diff --git a/doc/src/Eqs/angle_charmm.jpg b/doc/src/Eqs/angle_charmm.jpg deleted file mode 100644 index c6e6c297d2..0000000000 Binary files a/doc/src/Eqs/angle_charmm.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_charmm.tex b/doc/src/Eqs/angle_charmm.tex deleted file mode 100644 index 00b37ba335..0000000000 --- a/doc/src/Eqs/angle_charmm.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_class2.jpg b/doc/src/Eqs/angle_class2.jpg deleted file mode 100644 index f0f2a5152e..0000000000 Binary files a/doc/src/Eqs/angle_class2.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_class2.tex b/doc/src/Eqs/angle_class2.tex deleted file mode 100644 index e5a542e87a..0000000000 --- a/doc/src/Eqs/angle_class2.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E & = & E_a + E_{bb} + E_{ba} \\ - E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\ - E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\ - E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0) -\end{eqnarray*} - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_cosine.jpg b/doc/src/Eqs/angle_cosine.jpg deleted file mode 100644 index 23b9b64310..0000000000 Binary files a/doc/src/Eqs/angle_cosine.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine.tex b/doc/src/Eqs/angle_cosine.tex deleted file mode 100644 index e766676099..0000000000 --- a/doc/src/Eqs/angle_cosine.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [1 + \cos(\theta)] -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_cosine_delta.jpg b/doc/src/Eqs/angle_cosine_delta.jpg deleted file mode 100644 index c6e90bb2c5..0000000000 Binary files a/doc/src/Eqs/angle_cosine_delta.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_delta.tex b/doc/src/Eqs/angle_cosine_delta.tex deleted file mode 100644 index 918e9e5046..0000000000 --- a/doc/src/Eqs/angle_cosine_delta.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [1 - \cos(\theta - \theta_0)] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_cosine_periodic.jpg b/doc/src/Eqs/angle_cosine_periodic.jpg deleted file mode 100644 index a9d7d50cb3..0000000000 Binary files a/doc/src/Eqs/angle_cosine_periodic.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_periodic.tex b/doc/src/Eqs/angle_cosine_periodic.tex deleted file mode 100644 index 69aa1bba6a..0000000000 --- a/doc/src/Eqs/angle_cosine_periodic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_cosine_shift.jpg b/doc/src/Eqs/angle_cosine_shift.jpg deleted file mode 100644 index d9929939c8..0000000000 Binary files a/doc/src/Eqs/angle_cosine_shift.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_shift.tex b/doc/src/Eqs/angle_cosine_shift.tex deleted file mode 100644 index e795d6beff..0000000000 --- a/doc/src/Eqs/angle_cosine_shift.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_cosine_shift_exp.jpg b/doc/src/Eqs/angle_cosine_shift_exp.jpg deleted file mode 100644 index 294986de4b..0000000000 Binary files a/doc/src/Eqs/angle_cosine_shift_exp.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_shift_exp.tex b/doc/src/Eqs/angle_cosine_shift_exp.tex deleted file mode 100644 index 4afa01356c..0000000000 --- a/doc/src/Eqs/angle_cosine_shift_exp.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E=-U_{min} -\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} -\quad\mbox{with}\quad -U(\theta,\theta_0) -=-0.5 \left(1+\cos(\theta-\theta_0) \right) -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_cosine_squared.jpg b/doc/src/Eqs/angle_cosine_squared.jpg deleted file mode 100644 index b992398b7d..0000000000 Binary files a/doc/src/Eqs/angle_cosine_squared.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_cosine_squared.tex b/doc/src/Eqs/angle_cosine_squared.tex deleted file mode 100644 index 57ae47ae45..0000000000 --- a/doc/src/Eqs/angle_cosine_squared.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [\cos(\theta) - \cos(\theta_0)]^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_dipole_couple.jpg b/doc/src/Eqs/angle_dipole_couple.jpg deleted file mode 100644 index f16849b2f9..0000000000 Binary files a/doc/src/Eqs/angle_dipole_couple.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_dipole_couple.tex b/doc/src/Eqs/angle_dipole_couple.tex deleted file mode 100644 index a857d83d7a..0000000000 --- a/doc/src/Eqs/angle_dipole_couple.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} --\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\ -\vec{F_j} & = & -\vec{F_i} \\ -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/angle_dipole_gamma.jpg b/doc/src/Eqs/angle_dipole_gamma.jpg deleted file mode 100644 index 4bf618e252..0000000000 Binary files a/doc/src/Eqs/angle_dipole_gamma.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_dipole_gamma.tex b/doc/src/Eqs/angle_dipole_gamma.tex deleted file mode 100644 index 965b74ad96..0000000000 --- a/doc/src/Eqs/angle_dipole_gamma.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - \cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}} -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_dipole_potential.jpg b/doc/src/Eqs/angle_dipole_potential.jpg deleted file mode 100644 index b1285e8957..0000000000 Binary files a/doc/src/Eqs/angle_dipole_potential.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_dipole_potential.tex b/doc/src/Eqs/angle_dipole_potential.tex deleted file mode 100644 index 8949835eb7..0000000000 --- a/doc/src/Eqs/angle_dipole_potential.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\cos\gamma - \cos\gamma_0)^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_dipole_torque.jpg b/doc/src/Eqs/angle_dipole_torque.jpg deleted file mode 100644 index 996a9df3cb..0000000000 Binary files a/doc/src/Eqs/angle_dipole_torque.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_dipole_torque.tex b/doc/src/Eqs/angle_dipole_torque.tex deleted file mode 100644 index 9527459fdc..0000000000 --- a/doc/src/Eqs/angle_dipole_torque.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\, - \vec{r_{ij}} \times \vec{\mu_j} -$$ -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_fourier.jpg b/doc/src/Eqs/angle_fourier.jpg deleted file mode 100644 index e748e67430..0000000000 Binary files a/doc/src/Eqs/angle_fourier.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_fourier.tex b/doc/src/Eqs/angle_fourier.tex deleted file mode 100644 index f7f76462e3..0000000000 --- a/doc/src/Eqs/angle_fourier.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_fourier_simple.jpg b/doc/src/Eqs/angle_fourier_simple.jpg deleted file mode 100644 index 6c9297b970..0000000000 Binary files a/doc/src/Eqs/angle_fourier_simple.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_fourier_simple.tex b/doc/src/Eqs/angle_fourier_simple.tex deleted file mode 100644 index 3228315a13..0000000000 --- a/doc/src/Eqs/angle_fourier_simple.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [ 1.0 + c \cos ( n \theta) ] -$$ - -\end{document} diff --git a/doc/src/Eqs/angle_harmonic.jpg b/doc/src/Eqs/angle_harmonic.jpg deleted file mode 100644 index 352be0b544..0000000000 Binary files a/doc/src/Eqs/angle_harmonic.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_harmonic.tex b/doc/src/Eqs/angle_harmonic.tex deleted file mode 100644 index c566376b5b..0000000000 --- a/doc/src/Eqs/angle_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\theta - \theta_0)^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_quartic.jpg b/doc/src/Eqs/angle_quartic.jpg deleted file mode 100644 index 744ce7a35f..0000000000 Binary files a/doc/src/Eqs/angle_quartic.jpg and /dev/null differ diff --git a/doc/src/Eqs/angle_quartic.tex b/doc/src/Eqs/angle_quartic.tex deleted file mode 100644 index ff9ff9a7dc..0000000000 --- a/doc/src/Eqs/angle_quartic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 -$$ - -\end{document} diff --git a/doc/src/Eqs/bond_class2.jpg b/doc/src/Eqs/bond_class2.jpg deleted file mode 100644 index 493048100e..0000000000 Binary files a/doc/src/Eqs/bond_class2.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_class2.tex b/doc/src/Eqs/bond_class2.tex deleted file mode 100644 index 0735b61025..0000000000 --- a/doc/src/Eqs/bond_class2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/bond_fene.jpg b/doc/src/Eqs/bond_fene.jpg deleted file mode 100644 index e8b909c08f..0000000000 Binary files a/doc/src/Eqs/bond_fene.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_fene.tex b/doc/src/Eqs/bond_fene.tex deleted file mode 100644 index ec4dd8efa2..0000000000 --- a/doc/src/Eqs/bond_fene.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + - 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/bond_fene_expand.jpg b/doc/src/Eqs/bond_fene_expand.jpg deleted file mode 100644 index 1d04acec32..0000000000 Binary files a/doc/src/Eqs/bond_fene_expand.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_fene_expand.tex b/doc/src/Eqs/bond_fene_expand.tex deleted file mode 100644 index 5fd96e7ad5..0000000000 --- a/doc/src/Eqs/bond_fene_expand.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = -0.5 K R_0^2 - \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + - 4 \epsilon \left[ \left(\frac{\sigma}{\left(r - - \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - - \Delta\right)}\right)^6 \right] + \epsilon -$$ - -\end{document} diff --git a/doc/src/Eqs/bond_harmonic.jpg b/doc/src/Eqs/bond_harmonic.jpg deleted file mode 100644 index fe9ef5619b..0000000000 Binary files a/doc/src/Eqs/bond_harmonic.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_harmonic.tex b/doc/src/Eqs/bond_harmonic.tex deleted file mode 100644 index 2461086898..0000000000 --- a/doc/src/Eqs/bond_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (r - r_0)^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/bond_harmonic_shift.jpg b/doc/src/Eqs/bond_harmonic_shift.jpg deleted file mode 100644 index 3e66d853a5..0000000000 Binary files a/doc/src/Eqs/bond_harmonic_shift.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_harmonic_shift.tex b/doc/src/Eqs/bond_harmonic_shift.tex deleted file mode 100644 index 3daa16724f..0000000000 --- a/doc/src/Eqs/bond_harmonic_shift.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/bond_harmonic_shift_cut.jpg b/doc/src/Eqs/bond_harmonic_shift_cut.jpg deleted file mode 100644 index 06640e4fe0..0000000000 Binary files a/doc/src/Eqs/bond_harmonic_shift_cut.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_harmonic_shift_cut.tex b/doc/src/Eqs/bond_harmonic_shift_cut.tex deleted file mode 100644 index 3daa16724f..0000000000 --- a/doc/src/Eqs/bond_harmonic_shift_cut.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/bond_morse.jpg b/doc/src/Eqs/bond_morse.jpg deleted file mode 100644 index 6795c9e527..0000000000 Binary files a/doc/src/Eqs/bond_morse.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_morse.tex b/doc/src/Eqs/bond_morse.tex deleted file mode 100644 index a0d7a89961..0000000000 --- a/doc/src/Eqs/bond_morse.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2 - E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/bond_nonlinear.jpg b/doc/src/Eqs/bond_nonlinear.jpg deleted file mode 100644 index 0f18d8e73f..0000000000 Binary files a/doc/src/Eqs/bond_nonlinear.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_nonlinear.tex b/doc/src/Eqs/bond_nonlinear.tex deleted file mode 100644 index b8cdc96169..0000000000 --- a/doc/src/Eqs/bond_nonlinear.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]} -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/bond_quartic.jpg b/doc/src/Eqs/bond_quartic.jpg deleted file mode 100644 index 9d092883b2..0000000000 Binary files a/doc/src/Eqs/bond_quartic.jpg and /dev/null differ diff --git a/doc/src/Eqs/bond_quartic.tex b/doc/src/Eqs/bond_quartic.tex deleted file mode 100644 index 0d0cceb353..0000000000 --- a/doc/src/Eqs/bond_quartic.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 + - 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/box.jpg b/doc/src/Eqs/box.jpg deleted file mode 100644 index 4cb43df953..0000000000 Binary files a/doc/src/Eqs/box.jpg and /dev/null differ diff --git a/doc/src/Eqs/box.tex b/doc/src/Eqs/box.tex deleted file mode 100644 index 8442ea85b6..0000000000 --- a/doc/src/Eqs/box.