(np.abs(d[t, 3, :]))))
# if t == maxt:
# print "at last t"
# for particle1 in range(shape[2]):
# for particle2 in range(shape[2]):
# if particle1 == particle2:
# continue
# minsep = min(minsep, dist(d[t,:,particle1], d[t,:,particle2]))
# maxsep = max(maxsep, dist(d[t,:,particle1], d[t,:,particle2]))
# print minsep, maxsep
for t in range(shape[0]):
# plt.scatter(d[t, 1, :], d[t, 3, :], s=maxsize*m/np.max(m))
plt3d.scatter(ax,
d[t, 1, :],
d[t, 2, :],
d[t, 3, :],
c='k',
s=maxsize * m / np.max(m))
plt.xlim([-maxxyz, maxxyz])
plt.ylim([-maxxyz, maxxyz])
ax.set_zlim([-maxxyz, maxxyz])
fname = "graphic_result_%03d.png" % t
sys.stdout.write("Writing " + fname + "\r")
sys.stdout.flush()
plt.savefig(fname)
plt.cla()
# plt.show()
sys.stdout.write("\nDone!\n")
sys.stdout.flush()
def check_tree():
m, x, cx, y, cy, z, cz = np.loadtxt(inname, unpack=True)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
maxsize = 30
plt3d.scatter(ax,
x,
y,
z,
c='r',
s=maxsize * m / np.max(m),
label="Particles")
w, x, cx, y, cy, z, cz = np.loadtxt(outname, unpack=True)
maxsize = 20
# plt3d.scatter(ax, x, y, z, 'x', c='g', s=maxsize/4, label="Centers")
# plt3d.scatter(ax, cz, cy, cz, c='hotpink', s=2*w/np.max(w), label="COMs")
# for width, j, k, i in zip(w, x, y, z):
for width, i, j, k in zip(w, x, y, z):
# plt3d.scatter(ax, [i], [j], [k], c='r')
for top in range(2):
for side in range(2):
plt3d.plot(ax, [i - width / 2, i + width / 2], [
j - width / 2 + side * width, j - width / 2 + side * width
], [k - width / 2 + top * width, k - width / 2 + top * width],
c='k',
linewidth=.2)
plt3d.plot(
ax, [
i - width / 2 + side * width,
i - width / 2 + side * width
], [j - width / 2, j + width / 2],
[k - width / 2 + top * width, k - width / 2 + top * width],
c='k',
linewidth=.2)
plt3d.plot(ax, [
i - width / 2 + top * width, i - width / 2 + top * width
], [
j - width / 2 + side * width, j - width / 2 + side * width
], [k - width / 2, k + width / 2],
c='k',
linewidth=.2)
plt.legend()
plt.xlabel("X")
plt.ylabel("Y")
ax.set_zlabel("Z")
plt.show()
def main():
global rR
global v
#v = polynomial_surface2(rR)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
v=[ 345.01147843, -731.53883648, 701.43498064, -333.41157482, 61.69405675, 434.95848754, -734.92037163, 468.45066799, -108.66899203, 197.05683428, -229.38490931, 73.72852732, 38.62490216, -23.11704968, 2.79760705, 1112.02959271, -1850.90352232, 1243.44148281, -301.1366546, 1096.50133704, -1278.21349214, 419.17838208, 338.80540403, -201.95899053, 33.68403733, 1333.97626976, -1566.15905716, 552.3302448, 922.09578713, -558.92492054, 145.7445413, 705.90344671, -442.88105472, 259.89354682, 138.22604583]
#ax=implicit.plot_implicit(fn4,bbox=(-1.5,0,-3.5,-1.5,-2,1),rc=200,ns=30,colors='b', ax=ax)
v=[ 2.18930311, 0.24260729, 57.46589779, 3.38543536, -9.56889825, 34.36258001, -36.2221404, 4.86597348, 12.89329227, 21.10709896, -4.36372996, -5.89323474, 3.98227029, 0.9848254, 0.23593784, -36.46890674, -25.34400559, 81.86028261, 14.43120124, 44.89510312, -52.04801532, -9.90597384, 16.49023335, 2.29875215, 0.40597427, -55.46318028, -39.9563639, 26.95078929, 35.15384941, -18.2399162, 5.13417155, -31.78519693, -14.89522473, 10.38829065, -6.66988281]
#ax=implicit.plot_implicit(fn4,bbox=(-1.5,0,-3.5,-1.5,-2,1),rc=200,ns=30,colors='r', ax=ax)
#rR = tree_time.tree_time(rR,0.05)
rR=array(rR)
Axes3D.scatter(ax,rR[:,0],rR[:,1],rR[:,2])
Axes3D.scatter(ax,-0.87676517,-2.5211104,-0.76908632,color='green')
plt.show()
def PCAChart(X_pca, alpha=0.2):
n = X_pca.shape[
1] #second dimension is the number of colums which is the number of components
if n == 2:
plt.scatter(X_pca[:, 0], X_pca[:, 1], alpha=alpha)
elif n == 3:
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,
xs=X_pca[:, 0],
ys=X_pca[:, 1],
zs=X_pca[:, 2],
alpha=alpha)
else:
print("n should be either 2 or 3")
def updatePlot(self, X, Y, Z, population=None):
self.activePlot = (X,Y,Z)
x, y = np.meshgrid(X,Y)
if self.surface is not None:
self.surface.remove()
if self.scatter is not None:
self.scatter.remove()
# surface
self.surface = Axes3D.plot_surface(
self.axes,
x, y, Z,
rstride=1,
cstride=1,
cmap=cm.coolwarm,
linewidth=0,
antialiased=False,
shade=False,
alpha=0.5
)
# population
if population is not None:
self.activePopulation = population
x, y, z = self.preparePopulationData(population)
self.scatter = Axes3D.scatter(self.axes, x, y, z, c="r", marker="o")
self.scatter.set_alpha(1.0)
# Draw all
self.canvas.draw()
self.canvas.flush_events()
def plotFiguresTemp(xSolid, ySolid, zSolid, xFFDDeform, yFFDDeform, zFFDDeform):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
Axes3D.scatter(ax, zSolid, xSolid, ySolid, s=10, c='b')
Axes3D.scatter(ax, zFFDDeform, xFFDDeform, yFFDDeform, s=30, c='r')
# Axes3D.set_ylim(ax, [-0.5,4.5])
# Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.7, 0.7])
plt.show(block=True)
def plotFiguresTemp(xSolid, ySolid, zSolid, xFFDDeform, yFFDDeform, zFFDDeform):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
Axes3D.scatter(ax, zSolid, xSolid, ySolid, s=10, c='b')
Axes3D.scatter(ax, zFFDDeform, xFFDDeform, yFFDDeform, s=30, c='r')
# Axes3D.set_ylim(ax, [-0.5,4.5])
# Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.7, 0.7])
plt.show(block=True)
def visualize_pointclouds(pc0, pc1, subsample0=False, subsample1=False):
pc0 = np.copy(pc0)
pcl = np.copy(pc1)
if subsample0:
mask = np.random.rand(pc0.shape[0])
pc0 = pc0[mask < .005]
if subsample1:
mask = np.random.rand(pc1.shape[0])
pc1 = pc1[mask < .005]
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax, pc0[:, 0], pc0[:, 1], pc0[:, 2], c='b')
Axes3D.scatter(ax, pc1[:, 0], pc1[:, 1], pc1[:, 2], c='r')
plt.xlabel('X')
plt.ylabel('Y')
fig.show()
def plotElements(PhysicalElementMatrix):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('X axis')
ax.set_ylabel('Y axis')
ax.set_zlabel('Z axis')
xVector = []
yVector = []
zVector = []
for i in range(CONST_DIMENSION_X):
for j in range(CONST_DIMENSION_Y):
for k in range(CONST_DIMENSION_Z):
elementObject = PhysicalElementMatrix[i][j][k]
for gridPointObject in elementObject.gridPointList:
xVector.append(gridPointObject.getX())
