Fixed python calculations, added gitignore

.gitignore

@@ -0,0 +1,5 @@
+# Python
+__pycache__/
+*.pyc
+# Matlab
+*.asv

Matlab/bessel.m

@@ -1,6 +1,6 @@
 % Bessel beam
 function b = bessel(r, w0, r_max)
-    ring_radius = 2.405; % radisu of the first ring of the besselj_0
+    ring_radius = 2.405; % radius of the first ring of the besselj_0
     A = 2 * ring_radius / (w0 * r_max * exp(0.5)) * 2 * pi * integral(@(r) r.*besselj(0, ring_radius/w0 * r).^2, 0, r_max);
-    b = A * besselj(0, 2.405/w0 * r).^2;
+    b = A * besselj(0, ring_radius/w0 * r).^2;
 end

Matlab/test.m

@@ -0,0 +1,16 @@
+load_constants
+
+fprintf('q_s = %e\n', qs_factor(pi / 4, pi / 4, n1, n2))
+fprintf('q_g = %e\n', qg_factor(pi / 4, pi / 4, n1, n2))
+fprintf('q_mag = %e\n', qmag_factor(pi / 4, pi / 4, n1, n2))
+fprintf('qs_avg = %e\n', qs_avg_factor(pi / 4, n1, n2))
+fprintf('qg_avg = %e\n', qg_avg_factor(pi / 4, n1, n2))
+fprintf('q_mag_avg = %e\n', qmag_avg_factor(pi / 4, n1, n2))
+fprintf('phi_i = %e\n', phi_i(Rsp, f))
+fprintf('gamma = %e\n', gamma_angle(pi / 4, Rsp, f))
+fprintf('th_i_z = %e\n', th_i_z(Rsp, Rsp, Rsp, f))
+fprintf('th_i_y = %e\n', th_i_y(pi / 4, Rsp, Rsp, Rsp, f))
+fprintf('qg_z = %e\n', qg_z_factor(Rsp, Rsp, n1, n2, Rsp, f))
+fprintf('qs_z = %e\n', qs_z_factor(Rsp, Rsp, n1, n2, Rsp, f))
+fprintf('qg_y = %e\n', qg_y_factor(pi / 4, Rsp, Rsp, n1, n2, Rsp, f))
+fprintf('qs_y = %e\n', qs_y_factor(pi / 4, Rsp, Rsp, n1, n2, Rsp, f))

Matlab/trap_forces_axial.m

@@ -20,13 +20,13 @@ xlabel('r, м')
 ylabel('I(r)')
 
 % Integration
-Qres_g = @(z) 1 / (pi * w0 ^ 2) * integral2(@(beta, r) r .* gauss(r, w0, r_max) .* ...
-    iscomplex(qg_z_factor(r, z, n1, n2, Rsp, f)), 0, 2*pi, 0, r_max, ...
-    'Method', 'iterated', 'AbsTol', 1e-12, 'RelTol', 1e-6);
+Qres_g = @(z) 2*pi / (pi * w0 ^ 2) * integral(@(r) r .* gauss(r, w0, r_max) .* ...
+    iscomplex(qg_z_factor(r, z, n1, n2, Rsp, f)), 0, r_max, ...
+    'AbsTol', 1e-12, 'RelTol', 1e-6);
 
-Qres_s = @(z) 1 / (pi * w0 ^ 2) * integral2(@(beta, r) r .* gauss(r, w0, r_max) .* ...
-    iscomplex(qs_z_factor(r, z, n1, n2, Rsp, f)), 0, 2*pi, 0, r_max, ...
-    'Method', 'iterated', 'AbsTol', 1e-12, 'RelTol', 1e-6);
+Qres_s = @(z) 2*pi / (pi * w0 ^ 2) * integral(@(r) r .* gauss(r, w0, r_max) .* ...
+    iscomplex(qs_z_factor(r, z, n1, n2, Rsp, f)), 0, r_max, ...
+    'AbsTol', 1e-12, 'RelTol', 1e-6);
 
 % Calulation
 N = 200;