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -a &=& {\rm lx} \\ -b^2 &=& {\rm ly}^2 + {\rm xy}^2 \\ -c^2 &=& {\rm lz}^2 + {\rm xz}^2 + {\rm yz}^2 \\ -\cos{\alpha} &=& \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\ -\cos{\beta} &=& \frac{\rm xz}{c} \\ -\cos{\gamma} &=& \frac{\rm xy}{b} \\ -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/box_inverse.jpg b/doc/src/Eqs/box_inverse.jpg deleted file mode 100644 index 5d0895b87e..0000000000 Binary files a/doc/src/Eqs/box_inverse.jpg and /dev/null differ diff --git a/doc/src/Eqs/box_inverse.tex b/doc/src/Eqs/box_inverse.tex deleted file mode 100644 index 68994f2868..0000000000 --- a/doc/src/Eqs/box_inverse.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -{\rm lx} &=& a \\ -{\rm xy} &=& b \cos{\gamma} \\ -{\rm xz} &=& c \cos{\beta}\\ -{\rm ly}^2 &=& b^2 - {\rm xy}^2 \\ -{\rm yz} &=& \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\ -{\rm lz}^2 &=& c^2 - {\rm xz}^2 - {\rm yz}^2 \\ -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/centro_symmetry.jpg b/doc/src/Eqs/centro_symmetry.jpg deleted file mode 100644 index 1e89d11a11..0000000000 Binary files a/doc/src/Eqs/centro_symmetry.jpg and /dev/null differ diff --git a/doc/src/Eqs/centro_symmetry.tex b/doc/src/Eqs/centro_symmetry.tex deleted file mode 100644 index 8d9a9a33e6..0000000000 --- a/doc/src/Eqs/centro_symmetry.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - CS = \sum_{i = 1}^{N/2} | \vec{R}_i + \vec{R}_{i+N/2} |^2 -$$ - -\end{document} diff --git a/doc/src/Eqs/cna_cutoff1.jpg b/doc/src/Eqs/cna_cutoff1.jpg deleted file mode 100644 index fae5c6b636..0000000000 Binary files a/doc/src/Eqs/cna_cutoff1.jpg and /dev/null differ diff --git a/doc/src/Eqs/cna_cutoff1.tex b/doc/src/Eqs/cna_cutoff1.tex deleted file mode 100644 index f74166e608..0000000000 --- a/doc/src/Eqs/cna_cutoff1.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt,article]{article} - -\usepackage{indentfirst} -\usepackage{amsmath} - -\begin{document} - -\begin{eqnarray*} - r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\ - r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\ - r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a} -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/cna_cutoff2.jpg b/doc/src/Eqs/cna_cutoff2.jpg deleted file mode 100644 index 744b61e9b4..0000000000 Binary files a/doc/src/Eqs/cna_cutoff2.jpg and /dev/null differ diff --git a/doc/src/Eqs/cna_cutoff2.tex b/doc/src/Eqs/cna_cutoff2.tex deleted file mode 100644 index fcec31fd24..0000000000 --- a/doc/src/Eqs/cna_cutoff2.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentclass[12pt,article]{article} - -\usepackage{indentfirst} -\usepackage{amsmath} - -\begin{document} - -$$ - Rc + Rs > 2*{\rm cutoff} -$$ - -\end{document} diff --git a/doc/src/Eqs/compute_dpd.jpg b/doc/src/Eqs/compute_dpd.jpg deleted file mode 100644 index 42ed03db15..0000000000 Binary files a/doc/src/Eqs/compute_dpd.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_dpd.tex b/doc/src/Eqs/compute_dpd.tex deleted file mode 100644 index 3d4338db08..0000000000 --- a/doc/src/Eqs/compute_dpd.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentstyle[12pt]{article} -\pagestyle{empty} -\begin{document} - -\begin{eqnarray*} - U^{cond} = \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ - U^{mech} = \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\ - U = \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech}) \\ - \theta_{avg} = (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\ -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/compute_fep_bar.jpg b/doc/src/Eqs/compute_fep_bar.jpg deleted file mode 100644 index 772ec9c045..0000000000 Binary files a/doc/src/Eqs/compute_fep_bar.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_fep_bar.tex b/doc/src/Eqs/compute_fep_bar.tex deleted file mode 100644 index a40aa1c297..0000000000 --- a/doc/src/Eqs/compute_fep_bar.tex +++ /dev/null @@ -1,7 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\[ \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /kT \right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 + \Delta_0^1A \right) /kT \right]} \right>_1 \] - -\end{document} diff --git a/doc/src/Eqs/compute_fep_fdti.jpg b/doc/src/Eqs/compute_fep_fdti.jpg deleted file mode 100644 index ae8de241cc..0000000000 Binary files a/doc/src/Eqs/compute_fep_fdti.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_fep_fdti.tex b/doc/src/Eqs/compute_fep_fdti.tex deleted file mode 100644 index fdea6faa3d..0000000000 --- a/doc/src/Eqs/compute_fep_fdti.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left( \frac{\partial - A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda -\approx \sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) - - A(\lambda_i)}{\delta} \] - -\end{document} diff --git a/doc/src/Eqs/compute_fep_fep.jpg b/doc/src/Eqs/compute_fep_fep.jpg deleted file mode 100644 index d84a76b0dd..0000000000 Binary files a/doc/src/Eqs/compute_fep_fep.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_fep_fep.tex b/doc/src/Eqs/compute_fep_fep.tex deleted file mode 100644 index 718aad3c40..0000000000 --- a/doc/src/Eqs/compute_fep_fep.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\[ \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A = -- kT \sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) - - U(\lambda_i)}{kT} \right) \right>_{\lambda_i} \] - -\end{document} diff --git a/doc/src/Eqs/compute_fep_lambda.jpg b/doc/src/Eqs/compute_fep_lambda.jpg deleted file mode 100644 index 5ef9e8b9f2..0000000000 Binary files a/doc/src/Eqs/compute_fep_lambda.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_fep_lambda.tex b/doc/src/Eqs/compute_fep_lambda.tex deleted file mode 100644 index 08c8faaa3c..0000000000 --- a/doc/src/Eqs/compute_fep_lambda.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - \lambda = 0 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_0 \\ - \lambda = 1 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_1 -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/compute_fep_ti.jpg b/doc/src/Eqs/compute_fep_ti.jpg deleted file mode 100644 index 6b0c8fdc19..0000000000 Binary files a/doc/src/Eqs/compute_fep_ti.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_fep_ti.tex b/doc/src/Eqs/compute_fep_ti.tex deleted file mode 100644 index 6222dbd503..0000000000 --- a/doc/src/Eqs/compute_fep_ti.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left< \frac{\partial - U(\lambda)}{\partial\lambda} \right>_\lambda \mathrm{d}\lambda -\approx \sum_{i=0}^{n-1} w_i \left< \frac{U(\lambda_{i} + \delta) - - U(\lambda_i)}{\delta} \right>_{\lambda_i} \] - -\end{document} diff --git a/doc/src/Eqs/compute_fep_u.jpg b/doc/src/Eqs/compute_fep_u.jpg deleted file mode 100644 index 62df5dd0c0..0000000000 Binary files a/doc/src/Eqs/compute_fep_u.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_fep_u.tex b/doc/src/Eqs/compute_fep_u.tex deleted file mode 100644 index e847a9ac44..0000000000 --- a/doc/src/Eqs/compute_fep_u.tex +++ /dev/null @@ -1,7 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\[ U(\lambda) = U_{\mathrm{bg}} + U_1(\lambda) + U_0(\lambda) \] - -\end{document} diff --git a/doc/src/Eqs/compute_fep_vol.jpg b/doc/src/Eqs/compute_fep_vol.jpg deleted file mode 100644 index a66facad39..0000000000 Binary files a/doc/src/Eqs/compute_fep_vol.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_fep_vol.tex b/doc/src/Eqs/compute_fep_vol.tex deleted file mode 100644 index 0301e39788..0000000000 --- a/doc/src/Eqs/compute_fep_vol.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\[ \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( - - \frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right) -\right>_{\lambda_i}}{\left< V \right>_{\lambda_i}} \] - -\end{document} diff --git a/doc/src/Eqs/compute_gyration.jpg b/doc/src/Eqs/compute_gyration.jpg deleted file mode 100644 index 2285444434..0000000000 Binary files a/doc/src/Eqs/compute_gyration.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_gyration.tex b/doc/src/Eqs/compute_gyration.tex deleted file mode 100644 index 97204f1ded..0000000000 --- a/doc/src/Eqs/compute_gyration.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/compute_msd_nongauss.jpg b/doc/src/Eqs/compute_msd_nongauss.jpg deleted file mode 100644 index d57f6a4af8..0000000000 Binary files a/doc/src/Eqs/compute_msd_nongauss.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_msd_nongauss.tex b/doc/src/Eqs/compute_msd_nongauss.tex deleted file mode 100644 index 168d8f72ed..0000000000 --- a/doc/src/Eqs/compute_msd_nongauss.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1 -$$ - -\end{document} diff --git a/doc/src/Eqs/compute_saed1.jpg b/doc/src/Eqs/compute_saed1.jpg deleted file mode 100644 index 6bad3a6104..0000000000 Binary files a/doc/src/Eqs/compute_saed1.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_saed1.tex b/doc/src/Eqs/compute_saed1.tex deleted file mode 100644 index 0db2f55ecd..0000000000 --- a/doc/src/Eqs/compute_saed1.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - I=\frac{F^{*}F}{N} -$$ - -\end{document} - diff --git a/doc/src/Eqs/compute_saed2.jpg b/doc/src/Eqs/compute_saed2.jpg deleted file mode 100644 index 2b3b0bc090..0000000000 Binary files a/doc/src/Eqs/compute_saed2.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_saed2.tex b/doc/src/Eqs/compute_saed2.tex deleted file mode 100644 index d005602339..0000000000 --- a/doc/src/Eqs/compute_saed2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j) -$$ -\end{document} - diff --git a/doc/src/Eqs/compute_saed3.jpg b/doc/src/Eqs/compute_saed3.jpg deleted file mode 100644 index 1bbc920908..0000000000 Binary files a/doc/src/Eqs/compute_saed3.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_saed3.tex b/doc/src/Eqs/compute_saed3.tex deleted file mode 100644 index 5988a620c7..0000000000 --- a/doc/src/Eqs/compute_saed3.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5} -a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right ) -$$ -\end{document} - diff --git a/doc/src/Eqs/compute_sna_atom1.jpg b/doc/src/Eqs/compute_sna_atom1.jpg deleted file mode 100644 index fe4b641aa6..0000000000 Binary files a/doc/src/Eqs/compute_sna_atom1.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_sna_atom1.tex b/doc/src/Eqs/compute_sna_atom1.tex deleted file mode 100644 index 93e2709bf9..0000000000 --- a/doc/src/Eqs/compute_sna_atom1.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[24pt]{article} - -\pagestyle{empty} - -\begin{document} - -\begin{eqnarray*} -\theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/compute_sna_atom2.jpg b/doc/src/Eqs/compute_sna_atom2.jpg deleted file mode 100644 index 7a4b2c2111..0000000000 Binary files a/doc/src/Eqs/compute_sna_atom2.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_sna_atom2.tex b/doc/src/Eqs/compute_sna_atom2.tex deleted file mode 100644 index 98d8f2efa6..0000000000 --- a/doc/src/Eqs/compute_sna_atom2.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[24pt]{article} - -\pagestyle{empty} - -\begin{document} - -\begin{eqnarray*} -u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)} -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/compute_sna_atom3.jpg b/doc/src/Eqs/compute_sna_atom3.jpg deleted file mode 100644 index 41d6774e9c..0000000000 Binary files a/doc/src/Eqs/compute_sna_atom3.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_sna_atom3.tex b/doc/src/Eqs/compute_sna_atom3.tex deleted file mode 100644 index 5e3212f7bd..0000000000 --- a/doc/src/Eqs/compute_sna_atom3.tex +++ /dev/null @@ -1,16 +0,0 @@ -\documentclass[24pt]{article} - -\pagestyle{empty} - -\begin{document} - -\newcommand{\hcoeff}[9]{H\!\!{\tiny\begin{array}{l}#1 #2 #3 \\ #4 #5 #6 \\ #7 #8 #9 \end{array}}} - -\begin{equation} -B_{j_1,j_2,j} = \\ -\sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^* -\hcoeff{j}{m}{m'}{j_1}{\!m_1}{\!m'_1}{j_2}{m_2}{m'_2} -u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2} -\end{equation} - -\end{document} diff --git a/doc/src/Eqs/compute_sna_atom4.jpg b/doc/src/Eqs/compute_sna_atom4.jpg deleted file mode 100644 index 5d53943bf4..0000000000 Binary files a/doc/src/Eqs/compute_sna_atom4.