yVector.append(gridPointObject.getY())
zVector.append(gridPointObject.getZ())
Axes3D.scatter(ax, xVector, yVector, zVector, s=30, c='r')
#Axes3D.plot_wireframe(ax, zSolid, xSolid, ySolid, rstride = 1, cstride = 1, color="b")
# create the lines around all the elements
for i in range(CONST_DIMENSION_X):
for j in range(CONST_DIMENSION_Y):
for k in range(CONST_DIMENSION_Z):
elementObject = PhysicalElementMatrix[i][j][k]
ListXVectors,ListYVectors,ListZVectors = elementObject.getOuterLineVectors()
for l in range(len(ListXVectors)):
plt.plot(ListXVectors[l],ListYVectors[l], ListZVectors[l], c = 'b')
Axes3D.set_ylim(ax, [-10,10])
Axes3D.set_xlim(ax, [-10,10])
Axes3D.set_zlim(ax, [-10, 10])
plt.show(block=True)
def addcurve( ax, path, endpoints, color ) : px = path[ :,0 ] py = path[ :,1 ] pz = path[ :,2 ] n = len(px) - 1 q = Axes3D.plot(ax, px, py, zs=pz, c=color, linewidth=2 ) px = endpoints[ :,0 ] py = endpoints[ :,1 ] pz = endpoints[ :,2 ] print px, py, pz q = Axes3D.scatter(ax, px,py, zs=pz, c=color, marker='o', s=60)
def plotInitialState(xsolidInitial,ysolidInitial, zsolidInitial,
xFFDInitial, yFFDInitial, zFFDInitial):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
Axes3D.scatter(ax, zsolidInitial, xsolidInitial, ysolidInitial, s=10, c='b')
#Axes3D.plot_wireframe(ax, zsolidInitial, xsolidInitial, ysolidInitial,rstride = 1, cstride = 1, color="y")
Axes3D.scatter(ax, zFFDInitial, xFFDInitial, yFFDInitial, s=30, c='r')
#Axes3D.set_ylim(ax, [-0.5,4.5])
#Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.7, 0.7])
plt.show(block=True)
def updatePopulation(self, population):
self.activePopulation = population
x, y, z = self.preparePopulationData(population)
if self.scatter is not None:
self.scatter.remove()
self.scatter = Axes3D.scatter(self.axes, x, y, z, c="r", marker="o")
# self.surface.set_zorder(2)
# self.scatter.set_zorder(100)
self.scatter.set_alpha(1.0)
self.canvas.draw()
self.canvas.flush_events()
def plotElements(fig, ax, ElementsSbpData, ElementsFFDData, NumElements,c1,c2,\
c3,c4):
for i in range(NumElements):
xSolid = []
ySolid = []
zSolid = []
xFFD = []
yFFD = []
zFFD = []
#fill the Solid body points
for SBPTuple in ElementsSbpData[i]:
xSolid.append(SBPTuple[0][0])
ySolid.append(SBPTuple[0][1])
zSolid.append(SBPTuple[0][2])
for FFDTuple in ElementsFFDData[i]:
xFFD.append(FFDTuple[1][0])
yFFD.append(FFDTuple[1][1])
zFFD.append(FFDTuple[1][2])
# element 1 is the fuselage whose x and z values were switched
# to make z cross sections. So switch these back when plotting
if(i == 0):
#ax.plot_trisurf(zSolid, xSolid, ySolid, cmap=cm.jet, linewidth=0.2)
Axes3D.scatter(ax, zSolid,xSolid, ySolid, s=20, c=c1)
Axes3D.scatter(ax, zFFD, xFFD, yFFD, s=30, c= c2)
#Axes3D.plot_wireframe(ax, zFFD, xFFD, yFFD)
if(i == 1):
#ax.plot_trisurf(xSolid, zSolid, ySolid, cmap=cm.jet, linewidth=0.2)
Axes3D.scatter(ax, zSolid,xSolid, ySolid, s=20, c=c3)
Axes3D.scatter(ax, zFFD, xFFD, yFFD, s=30, c= c4)
def makeacluster(radius,charges = 0, distance =4,cadmium_term=False,
module = 'nwchem',
removehangeroners = True, surfacepassivation=True,_plot=True):
""" Prepare an xyzfile of cluster of CdS or CdSe with a specified radius and a certain number of point charges around it"""
#########cell vectors in angstroms
a = array([4.16,0,0])
b = 4.16*array([cos(radians(60)),sin(radians(60)),0])
c = array([0,0,6.756])
###### cell vectors in angstroms for CdSe
a = array([4.2985,0,0])
b = 4.2985*array([cos(radians(60)),sin(radians(60)),0])
c = array([0,0,7.0152])
cellvectors = array([a,b,c])
##Atomic positions in fractional coordinates in cell
### For Wurtzite#####
Cdcoord = array([[0,0,0],[0.33,0.333,0.5]])
Scoord = array([[0,0,0.375],[0.3333,0.3333,0.875]])
tetarray = array([[0,0,0.375],[-0.333,-0.333,-0.125],[0.6666,-0.3333,-0.125],[-0.3333,0.6666,-0.125]])
Cdcoord= dot(Cdcoord,cellvectors)
Scoord=dot(Scoord,cellvectors)
Cdcoordlist1 = ndarray((0,3))
Cdcoordlist2 = ndarray((0,3))
Scoordlist1 = ndarray((0,3))
Scoordlist2 = ndarray((0,3))
OHcoordlist=ndarray((0,3))
Hcoordlist=ndarray((0,3))
numbertorepeat = int(radius/b[1])+2
for p in itertools.product(range(-numbertorepeat,numbertorepeat+1),repeat=3):
x= dot(array([p]),cellvectors)+Cdcoord[0]
x2=dot(array([p]),cellvectors)+Cdcoord[1]
y = dot(array([p]),cellvectors)+Scoord[0]
y2 = dot(array([p]),cellvectors)+Scoord[1]
Cdcoordlist1 = append(Cdcoordlist1,x,axis=0)
Cdcoordlist2 = append(Cdcoordlist2,x2,axis=0)
Scoordlist1 = append(Scoordlist1,y,axis=0)
Scoordlist2 = append(Scoordlist2,y2,axis=0)
tetcoord=array([[ -2.08208000e+00, 1.19968767e+00, -8.44500000e-01],
[ -2.08000000e-03, -2.40297801e+00 , -8.44500000e-01],
[ 2.07792000e+00, 1.19968767e+00, -8.44500000e-01],
[ 0.00000000e+00, 0.00000000e+00, 2.53350000e+00]])#ndarray((0,3))
tetcoord2 = array( [[ -2.06544000e+00, -1.19968767e+00, -8.44500000e-01],
[ 1.43520000e-02, 1.08079970e-03, 2.53350000e+00],
[ 1.45600000e-02, 2.40297801e+00, -8.44500000e-01],
[ 2.09456000e+00, -1.19968767e+00, -8.44500000e-01]])
Cdtetcoord1=tetcoord*array([[1,1,-1]])
Cdtetcoord2=tetcoord2*array([[1,1,-1]])
extrashift = (a+b+c)/2
Cdcoordlist1[:]+=extrashift#array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Scoordlist1[:]+=extrashift#array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Cdcoordlist2[:]+=extrashift#array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Scoordlist2[:]+=extrashift#array([[radius+extrashift,radius+extrashift,radius+extrashift]])
x= where(numpy.sum(Cdcoordlist1**2,axis=1)<radius**2)[0]
Cdcoordlist1=Cdcoordlist1[x]
x= where(numpy.sum(Cdcoordlist2**2,axis=1)<radius**2)[0]
Cdcoordlist2=Cdcoordlist2[x]
Scoordlist1=Scoordlist1[numpy.sum(Scoordlist1**2,axis=1)<radius**2]
Scoordlist2=Scoordlist2[numpy.sum(Scoordlist2**2,axis=1)<radius**2]
extrashift = 10
Cdcoordlist1[:]+=array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Scoordlist1[:]+=array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Cdcoordlist2[:]+=array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Scoordlist2[:]+=array([[radius+extrashift,radius+extrashift,radius+extrashift]])
print '--------------'
if cadmium_term:
"""Cadmium Termination. Still not working"""