Matlab/uniform.m

@@ -1,4 +1,4 @@
 % Beam with uniform distribution
-function u = uniform(r, w0, r_max, P)
-    u = P / (pi*r_max^2);
+function u = uniform(r, w0, r_max)
+    u = ones(size(r));
 end

Python/functions.py

@@ -8,7 +8,7 @@ n2 = 1.4607  # index of refraction of the fused silica at wavelength 523 nm
 NA = 1.25  # numerical aperture
 f = 2.0e-3  # objective lens focus or WD
 Rsp = 1.03e-6  # sphere radius
-P = 4.4e-3  # power of the laser
+P = 51.7e-3  # power of the laser
 ratio = 1.0  # the ratio of the beam radius to the aperture radius
 
 th_max = np.arcsin(NA / n1)  # maximum angle of incidence
@@ -106,23 +106,37 @@ def q_s_y(beta, r, y):
 
 
 # Intensity distributions
-def gauss_peak():
-    A = (1 - np.exp(-2*r_max ** 2 / w0 ** 2))
-    return 2*A / (np.pi * w0 ** 2)
-
-
 def gauss(r):
-    return np.exp(-2 * r ** 2 / w0 ** 2)
+    # the fraction of power that falls on the pupil of the micro lens
+    A = (1 - np.exp(-2*r_max ** 2 / w0 ** 2))
+    return 2 * A * np.exp(-2 * r ** 2 / w0 ** 2)
 
 
 def bessel(r):
-    return special.jv(0, 2.405 / w0 * r) ** 2
-
-
-def bessel_peak():
-    return 4.81 / (w0 * r_max * np.exp(0.5)) * 2 * np.pi * integrate.quad(lambda r: r * special.jv(0, 2.405 / w0 * r) ** 2,
+    ring_radius = 2.405; # radius of the first ring of the besselj_0
+    # the fraction of power that falls on the pupil of the micro lens
+    A = ring_radius / (w0 * r_max * np.exp(0.5)) * 2 * np.pi * \
+        integrate.quad(lambda r: r * special.jv(0, ring_radius / w0 * r) ** 2,
                        0, r_max, epsabs=1e-12, epsrel=1e-6)[0]
+    return 2 * A* special.jv(0, ring_radius / w0 * r) ** 2
 
 
 def uniform(r):
-    return P / (np.pi * r_max ** 2) * np.ones(r.shape)
+    return np.ones(r.shape)
+
+def test():
+    print("q_s = ", q_s(np.pi / 4, np.pi / 4))
+    print("q_g = ", q_g(np.pi / 4, np.pi / 4))
+    print("q_mag = ", q_mag(np.pi / 4, np.pi / 4))
+    print("q_s_avg = ", q_s_avg(np.pi / 4))
+    print("q_g_avg = ", q_g_avg(np.pi / 4))
+    print("q_mag_avg = ", q_mag_avg(np.pi / 4))
+    print("phi_i = ", phi_i(Rsp))
+    print("gamma = ", gamma(np.pi / 4, Rsp))
+    print("th_i_z = ", th_i_z(Rsp, Rsp))
+    print("th_i_y = ", th_i_y(np.pi / 4, Rsp, Rsp))
+    print("q_g_z = ", q_g_z(Rsp, Rsp))
+    print("q_s_z = ", q_s_z(Rsp, Rsp))
+    print("q_g_y = ", q_g_y(np.pi / 4, Rsp, Rsp))
+    print("q_s_y = ", q_s_y(np.pi / 4, Rsp, Rsp))
+    

Python/trap_forces_axial.py

@@ -24,36 +24,33 @@ plt.ylabel('I(r)', fontsize=18)
 