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_sna_atom4.tex b/doc/src/Eqs/compute_sna_atom4.tex deleted file mode 100644 index 3477d163e3..0000000000 --- a/doc/src/Eqs/compute_sna_atom4.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[24pt]{article} - -\pagestyle{empty} - -\begin{document} - -\begin{eqnarray*} -\label{eqn:f_c} -f_c(r) & = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\ -& = & 0, r > R_{ii'} -\end{eqnarray*} - - -\end{document} diff --git a/doc/src/Eqs/compute_sna_atom5.jpg b/doc/src/Eqs/compute_sna_atom5.jpg deleted file mode 100644 index 732731fe13..0000000000 Binary files a/doc/src/Eqs/compute_sna_atom5.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_sna_atom5.tex b/doc/src/Eqs/compute_sna_atom5.tex deleted file mode 100644 index 72f5a0fe7c..0000000000 --- a/doc/src/Eqs/compute_sna_atom5.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentclass[24pt]{article} - -\pagestyle{empty} - -\begin{document} - - -\begin{equation} -- \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial {\bf r}_i} -\end{equation} - -\end{document} diff --git a/doc/src/Eqs/compute_sna_atom6.jpg b/doc/src/Eqs/compute_sna_atom6.jpg deleted file mode 100644 index 963dd81416..0000000000 Binary files a/doc/src/Eqs/compute_sna_atom6.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_sna_atom6.tex b/doc/src/Eqs/compute_sna_atom6.tex deleted file mode 100644 index 7da589548b..0000000000 --- a/doc/src/Eqs/compute_sna_atom6.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentclass[24pt]{article} - -\pagestyle{empty} - -\begin{document} - - -\begin{eqnarray*} -- {\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i} -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/compute_xrd1.jpg b/doc/src/Eqs/compute_xrd1.jpg deleted file mode 100644 index 8432fad4aa..0000000000 Binary files a/doc/src/Eqs/compute_xrd1.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_xrd1.tex b/doc/src/Eqs/compute_xrd1.tex deleted file mode 100644 index 6e749c768d..0000000000 --- a/doc/src/Eqs/compute_xrd1.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - I=Lp(\theta)\frac{F^{*}F}{N} -$$ - -\end{document} - diff --git a/doc/src/Eqs/compute_xrd2.jpg b/doc/src/Eqs/compute_xrd2.jpg deleted file mode 100644 index 1bcf0494ea..0000000000 Binary files a/doc/src/Eqs/compute_xrd2.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_xrd2.tex b/doc/src/Eqs/compute_xrd2.tex deleted file mode 100644 index d005602339..0000000000 --- a/doc/src/Eqs/compute_xrd2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j) -$$ -\end{document} - diff --git a/doc/src/Eqs/compute_xrd3.jpg b/doc/src/Eqs/compute_xrd3.jpg deleted file mode 100644 index 19f7aa99b5..0000000000 Binary files a/doc/src/Eqs/compute_xrd3.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_xrd3.tex b/doc/src/Eqs/compute_xrd3.tex deleted file mode 100644 index da0254134c..0000000000 --- a/doc/src/Eqs/compute_xrd3.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - Lp(\theta)=\frac{1+cos^{2}(2\theta)}{cos(\theta)sin^{2}(\theta)} -$$ -\end{document} - diff --git a/doc/src/Eqs/compute_xrd4.jpg b/doc/src/Eqs/compute_xrd4.jpg deleted file mode 100644 index 385bb1efd7..0000000000 Binary files a/doc/src/Eqs/compute_xrd4.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_xrd4.tex b/doc/src/Eqs/compute_xrd4.tex deleted file mode 100644 index d4deb7ca55..0000000000 --- a/doc/src/Eqs/compute_xrd4.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - \frac{sin(\theta)}{\lambda}=\frac{\left | \mathbf{k} \right |}{2} -$$ -\end{document} - diff --git a/doc/src/Eqs/compute_xrd5.jpg b/doc/src/Eqs/compute_xrd5.jpg deleted file mode 100644 index c6f0a2609a..0000000000 Binary files a/doc/src/Eqs/compute_xrd5.jpg and /dev/null differ diff --git a/doc/src/Eqs/compute_xrd5.tex b/doc/src/Eqs/compute_xrd5.tex deleted file mode 100644 index 2d97a3288b..0000000000 --- a/doc/src/Eqs/compute_xrd5.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4} -a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )+c -$$ -\end{document} - diff --git a/doc/src/Eqs/dihedral_charmm.jpg b/doc/src/Eqs/dihedral_charmm.jpg deleted file mode 100644 index 810afa3cd2..0000000000 Binary files a/doc/src/Eqs/dihedral_charmm.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_charmm.tex b/doc/src/Eqs/dihedral_charmm.tex deleted file mode 100644 index c3d860b265..0000000000 --- a/doc/src/Eqs/dihedral_charmm.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [ 1 + \cos (n \phi - d) ] -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/dihedral_class2.jpg b/doc/src/Eqs/dihedral_class2.jpg deleted file mode 100644 index 6a6780e769..0000000000 Binary files a/doc/src/Eqs/dihedral_class2.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_class2.tex b/doc/src/Eqs/dihedral_class2.tex deleted file mode 100644 index 02acc16fb9..0000000000 --- a/doc/src/Eqs/dihedral_class2.tex +++ /dev/null @@ -1,17 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E & = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\ - E_d & = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\ - E_{mbt} & = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\ - E_{ebt} & = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\ - & & (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\ - E_{at} & = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\ - & & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\ - E_{aat} & = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\ - E_{bb13} & = & N (r_{ij} - r_1) (r_{kl} - r_3) -\end{eqnarray*} - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/dihedral_cosine_shift_exp.jpg b/doc/src/Eqs/dihedral_cosine_shift_exp.jpg deleted file mode 100644 index ea0a7550f8..0000000000 Binary files a/doc/src/Eqs/dihedral_cosine_shift_exp.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_cosine_shift_exp.tex b/doc/src/Eqs/dihedral_cosine_shift_exp.tex deleted file mode 100644 index 4afa01356c..0000000000 --- a/doc/src/Eqs/dihedral_cosine_shift_exp.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E=-U_{min} -\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} -\quad\mbox{with}\quad -U(\theta,\theta_0) -=-0.5 \left(1+\cos(\theta-\theta_0) \right) -$$ - -\end{document} diff --git a/doc/src/Eqs/dihedral_fourier.jpg b/doc/src/Eqs/dihedral_fourier.jpg deleted file mode 100644 index 663ac17ee6..0000000000 Binary files a/doc/src/Eqs/dihedral_fourier.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_fourier.tex b/doc/src/Eqs/dihedral_fourier.tex deleted file mode 100644 index 960d3a8ea8..0000000000 --- a/doc/src/Eqs/dihedral_fourier.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \sum_{i=1,m} K_i [ 1.0 + \cos ( n_i \phi - d_i ) ] -$$ - -\end{document} diff --git a/doc/src/Eqs/dihedral_harmonic.jpg b/doc/src/Eqs/dihedral_harmonic.jpg deleted file mode 100644 index cb5c16a8ca..0000000000 Binary files a/doc/src/Eqs/dihedral_harmonic.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_harmonic.tex b/doc/src/Eqs/dihedral_harmonic.tex deleted file mode 100644 index 9d02036fcc..0000000000 --- a/doc/src/Eqs/dihedral_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [ 1 + d \cos (n \phi) ] -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/dihedral_helix.jpg b/doc/src/Eqs/dihedral_helix.jpg deleted file mode 100644 index 01a0ec982c..0000000000 Binary files a/doc/src/Eqs/dihedral_helix.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_helix.tex b/doc/src/Eqs/dihedral_helix.tex deleted file mode 100644 index ae25776f2c..0000000000 --- a/doc/src/Eqs/dihedral_helix.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + - C [1 + \cos(\theta + \frac{\pi}{4})] -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/dihedral_multi_harmonic.jpg b/doc/src/Eqs/dihedral_multi_harmonic.jpg deleted file mode 100644 index d066cd212b..0000000000 Binary files a/doc/src/Eqs/dihedral_multi_harmonic.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_multi_harmonic.tex b/doc/src/Eqs/dihedral_multi_harmonic.tex deleted file mode 100644 index 819aa7c57c..0000000000 --- a/doc/src/Eqs/dihedral_multi_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \sum_{n=1,5} A_n \cos^{n-1}(\phi) -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/dihedral_nharmonic.jpg b/doc/src/Eqs/dihedral_nharmonic.jpg deleted file mode 100644 index 4f4928bdd5..0000000000 Binary files a/doc/src/Eqs/dihedral_nharmonic.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_nharmonic.tex b/doc/src/Eqs/dihedral_nharmonic.tex deleted file mode 100644 index 57a1d25284..0000000000 --- a/doc/src/Eqs/dihedral_nharmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \sum_{n=1,n} A_n \cos^{n-1}(\phi) -$$ - -\end{document} diff --git a/doc/src/Eqs/dihedral_opls.jpg b/doc/src/Eqs/dihedral_opls.jpg deleted file mode 100644 index 0546aebfde..0000000000 Binary files a/doc/src/Eqs/dihedral_opls.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_opls.tex b/doc/src/Eqs/dihedral_opls.tex deleted file mode 100644 index 5e4aada53a..0000000000 --- a/doc/src/Eqs/dihedral_opls.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] + - \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)] -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/dihedral_quadratic.jpg b/doc/src/Eqs/dihedral_quadratic.jpg deleted file mode 100644 index 8fb17622f8..0000000000 Binary files a/doc/src/Eqs/dihedral_quadratic.jpg and /dev/null differ diff --git a/doc/src/Eqs/dihedral_quadratic.tex b/doc/src/Eqs/dihedral_quadratic.tex deleted file mode 100644 index 049e4b2ec4..0000000000 --- a/doc/src/Eqs/dihedral_quadratic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\phi - \phi_0)^2 -$$ - -\end{document} diff --git a/doc/src/Eqs/dihedral_sign.jpg b/doc/src/Eqs/dihedral_sign.jpg deleted file mode 100644 index 8d8352e8fc..0000000000 Binary files a/doc/src/Eqs/dihedral_sign.jpg and /dev/null differ diff --git a/doc/src/Eqs/dreiding_hbond.jpg b/doc/src/Eqs/dreiding_hbond.jpg deleted file mode 100644 index 76cc42a45b..0000000000 Binary files a/doc/src/Eqs/dreiding_hbond.jpg and /dev/null differ diff --git a/doc/src/Eqs/eff_ECP1.jpg b/doc/src/Eqs/eff_ECP1.jpg deleted file mode 100644 index 3b8a3f8ff3..0000000000 Binary files a/doc/src/Eqs/eff_ECP1.jpg and /dev/null differ diff --git a/doc/src/Eqs/eff_ECP1.tex b/doc/src/Eqs/eff_ECP1.tex deleted file mode 100644 index ebd581163c..0000000000 --- a/doc/src/Eqs/eff_ECP1.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E_{Pauli(ECP_s)}=p_1\exp\left(-\frac{p_2r^2}{p_3+s^2} \right) -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/eff_ECP2.jpg b/doc/src/Eqs/eff_ECP2.jpg deleted file mode 100644 index 195ed55e43..0000000000 Binary files a/doc/src/Eqs/eff_ECP2.jpg and /dev/null differ diff --git a/doc/src/Eqs/eff_ECP2.tex b/doc/src/Eqs/eff_ECP2.tex deleted file mode 100644 index 0c3c366562..0000000000 --- a/doc/src/Eqs/eff_ECP2.tex +++ /dev/null @@ -1,8 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E_{Pauli(ECP_p)}=p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right] -$$ - \end{document} \ No newline at end of file diff --git a/doc/src/Eqs/eff_KE.jpg b/doc/src/Eqs/eff_KE.jpg deleted file mode 100644 index 40eed0df65..0000000000 Binary files a/doc/src/Eqs/eff_KE.jpg and /dev/null differ diff --git a/doc/src/Eqs/eff_KE.tex b/doc/src/Eqs/eff_KE.tex deleted file mode 100644 index 9f9af2fa25..0000000000 --- a/doc/src/Eqs/eff_KE.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -E_{KE} = \frac{\hbar^2 }{{m_{e} }}\sum\limits_i {\frac{3}{{2s_i^2 }}} -$$ - -\end{document} diff --git a/doc/src/Eqs/eff_NN.jpg b/doc/src/Eqs/eff_NN.jpg deleted file mode 100644 index c3c52e19b4..0000000000 Binary files a/doc/src/Eqs/eff_NN.jpg and /dev/null differ diff --git a/doc/src/Eqs/eff_NN.tex b/doc/src/Eqs/eff_NN.tex deleted file mode 100644 index 4f9bb6d132..0000000000 --- a/doc/src/Eqs/eff_NN.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -E_{NN} = \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i < j} {\frac{{Z_i Z_j }}{{R_{ij} }}} -$$ - -\end{document} diff --git a/doc/src/Eqs/eff_Ne.jpg b/doc/src/Eqs/eff_Ne.jpg deleted file mode 100644 index e23ceacc88..0000000000 Binary files a/doc/src/Eqs/eff_Ne.jpg and /dev/null differ diff --git a/doc/src/Eqs/eff_Ne.tex b/doc/src/Eqs/eff_Ne.tex deleted file mode 100644 index e6813b125c..0000000000 --- a/doc/src/Eqs/eff_Ne.