### TODO implement this.
print 'terminating the surface with cadmium atoms'
for i in Scoordlist1:
remove = array([])
bondlength=1.83 ## angstroms
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
for s in Cdtetcoord1:
if not any(sum((x[:]-s)**2,axis=1)<0.5):
print " adding Cd1 Atom at",[i+s]
Cdcoordlist1= append(Cdcoordlist1,[i+s],axis=0)
for i in Scoordlist2:
bondlength=1.83 ## angstroms
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
for s in Cdtetcoord2:
if not any(sum((x[:]-s)**2,axis=1)<0.5):
print " adding Cd2 Atom at",[i+s]
Cdcoordlist2= append(Cdcoordlist2,[i+s],axis=0)
if removehangeroners:
"""removing Cd or S/Se atoms connected by only one bond"""
print '--------------'
print "removing core atoms connected by only one bond"
removefromCd1 = []
removefromCd2 = []
removefromS1 = []
removefromS2 = []
removefromS2_2 = array([])
removefromCd1_2 = array([])
for i in Cdcoordlist1:
x= append(Scoordlist1,Scoordlist2,axis=0)[numpy.sum((append(Scoordlist1,Scoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==1:
removefromCd1 = append(removefromCd1,where(all(Cdcoordlist1==i,axis=1))[0])
for i in Cdcoordlist2:
x= append(Scoordlist1,Scoordlist2,axis=0)[numpy.sum((append(Scoordlist1,Scoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==1:
removefromCd2 = append(removefromCd2,where(all(Cdcoordlist2==i,axis=1))[0])
for i in Scoordlist1:
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==1:
removefromS1 = append(removefromS1,where(all(Scoordlist1==i,axis=1))[0])
for i in Scoordlist2:
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==1:
removefromS2 = append(removefromS2,where(all(Scoordlist2==i,axis=1))[0])
print " removed", len(removefromCd1), "atoms from Cd1"
print " removed", len(removefromCd2), "atoms from Cd2"
print " removed", len(removefromS1), "atoms from S1"
print " removed", len(removefromS2), "atoms from S2"
Cdcoordlist1 = delete(Cdcoordlist1,removefromCd1,axis=0)
Cdcoordlist2 = delete(Cdcoordlist2,removefromCd2,axis=0)
Scoordlist1 = delete(Scoordlist1,removefromS1,axis=0)
Scoordlist2 = delete(Scoordlist2,removefromS2,axis=0)
listofcoordlists = [Cdcoordlist1,Cdcoordlist2,Scoordlist1,Scoordlist2,OHcoordlist,Hcoordlist]
alllists = ndarray((0,3))
surface_atoms_count = 0
"""Surface passivation with cations and anions"""
if surfacepassivation:
CdOHbondlength =2.7
for i in Cdcoordlist1:
bondlength=CdOHbondlength
x= append(Scoordlist1,Scoordlist2,axis=0)[numpy.sum((append(Scoordlist1,Scoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
surface_atoms_count +=1
for s in tetcoord:
if not any(sum((x[:]-s)**2,axis=1)<0.5):# and not any(sum((OHcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1)<0.5):
OHcoordlist= append(OHcoordlist,[i+s/sqrt(sum(s**2))*bondlength],axis=0)
else:
pass
# print min(sum((OHcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1))
for i in Cdcoordlist2:
bondlength=CdOHbondlength ## angstroms
x= append(Scoordlist1,Scoordlist2,axis=0)[numpy.sum((append(Scoordlist1,Scoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
surface_atoms_count +=1
for s in tetcoord2:
if not any(sum((x[:]-s)**2,axis=1)<0.5):# and not any(sum((OHcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1)<0.5):
OHcoordlist= append(OHcoordlist,[i+s/sqrt(sum(s**2))*bondlength],axis=0)
else:
pass#print min(sum((OHcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1))
for i in Scoordlist1:
remove = array([])
bondlength=1.83 ## angstroms
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
surface_atoms_count +=1
for s in Cdtetcoord1:
if not any(sum((x[:]-s)**2,axis=1)<0.5) and not any(sum((Hcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1)<2):
Hcoordlist= append(Hcoordlist,[i+s/sqrt(sum(s**2))*bondlength],axis=0)
for i in Scoordlist2:
bondlength=1.83 ## angstroms
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
surface_atoms_count +=1
for s in Cdtetcoord2:
if not any(sum((x[:]-s)**2,axis=1)<0.5) and not any(sum((Hcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1)<2):
Hcoordlist= append(Hcoordlist,[i+s/sqrt(sum(s**2))*bondlength],axis=0)
listofcoordlists = [Cdcoordlist1,Cdcoordlist2,Scoordlist1,Scoordlist2,OHcoordlist,Hcoordlist]
###########Remove Duplicate Atoms
for i in listofcoordlists[0:4]:
OHcoordlist = delete(OHcoordlist,checkduplicates(i,OHcoordlist)[1],axis=0)
Hcoordlist = delete(Hcoordlist,checkduplicates(i,Hcoordlist)[1],axis=0)
listofcoordlists = [Cdcoordlist1,Cdcoordlist2,Scoordlist1,Scoordlist2,OHcoordlist,Hcoordlist]
for i in range(len(listofcoordlists)):
for j in range(i,len(listofcoordlists)):
x = checkduplicates(listofcoordlists[i],listofcoordlists[j],threshold=1)
if x[0].size>0:
if j==i:
# print i,j,x
# print listofcoordlists[i][x[0]]
# print listofcoordlists[i][x[1]]
listofcoordlists[i]=delete(listofcoordlists[i],x[1],axis=0)
print 'duplicate atoms found in same list! THE DUPLICATE ATOMS WERE REMOVED'
else:
print i,j,x
print 'duplicate atoms found! ERROR YOU NEED TO FIX THIS'
(Cdcoordlist1,Cdcoordlist2,Scoordlist1,Scoordlist2,OHcoordlist,Hcoordlist)=listofcoordlists[:]
####################3 add charges aroundthe particls
chargecoordlist=pointsonsphere(charges,radius+distance)+array([[radius,radius,radius]])
###############################
if _plot:
fig=figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,Cdcoordlist1[:,0],Cdcoordlist1[:,1],Cdcoordlist1[:,2],c='b')
Axes3D.scatter(ax,Cdcoordlist2[:,0],Cdcoordlist2[:,1],Cdcoordlist2[:,2],c='b')
Axes3D.scatter(ax,Scoordlist1[:,0],Scoordlist1[:,1],Scoordlist1[:,2],c='r')
Axes3D.scatter(ax,Scoordlist2[:,0],Scoordlist2[:,1],Scoordlist2[:,2],c='r')
Axes3D.scatter(ax,OHcoordlist[:,0],OHcoordlist[:,1],OHcoordlist[:,2],c='y')
Axes3D.scatter(ax,Hcoordlist[:,0],Hcoordlist[:,1],Hcoordlist[:,2],c='k')
Axes3D.scatter(ax,chargecoordlist[:,0],chargecoordlist[:,1],chargecoordlist[:,2],c='k')
numcoreatoms = Cdcoordlist1.shape[0]*1+Cdcoordlist2.shape[0]+Scoordlist1.shape[0]*1+Scoordlist2.shape[0]*1
print 'cadmium atoms:',Cdcoordlist1.shape[0]*1+Cdcoordlist2.shape[0]
print 'sulfur atoms:', Scoordlist1.shape[0]*1+Scoordlist2.shape[0]
print 'negative cations:', OHcoordlist.shape[0]
print 'positive cations:', Hcoordlist.shape[0]
print 'number of core atoms', numcoreatoms
numatoms= Cdcoordlist1.shape[0]*1+Cdcoordlist2.shape[0]+Scoordlist1.shape[0]*1+Scoordlist2.shape[0]*1+OHcoordlist.shape[0]*1+Hcoordlist.shape[0]*1
print 'num electrons with ECP:', str(10*(Cdcoordlist1.shape[0]+Cdcoordlist2.shape[0])+
8*(Scoordlist1.shape[0]+Scoordlist2.shape[0])+
OHcoordlist.shape[0]*10+
Hcoordlist.shape[0]*0)
print 'num atoms:', numatoms, 'total charge:', str(Cdcoordlist1.shape[0]*2+Cdcoordlist2.shape[0]*2+
Scoordlist1.shape[0]*-2+Scoordlist2.shape[0]*-2+
OHcoordlist.shape[0]*-1+
Hcoordlist.shape[0]*1)
commentline = str('cadmium atoms: '+str(Cdcoordlist1.shape[0]*1+Cdcoordlist2.shape[0])+
', sulfur atoms: '+ str(Scoordlist1.shape[0]*1+Scoordlist2.shape[0])+
', total charge of cluster: '+ str(Cdcoordlist1.shape[0]*2+
+Cdcoordlist2.shape[0]*2
+Scoordlist1.shape[0]*-2
+Scoordlist2.shape[0]*-2
+OHcoordlist.shape[0]*-1
+Hcoordlist.shape[0]*1)+
', number of point charges:'+str(charges)+