 # Integration
 def q_res_g(z, func):
-    ans = integrate.quad(lambda x: x * func(x) * q_g_z(x, z) * (~np.iscomplex(q_g_z(x, z))).astype(float),
+    ans = integrate.quad(lambda dr: dr * func(dr) * q_g_z(dr, z) * (~np.iscomplex(q_g_z(dr, z))).astype(float),
                          0, r_max, epsabs=1e-12, epsrel=1e-6)
-    return ans[0]
-
+    return 2 * np.pi * ans[0] / (np.pi * w0 ** 2)
 
 def q_res_s(z, func):
-    ans = integrate.quad(lambda x: x * func(x) * q_s_z(x, z) * (~np.iscomplex(q_s_z(x, z))).astype(float),
+    ans = integrate.quad(lambda dr: dr * func(dr) * q_s_z(dr, z) * (~np.iscomplex(q_s_z(dr, z))).astype(float),
                          0, r_max, epsabs=1e-12, epsrel=1e-6)
-    return ans[0]
+    return 2 * np.pi * ans[0] / (np.pi * w0 ** 2)
 
 
 # Calculation
 n = 200
 z = np.linspace(-2 * Rsp, 2 * Rsp, n)
 
-axial_g = gauss_peak() * [q_res_g(x, gauss) for x in z]
-axial_s = gauss_peak() * [q_res_s(x, gauss) for x in z]
+axial_g = [q_res_g(dz, gauss) for dz in z]
+axial_s = [q_res_s(dz, gauss) for dz in z]
 
-f_0 = n1 * P / constants.c  # net force
-
-axial_g = np.array(axial_g[::-1])
-axial_s = np.array(axial_s[::-1])
+axial_g = F0 * np.array(axial_g[::-1])
+axial_s = F0 * np.array(axial_s[::-1])
 axial = axial_g + axial_s
 z = -z[::-1]
 
 # Graphics
 fig2 = plt.figure(2, figsize=(10, 6))
-plt.plot(z, f_0*axial_g, '-.', lw=1, label='$F_{g}$')
-plt.plot(z, f_0*axial_s, '--', lw=1, label='$F_{s}$')
-plt.plot(z, f_0*axial, lw=1, label='$F_{t}$')
+plt.plot(z, axial_g, '-.', lw=1, label='$F_{g}$')
+plt.plot(z, axial_s, '--', lw=1, label='$F_{s}$')
+plt.plot(z, axial, lw=1, label='$F_{t}$')
 plt.xlabel('r, m', fontsize=18)
 plt.ylabel('F, N', fontsize=18)
 plt.legend(fontsize=18)

Python/trap_forces_transverse.py

@@ -26,23 +26,22 @@ plt.ylabel('I(r)', fontsize=18)
 def q_res_g(dy, func):
     ans = integrate.dblquad(lambda dr, db, dy: dr * func(dr) * q_g_y(db, dr, dy) * (~np.iscomplex(q_g_y(db, dr, dy))).astype(float),
                             0, 2 * np.pi, 0, r_max, args=(dy, ),
-                            epsabs=1e-8, epsrel=1e-6)
-    return ans[0]
+                            epsabs=1e-6, epsrel=1e-6)
+    return ans[0] / (np.pi * w0 ** 2)
 
 
 def q_res_s(dy, func):
     ans = integrate.dblquad(lambda dr, db: dr * func(dr) * q_s_y(db, dr, dy) * (~np.iscomplex(q_g_y(db, dr, dy))).astype(float),
                             0, 2 * np.pi, 0, r_max,
-                            epsabs=1e-8, epsrel=1e-6)
-    return ans[0]
-
+                            epsabs=1e-6, epsrel=1e-6)
+    return ans[0] / (np.pi * w0 ** 2)
 
 # Calculation
 n = 150
 y = np.linspace(-2 * Rsp, 2 * Rsp, n)
 
-transverse_g = gauss_peak() * F0 * np.abs(np.array([q_res_g(x, gauss) for x in y]))
-transverse_s = gauss_peak() * F0 * np.array([q_res_s(x, gauss) for x in y])
+transverse_g = F0 * np.abs(np.array([q_res_g(dy, gauss) for dy in y]))
+transverse_s = F0 * np.array([q_res_s(dy, gauss) for dy in y])
 transverse = transverse_g + transverse_s
 
 

README.md

@@ -1 +1 @@
-# optical-trap-forces
+# Optical Trap Forces