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -E_{Ne} = - \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i,j} {\frac{{Z_i }}{{R_{ij} }}Erf\left( {\frac{{\sqrt 2 R_{ij} }}{{s_j }}} \right)} -$$ - -\end{document} diff --git a/doc/src/Eqs/eff_Pauli.jpg b/doc/src/Eqs/eff_Pauli.jpg deleted file mode 100644 index 61bb8652e3..0000000000 Binary files a/doc/src/Eqs/eff_Pauli.jpg and /dev/null differ diff --git a/doc/src/Eqs/eff_Pauli.tex b/doc/src/Eqs/eff_Pauli.tex deleted file mode 100644 index b6b8070cc7..0000000000 --- a/doc/src/Eqs/eff_Pauli.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -E_{Pauli} = \sum\limits_{\sigma _i = \sigma _j } {E\left( { \uparrow \uparrow } \right)_{ij}} + \sum\limits_{\sigma _i \ne \sigma _j } {E\left( { \uparrow \downarrow } \right)_{ij}} -$$ - -\end{document} diff --git a/doc/src/Eqs/eff_ee.jpg b/doc/src/Eqs/eff_ee.jpg deleted file mode 100644 index aef84d0fd4..0000000000 Binary files a/doc/src/Eqs/eff_ee.jpg and /dev/null differ diff --git a/doc/src/Eqs/eff_ee.tex b/doc/src/Eqs/eff_ee.tex deleted file mode 100644 index 5d17e5557b..0000000000 --- a/doc/src/Eqs/eff_ee.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -E_{ee} = \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i < j} {\frac{1}{{r_{ij} }}Erf\left( {\frac{{\sqrt 2 r_{ij} }}{{\sqrt {s_i^2 + s_j^2 } }}} \right)} -$$ - -\end{document} diff --git a/doc/src/Eqs/eff_energy_expression.jpg b/doc/src/Eqs/eff_energy_expression.jpg deleted file mode 100644 index e06fe8ff2f..0000000000 Binary files a/doc/src/Eqs/eff_energy_expression.jpg and /dev/null differ diff --git a/doc/src/Eqs/eff_energy_expression.tex b/doc/src/Eqs/eff_energy_expression.tex deleted file mode 100644 index f56380f646..0000000000 --- a/doc/src/Eqs/eff_energy_expression.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -U\left(R,r,s\right) = E_{NN} \left( R \right) + E_{Ne} \left( {R,r,s} \right) + E_{ee} \left( {r,s} \right) + E_{KE} \left( {r,s} \right) + E_{PR} \left( { \uparrow \downarrow ,S} \right) -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_box_relax1.jpg b/doc/src/Eqs/fix_box_relax1.jpg deleted file mode 100644 index d425526046..0000000000 Binary files a/doc/src/Eqs/fix_box_relax1.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_box_relax1.tex b/doc/src/Eqs/fix_box_relax1.tex deleted file mode 100644 index a332360666..0000000000 --- a/doc/src/Eqs/fix_box_relax1.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -E = U + P_t \left(V-V_0 \right) + E_{strain} -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_box_relax2.jpg b/doc/src/Eqs/fix_box_relax2.jpg deleted file mode 100644 index 8fac42e0fa..0000000000 Binary files a/doc/src/Eqs/fix_box_relax2.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_box_relax2.tex b/doc/src/Eqs/fix_box_relax2.tex deleted file mode 100644 index bc9cddef4e..0000000000 --- a/doc/src/Eqs/fix_box_relax2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\mathbf P = P_t \mathbf I + {\mathbf S_t} \left( \mathbf h_0^{-1} \right)^t \mathbf h_{0d} -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_eos-cv.jpg b/doc/src/Eqs/fix_eos-cv.jpg deleted file mode 100644 index 37eeac8e2d..0000000000 Binary files a/doc/src/Eqs/fix_eos-cv.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_eos-cv.tex b/doc/src/Eqs/fix_eos-cv.tex deleted file mode 100644 index e084bac9bc..0000000000 --- a/doc/src/Eqs/fix_eos-cv.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} -\pagestyle{empty} -\begin{document} - -$$ - u_{i} = u^{mech}_{i} + u^{cond}_{i} = C_{V} \theta_{i} -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_gld1.jpg b/doc/src/Eqs/fix_gld1.jpg deleted file mode 100644 index d54ce57a6c..0000000000 Binary files a/doc/src/Eqs/fix_gld1.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_gld1.tex b/doc/src/Eqs/fix_gld1.tex deleted file mode 100644 index baa0f32a5b..0000000000 --- a/doc/src/Eqs/fix_gld1.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\usepackage{amsmath} - -\begin{document} - -\begin{align*} - &{\bf F}_{j}(t) = {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\ - &\Gamma_j(t-s) = \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ - &\langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = \text{k$_\text{B}$T} ~\Gamma_j(t-s) -\end{align*} - -\end{document} diff --git a/doc/src/Eqs/fix_lb_fluid_boltzmann.jpg b/doc/src/Eqs/fix_lb_fluid_boltzmann.jpg deleted file mode 100644 index 9d82b40ecb..0000000000 Binary files a/doc/src/Eqs/fix_lb_fluid_boltzmann.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_lb_fluid_boltzmann.tex b/doc/src/Eqs/fix_lb_fluid_boltzmann.tex deleted file mode 100755 index 4a6ca6fe01..0000000000 --- a/doc/src/Eqs/fix_lb_fluid_boltzmann.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\left(\partial_t + e_{i\alpha}\partial_{\alpha}\right)f_i = -\frac{1}{\tau}\left(f_i - f_i^{eq}\right) + W_i -$$ - - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_lb_fluid_fluidforce.jpg b/doc/src/Eqs/fix_lb_fluid_fluidforce.jpg deleted file mode 100644 index d3149616ca..0000000000 Binary files a/doc/src/Eqs/fix_lb_fluid_fluidforce.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_lb_fluid_fluidforce.tex b/doc/src/Eqs/fix_lb_fluid_fluidforce.tex deleted file mode 100755 index 8433c9264a..0000000000 --- a/doc/src/Eqs/fix_lb_fluid_fluidforce.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -{\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha} -$$ - - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_lb_fluid_gammadefault.jpg b/doc/src/Eqs/fix_lb_fluid_gammadefault.jpg deleted file mode 100644 index cd10239c9b..0000000000 Binary files a/doc/src/Eqs/fix_lb_fluid_gammadefault.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_lb_fluid_gammadefault.tex b/doc/src/Eqs/fix_lb_fluid_gammadefault.tex deleted file mode 100755 index 1af82c4972..0000000000 --- a/doc/src/Eqs/fix_lb_fluid_gammadefault.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right) -$$ - - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_lb_fluid_navierstokes.jpg b/doc/src/Eqs/fix_lb_fluid_navierstokes.jpg deleted file mode 100644 index 0a1c104141..0000000000 Binary files a/doc/src/Eqs/fix_lb_fluid_navierstokes.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_lb_fluid_navierstokes.tex b/doc/src/Eqs/fix_lb_fluid_navierstokes.tex deleted file mode 100755 index 41ca4674e9..0000000000 --- a/doc/src/Eqs/fix_lb_fluid_navierstokes.tex +++ /dev/null @@ -1,16 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\partial_t \rho + \partial_{\beta}\left(\rho u_{\beta}\right)= 0 -$$ -$$ -\partial_t\left(\rho u_{\alpha}\right) + \partial_{\beta}\left(\rho u_{\alpha} u_{\beta}\right) = \partial_{\beta}\sigma_{\alpha \beta} + F_{\alpha} + \partial_{\beta}\left(\eta_{\alpha \beta \gamma \nu}\partial_{\gamma} u_{\nu}\right) -$$ - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_lb_fluid_properties.jpg b/doc/src/Eqs/fix_lb_fluid_properties.jpg deleted file mode 100644 index 3d70cd7667..0000000000 Binary files a/doc/src/Eqs/fix_lb_fluid_properties.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_lb_fluid_properties.tex b/doc/src/Eqs/fix_lb_fluid_properties.tex deleted file mode 100755 index fe1290be12..0000000000 --- a/doc/src/Eqs/fix_lb_fluid_properties.tex +++ /dev/null @@ -1,17 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\rho = \displaystyle\sum\limits_{i} f_i -$$ -$$ -\rho u_{\alpha} = \displaystyle\sum\limits_{i} f_i e_{i\alpha} -$$ - - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_lb_fluid_stress.jpg b/doc/src/Eqs/fix_lb_fluid_stress.jpg deleted file mode 100644 index 8f730e9d70..0000000000 Binary files a/doc/src/Eqs/fix_lb_fluid_stress.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_lb_fluid_stress.tex b/doc/src/Eqs/fix_lb_fluid_stress.tex deleted file mode 100755 index b4e0982536..0000000000 --- a/doc/src/Eqs/fix_lb_fluid_stress.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\sigma_{\alpha \beta} = -P_{\alpha \beta} = -\rho a_0 \delta_{\alpha \beta} -$$ - - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_lb_fluid_viscosity.jpg b/doc/src/Eqs/fix_lb_fluid_viscosity.jpg deleted file mode 100644 index 1816317ee6..0000000000 Binary files a/doc/src/Eqs/fix_lb_fluid_viscosity.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_lb_fluid_viscosity.tex b/doc/src/Eqs/fix_lb_fluid_viscosity.tex deleted file mode 100755 index d5925f213f..0000000000 --- a/doc/src/Eqs/fix_lb_fluid_viscosity.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\eta_{\alpha \beta \gamma \nu} = \eta\left[\delta_{\alpha \gamma}\delta_{\beta \nu} + \delta_{\alpha \nu}\delta_{\beta \gamma} - \frac{2}{3}\delta_{\alpha \beta}\delta_{\gamma \nu}\right] + \Lambda \delta_{\alpha \beta}\delta_{\gamma \nu} -$$ - - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_nh1.jpg b/doc/src/Eqs/fix_nh1.jpg deleted file mode 100644 index af07ea3a4b..0000000000 Binary files a/doc/src/Eqs/fix_nh1.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_nh1.tex b/doc/src/Eqs/fix_nh1.tex deleted file mode 100644 index 3e780f2772..0000000000 --- a/doc/src/Eqs/fix_nh1.tex +++ /dev/null @@ -1,36 +0,0 @@ -\documentclass[24pt]{article} - -\pagestyle{empty} -\Huge - -\begin{document} - -\mathchardef\mhyphen="2D - -% The imaginary unit -\providecommand*{\iu}% - {\ensuremath{{\rm i}}} - - -\begin{eqnarray*} -\exp \left(\iu{} L \Delta t \right) &=&Ê -\exp \left(\iu{} L_{\rm T\mhyphen baro} \frac{\Delta t}{2} \right) -\exp \left(\iu{} L_{\rm T\mhyphen part} \frac{\Delta t}{2} \right) -\exp \left(\iu{} L_{\epsilon , 2} \frac{\Delta t}{2} \right) -\exp \left(\iu{} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\ -&&\times \left[ -\exp \left(\iu{} L_{2}^{(1)} \frac{\Delta t}{2n} \right) -\exp \left(\iu{} L_{\epsilon , 1} \frac{\Delta t}{2n} \right) -\exp \left(\iu{} L_1 \frac{\Delta t}{n} \right) -\exp \left(\iu{} L_{\epsilon , 1} \frac{\Delta t}{2n} \right) -\exp \left(\iu{} L_{2}^{(1)} \frac{\Delta t}{2n} \right) -\right]^n \\ -&&\times -\exp \left(\iu{} L_{2}^{(2)} \frac{\Delta t}{2} \right) -\exp \left(\iu{} L_{\epsilon , 2} \frac{\Delta t}{2} \right) -\exp \left(\iu{} L_{\rm T\mhyphen part} \frac{\Delta t}{2} \right) -\exp \left(\iu{} L_{\rm T\mhyphen baro} \frac{\Delta t}{2} \right) \\ -&&+ \mathcal{O} \left(\Delta t^3 \right) -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/fix_nphug.jpg b/doc/src/Eqs/fix_nphug.jpg deleted file mode 100644 index a3a67e7b7b..0000000000 Binary files a/doc/src/Eqs/fix_nphug.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_nphug.tex b/doc/src/Eqs/fix_nphug.tex deleted file mode 100644 index 4e162b69b7..0000000000 --- a/doc/src/Eqs/fix_nphug.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -T_t - T = \frac{\left(\frac{1}{2}\left(P + P_0\right)\left(V_0 - V\right) + E_0 - E\right)}{N_{dof} k_B } = Delta -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_orient_fcc.jpg b/doc/src/Eqs/fix_orient_fcc.jpg deleted file mode 100644 index b22e6c9c20..0000000000 Binary files a/doc/src/Eqs/fix_orient_fcc.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_orient_fcc.tex b/doc/src/Eqs/fix_orient_fcc.tex deleted file mode 100644 index 5596848eb5..0000000000 --- a/doc/src/Eqs/fix_orient_fcc.tex +++ /dev/null @@ -1,30 +0,0 @@ -\newcommand{\br}{\mathbf{r}} - -\documentclass[12pt]{article} - -\begin{document} - -\begin{equation} - \xi_{i} = \sum_{j=1}^{12} \left| \br_{j} - \br_{j}^{\rm I} \right| -\end{equation} - -\begin{equation} - \xi_{\rm IJ} = \sum_{j=1}^{12} \left| \br_{j}^{\rm J} - \br_{j}^{\rm I} \right| -\end{equation} - -\begin{eqnarray} - \xi_{\rm low} &=& {\rm cutlo} \, \xi_{\rm IJ} \\ - \xi_{\rm high} &=& {\rm cuthi} \, \xi_{\rm IJ} -\end{eqnarray} - -\begin{eqnarray} - \omega_{i} &=& \frac{\pi}{2} - \frac{\xi_{i} - \xi_{\rm low}}{\xi_{\rm high} - \xi_{\rm low}} \\ - \mbox{\hspace*{72pt}} \nonumber \\ - u_{i} &=& 0 \mbox{\hspace{84pt} for } \xi_{i} < \xi_{\rm low} \nonumber \\ - &=& {\rm dE}\,\frac{1 - \cos(2 \omega_{i})}{2} - \mbox{\hspace{10pt} for } \xi_{\rm low} < \xi_{i} < \xi_{\rm high} \\ - &=& {\rm dE} \mbox{\hspace{80pt} for } \xi_{\rm high} < \xi_{i} - \nonumber -\end{eqnarray} -\end{document} diff --git a/doc/src/Eqs/fix_pimd.jpg b/doc/src/Eqs/fix_pimd.jpg deleted file mode 100644 index b6e8f5831b..0000000000 Binary files a/doc/src/Eqs/fix_pimd.