' removehangeroners= '+str(removehangeroners)
+'\n')
print 'number of surface atoms counted', surface_atoms_count
with open('/home/chris/Desktop/CdSParticle.xyz','wb') as f:#'+str(numcoreatoms)+'core'+str(charges)+'charges.xyz','wb') as f:
f.write(str(numatoms)+'\n')
f.write(commentline)
for i in append(Cdcoordlist1,Cdcoordlist2,axis=0):
f.write('Cd '+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
for i in append(Scoordlist1,Scoordlist2,axis=0):
f.write('S '+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
for i in OHcoordlist:
f.write('Cl '+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
for i in Hcoordlist:
f.write('H '+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
for i in chargecoordlist:
if module == 'nwchem':
f.write('bq1 '+str(i[0])+' '+str(i[1])+' '+str(i[2])+' charge -1\n')
elif module == 'orca':
f.write('Q -1'+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
f.close()
return None
def plotFFDPointsAndPlane(xsolidInitial,ysolidInitial, zsolidInitial, xFFDInitial, yFFDInitial, zFFDInitial,
LeadingEdgeX, LeadingEdgeY, LeadingEdgeZ):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
Axes3D.scatter(ax, zsolidInitial, xsolidInitial, ysolidInitial, s=10, c='y')
#Axes3D.plot_wireframe(ax, zsolidInitial, xsolidInitial, ysolidInitial, rstride = 1, cstride = 1, color='y')
#Axes3D.scatter(ax, LeadingEdgeZ, LeadingEdgeX, LeadingEdgeY, s=10, c='y')
#Axes3D.plot_wireframe(ax, zSolid, xSolid, ySolid, rstride = 1, cstride = 1, color="b")
Axes3D.scatter(ax, zFFDInitial, xFFDInitial, yFFDInitial, s=10, c='r')
LeadingEdgeX1 = []
LeadingEdgeY1 = []
LeadingEdgeZ1 = []
#Find all the leading edge points:
for element in solidBoundaryPointArray:
if((element.getLabel() == "LeadingEdge") or (element.getLabel() == "TrailingEdge")
or (element.getLabel() == "WingTip") or (element.getLabel() == "WingRoot")):
LeadingEdgeX1.append(element.getX())
LeadingEdgeY1.append(element.getY())
LeadingEdgeZ1.append(element.getZ())
#Axes3D.scatter(ax, LeadingEdgeZ1, LeadingEdgeX1, LeadingEdgeY1, s=100, c='r')
#plot the deformed wing and FFD point data
xDeformed = []
yDeformed = []
zDeformed = []
xFFDDeformed = []
yFFDDeformed = []
zFFDDeformed = []
for element in solidBoundaryPointArray:
xDeformed.append(element.getX())
yDeformed.append(element.getY())
zDeformed.append(element.getZ())
# filling the FFD arrays
for i in range(CONST_nXFDD):
for j in range(CONST_nYFDD):
for k in range(CONST_nZFDD):
element = FFDPointArray[i][j][k]
xFFDDeformed.append(element.getX())
yFFDDeformed.append(element.getY())
zFFDDeformed.append(element.getZ())
"""
Axes3D.plot_wireframe(ax, zDeformed, xDeformed, yDeformed, rstride =1, cstride = 1, color='b')
"""
Axes3D.scatter(ax, zDeformed, xDeformed, yDeformed, s=10, color='b')
Axes3D.scatter(ax, zFFDDeformed, xFFDDeformed, yFFDDeformed, s=10, c='g')
#takes a value for t,u,v. When a value is set to -1, then that parameter is free
# to change while the one that is not set to -1 is the plane that needs to be drawn
tuplesArray = plotIsoparametricLine(-1,-1,-1)
xArray = []
yArray = []
zArray = []
for a in tuplesArray:
xArray.append(a[0])
yArray.append(a[1])
zArray.append(a[2])
tuplesArray2 = plotIsoparametricLine(-1,-1,-1)
xArray2 = []
yArray2 = []
zArray2 = []
for a in tuplesArray2:
xArray2.append(a[0])
yArray2.append(a[1])
zArray2.append(a[2])
#Axes3D.scatter(ax, zArray, xArray, yArray, s=10, c='y')
Axes3D.plot_wireframe(ax, zArray, xArray, yArray, rstride=1, cstride =1, color='g')
Axes3D.plot_wireframe(ax, zArray2, xArray2, yArray2, rstride=1, cstride =1, color='g')
#Axes3D.set_ylim(ax, [-0.5,4.5])
#Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.9, 0.9])
plt.show(block=True)
plt.xlim([4, 8])
plt.title('Classified data')
#plt.legend(loc='best')
# Plot samples according to their original class
w0 = [6.5, 3]
plt.figure()
plt.plot(C1[0, :], C1[1, :], 'ro', label='Class 1')
plt.plot(C2[0, :], C2[1, :], 'go', label='Class 2')
plt.plot(C3[0, :], C3[1, :], 'bo', label='Class 3')
plt.plot([w0[0], w[0, 0] + w0[0]], [w0[1], w[0, 1] + w0[1]], '-r', label='1-2')
plt.plot([w0[0], w[1, 0] + w0[0]], [w0[1], w[1, 1] + w0[1]], '-g', label='1-3')
plt.plot([w0[0], w[2, 0] + w0[0]], [w0[1], w[2, 1] + w0[1]], '-b', label='2-3')
plt.ylim([1, 5])
plt.xlim([4, 8])
plt.title('Original classes')
plt.legend(loc='best')
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# plt.plot(C1_12.T, C1_13.T)
Axes3D.scatter(ax, C1_p[0, :], C1_p[1, :], zs=C1_p[2, :], c='r', label='Class 1')
Axes3D.scatter(ax, C2_p[0, :], C2_p[1, :], zs=C2_p[2, :], c='g', label='Class 2')
Axes3D.scatter(ax, C3_p[0, :], C3_p[1, :], zs=C3_p[2, :], c='b', label='Class 3')
plt.legend(loc='best')
ax.set_xlabel('Separating 1-2')
ax.set_ylabel('Separating 1-3')
ax.set_zlabel('Separating 2-3')
plt.show()
def plot():
ax = implicit.plot_implicit(f3,bbox=(-5,5,-5,5,-5,5))
Axes3D.scatter(ax,rays[:,0],rays[:,1],rays[:,2])
plt.show()
nxarray = []
nyarray = []
nzarray = []
for nonFeasibleTReference in nonFeasibleTReferences:
nxarray.append(nonFeasibleTReference[0])
nyarray.append(nonFeasibleTReference[1])
nzarray.append(nonFeasibleTReference[2])
xarray = []
yarray = []
zarray = []
for FeasibleTReference in FeasibleTReferences:
xarray.append(FeasibleTReference[0])
yarray.append(FeasibleTReference[1])
zarray.append(FeasibleTReference[2])
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
Axes3D.scatter(ax, nxarray, nyarray, nzarray, c="r")
Axes3D.scatter(ax, xarray, yarray, zarray)
ax.axis("off")
savez_compressed("FeasibleTPoints0_HD.npz", array=FeasibleTPoints)
savez_compressed("FeasibleTAlphas0_HD.npz", array=FeasibleTAlphas)
savez_compressed("FeasibleTOmegas0_HD.npz", array=FeasibleTOmegas)
savez_compressed("FeasibleTThetas0_HD.npz", array=FeasibleTThetas)
plt.show()
# with open(filename, 'wb') as handle: # cPickle.dump([difficulties, generosities, ave_switches], handle) #read with open(filename, 'rb') as handle: data = cPickle.load(handle) difficulties=data[0] generosities=data[1] ave_switches=data[2] fig = plt.figure() ax = Axes3D(fig) Axes3D.scatter(ax, difficulties, generosities, ave_switches, cmap=cm.jet) Axes3D.plot_trisurf(ax, difficulties, generosities, ave_switches, cmap=cm.jet) plt.show() print ave_switches # griddata and contour. xi = np.linspace(min(difficulties),max(difficulties),15) yi = np.linspace(min(generosities),max(generosities),15) xi = np.linspace(0,1,15) yi = np.linspace(0,1,15) print len(difficulties), len(generosities), len(ave_switches)
current_point = seed
for idx in xrange(0, N):
ndx = rnd.randint(0, nVerts)
vert = polygon[:, ndx]
next_point = current_point + f*(vert-current_point)
fractal[:,idx] = next_point
current_point = next_point
return fractal
seed_x = np.array([])
if __name__ == '__main__':
n = 4
N = int(1e4)
f = 1.0/2.0
seed = [0.5,0.5,0.5]
#nGon = get_regular_polygon(n)
nGon = np.array([[0,1,1/2,1/2],
[0,0,np.sqrt(3)/2, np.sqrt(3)/4],
[0,0,0, np.sqrt(3)/2]])
fractal = chaos_game(nGon, seed, N, f)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax, fractal[0,:], fractal[1,:], fractal[2,:])
plt.show()
#plt.plot(fractal[0,:], fractal[1,:], 'b.')
