Fixed documentation and tests for polarisability functions

ilent2 · Apr 6, 2020 · b6aef2b · b6aef2b
1 parent 6eaf524
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Showing 7 changed files with 20 additions and 25 deletions.
diff --git a/+ott/+utils/+polarizability/CM.m b/+ott/+utils/+polarizability/CM.m
@@ -1,26 +1,21 @@
-function alpha_CM = polarizability_CM(d, index)
+function alpha_CM = CM(spacing, index)
 % Clausius-Mossoti Polarizability 
 %
 % Usage
-%   alpha = polarizability_LDR(spacing, index)
+%   alpha = CM(spacing, index)
 %   Calculates a Nx1 element vector containing the isotropic
 %   polarisabilities for N dipoles.
 %
-%   alpha = polarizability_LDR(spacing, index, kvec, E0)
-%   As above but specifies the polarisability information for use
-%   with plane wave illumination.
-%
 % Parameters
 %   - spacing (numeric scalar) -- lattice spacing parameter
 %   - index (Nx1 numeric) -- Relative refractive indices for N dipoles.
-%   - kvec (1x3 numeric) -- Wave vector [kx, ky, kz]
-%   - E0 (1x3 numeric) -- E-field polarisation [Ex, Ey, Ez]
 
 % Based on the script by Vincent Loke.
 % This file is part of the optical tweezers toolbox.
 % See LICENSE.md for information about using/distributing this file.
 
 msqr = index(:).^2;
-dcube = d^3;
+dcube = spacing^3;
 
 alpha_CM = 3*dcube/(4*pi)*(msqr - 1)./(msqr + 2); % Clausius-Mossotti
+
diff --git a/+ott/+utils/+polarizability/Contents.m b/+ott/+utils/+polarizability/Contents.m
@@ -1,5 +1,5 @@
 % +OTT/+UTILS/+POLARIZABILITY Polarizability calculation methods for DDA
 %
-%   polarizability_CM     - Clausius-Mossoti Polarizability 
-%   polarizability_FCD    - Filtered coupled dipole polarizability
-%   polarizability_LDR    - Lattice dispersion relation polarizablity
+%   CM     - Clausius-Mossoti Polarizability 
+%   FCD    - Filtered coupled dipole polarizability
+%   LDR    - Lattice dispersion relation polarizablity
diff --git a/+ott/+utils/+polarizability/FCD.m b/+ott/+utils/+polarizability/FCD.m
@@ -1,10 +1,10 @@
-function alpha_FCD = polarizability_FCD(spacing, index, varargin)
+function alpha_FCD = FCD(spacing, index, varargin)
 % Filtered coupled dipole polarizability
 %
 % Usage
-%   alpha = polarizability_FCD(spacing, index)
+%   alpha = FCD(spacing, index)
 %   Calculates a Nx1 element vector containing the isotropic
-%   polarisabilities for N dipoles.
+%   polarizabilities for N dipoles.
 %
 % Parameters
 %   - spacing (numeric scalar) -- lattice spacing parameter

diff --git a/+ott/+utils/+polarizability/LDR.m b/+ott/+utils/+polarizability/LDR.m
@@ -1,4 +1,4 @@
-function alpha_LDR = polarizability_LDR(spacing,index,varargin)
+function alpha_LDR = LDR(spacing,index,varargin)
 % Lattice dispersion relation polarizablity
 %
 % Polarizability calculation based on
@@ -8,11 +8,11 @@
 %   The Astrophysical Journal, 405:685-697, 1993 March 10
 %
 % Usage
-%   alpha = polarizability_LDR(spacing, index, ...)
+%   alpha = LDR(spacing, index, ...)
 %   Calculates a Nx1 element vector containing the isotropic
 %   polarisabilities for N dipoles.
 %
-%   alpha = polarizability_LDR(spacing, index, kvec, E0, ...)
+%   alpha = LDR(spacing, index, kvec, E0, ...)
 %   As above but specifies the polarisability information for use
 %   with plane wave illumination.
 %

diff --git a/tests/utils/testPolarizabilityCm.m b/tests/utils/testPolarizabilityCm.m
@@ -11,7 +11,7 @@ function testAlphaValues(testCase)
   spacing = 1.0;
   index = [1, 2];
 
-  alpha = ott.utils.polarizability_CM(spacing,index);
+  alpha = ott.utils.polarizability.CM(spacing,index);
 
   targetAlpha = [0; 0.119366207318922];
 

diff --git a/tests/utils/testPolarizabilityFcd.m b/tests/utils/testPolarizabilityFcd.m
@@ -11,7 +11,7 @@ function testAlphaValues(testCase)
   spacing = 1.0;
   index = [1, 2];
 
-  alpha = ott.utils.polarizability_FCD(spacing,index);
+  alpha = ott.utils.polarizability.FCD(spacing,index);
 
   targetAlpha = [0; 0.000029131505380 - 0.003023300651752i];
 

diff --git a/tests/utils/testPolarizabilityLdr.m b/tests/utils/testPolarizabilityLdr.m
@@ -13,13 +13,13 @@ function testArgumentCount(testCase)
   kvec = [0, 0, 1];
   E0 = [1, 0, 0];
 
-  alpha = ott.utils.polarizability_LDR(spacing,index,kvec,E0);
+  alpha = ott.utils.polarizability.LDR(spacing,index,kvec,E0);
 
-  alpha = ott.utils.polarizability_LDR(spacing,index,kvec,E0, 'k0', 2*pi);
+  alpha = ott.utils.polarizability.LDR(spacing,index,kvec,E0, 'k0', 2*pi);
 
-  alpha = ott.utils.polarizability_LDR(spacing,index);
+  alpha = ott.utils.polarizability.LDR(spacing,index);
 
-  alpha = ott.utils.polarizability_LDR(spacing,index, 'k0', 2*pi);
+  alpha = ott.utils.polarizability.LDR(spacing,index, 'k0', 2*pi);
 
 end
 
@@ -28,7 +28,7 @@ function testAlphaValues(testCase)
   spacing = 1.0;
   index = [1, 2];
 
-  alpha = ott.utils.polarizability_LDR(spacing,index);
+  alpha = ott.utils.polarizability.LDR(spacing,index);
 
   targetAlpha = [0; -0.002627924391542 + 0.004518926661470i];