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_pimd.tex b/doc/src/Eqs/fix_pimd.tex deleted file mode 100644 index 983fead8e4..0000000000 --- a/doc/src/Eqs/fix_pimd.tex +++ /dev/null @@ -1,17 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - Z = \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ] -$$ - -$$ - H_{eff} = \bigg(\sum_{i=1}^P \frac{p_i^2}{2m_i}\bigg) + V_{eff} -$$ - -$$ - V_{eff} = \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg] -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_rattle_constraints.jpg b/doc/src/Eqs/fix_rattle_constraints.jpg deleted file mode 100644 index 2ba86095cd..0000000000 Binary files a/doc/src/Eqs/fix_rattle_constraints.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_rattle_constraints.tex b/doc/src/Eqs/fix_rattle_constraints.tex deleted file mode 100644 index daff0ce775..0000000000 --- a/doc/src/Eqs/fix_rattle_constraints.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} -\usepackage{amsmath} - -\begin{document} -\begin{align*} -\mathbf r^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= d^2_{ij} \quad \text{and} \\ -\mathbf v^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= 0, \label{eq:velcon} -\end{align*} -\end{document} diff --git a/doc/src/Eqs/fix_rattle_rij.jpg b/doc/src/Eqs/fix_rattle_rij.jpg deleted file mode 100644 index b08e2fe02e..0000000000 Binary files a/doc/src/Eqs/fix_rattle_rij.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_rattle_rij.tex b/doc/src/Eqs/fix_rattle_rij.tex deleted file mode 100644 index fae0457c60..0000000000 --- a/doc/src/Eqs/fix_rattle_rij.tex +++ /dev/null @@ -1,8 +0,0 @@ -\documentclass[12pt]{article} -\usepackage{amsmath} -\begin{document} -$$ - \mathbf r^{n+1}_{ij} = \mathbf r^n_j - \mathbf r^n_i -$$ -\end{document} - diff --git a/doc/src/Eqs/fix_spring_rg.jpg b/doc/src/Eqs/fix_spring_rg.jpg deleted file mode 100644 index 313844f555..0000000000 Binary files a/doc/src/Eqs/fix_spring_rg.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_spring_rg.tex b/doc/src/Eqs/fix_spring_rg.tex deleted file mode 100644 index b772aaf652..0000000000 --- a/doc/src/Eqs/fix_spring_rg.tex +++ /dev/null @@ -1,19 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -{R_G}^2 = \frac{1}{M}\sum_{i}^{N}{m_{i}\left( x_{i} - -\frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right)^{2}} -$$ - -$$ - E = K\left( R_G - R_{G0} \right)^{2} -$$ - -$$ -F_{i} = 2K\frac{m_{i}}{M}\left( 1-\frac{R_{G0}}{R_G} -\right)\left( x_{i} - \frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right) -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/fix_ti_rs_force.jpg b/doc/src/Eqs/fix_ti_rs_force.jpg deleted file mode 100644 index a09bcb66c5..0000000000 Binary files a/doc/src/Eqs/fix_ti_rs_force.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ti_rs_force.tex b/doc/src/Eqs/fix_ti_rs_force.tex deleted file mode 100644 index 849c0ccc97..0000000000 --- a/doc/src/Eqs/fix_ti_rs_force.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\usepackage{amsmath} - -\begin{document} - -$$ - F_{\text{total}} = \lambda F_{\text{int}} -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_ti_rs_function_1.jpg b/doc/src/Eqs/fix_ti_rs_function_1.jpg deleted file mode 100644 index 478dc5781d..0000000000 Binary files a/doc/src/Eqs/fix_ti_rs_function_1.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ti_rs_function_1.tex b/doc/src/Eqs/fix_ti_rs_function_1.tex deleted file mode 100644 index 033d8d7559..0000000000 --- a/doc/src/Eqs/fix_ti_rs_function_1.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - \lambda(\tau) = \lambda_i + \tau \left( \lambda_f - \lambda_i \right) -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_ti_rs_function_2.jpg b/doc/src/Eqs/fix_ti_rs_function_2.jpg deleted file mode 100644 index 4fbfe45c63..0000000000 Binary files a/doc/src/Eqs/fix_ti_rs_function_2.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ti_rs_function_2.tex b/doc/src/Eqs/fix_ti_rs_function_2.tex deleted file mode 100644 index a1dd377dcc..0000000000 --- a/doc/src/Eqs/fix_ti_rs_function_2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - \lambda(\tau) = \frac{\lambda_i}{1 + \tau \left( \frac{\lambda_i}{\lambda_f} - 1 \right)} -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_ti_rs_function_3.jpg b/doc/src/Eqs/fix_ti_rs_function_3.jpg deleted file mode 100644 index 94ab0f468c..0000000000 Binary files a/doc/src/Eqs/fix_ti_rs_function_3.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ti_rs_function_3.tex b/doc/src/Eqs/fix_ti_rs_function_3.tex deleted file mode 100644 index 2d2790fa97..0000000000 --- a/doc/src/Eqs/fix_ti_rs_function_3.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - \lambda(\tau) = \frac{\lambda_i}{ 1 + \log_2(1+\tau) \left( \frac{\lambda_i}{\lambda_f} - 1 \right)} -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_ti_spring_force.jpg b/doc/src/Eqs/fix_ti_spring_force.jpg deleted file mode 100644 index 347102b3e7..0000000000 Binary files a/doc/src/Eqs/fix_ti_spring_force.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ti_spring_force.tex b/doc/src/Eqs/fix_ti_spring_force.tex deleted file mode 100644 index 0acd0e54ae..0000000000 --- a/doc/src/Eqs/fix_ti_spring_force.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\usepackage{amsmath} - -\begin{document} - -$$ - F_{\text{total}} = \left( 1-\lambda \right) F_{\text{solid}} + \lambda F_{\text{harm}} -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_ti_spring_function_1.jpg b/doc/src/Eqs/fix_ti_spring_function_1.jpg deleted file mode 100644 index 8d3c9a78e3..0000000000 Binary files a/doc/src/Eqs/fix_ti_spring_function_1.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ti_spring_function_1.tex b/doc/src/Eqs/fix_ti_spring_function_1.tex deleted file mode 100644 index 0673410b00..0000000000 --- a/doc/src/Eqs/fix_ti_spring_function_1.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - \lambda(\tau) = \tau -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_ti_spring_function_2.jpg b/doc/src/Eqs/fix_ti_spring_function_2.jpg deleted file mode 100644 index 96a17e63e6..0000000000 Binary files a/doc/src/Eqs/fix_ti_spring_function_2.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ti_spring_function_2.tex b/doc/src/Eqs/fix_ti_spring_function_2.tex deleted file mode 100644 index f2cb51e47d..0000000000 --- a/doc/src/Eqs/fix_ti_spring_function_2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - \lambda(\tau) = \tau^5 \left( 70 \tau^4 - 315 \tau^3 + 540 \tau^2 - 420 \tau + 126 \right) -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_ttm.jpg b/doc/src/Eqs/fix_ttm.jpg deleted file mode 100644 index 8d9fac3fed..0000000000 Binary files a/doc/src/Eqs/fix_ttm.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ttm.tex b/doc/src/Eqs/fix_ttm.tex deleted file mode 100644 index d5a3238f82..0000000000 --- a/doc/src/Eqs/fix_ttm.tex +++ /dev/null @@ -1,15 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - C_e \rho_e \frac{\partial T_e}{\partial t} = - \bigtriangledown (\kappa_e \bigtriangledown T_e) - - g_p (T_e - T_a) + g_s T_a' -$$ - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_ttm_blast.jpg b/doc/src/Eqs/fix_ttm_blast.jpg deleted file mode 100644 index d4ffe05f12..0000000000 Binary files a/doc/src/Eqs/fix_ttm_blast.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ttm_blast.tex b/doc/src/Eqs/fix_ttm_blast.tex deleted file mode 100644 index 6871ed5cc6..0000000000 --- a/doc/src/Eqs/fix_ttm_blast.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - {\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec F}_{langevin} - \nabla P_e/n_{ion} -$$ - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_ttm_blast1.jpg b/doc/src/Eqs/fix_ttm_blast1.jpg deleted file mode 100644 index 1106c627cb..0000000000 Binary files a/doc/src/Eqs/fix_ttm_blast1.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ttm_blast1.tex b/doc/src/Eqs/fix_ttm_blast1.tex deleted file mode 100644 index 642afe4300..0000000000 --- a/doc/src/Eqs/fix_ttm_blast1.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - \nabla_x P_e = \left[\frac{C_e{}T_e(x)\lambda}{(x+\lambda)^2} + \frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta x}-(C_e{}T_e)_{x}}{\Delta x} \right] -$$ - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_ttm_ce.jpg b/doc/src/Eqs/fix_ttm_ce.jpg deleted file mode 100644 index 4f439e31e6..0000000000 Binary files a/doc/src/Eqs/fix_ttm_ce.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ttm_ce.tex b/doc/src/Eqs/fix_ttm_ce.tex deleted file mode 100644 index f787590b8f..0000000000 --- a/doc/src/Eqs/fix_ttm_ce.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2) -$$ - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_ttm_mod.jpg b/doc/src/Eqs/fix_ttm_mod.jpg deleted file mode 100644 index 7cc67200f9..0000000000 Binary files a/doc/src/Eqs/fix_ttm_mod.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_ttm_mod.tex b/doc/src/Eqs/fix_ttm_mod.tex deleted file mode 100644 index d0a313e676..0000000000 --- a/doc/src/Eqs/fix_ttm_mod.tex +++ /dev/null @@ -1,15 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - C_e \rho_e \frac{\partial T_e}{\partial t} = - \bigtriangledown (\kappa_e \bigtriangledown T_e) - - g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin}) -$$ - -\end{document} - - - - diff --git a/doc/src/Eqs/fix_wall_colloid.jpg b/doc/src/Eqs/fix_wall_colloid.jpg deleted file mode 100644 index 8168d3a792..0000000000 Binary files a/doc/src/Eqs/fix_wall_colloid.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_wall_colloid.tex b/doc/src/Eqs/fix_wall_colloid.tex deleted file mode 100644 index 3ed716c263..0000000000 --- a/doc/src/Eqs/fix_wall_colloid.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{eqnarray} -E &=& \epsilon \left[ \frac{\sigma^{6}}{7560} - \left(\frac{6R-D}{D^{7}} + \frac{D+8R}{(D+2R)^{7}} \right) - - \frac{}{} \right. \nonumber \\ - &&\qquad \left. \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R) - \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] -\qquad r < r_c \nonumber -\end{eqnarray} - -\end{document} diff --git a/doc/src/Eqs/fix_wall_harmonic.jpg b/doc/src/Eqs/fix_wall_harmonic.jpg deleted file mode 100644 index 3c605690c3..0000000000 Binary files a/doc/src/Eqs/fix_wall_harmonic.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_wall_harmonic.tex b/doc/src/Eqs/fix_wall_harmonic.tex deleted file mode 100644 index 86dcb80a0e..0000000000 --- a/doc/src/Eqs/fix_wall_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - E = \epsilon \hspace{0.1cm} (r - r_c)^2 \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/fix_wall_lj1043.jpg b/doc/src/Eqs/fix_wall_lj1043.jpg deleted file mode 100644 index 303743bf3e..0000000000 Binary files a/doc/src/Eqs/fix_wall_lj1043.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_wall_lj1043.tex b/doc/src/Eqs/fix_wall_lj1043.tex deleted file mode 100644 index 06fc4dd33e..0000000000 --- a/doc/src/Eqs/fix_wall_lj1043.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} - - \left(\frac{\sigma}{r}\right)^4 - - \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right] - \qquad r < r_c -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/fix_wall_lj93.jpg b/doc/src/Eqs/fix_wall_lj93.jpg deleted file mode 100644 index 18e502cfbf..0000000000 Binary files a/doc/src/Eqs/fix_wall_lj93.jpg and /dev/null differ diff --git a/doc/src/Eqs/fix_wall_lj93.tex b/doc/src/Eqs/fix_wall_lj93.tex deleted file mode 100644 index 7372e55c15..0000000000 --- a/doc/src/Eqs/fix_wall_lj93.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} - - \left(\frac{\sigma}{r}\right)^3 \right] - \qquad r < r_c -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/fld.jpg b/doc/src/Eqs/fld.jpg deleted file mode 100644 index 3d80d436ff..0000000000 Binary files a/doc/src/Eqs/fld.jpg and /dev/null differ diff --git a/doc/src/Eqs/fld.tex b/doc/src/Eqs/fld.tex deleted file mode 100644 index 7c75cfbe60..0000000000 --- a/doc/src/Eqs/fld.