#plt.grid()
#plt.show()
def run(self):
nat = 4 # number of atoms first and last mimic walls.
x0 = zeros(nat)
y0 = zeros(nat)
xm = zeros(nat)
t = 0.0
#--------- potential setting
epsilon = 1
eps = zeros(nat-1)
eps[0] = epsilon*self.frac_stif
eps[1] = epsilon
eps[2] = epsilon*self.frac_stif
sig = 1
d_eq = sig*2.0**(1./6.0) # vdW eq. distance
mass = 2.0 # mass of each atom
red_mass = mass/2.0 # reduced mass (mass of the optical oscillator)
aco_mass = mass*2.0 # mass of the acoustic oscillator
period = (2.0*pi*sig/(6.0*2.**(1./3)))*(red_mass/epsilon)**0.5 #--------- period of a free LJ dimer
if self.i_potential == "stiffer_lj":
per_opt = (2.0*pi*sig/(6.0*2.**(1./3)))*(red_mass/((0.5*eps[0])+eps[1]))**0.5 #--------- period of the optical mode (stiffer single backbond)
per_aco = (2.0*pi*sig/(6.0*2.**(1./3)))*(aco_mass/(2.0*eps[0]))**0.5 #--------- period of the acoustic mode
elif self.i_potential == "triple_back":
per_opt = (2.0*pi*sig/(6.0*2.**(1./3)))*(red_mass/(0.5*eps[0]/3.+eps[1]))**0.5 #--------- period of the optical mode
per_aco = (2.0*pi*sig/(6.0*2.**(1./3)))*(aco_mass/(2.*eps[0]/3.))**0.5
speed_of_sound = 6.0*(2.*epsilon/mass)**0.5
w_lj = 2*pi/period # --------- angular frequencies
w_opt = 2*pi/per_opt
w_aco = 2*pi/per_aco
# --------- opening velocity & time step
vel = self.frac_vel * speed_of_sound # velocity as fraction of the speed of sound of a LJ 1D lattice
dt = self.frac_tim * period # time step as fraction of the period of a LJ dimer
works = []
en_mask = 0
pos1 = []
pos2 = []
pos0 = []
pos3 = []
times = []
eq = []
disp = []
maxes = []
for i_sample in range(0, self.nconfig):
if i_sample == 0:
start_time = time.time()
# ---------equilibrium atoms positions
if self.i_potential == "stiffer_lj":
for i in range(nat):
x0[i] = (-float(nat-1)/2.0 + float(i))*d_eq
elif self.i_potential == "triple_back":
x0[1] = -0.5*d_eq
x0[2] = 0.5*d_eq
x0[0] = x0[1]-d_eq/3.
x0[3] = x0[2]+d_eq/3.
# PHONON SETUPS
en_opt = self.frac_opt*epsilon # ---------energy of the opt phonon in units of epsilon
en_aco = self.frac_aco*epsilon # ---------energy of the opt phonon in units of epsilon
# -------------
dis_opt = (2.0*en_opt/(red_mass * w_opt**2))**0.5 # displacement for the opt phonon to have that energy
dis_aco = (2.0*en_aco/(2.*mass * w_aco**2))**0.5 # displacement for the opt phonon to have that energy
phs_opt = 2.0*pi*rand() # Present positions in relative phon coord (with random phases)
xopt = dis_opt*cos(w_opt*t + phs_opt)
xoptm = dis_opt*cos(w_opt*(t-dt) + phs_opt)
phs_aco = 2.0*pi*rand() # past positions in relative phon coord (with random phases)
xaco = dis_aco*cos(w_aco*t + phs_aco)
xacom = dis_aco*cos(w_aco*(t-dt) + phs_aco)
xdtot=zeros(2) # total current displ vector in relative phon coord
xdtot[0]=+xopt/2.0 + xaco
xdtot[1]=-xopt/2.0 + xaco
xdmtot=zeros(2) # total past displ vector in relative phon coords
xdmtot[0]=+xoptm/2.0 + xacom
xdmtot[1]=-xoptm/2.0 + xacom
# setting up atomic positions in absolute coords
xm[:] = x0[:]
x0[1] = x0[1]+xdtot[0] # present
x0[2] = x0[2]+xdtot[1]
xm[1] = xm[1]+xdmtot[0] # past time step
xm[2] = xm[2]+xdmtot[1]
delxd = zeros(2)
delxd[0] = xm[1]-x0[1]
delxd[1] = xm[2]-x0[2]
# correction section for anharmonicity essentially this will be microcanonic dynamics with kin + pot fixed at the desired target
# while epot and ekin won't necessarily be equal, so that half the target does not immediately give temperature (just a very good estimate)
#
# estimated potential: -(eps[0]+eps[1]+eps[2]) + phonon energy
if self.i_potential == "stiffer_lj":
e_bottom = -(eps[0]+eps[1]+eps[2])
elif self.i_potential == "triple_back":
e_bottom = -(3.0*eps[0]+eps[1]+3.*eps[2])
e_est = 0.5*red_mass*w_opt**2*xopt**2 + 0.5*aco_mass*w_aco**2*xaco**2
epot, fc = self.en_and_for(x0, nat, sig, eps)
#print("estimated and real epots: ",e_est,epot + (eps[0]+eps[1]+eps[2]))
for i in range(1, 7): # iterative trick.
rat_corr = e_est/(epot - e_bottom)
x0[1] = x0[1]-xdtot[0] # present
x0[2] = x0[2]-xdtot[1]
xdtot[:] = xdtot[:]*rat_corr**0.5
x0[1] = x0[1]+xdtot[0]
x0[2] = x0[2]+xdtot[1]
epot, fc = self.en_and_for(x0, nat, sig, eps)
#print("estimated and real epots: ",e_est,epot + (eps[0]+eps[1]+eps[2]))
xm[1] = x0[1] + delxd[0]
xm[2] = x0[2] + delxd[1]
#nstep = 10000
nstep = int(self.n_sigmas*sig/(vel*dt))
work = 0.0
veldrift = zeros(4)
veldrift[0] = -vel/2.
veldrift[1] = -vel/2.
veldrift[2] = vel/2.
veldrift[3] = vel/2.
clf()
ekin_total = 0
epot_total = 0
for i in range(1, nstep):
epot, fc = self.en_and_for(x0, nat, sig, eps)
# current_time = dt*float(i)
# tau = 0.2*period
# vell = self.velocity(current_time, tau, vel)
xp, dwork = self.verlet(x0, xm, dt, fc, mass, nat, vel)
work += dwork
velo = (xp - xm)/(2.0*dt)
ekin = 0.5*mass*(velo[1]**2+velo[2]**2)
etot = epot + ekin
# ekinotto = ekinotto + epot + 0.25*mass*vel**2 + eps[0]+eps[2] -en_opt - en_aco
#
# A DEFINITION OF WORK DONE BY THE TWO FORCES:
if (abs(x0[1]-x0[0]) < 3.0*sig): # left atom drifting left with left wall
veldrift[1]=-vel/2.