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -F^{H} = -R_{FU}(U-U^{\infty}) + R_{FE}E^{\infty} -$$ - -\end{document} diff --git a/doc/src/Eqs/fld2.jpg b/doc/src/Eqs/fld2.jpg deleted file mode 100644 index 42de943c90..0000000000 Binary files a/doc/src/Eqs/fld2.jpg and /dev/null differ diff --git a/doc/src/Eqs/fld2.tex b/doc/src/Eqs/fld2.tex deleted file mode 100644 index 43adae11db..0000000000 --- a/doc/src/Eqs/fld2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ --R_{FU}(U-U^{\infty}) = -R_{FE}E^{\infty} - F^{rest} -$$ - -\end{document} diff --git a/doc/src/Eqs/heat_flux_J.jpg b/doc/src/Eqs/heat_flux_J.jpg deleted file mode 100644 index cf3e220caa..0000000000 Binary files a/doc/src/Eqs/heat_flux_J.jpg and /dev/null differ diff --git a/doc/src/Eqs/heat_flux_J.tex b/doc/src/Eqs/heat_flux_J.tex deleted file mode 100644 index 53c0ff494a..0000000000 --- a/doc/src/Eqs/heat_flux_J.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -\mathbf{J} & = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i - \sum_{i} \mathbf{S}_{i} \mathbf{v}_i \right] \\ -& = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \sum_{i r_{\rm out} \\ - E & = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\ - & = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ - & = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ - LJ(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] \\ - C(r) & = & \frac{C q_i q_j}{ \epsilon r} \\ - S(r) & = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 - \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} - { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } -\end{eqnarray*} - -\end{document} - - diff --git a/doc/src/Eqs/pair_class2.jpg b/doc/src/Eqs/pair_class2.jpg deleted file mode 100644 index abec072e79..0000000000 Binary files a/doc/src/Eqs/pair_class2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_class2.tex b/doc/src/Eqs/pair_class2.tex deleted file mode 100644 index e2acc00bb6..0000000000 --- a/doc/src/Eqs/pair_class2.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 - - 3 \left(\frac{\sigma}{r}\right)^6 \right] - \qquad r < r_c -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_cmm.jpg b/doc/src/Eqs/pair_cmm.jpg deleted file mode 100644 index 1ec60f7305..0000000000 Binary files a/doc/src/Eqs/pair_cmm.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_cmm.tex b/doc/src/Eqs/pair_cmm.tex deleted file mode 100644 index 9bab1e9002..0000000000 --- a/doc/src/Eqs/pair_cmm.tex +++ /dev/null @@ -1,16 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} - - \left(\frac{\sigma}{r}\right)^6 \right] & - \qquad r < r_c \\ - E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^4 \right] & - \qquad r < r_c \\ - E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] & - \qquad r < r_c -\end{eqnarray*} -\end{document} diff --git a/doc/src/Eqs/pair_colloid_cc.jpg b/doc/src/Eqs/pair_colloid_cc.jpg deleted file mode 100644 index a64094ddad..0000000000 Binary files a/doc/src/Eqs/pair_colloid_cc.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_colloid_cc.tex b/doc/src/Eqs/pair_colloid_cc.tex deleted file mode 100644 index e1485d325a..0000000000 --- a/doc/src/Eqs/pair_colloid_cc.tex +++ /dev/null @@ -1,31 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{eqnarray} -U_A &=& - \frac{A_{cc}}{6} \left[ - \frac{2 a_1 a_2}{r^2-\left(a_1+a_2\right)^2} - + \frac{2 a_1 a_2}{r^2 - \left(a_1 - a_2\right)^2} - + \mathrm{ln} - \left( - \frac{r^2-\left(a_1+a_2\right)^2}{r^2-\left(a_1-a_2\right)^2} - \right) - \right] \nonumber \\ -\nonumber \\ -U_R &=& \frac{A_{cc}}{37800} \frac{\sigma^6}{r} -\left[ \frac{}{} \right. \nonumber \\ - &&\qquad \frac{r^2-7r\left(a_1+a_2\right)+6\left(a_1^2+7a_1a_2+a_2^2\right)} - {\left(r-a_1-a_2\right)^7} \nonumber \\ - &&\qquad +\frac{r^2+7r\left(a_1+a_2\right)+6\left(a_1^2+7a_1a_2+a_2^2\right)} - {\left(r+a_1+a_2\right)^7} \nonumber \\ - &&\qquad -\frac{r^2+7r\left(a_1-a_2\right)+6\left(a_1^2-7a_1a_2+a_2^2\right)} - {\left(r+a_1-a_2\right)^7} \nonumber \\ - &&\qquad \left. -\frac{r^2-7r\left(a_1-a_2\right)+6\left(a_1^2-7a_1a_2+a_2^2\right)} - {\left(r-a_1+a_2\right)^7} - \right] \nonumber \\ -\nonumber \\ -U &=& U_A + U_R, \qquad r < r_c \nonumber -\end{eqnarray} - -\end{document} - diff --git a/doc/src/Eqs/pair_colloid_cs.jpg b/doc/src/Eqs/pair_colloid_cs.jpg deleted file mode 100644 index 8f5948fa54..0000000000 Binary files a/doc/src/Eqs/pair_colloid_cs.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_colloid_cs.tex b/doc/src/Eqs/pair_colloid_cs.tex deleted file mode 100644 index 760215ee08..0000000000 --- a/doc/src/Eqs/pair_colloid_cs.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{eqnarray} - U &=& \frac{2 ~ a^3 ~ \sigma^3 ~ A_{cs}}{9 \left( a^2 - r^2 \right)^3} - \left[ 1 - \frac{\left(5 ~ a^6+45~a^4~r^2+63~a^2~r^4+15~r^6\right) \sigma^6} - {15 \left(a-r\right)^6 \left( a+r \right)^6} \right], ~~ r < r_c \nonumber -\end{eqnarray} - -\end{document} - diff --git a/doc/src/Eqs/pair_colloid_ss.jpg b/doc/src/Eqs/pair_colloid_ss.jpg deleted file mode 100644 index 4ce19ba1e8..0000000000 Binary files a/doc/src/Eqs/pair_colloid_ss.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_colloid_ss.tex b/doc/src/Eqs/pair_colloid_ss.tex deleted file mode 100644 index 1cc511ed06..0000000000 --- a/doc/src/Eqs/pair_colloid_ss.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{eqnarray} - U &=& \frac{A_{ss}}{36} \left[ \left( \frac{\sigma}{r} - \right)^{12} - \left( \frac{ \sigma}{r} \right)^6 \right], ~~ - r < r_c \nonumber -\end{eqnarray} - -\end{document} - diff --git a/doc/src/Eqs/pair_comb1.jpg b/doc/src/Eqs/pair_comb1.jpg deleted file mode 100644 index e0711ca972..0000000000 Binary files a/doc/src/Eqs/pair_comb1.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_comb1.tex b/doc/src/Eqs/pair_comb1.tex deleted file mode 100644 index 82c6be056e..0000000000 --- a/doc/src/Eqs/pair_comb1.tex +++ /dev/null @@ -1,7 +0,0 @@ -\documentclass[12pt]{article} -\begin{document} \large -\begin{eqnarray*} -E_T & = & \sum_i [ E_i^{self} (q_i) + \sum_{j>i} [E_{ij}^{short} (r_{ij}, q_i, q_j) + E_{ij}^{Coul} (r_{ij}, q_i, q_j)] + \\ -&& E^{polar} (q_i, r_{ij}) + E^{vdW} (r_{ij}) + E^{barr} (q_i) + E^{corr} (r_{ij}, \theta_{jik})] \\ -\end{eqnarray*} -\end{document} diff --git a/doc/src/Eqs/pair_comb2.jpg b/doc/src/Eqs/pair_comb2.jpg deleted file mode 100644 index 8b0e5ba51a..0000000000 Binary files a/doc/src/Eqs/pair_comb2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_comb2.tex b/doc/src/Eqs/pair_comb2.tex deleted file mode 100644 index 3ba72f0726..0000000000 --- a/doc/src/Eqs/pair_comb2.tex +++ /dev/null @@ -1,23 +0,0 @@ -\documentclass[10pt]{article} - -\begin{document} - -\begin{table}[h] -\begin{tabular}{|c|c|c|c|c|c|c|c|c|} -\hline - & $O$ & $Cu$ & $N$ & $C$ & $H$ & $Ti$ & $Zn$ & $Zr$ \\ \hline -$O$ & F & F & F & F & F & F & F & F\\ \hline -$Cu$ & F & F & P & F & F & P & F & P \\ \hline -$N$ & F & P & F & M & F & P & P & P \\ \hline -$C$ & F & F & M & F & F & M & M & M \\ \hline -$H$ & F & F & F & F & F & M & M & F \\ \hline -$Ti$ & F & P & P & M & M & F & P & P \\ \hline -$Zn$ & F & F & P & M & M & P & F & P \\ \hline -$Zr$ & F & P & P & M & F & P & P & F \\ \hline -\multicolumn{9}{l}{F: Fully optimized} \\ -\multicolumn{9}{l}{M: Only optimized for dimer molecule} \\ -\multicolumn{9}{l}{P: in Progress but have it from mixing rule} \\ -\end{tabular} -\end{table} - -\end{document} diff --git a/doc/src/Eqs/pair_coul_diel.jpg b/doc/src/Eqs/pair_coul_diel.jpg deleted file mode 100644 index 70cb84f7a5..0000000000 Binary files a/doc/src/Eqs/pair_coul_diel.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_coul_diel.tex b/doc/src/Eqs/pair_coul_diel.tex deleted file mode 100644 index f0b893d887..0000000000 --- a/doc/src/Eqs/pair_coul_diel.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} -\pagestyle{empty} -\begin{document} - -\begin{eqnarray*} - E & = & \frac{Cq_iq_j}{\epsilon r} \left( \frac{\epsilon}{\epsilon_D(r)}-1\right) \qquad r < r_c \\ - \epsilon_D(r) & = & \frac{5.2+\epsilon}{2} + \frac{\epsilon-5.2}{2}\tanh\left(\frac{r-r_{me}}{\sigma_e}\right) -\end{eqnarray*} -\end{document} diff --git a/doc/src/Eqs/pair_coul_dsf.jpg b/doc/src/Eqs/pair_coul_dsf.jpg deleted file mode 100644 index a891b3ad15..0000000000 Binary files a/doc/src/Eqs/pair_coul_dsf.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_coul_dsf.tex b/doc/src/Eqs/pair_coul_dsf.tex deleted file mode 100644 index ec69680fc8..0000000000 --- a/doc/src/Eqs/pair_coul_dsf.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} -$$ - E = - q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + - \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_coul_soft.jpg b/doc/src/Eqs/pair_coul_soft.jpg deleted file mode 100644 index dad9c745ba..0000000000 Binary files a/doc/src/Eqs/pair_coul_soft.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_coul_soft.tex b/doc/src/Eqs/pair_coul_soft.tex deleted file mode 100644 index 2ff42a25b6..0000000000 --- a/doc/src/Eqs/pair_coul_soft.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\[ -E = \lambda^n \frac{ C q_i q_j}{\epsilon -\left[ \alpha_{\mathrm{C}} (1-\lambda)^2 + r^2 \right]^{1/2}} \qquad r < r_c -\] - -\end{document} diff --git a/doc/src/Eqs/pair_coul_wolf.jpg b/doc/src/Eqs/pair_coul_wolf.jpg deleted file mode 100644 index fd64cb6c03..0000000000 Binary files a/doc/src/Eqs/pair_coul_wolf.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_coul_wolf.tex b/doc/src/Eqs/pair_coul_wolf.tex deleted file mode 100644 index 4a6592638f..0000000000 --- a/doc/src/Eqs/pair_coul_wolf.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} -$$ - E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + - \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_coulomb.jpg b/doc/src/Eqs/pair_coulomb.jpg deleted file mode 100644 index 39aaebac31..0000000000 Binary files a/doc/src/Eqs/pair_coulomb.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_coulomb.tex b/doc/src/Eqs/pair_coulomb.tex deleted file mode 100644 index 9dacdc1af3..0000000000 --- a/doc/src/Eqs/pair_coulomb.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_cs.jpg b/doc/src/Eqs/pair_cs.jpg deleted file mode 100644 index b870a3bdf4..0000000000 Binary files a/doc/src/Eqs/pair_cs.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_cs.tex b/doc/src/Eqs/pair_cs.tex deleted file mode 100644 index b7eacb8d5b..0000000000 --- a/doc/src/Eqs/pair_cs.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - E = \frac{C q_i q_j}{\epsilon (r + r_{min})} \qquad r \rightarrow 0 -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_debye.jpg b/doc/src/Eqs/pair_debye.jpg deleted file mode 100644 index 42bcb5cc63..0000000000 Binary files a/doc/src/Eqs/pair_debye.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_debye.tex b/doc/src/Eqs/pair_debye.tex deleted file mode 100644 index 392a6516ce..0000000000 --- a/doc/src/Eqs/pair_debye.tex +++ /dev/null @@ -1,8 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} -$$ - E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_dipole.jpg b/doc/src/Eqs/pair_dipole.jpg deleted file mode 100644 index e106c17c91..0000000000 Binary files a/doc/src/Eqs/pair_dipole.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_dipole.tex b/doc/src/Eqs/pair_dipole.tex deleted file mode 100644 index bc0ae82f80..0000000000 --- a/doc/src/Eqs/pair_dipole.tex +++ /dev/null @@ -1,38 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -E_{LJ} & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] \\ -E_{qq} & = & \frac{q_i q_j}{r} \\ -E_{qp} & = & \frac{q}{r^3} (p \bullet \vec{r}) \\ -E_{pp} & = & \frac{1}{r^3} (\vec{p_i} \bullet \vec{p_j}) - - \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r}) -\end{eqnarray*} - -\begin{eqnarray*} -F_{qq} & = & \frac{q_i q_j}{r^3} \vec{r} \\ -F_{qp} & = & -\frac{q}{r^3} \vec{p} + \frac{3q}{r^5} - (\vec{p} \bullet \vec{r}) \vec{r} \\ -F_{pp} & = & \frac{3}{r^5} (\vec{p_i} \bullet \vec{p_j}) \vec{r} - - \frac{15}{r^7} (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \bullet \vec{r}) \vec{r} + - \frac{3}{r^5} \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + - (\vec{p_i} \bullet \vec{r}) \vec{p_j} \right] -\end{eqnarray*} - -\begin{eqnarray*} -T_{pq} = T_{ij} & = & \frac{q_j}{r^3} (\vec{p_i} \times \vec{r}) \\ -T_{qp} = T_{ji} & = & - \frac{q_i}{r^3} (\vec{p_j} \times \vec{r}) \\ -T_{pp} = T_{ij} & = & -\frac{1}{r^3} (\vec{p_i} \times \vec{p_j}) + - \frac{3}{r^5} (\vec{p_j} \bullet \vec{r}) - (\vec{p_i} \times \vec{r}) \\ -T_{pp} = T_{ji} & = & -\frac{1}{r^3} (\vec{p_j} \times \vec{p_i}) + - \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \times \vec{r}) \\ -\end{eqnarray*} - -\end{document} - - diff --git a/doc/src/Eqs/pair_dipole_sf.jpg b/doc/src/Eqs/pair_dipole_sf.jpg deleted file mode 100644 index c591534550..0000000000 Binary files a/doc/src/Eqs/pair_dipole_sf.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_dipole_sf.tex b/doc/src/Eqs/pair_dipole_sf.tex deleted file mode 100644 index c653a37740..0000000000 --- a/doc/src/Eqs/pair_dipole_sf.tex +++ /dev/null @@ -1,51 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -E_{LJ} & = & 4\epsilon \left\{ \left[ \left( \frac{\sigma}{r} \right)^{\!12} - - \left( \frac{\sigma}{r} \right)^{\!6} \right] + - \left[ 6\left( \frac{\sigma}{r_c} \right)^{\!12} - - 3\left(\frac{\sigma}{r_c}\right)^{\!6}\right]\left(\frac{r}{r_c}\right)^{\!2} - - 7\left( \frac{\sigma}{r_c} \right)^{\!12} + - 4\left( \frac{\sigma}{r_c} \right)^{\!6}\right\} \\ -E_{qq} & = & \frac{q_i q_j}{r}\left(1-\frac{r}{r_c}\right)^{\!2} \\ -E_{pq} & = & E_{ji} = -\frac{q}{r^3} \left[ 1 - - 3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\ -E_{qp} & = & E_{ij} = \frac{q}{r^3} \left[ 1 - - 3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\ -E_{pp} & = & \left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right]\left[\frac{1}{r^3} - (\vec{p_i} \bullet \vec{p_j}) - \frac{3}{r^5} - (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})\right] \\ -\end{eqnarray*} - -\begin{eqnarray*} -F_{LJ} & = & \left\{\left[48\epsilon \left(\frac{\sigma}{r}\right)^{\!12} - - 24\epsilon \left(\frac{\sigma}{r}\right)^{\!6} \right]\frac{1}{r^2} - - \left[48\epsilon \left(\frac{\sigma}{r_c}\right)^{\!12} - 24\epsilon - \left(\frac{\sigma}{r_c}\right)^{\!6} \right]\frac{1}{r_c^2}\right\}\vec{r}\\ -F_{qq} & = & \frac{q_i q_j}{r}\left(\frac{1}{r^2} - - \frac{1}{r_c^2}\right)\vec{r} \\ -F_{pq} &=& F_{ij } = -\frac{3q}{r^5} \left[ 1 - - \left(\frac{r}{r_c}\right)^{\!2}\right](\vec{p}\bullet\vec{r})\vec{r} + - \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\ -F_{qp} &=& F_{ij} = \frac{3q}{r^5} \left[ 1 - - \left(\frac{r}{r_c}\right)^{\!2}\right] (\vec{p}\bullet\vec{r})\vec{r} - - \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\ -F_{pp} & = &\frac{3}{r^5}\Bigg\{\left[1-\left(\frac{r}{r_c}\right)^{\!4}\right] - \left[(\vec{p_i}\bullet\vec{p_j}) - \frac{3}{r^2} (\vec{p_i}\bullet\vec{r}) - (\vec{p_j} \bullet \vec{r})\right] \vec{r} + \\ - & & \left[1 - - 4\left(\frac{r}{r_c}\right)^{\!3}+3\left(\frac{r}{r_c}\right)^{\!4}\right] - \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + (\vec{p_i} \bullet \vec{r}) - \vec{p_j} -\frac{2}{r^2} (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \bullet \vec{r})\vec{r}\right] \Bigg\} \\ -\end{eqnarray*} - -\end{document} - diff --git a/doc/src/Eqs/pair_dipole_sf2.jpg b/doc/src/Eqs/pair_dipole_sf2.jpg deleted file mode 100644 index b9e57becf6..0000000000 Binary files a/doc/src/Eqs/pair_dipole_sf2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_dipole_sf2.tex b/doc/src/Eqs/pair_dipole_sf2.tex deleted file mode 100644 index 74758ba230..0000000000 --- a/doc/src/Eqs/pair_dipole_sf2.tex +++ /dev/null @@ -1,24 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -T_{pq} = T_{ij} & = & \frac{q_j}{r^3} \left[ 1 - - 3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p_i}\times\vec{r}) \\ -T_{qp} = T_{ji} & = & - \frac{q_i}{r^3} \left[ 1 - - 3\left(\frac{r}{r_c}\right)^{\!2} + - 2\left(\frac{r}{r_c}\right)^{\!3} \right] (\vec{p_j}\times\vec{r}) \\ -T_{pp} = T_{ij} & = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - e3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \times \vec{p_j}) + \\ - & & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_j}\bullet\vec{r}) - (\vec{p_i} \times \vec{r}) \\ -T_{pp} = T_{ji} & = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right](\vec{p_j} \times \vec{p_i}) + \\ - & & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \times \vec{r}) \\ -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_dpd.jpg b/doc/src/Eqs/pair_dpd.jpg deleted file mode 100644 index e9bb8a69af..0000000000 Binary files a/doc/src/Eqs/pair_dpd.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_dpd.tex b/doc/src/Eqs/pair_dpd.tex deleted file mode 100644 index ba47f0d6b6..0000000000 --- a/doc/src/Eqs/pair_dpd.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - \vec{f} & = & (F^C + F^D + F^R) \hat{r_{ij}} \qquad \qquad r < r_c \\ - F^C & = & A w(r) \\ - F^D & = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v_{ij}}) \\ - F^R & = & \sigma w(r) \alpha (\Delta t)^{-1/2} \\ - w(r) & = & 1 - r/r_c -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_dpd_conservative.jpg b/doc/src/Eqs/pair_dpd_conservative.jpg deleted file mode 100644 index aa0006caa2..0000000000 Binary files a/doc/src/Eqs/pair_dpd_conservative.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_dpd_conservative.tex b/doc/src/Eqs/pair_dpd_conservative.tex deleted file mode 100644 index db89b987aa..0000000000 --- a/doc/src/Eqs/pair_dpd_conservative.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} -\pagestyle{empty} -\begin{document} - -$$ -F^C = A \omega_{ij} \qquad \qquad r_{ij} < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_dpd_omega.jpg b/doc/src/Eqs/pair_dpd_omega.jpg deleted file mode 100644 index fd25f00f19..0000000000 Binary files a/doc/src/Eqs/pair_dpd_omega.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_dpd_omega.tex b/doc/src/Eqs/pair_dpd_omega.tex deleted file mode 100644 index fbd533abfa..0000000000 --- a/doc/src/Eqs/pair_dpd_omega.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} -\pagestyle{empty} -\begin{document} - -$$ - \omega_{ij} = 1 - \frac{r_{ij}}{r_{c}} -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_eam.jpg b/doc/src/Eqs/pair_eam.jpg deleted file mode 100644 index 95c86b4ced..0000000000 Binary files a/doc/src/Eqs/pair_eam.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_eam.tex b/doc/src/Eqs/pair_eam.tex deleted file mode 100644 index 2ea20b2198..0000000000 --- a/doc/src/Eqs/pair_eam.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E_i = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) + - \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij}) -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_eam_fs.jpg b/doc/src/Eqs/pair_eam_fs.jpg deleted file mode 100644 index fa72f8fc73..0000000000 Binary files a/doc/src/Eqs/pair_eam_fs.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_eam_fs.tex b/doc/src/Eqs/pair_eam_fs.tex deleted file mode 100644 index 32ca605e2e..0000000000 --- a/doc/src/Eqs/pair_eam_fs.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E_i = F_\alpha \left(\sum_{j \neq i}\ - \rho_{\alpha\beta} (r_{ij})\right) + - \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij}) -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_edip.jpg b/doc/src/Eqs/pair_edip.jpg deleted file mode 100644 index 3933280480..0000000000 Binary files a/doc/src/Eqs/pair_edip.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_edip.tex b/doc/src/Eqs/pair_edip.tex deleted file mode 100644 index 27f5dd9eec..0000000000 --- a/doc/src/Eqs/pair_edip.tex +++ /dev/null @@ -1,22 +0,0 @@ -\documentclass[12pt]{article} - -\usepackage{amssymb,amsmath} - -\begin{document} - -\begin{eqnarray*} -E & = & \sum_{j \ne i} \phi_{2}(R_{ij}, Z_{i}) + \sum_{j \ne i} \sum_{k \ne i,k > j} \phi_{3}(R_{ij}, R_{ik}, Z_{i}) \\ -\phi_{2}(r, Z) & = & A\left[\left(\frac{B}{r}\right)^{\rho} - e^{-\beta Z^2}\right]exp{\left(\frac{\sigma}{r-a}\right)} \\ -\phi_{3}(R_{ij}, R_{ik}, Z_i) & = & exp{\left(\frac{\gamma}{R_{ij}-a}\right)}exp{\left(\frac{\gamma}{R_{ik}-a}\right)}h(cos\theta_{ijk},Z_i) \\ -Z_i & = & \sum_{m \ne i} f(R_{im}) \qquad - f(r) = \begin{cases} - 1 & \quad ra - \end{cases} \\ -h(l,Z) & = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\ -Q(Z) & = & Q_0 e^{-\mu Z} \qquad \tau(Z) = u_1 + u_2 (u_3 e^{-u_4 Z} - e^{-2u_4 Z}) -\end{eqnarray*} - -\end{document} - diff --git a/doc/src/Eqs/pair_eim1.jpg b/doc/src/Eqs/pair_eim1.jpg deleted file mode 100644 index c243120b2a..0000000000 Binary files a/doc/src/Eqs/pair_eim1.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_eim1.tex b/doc/src/Eqs/pair_eim1.tex deleted file mode 100644 index bfa5b6ebc4..0000000000 --- a/doc/src/Eqs/pair_eim1.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E = \frac{1}{2} \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \phi_{ij} \left(r_{ij}\right) + \sum_{i=1}^{N}E_i\left(q_i,\sigma_i\right) -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_eim2.jpg b/doc/src/Eqs/pair_eim2.jpg deleted file mode 100644 index 4896f658f1..0000000000 Binary files a/doc/src/Eqs/pair_eim2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_eim2.tex b/doc/src/Eqs/pair_eim2.tex deleted file mode 100644 index d8c4181342..0000000000 --- a/doc/src/Eqs/pair_eim2.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -q_i & = & \sum_{j=i_1}^{i_N} \eta_{ji}\left(r_{ij}\right) \\ -\sigma_i & = & \sum_{j=i_1}^{i_N} q_j \cdot \psi_{ij} \left(r_{ij}\right) \\ -E_i\left(q_i,\sigma_i\right) & = & \frac{1}{2} \cdot q_i \cdot \sigma_i -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_eim3.jpg b/doc/src/Eqs/pair_eim3.jpg deleted file mode 100644 index 57366bc15d..0000000000 Binary files a/doc/src/Eqs/pair_eim3.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_eim3.tex b/doc/src/Eqs/pair_eim3.tex deleted file mode 100644 index 84343c6acf..0000000000 --- a/doc/src/Eqs/pair_eim3.tex +++ /dev/null @@ -1,25 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -\phi_{ij}\left(r\right) = \left\{ \begin{array}{lr} -\left[\frac{E_{b,ij}\beta_{ij}}{\beta_{ij}-\alpha_{ij}}\exp\left(-\alpha_{ij} \frac{r-r_{e,ij}}{r_{e,ij}}\right)-\frac{E_{b,ij}\alpha_{ij}}{\beta_{ij}-\alpha_{ij}}\exp\left(-\beta_{ij} \frac{r-r_{e,ij}}{r_{e,ij}}\right)\right]f_c\left(r,r_{e,ij},r_{c,\phi,ij}\right),& p_{ij}=1 \\ -\left[\frac{E_{b,ij}\beta_{ij}}{\beta_{ij}-\alpha_{ij}} \left(\frac{r_{e,ij}}{r}\right)^{\alpha_{ij}} -\frac{E_{b,ij}\alpha_{ij}}{\beta_{ij}-\alpha_{ij}} \left(\frac{r_{e,ij}}{r}\right)^{\beta_{ij}}\right]f_c\left(r,r_{e,ij},r_{c,\phi,ij}\right),& p_{ij}=2 -\end{array} -\right. -\end{eqnarray*} - -$$ -\eta_{ji} = A_{\eta,ij}\left(\chi_j-\chi_i\right)f_c\left(r,r_{s,\eta,ij},r_{c,\eta,ij}\right) -$$ - -$$ -\psi_{ij}\left(r\right) = A_{\psi,ij}\exp\left(-\zeta_{ij}r\right)f_c\left(r,r_{s,\psi,ij},r_{c,\psi,ij}\right) -$$ - -$$ -f_{c}\left(r,r_p,r_c\right) = 0.510204 erfc\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204 -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_gauss.jpg b/doc/src/Eqs/pair_gauss.jpg deleted file mode 100644 index 97c2f0ecb2..0000000000 Binary files a/doc/src/Eqs/pair_gauss.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_gauss.tex b/doc/src/Eqs/pair_gauss.tex deleted file mode 100644 index ed38e13943..0000000000 --- a/doc/src/Eqs/pair_gauss.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} -\pagestyle{empty} -\begin{document} - -$$ - E = - A \exp(-B r^2) \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_gauss_cut.jpg b/doc/src/Eqs/pair_gauss_cut.jpg deleted file mode 100644 index e47bb8cc06..0000000000 Binary files a/doc/src/Eqs/pair_gauss_cut.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_gauss_cut.tex b/doc/src/Eqs/pair_gauss_cut.tex deleted file mode 100644 index 5d0bb430f3..0000000000 --- a/doc/src/Eqs/pair_gauss_cut.tex +++ /dev/null @@ -1,8 +0,0 @@ -\documentclass[12pt]{article} -\pagestyle{empty} -\begin{document} - -\begin{eqnarray*} - E = & \frac{H}{\sigma_h\sqrt{2\pi}} \exp\left[-\frac{(r-r_{mh})^2}{2\sigma_h^2}\right] -\end{eqnarray*} -\end{document} diff --git a/doc/src/Eqs/pair_gayberne.jpg b/doc/src/Eqs/pair_gayberne.jpg deleted file mode 100644 index e9b1f3ca93..0000000000 Binary files a/doc/src/Eqs/pair_gayberne.