if(abs(x0[2]-x0[1]) < 3.0*sig): # right atom drifting left with left atom
veldrift[2]= -vel/2.
if (abs(x0[3]-x0[2]) < 3.0*sig): # right atom drifting right with right wall
veldrift[2]= vel/2.
if(abs(x0[2]-x0[1]) < 3.0*sig): # left atom drifting right with right atom
veldrift[1]= vel/2.
if( (abs(x0[1]-x0[0]) > 3.0*sig) or (abs(x0[3]-x0[2]) > 3.0*sig)): # non standard event
en_mask = 1 # flagged for later use
ekinotto = 0.5*mass*((velo[1]-veldrift[1])**2 + (velo[2]-veldrift[2])**2) # kinetic energy of the two oscillating fragments
# in the translating ref. frames
ekinotto += (epot - e_bottom) # total oscillator energy in the translating ref. frame
ekinotto -= (en_opt + en_aco) # ..minus the initial oscillator energy before the pull
ekinotto -= eps[1] # ..minus the energy it took to break the central bond
# (this correction can be excluded as as an offset)
# ekinotto = ekinotto + 2.*(0.5*mass*(vel/2.)**2) # ..plus translation kin. energy of the two atoms
# (this last correction is temperature independent and
# could be excluded from the definition)
# so this is the energy to break the bond at the net of the static bond energy and the translational kinetic energy
# it can be negative (in which case, initial oscillations helped the bond breaking)
# or positive (in which case, initial oscillations -temperature- made the bond breaking more difficult)
# or zero (typical of zero initial oscillation and fracture at very low velocity)
#if i%1000==1: print(("%6d"+"%12.8f"*6) % (i,ekin,epot,etot, work, etot + work, ekinotto))
if i % 1 == 0:
pos1.append(x0[1])
pos2.append(x0[2])
pos0.append(x0[0])
pos3.append(x0[3])
times.append(t)
i = len(pos1)
disp.append((pos1[i - 1]) - (pos2[i - 1]))
#print(pos1[i - 1], eq[i - 1], disp[i - 1])
if i > 3:
if pos1[i - 3] < pos1[i - 2] > pos1[i - 1]:
maxes.append(t)
xm[:] = x0[:]
x0[:] = xp[:]
t += dt
if ((x0[2]-x0[1]) > sig*(float(self.n_sigmas)-3.0)) :
print('LOST COHERENCE at frac_vel,frac_opt,frac_aco', self.frac_vel, self.frac_opt, self.frac_aco)
if( ((x0[1] < 0) and (x0[2] < 0)) or ((x0[1] > 0) and (x0[2] > 0)) ): # a stiff, not a weak bond was broken
print('STIFF BOND BROKEN, POSITIONS: ',x0)
elif( ((x0[1] < 0) and (x0[2] > 0)) or ((x0[1] > 0) and (x0[2] < 0)) ): # TWO stiff bonds were broken
if( ((x0[1]-x0[0]) > 2*sig) and ((x0[3]-x0[2]) > 2*sig)): # (making sure)
print('TWO STIFF BONDS BROKEN, POSITIONS: ',x0)
else:
print('DISASTER, POSITIONS: ',x0)
sys.exit(0)
periods = []
prev = 0
for t in maxes:
periods.append(t - prev)
prev = t
print(statistics.mean(periods), statistics.pstdev(periods))
# plt.plot(times, pos1, ls="none", marker="+", color=(0, 0.5, 0.5))
# plt.plot(times, disp, ls="none", marker="+", color=(0.5, 0, 0.5))
# fit = []
#
# def sin_fit(tl, amp, freq, phase, offset):
# q = []
# for t in tl:
# q.append(amp*math.sin((freq*t) + phase) - offset)
# return q
#
# #p0 = [0.05, 10, -0.5, 1.125]
# p0 = [1, (2*pi/statistics.mean(periods)), 1, 1]
#
#
# parms, cov = curve_fit(sin_fit, times, disp, p0)
#
# print(parms)
# for t in times:
# fit.append(parms[0]*math.sin((parms[1]*t) + parms[2]) - parms[3])
#
# plt.plot(times, fit, ls="none", marker="+", color=(0.5, 0, 0.5))
# plt.show()
param_string = "Optical Mode: f_opt = 0.005, Stiffness = 1.0"
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1], projection='3d')
plt.xlabel("x")
plt.ylabel("y")
#ax.axis('off')
fig.suptitle(param_string, fontsize=12)
x_init = [-0.5*d_eq, 0.5*d_eq]
y0 = [0, 0]
z0 = [0, 0]
d_lat = d_eq*(2/3)*(2**0.5)
x_bb_rel = [-d_lat/3, -d_lat/3, -d_lat/3, d_lat/3, d_lat/3, d_lat/3]
y_bb_rel = [d_lat, -d_lat, 0, -d_lat, d_lat, 0]
z_bb_rel = [-d_lat, -d_lat, d_lat, d_lat, d_lat, -d_lat]
# Set up figure & 3D axis for animation
ax.set_xlim((-5, 5))
ax.set_ylim((-3, 3))
ax.set_zlim((-3, 3))
atom_colours = [(0, 0.5, 0.5), (0, 0.5, 0.5),
(0.5, 0.5, 0), (0.5, 0.5, 0), (0.5, 0.5, 0),
(0.5, 0.5, 0), (0.5, 0.5, 0), (0.5, 0.5, 0)]
atoms = Axes3D.scatter(ax, [], [], [], c=atom_colours, s=200, depthshade=False)
bonds = [ax.plot([], [], ls="--", lw=2, color=(0, 1, 0.5), zorder=-1)]
back_bonds = [ax.plot([], [], ls="-", lw=2, color=(1, 0, 0.5), zorder=-1)]
for q in range(5):
back_bonds.append(ax.plot([], [], ls="-", lw=2, color=(1, 0, 0.5), zorder=-1))
ax.view_init(25, 100)
self.broken = False
text = True
speed_factor = 5
if text:
time_text = ax.text(4.9, -3, 3, "")
theoretical_period = ax.text(4.9, -3, 2.6, "Theoretical Period = " + str(round(per_opt, 3)))
period_text = ax.text(4.9, -3, 2.2, "")
def init():
elements = []
for bond in bonds:
bond = bond[0]
bond.set_data([], [])
bond.set_3d_properties([])
elements.append(bond)
for bond in back_bonds:
bond = bond[0]
bond.set_data([], [])
bond.set_3d_properties([])
elements.append(bond)
atoms._offsets3d = ([], [], [])
elements.append(atoms)
if text:
time_text.set_text('')
period_text.set_text('')
elements.append(time_text)
elements.append(period_text)
return elements
def animate(i):
if i == 0:
self.broken = False
i *= speed_factor
elements = []
bondx = []
bondy = []
bondz = []
for q in range(len(bonds)):
bondx.append([pos1[i], pos2[i]])
bondy.append([y0[q], y0[q]])
bondz.append([z0[q], z0[q]])
for bond in bonds:
q = bonds.index(bond)
bond = bond[0]
if abs(bondx[0][0] - bondx[0][1]) < 3 and not self.broken:
bond.set_data(bondx[q], bondy[q])
bond.set_3d_properties(bondz[q])
elements.append(bond)
else:
bond.set_data(0, 0)
bond.set_3d_properties(0)
self.broken = True
x_bb = []
y_bb = []
z_bb = []
for q in range(len(back_bonds)):
if q < 3:
x_bb.append(pos0[i])
y_bb.append(y_bb_rel[q] + y0[0])
z_bb.append(z_bb_rel[q] + z0[0])
else:
x_bb.append(pos3[i])
y_bb.append(y_bb_rel[q] + y0[1])
z_bb.append(z_bb_rel[q] + z0[1])
bondx = []
bondy = []
bondz = []
for q in range(len(back_bonds)):
if q < 3:
bondx.append([x_bb[q], pos1[i]])
bondy.append([y_bb[q], y0[0]])
bondz.append([z_bb[q], z0[0]])
else:
bondx.append([x_bb[q], pos2[i]])
bondy.append([y_bb[q], y0[1]])
bondz.append([z_bb[q], z0[1]])
for bond in back_bonds:
q = back_bonds.index(bond)
bond = bond[0]
bond.set_data(bondx[q], bondy[q])
bond.set_3d_properties(bondz[q])
elements.append(bond)
atomx = []
atomy = []
atomz = []
for q in range(8):
if q == 0:
atomx.append(pos1[i])
atomy.append(y0[0])
atomz.append(z0[0])
elif q == 1:
atomx.append(pos2[i])
atomy.append(y0[1])
atomz.append(z0[1])
elif 1 < q > 4:
atomx.append(pos3[i])
atomy.append(y_bb_rel[q - 2] + y0[1])
atomz.append(z_bb_rel[q - 2] + z0[1])
else:
atomx.append(pos0[i])
atomy.append(y_bb_rel[q - 2] + y0[0])
atomz.append(z_bb_rel[q - 2] + z0[0])
atoms._offsets3d = (atomx, atomy, atomz)
elements.append(atoms)
if text:
time_text.set_text("Time = " + format(times[i], ".3f"))
c_time = times[i]
c_max = 0
for max_i in range(len(maxes)):
q = len(maxes) - max_i - 1
if c_time <= maxes[q]:
c_max = max_i
period_text.set_text("Period = " + format(periods[c_max], ".3f"))
elements.append(time_text)
elements.append(period_text)
#ax.view_init(25, 125 - 60*(i/len(pos1)))
fig.canvas.draw()
return elements
n_frames = int(len(pos1)/speed_factor)
anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=n_frames, interval=1, blit=True)
print(n_frames, n_frames/60)
#anim.save('optical_3D_15.mp4', fps=60, extra_args=['-vcodec', 'libx264'])
plt.show()
colors = [out1, out1_HSV, out1_HLS, out1_Lab, out1_Luv, out1_YCrCb]
out1_colors = {}
i=0
for color in colors:
X = color.reshape((-1,3))
df = pd.DataFrame(X)
out1_colors['%s_uniq' % colors_name[i]] = df.drop_duplicates().values #get unique color value
i=i+1
#3-D plot
fig = plt.figure()
fig.suptitle('RGB', fontsize=20)
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax, xs=out1_colors["out1_uniq"][:,0], ys=out1_colors["out1_uniq"][:,1], zs=out1_colors["out1_uniq"][:,2], zdir='z', s=20, c='cyan', depthshade=True)
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')
ax.view_init(30,220)
plt.show()
fig = plt.figure()
fig.suptitle('HSV', fontsize=20)
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax, xs=out1_colors["out1_HSV_uniq"][:,0], ys=out1_colors["out1_HSV_uniq"][:,1], zs=out1_colors["out1_HSV_uniq"][:,2], zdir='z', s=20, c='yellow', depthshade=True)
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')
ax.view_init(30,220)
plt.show()
Max.append(amax(t[j]))
xarray.append(alltriopoints[i][0][0][0])
yarray.append(alltriopoints[i][0][0][1])
zarray.append(alltriopoints[i][0][0][2])
io = 0
break
if io:
nMax.append(amin(t))
xnarray.append(alltriopoints[i][0][0][0])
ynarray.append(alltriopoints[i][0][0][1])
znarray.append(alltriopoints[i][0][0][2])
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
Axes3D.scatter(ax, xnarray, ynarray, znarray, c="r")
Axes3D.scatter(ax, xarray, yarray, zarray)
ax.axis("off")
plt.show()
def scatter3d(x, y, z, cs, colorsMap="jet"):
cm = plt.get_cmap(colorsMap)
cNorm = clr.Normalize(vmin=min(cs), vmax=max(cs))
scalarMap = cmx.ScalarMappable(norm=cNorm, cmap=cm)
fig = plt.figure()
ax = Axes3D(fig)
ax.scatter(x, y, z, c=scalarMap.to_rgba(cs))
scalarMap.set_array(cs)
fig.colorbar(scalarMap)
ax.axis("off")
def prepdftcharged(charges,chargemag,totalcharge,d=0):
"""used to create input files for nwchem for Cd29S29 clusters with point charges"""
z=array([[3.73479929,4.70148859,1.08453093],
[-0.45777444,5.46389693,1.42922813],
[3.99256744,1.42776590,0.17101104],
[-3.23253881,2.73557278,0.17389669],
[0.00277074,-0.00738694,-0.25202305],
[0.00013075,-0.01651818,6.38550475],
[4.95224596, -2.34187282,1.40722903],
[-5.94120956,0.87524543,1.07437676],
[-4.49880283,-3.12964705,1.41125120],
[-0.75991343,-4.18114040,0.15674939],
[2.20650584,-5.59236598,1.05533723],
[0.96252338,4.36198028,-1.42717920],
[4.81764990,3.19485539,-2.77622069],
[-1.73138701,4.16471485,-3.46626689],
[-2.55306625,2.91594904,4.51767596],
[1.50206160,1.89218763,-4.09811156],
[0.98329346,2.34564526,3.5974529],
[4.46454220,-0.56369361,-3.47475802],
[3.80849139,0.73094006,4.51682402],
[-5.17525966,2.60395011,-2.77772471],
[-2.37975873,0.36837952,-4.07698444],
[-2.53045715,-0.33540920,3.59449188],
[0.88144546,-2.23348348,-4.09931249],
[1.54175224,-2.03600240,3.58132334],
[3.31038688,-3.02228474,-1.45695989],
[-4.27528734,-1.35796536,-1.44852313],
[-2.72513737,-3.56991001,-3.48209886],
[-1.25794100,-3.68787964,4.50492503],
[0.35261163,-5.75579556,-2.79552608],
[0.74123700,4.43697518,-4.02956973],
[-0.64622546,4.44077927,3.74595547],
[4.18920378,1.70873805,-4.66166552],
[3.47773976,2.51701231,2.54165082],
[-3.55947851,2.79106662,-4.65228042],
[-3.92545305,1.73860005,2.54076867],
[-0.00271263,0.01013464,-5.02518153],
[-0.00332939,-0.00785361,2.48730355],
[3.46776368,-2.83946171,-4.05736012],
[4.17115409,-1.67896151,3.73089394],
[-4.20196677,-1.57060486,-4.04933515],
[-3.53060015,-2.79614465,3.73504438],
[-0.62463325,-4.46372023,-4.67635054],
[0.44748177,-4.28341329,2.52481152],
[1.79334057,6.15314947,0.33208226],
[5.55303831,3.65754425,-0.46937522],
[-1.77455171,4.68869481,-0.74204629],
[1.74568849,1.79694051,-1.26045912],
[1.94632660,1.65173243,6.00004182],
[4.95599592,-0.80678637,-0.75922862],
[-5.94441654,2.98322195,-0.46759778],
[-2.43853084,0.59877699,-1.25432294],
[-2.41524712,0.83987083,5.99734552],
[0.69721678,-2.42073954,-1.26854049],
[0.46924459,-2.53096433,5.98775239],
[4.43666586,-4.63906404,0.30520008],
[-6.23050849,-1.53090073,0.31876024],
[-3.17891818,-3.89146035,-0.76368896],
[0.38866467,-6.64405085,-0.49626228]])
print z.shape
# z = numpy.loadtxt('/home/chris/Desktop/q16_cd29/Cd29.xyz',skiprows = 2, usecols = (1,2,3), delimiter = ' ',unpack=False)
chargemag = float(totalcharge)/charges
print "number of charges",charges
print 'total charge', totalcharge
print 'magnitude of each charge', chargemag
(x1,y1,z1) = tuple(numpy.mean(z,axis=0))
center = numpy.mean(z,axis=0)
minradius = max(sqrt(sum((z[:]-center)**2,axis = 1)))
radius = minradius + d
chargecoordlist = pointsonsphere(charges,radius) + center
# with open('/home/chris/Desktop/q16_cd29/Cd29.xyz','rb') as r:
# xyzcoords = r.read()[3:]
# r.close()
totalcharge = str(totalcharge)
print totalcharge
newfolder = 'Q'+totalcharge+'d'+str(charges)+'r'+str(d)+'_Cd29S29'
try:
os.mkdir('/home/chris/Desktop/charges/'+newfolder)
except:
pass
outputfilename = str('/home/chris/Desktop/charges/'+newfolder+'/'+newfolder+'.nw')
newfolder = 'Q'+totalcharge+'d'+str(charges)+'r'+str(d)+'_Cd29S29'
print "newfolder name", newfolder
print "saving as", outputfilename
with open(outputfilename,'wb') as f:
f.write('''start "'''+newfolder+'''"
echo
memory total 4096 mb
charge 0
geometry
Cd 3.73479929 4.70148859 1.08453093
Cd -0.45777444 5.46389693 1.42922813
Cd 3.99256744 1.42776590 0.17101104
Cd -3.23253881 2.73557278 0.17389669
Cd 0.00277074 -0.00738694 -0.25202305
Cd 0.00013075 -0.01651818 6.38550475
Cd 4.95224596 -2.34187282 1.40722903
Cd -5.94120956 0.87524543 1.07437676
Cd -4.49880283 -3.12964705 1.41125120
Cd -0.75991343 -4.18114040 0.15674939
Cd 2.20650584 -5.59236598 1.05533723
Cd 0.96252338 4.36198028 -1.42717920
Cd 4.81764990 3.19485539 -2.77622069
Cd -1.73138701 4.16471485 -3.46626689
Cd -2.55306625 2.91594904 4.51767596
Cd 1.50206160 1.89218763 -4.09811156
Cd 0.98329346 2.34564526 3.59745292
Cd 4.46454220 -0.56369361 -3.47475802
Cd 3.80849139 0.73094006 4.51682402
Cd -5.17525966 2.60395011 -2.77772471
Cd -2.37975873 0.36837952 -4.07698444
Cd -2.53045715 -0.33540920 3.59449188
Cd 0.88144546 -2.23348348 -4.09931249
Cd 1.54175224 -2.03600240 3.58132334
Cd 3.31038688 -3.02228474 -1.45695989
Cd -4.27528734 -1.35796536 -1.44852313
Cd -2.72513737 -3.56991001 -3.48209886
Cd -1.25794100 -3.68787964 4.50492503
Cd 0.35261163 -5.75579556 -2.79552608
S 0.74123700 4.43697518 -4.02956973
S -0.64622546 4.44077927 3.74595547
S 4.18920378 1.70873805 -4.66166552
S 3.47773976 2.51701231 2.54165082
S -3.55947851 2.79106662 -4.65228042
S -3.92545305 1.73860005 2.54076867
S -0.00271263 0.01013464 -5.02518153
S -0.00332939 -0.00785361 2.48730355
S 3.46776368 -2.83946171 -4.05736012
S 4.17115409 -1.67896151 3.73089394
S -4.20196677 -1.57060486 -4.04933515
S -3.53060015 -2.79614465 3.73504438
S -0.62463325 -4.46372023 -4.67635054
S 0.44748177 -4.28341329 2.52481152
S 1.79334057 6.15314947 0.33208226
S 5.55303831 3.65754425 -0.46937522
S -1.77455171 4.68869481 -0.74204629
S 1.74568849 1.79694051 -1.26045912
S 1.94632660 1.65173243 6.00004182
S 4.95599592 -0.80678637 -0.75922862
S -5.94441654 2.98322195 -0.46759778
S -2.43853084 0.59877699 -1.25432294
S -2.41524712 0.83987083 5.99734552
S 0.69721678 -2.42073954 -1.26854049
S 0.46924459 -2.53096433 5.98775239
S 4.43666586 -4.63906404 0.30520008
S -6.23050849 -1.53090073 0.31876024
S -3.17891818 -3.89146035 -0.76368896
S 0.38866467 -6.64405085 -0.49626228
end
bq\n''')
for i in chargecoordlist:
f.write(str(i[0])+' '+str(i[1])+' '+str(i[2])+' ' +str(chargemag) + '\n')
f.write('''
end
basis
Cd library "LANL2DZ ECP"
S library "LANL2DZ ECP"
end
ecp
Cd library "LANL2DZ ECP"
S library "LANL2DZ ECP"
end
dft
xc b3lyp
direct
mult 1
iterations 200
convergence energy 1E-5 density 5E-6 gradient 5e-5 ncysh 200
end
dplot
TITLE LUMO
GAUSSIAN
vectors ./'''+newfolder+'''.movecs
LimitXYZ
-10 10 50
-10 10 50
-10 10 50
orbitals view;1;262
output lumo.cube
end
task tddft gradient
task dplot
dplot
TITLE H**O
GAUSSIAN
vectors ./'''+newfolder+'''.movecs
LimitXYZ
-10 10 50
-10 10 50
-10 10 50
orbitals view;1;261
output h**o.cube
end
task dplot''')
f.close()
if False:
fig=figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,z[:,0],z[:,1],z[:,2],c='b')
Axes3D.scatter(ax,chargecoordlist[:,0],chargecoordlist[:,1],chargecoordlist[:,2],c='r')
return None
def CdSetddftcharged(charges,chargemag,totalcharge,d=0):
#### d distance of charges from surface in is in angstrom
z = numpy.loadtxt('/home/chris/Desktop/CdSe29_finalgeometry.xyz',skiprows = 2, usecols = (1,2,3), delimiter = ' ',unpack=False)
if z.shape[0]!=58:
return 0
chargemag = float(totalcharge)/charges
print "number of charges",charges
print 'total charge', totalcharge
print 'magnitude of each charge', chargemag
(x1,y1,z1) = tuple(numpy.mean(z,axis=0))
center = numpy.mean(z,axis=0)
minradius = max(sqrt(sum((z[:]-center)**2,axis = 1)))
radius = minradius + d
chargecoordlist = pointsonsphere(charges,radius) + center
# with open('/home/chris/Desktop/CdSe29_finalgeometry.xyz','rb') as r:
# xyzcoords = r.read()[3:]
# r.close()
totalcharge = str(totalcharge)
print totalcharge
newfolder = 'tddftQ'+totalcharge+'d'+str(charges)+'r'+str(d)+'_Cd29Se29'
try:
os.mkdir('/home/chris/Desktop/charges/'+newfolder)
except:
pass
outputfilename = str('/home/chris/Desktop/charges/'+newfolder+'/'+newfolder+'.nw')
newfolder = 'tddftQ'+totalcharge+'d'+str(charges)+'r'+str(d)+'_Cd29Se29'
print "newfolder name", newfolder
print "saving as", outputfilename
with open(outputfilename,'wb') as f:
f.write('''start "'''+newfolder+'''"
echo
memory total 4096 mb
charge 0
geometry
symmetry c1\n''')
for i in range(z.shape[0]):
if i<29: f.write('Cd '+str(z[i,0])+' '+str(z[i,1])+' '+str(z[i,2])+'\n')
elif i>30: f.write('Se '+str(z[i,0])+' '+str(z[i,1])+' '+str(z[i,2])+'\n')
f.write('''end
bq\n''')
for i in chargecoordlist:
f.write(str(i[0])+' '+str(i[1])+' '+str(i[2])+' ' +str(chargemag) + '\n')
f.write('''
end
basis
Cd library "LANL2DZ ECP"
Se library "LANL2DZ ECP"
end
ecp
Cd library "LANL2DZ ECP"
Se library "LANL2DZ ECP"
end
dft
xc b3lyp
direct
mult 1
iterations 200
convergence energy 1E-5 density 5E-6 gradient 5e-5 ncysh 200
end
tddft
nroots 10
civecs
notriplet
end
dplot
TITLE LUMO
GAUSSIAN
vectors ./'''+newfolder+'''.movecs
LimitXYZ
-10 10 50
-10 10 50
-10 10 50
orbitals view;1;262
output lumo.cube
end
task tddft energy
task dplot
dplot
TITLE H**O
GAUSSIAN
vectors ./'''+newfolder+'''movecs
LimitXYZ
-10 10 50
-10 10 50
-10 10 50
orbitals view;1;261
output h**o.cube
end
task dplot''')
f.close()
if False:
fig=figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,z[:,0],z[:,1],z[:,2],c='b')
Axes3D.scatter(ax,chargecoordlist[:,0],chargecoordlist[:,1],chargecoordlist[:,2],c='r')
return None