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_gayberne.tex b/doc/src/Eqs/pair_gayberne.tex deleted file mode 100644 index d3c199e826..0000000000 --- a/doc/src/Eqs/pair_gayberne.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ U ( \mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12} ) = U_r ( -\mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12}, \gamma ) \cdot \eta_{12} ( -\mathbf{A}_1, \mathbf{A}_2, \upsilon ) \cdot \chi_{12} ( \mathbf{A}_1, -\mathbf{A}_2, \mathbf{r}_{12}, \mu ) $$ - -$$ U_r = 4 \epsilon ( \varrho^{12} - \varrho^6) $$ - -$$ \varrho = \frac{\sigma}{ h_{12} + \gamma \sigma} $$ - -\end{document} diff --git a/doc/src/Eqs/pair_gayberne2.jpg b/doc/src/Eqs/pair_gayberne2.jpg deleted file mode 100644 index a4e6c6f70f..0000000000 Binary files a/doc/src/Eqs/pair_gayberne2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_gayberne2.tex b/doc/src/Eqs/pair_gayberne2.tex deleted file mode 100644 index 6efb755774..0000000000 --- a/doc/src/Eqs/pair_gayberne2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ \epsilon_a = \sigma \cdot { \frac{a}{ b \cdot c } }; \epsilon_b = -\sigma \cdot { \frac{b}{ a \cdot c } }; \epsilon_c = \sigma \cdot { -\frac{c}{ a \cdot b } } $$ - -\end{document} diff --git a/doc/src/Eqs/pair_gran_hertz.jpg b/doc/src/Eqs/pair_gran_hertz.jpg deleted file mode 100644 index 733875fee6..0000000000 Binary files a/doc/src/Eqs/pair_gran_hertz.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_gran_hertz.tex b/doc/src/Eqs/pair_gran_hertz.tex deleted file mode 100644 index d6e09493b2..0000000000 --- a/doc/src/Eqs/pair_gran_hertz.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - F_{hz} = \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}} F_{hk} = - \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}} - \Big[ (k_n \delta \mathbf{n}_{ij} - - m_{\mbox{\scriptsize{eff}}} \: \gamma_n \mathbf{ v}_n) - - (k_t \mathbf{ \Delta s}_t + - m_{\mbox{\scriptsize{eff}}} \: \gamma_t \mathbf{v}_t) \Big] -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_gran_hooke.jpg b/doc/src/Eqs/pair_gran_hooke.jpg deleted file mode 100644 index 36f34db6c6..0000000000 Binary files a/doc/src/Eqs/pair_gran_hooke.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_gran_hooke.tex b/doc/src/Eqs/pair_gran_hooke.tex deleted file mode 100644 index e1901e66a3..0000000000 --- a/doc/src/Eqs/pair_gran_hooke.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - F_{hk} = (k_n \delta \mathbf{n}_{ij} - - m_{\mbox{\scriptsize{eff}}} \gamma_n\mathbf{ v}_n) - - (k_t \mathbf{ \Delta s}_t + - m_{\mbox{\scriptsize{eff}}} \gamma_t \mathbf{v}_t) -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_gromacs.jpg b/doc/src/Eqs/pair_gromacs.jpg deleted file mode 100644 index 885c059e65..0000000000 Binary files a/doc/src/Eqs/pair_gromacs.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_gromacs.tex b/doc/src/Eqs/pair_gromacs.tex deleted file mode 100644 index 88dbe15909..0000000000 --- a/doc/src/Eqs/pair_gromacs.tex +++ /dev/null @@ -1,17 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -E_{LJ} & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] + S_{LJ}(r) - \qquad r < r_c \\ -E_C & = & \frac{C q_i q_j}{\epsilon r} + S_C(r) \qquad r < r_c \\ -S(r) & = & C \qquad r < r_1 \\ -S(r) & = & \frac{A}{3} (r - r_1)^3 + \frac{B}{4} (r - r_1)^4 + C \qquad r_1 < r < r_c \\ -A & = & (-3 E'(r_c) + (r_c - r_1) E''(r_c))/(r_c - r_1)^2 \\ -B & = & (2 E'(r_c) - (r_c - r_1) E''(r_c))/(r_c - r_1)^3 \\ -C & = & -E(r_c) + \frac{1}{2} (r_c - r_1) E'(r_c) - \frac{1}{12} (r_c - r_1)^2 E''(r_c)) \\ -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_hbond_dreiding.jpg b/doc/src/Eqs/pair_hbond_dreiding.jpg deleted file mode 100644 index b93044ed31..0000000000 Binary files a/doc/src/Eqs/pair_hbond_dreiding.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_hbond_dreiding.tex b/doc/src/Eqs/pair_hbond_dreiding.tex deleted file mode 100644 index 9663ee5608..0000000000 --- a/doc/src/Eqs/pair_hbond_dreiding.tex +++ /dev/null @@ -1,18 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} -\begin{eqnarray*} - E & = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_{\rm in} \\ - & = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ - & = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_{\rm out} \\ - LJ(r) & = & AR^{-12}-BR^{-10}cos^n\theta= - \epsilon\left\lbrace 5\left[ \frac{\sigma}{r}\right]^{12}- - 6\left[ \frac{\sigma}{r}\right]^{10} \right\rbrace cos^n\theta\\ - Morse(r) & = & D_0\left\lbrace \chi^2 - 2\chi\right\rbrace cos^n\theta= - D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} - \right\rbrace cos^n\theta \\ - S(r) & = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 - \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} - { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } -\end{eqnarray*} -\end{document} diff --git a/doc/src/Eqs/pair_lj.jpg b/doc/src/Eqs/pair_lj.jpg deleted file mode 100644 index 49cf7f5eb9..0000000000 Binary files a/doc/src/Eqs/pair_lj.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj.tex b/doc/src/Eqs/pair_lj.tex deleted file mode 100644 index 011fb8b769..0000000000 --- a/doc/src/Eqs/pair_lj.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] - \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_lj96.jpg b/doc/src/Eqs/pair_lj96.jpg deleted file mode 100644 index 6462de180e..0000000000 Binary files a/doc/src/Eqs/pair_lj96.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj96.tex b/doc/src/Eqs/pair_lj96.tex deleted file mode 100644 index e970624892..0000000000 --- a/doc/src/Eqs/pair_lj96.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} - - \left(\frac{\sigma}{r}\right)^6 \right] - \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_lj_cubic.jpg b/doc/src/Eqs/pair_lj_cubic.jpg deleted file mode 100644 index 69ec4f6e84..0000000000 Binary files a/doc/src/Eqs/pair_lj_cubic.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj_cubic.tex b/doc/src/Eqs/pair_lj_cubic.tex deleted file mode 100644 index e2e1b67dd7..0000000000 --- a/doc/src/Eqs/pair_lj_cubic.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E &=& u_{LJ}(r) \qquad r \leq r_s \\ - &=& u_{LJ}(r_s) + (r-r_s) u'_{LJ}(r_s) - \frac{1}{6} A_3 (r-r_s)^3 \qquad r_s < r \leq r_c \\ - &=& 0 \qquad r > r_c -\end{eqnarray*} - - -\end{document} diff --git a/doc/src/Eqs/pair_lj_expand.jpg b/doc/src/Eqs/pair_lj_expand.jpg deleted file mode 100644 index e274818892..0000000000 Binary files a/doc/src/Eqs/pair_lj_expand.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj_expand.tex b/doc/src/Eqs/pair_lj_expand.tex deleted file mode 100644 index 0aaa2f44d8..0000000000 --- a/doc/src/Eqs/pair_lj_expand.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = 4 \epsilon \left[ \left(\frac{\sigma}{r - \Delta}\right)^{12} - - \left(\frac{\sigma}{r - \Delta}\right)^6 \right] - \qquad r < r_c + \Delta -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_lj_sf.jpg b/doc/src/Eqs/pair_lj_sf.jpg deleted file mode 100644 index a702240003..0000000000 Binary files a/doc/src/Eqs/pair_lj_sf.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj_sf.tex b/doc/src/Eqs/pair_lj_sf.tex deleted file mode 100644 index e78e2ca75f..0000000000 --- a/doc/src/Eqs/pair_lj_sf.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\ - E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\ - \mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r) -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_lj_smooth.jpg b/doc/src/Eqs/pair_lj_smooth.jpg deleted file mode 100644 index d380fd345c..0000000000 Binary files a/doc/src/Eqs/pair_lj_smooth.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj_smooth.tex b/doc/src/Eqs/pair_lj_smooth.tex deleted file mode 100644 index 5aa5495c27..0000000000 --- a/doc/src/Eqs/pair_lj_smooth.tex +++ /dev/null @@ -1,15 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] - \qquad r < r_{in} \\ - F & = & C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3 - \qquad r_{in} < r < r_c -\end{eqnarray*} - -\end{document} - - diff --git a/doc/src/Eqs/pair_lj_smooth_linear.jpg b/doc/src/Eqs/pair_lj_smooth_linear.jpg deleted file mode 100644 index b0626abae1..0000000000 Binary files a/doc/src/Eqs/pair_lj_smooth_linear.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj_smooth_linear.tex b/doc/src/Eqs/pair_lj_smooth_linear.tex deleted file mode 100644 index b8980f8d25..0000000000 --- a/doc/src/Eqs/pair_lj_smooth_linear.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -\phi\left(r\right) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] \\ -E\left(r\right) & = & \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c -\end{eqnarray*} - -\end{document} - - diff --git a/doc/src/Eqs/pair_lj_soft.jpg b/doc/src/Eqs/pair_lj_soft.jpg deleted file mode 100644 index 856d6d5bbc..0000000000 Binary files a/doc/src/Eqs/pair_lj_soft.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj_soft.tex b/doc/src/Eqs/pair_lj_soft.tex deleted file mode 100644 index e32f11f0aa..0000000000 --- a/doc/src/Eqs/pair_lj_soft.tex +++ /dev/null @@ -1,15 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -\[ -E = \lambda^n 4 \epsilon -\left\{ - \frac{1}{ \left[ \alpha_{\mathrm{LJ}} (1-\lambda)^2 + - \left( \displaystyle\frac{r}{\sigma} \right)^6 \right]^2 } - - \frac{1}{ \alpha_{\mathrm{LJ}} (1-\lambda)^2 + - \left( \displaystyle\frac{r}{\sigma} \right)^6 } -\right\} \qquad r < r_c - \] - -\end{document} diff --git a/doc/src/Eqs/pair_lubricate.jpg b/doc/src/Eqs/pair_lubricate.jpg deleted file mode 100644 index 560591765a..0000000000 Binary files a/doc/src/Eqs/pair_lubricate.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lubricate.tex b/doc/src/Eqs/pair_lubricate.tex deleted file mode 100644 index c7e3dd96ed..0000000000 --- a/doc/src/Eqs/pair_lubricate.tex +++ /dev/null @@ -1,17 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - W & = & - a_{sq} | (v_1 - v_2) \bullet \mathbf{nn} |^2 - - a_{sh} | (\omega_1 + \omega_2) \bullet - (\mathbf{I} - \mathbf{nn}) - 2 \Omega_N |^2 - \\ - & & a_{pu} | (\omega_1 - \omega_2) \bullet (\mathbf{I} - \mathbf{nn}) |^2 - - a_{tw} | (\omega_1 - \omega_2) \bullet \mathbf{nn} |^2 \qquad r < r_c -\end{eqnarray*} - -$$ -\Omega_N = \mathbf{n} \times (v_1 - v_2) / r -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_mdf-1.jpg b/doc/src/Eqs/pair_mdf-1.jpg deleted file mode 100644 index fb0d9d644f..0000000000 Binary files a/doc/src/Eqs/pair_mdf-1.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_mdf-1.tex b/doc/src/Eqs/pair_mdf-1.tex deleted file mode 100644 index f3e6f36bcf..0000000000 --- a/doc/src/Eqs/pair_mdf-1.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E_{smooth}(r) = E(r)*f(r) -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_mdf-2.jpg b/doc/src/Eqs/pair_mdf-2.jpg deleted file mode 100644 index ae6358e5cc..0000000000 Binary files a/doc/src/Eqs/pair_mdf-2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_mdf-2.tex b/doc/src/Eqs/pair_mdf-2.tex deleted file mode 100644 index 9bb3be16c0..0000000000 --- a/doc/src/Eqs/pair_mdf-2.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\begin{array}{lcl} -f(r) = 1.0 &\mathrm{for}& r < r_m \\ -f(r) = (1 - x)^3*(1+3x+6x^2) &\mathrm{for}& r_m < r < r_{cut} \\ -f(r) = 0.0 &\mathrm{for}& r >= r_{cut} \\ -\end{array} -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_mdf-3.jpg b/doc/src/Eqs/pair_mdf-3.jpg deleted file mode 100644 index 45a1a68e05..0000000000 Binary files a/doc/src/Eqs/pair_mdf-3.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_mdf-3.tex b/doc/src/Eqs/pair_mdf-3.tex deleted file mode 100644 index 6ba1444466..0000000000 --- a/doc/src/Eqs/pair_mdf-3.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - x = \frac{(r-r_m)}{(r_{cut}-r_m)} -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_mdf-4.jpg b/doc/src/Eqs/pair_mdf-4.jpg deleted file mode 100644 index 05d08c01a0..0000000000 Binary files a/doc/src/Eqs/pair_mdf-4.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_mdf-4.tex b/doc/src/Eqs/pair_mdf-4.tex deleted file mode 100644 index 948be2e40f..0000000000 --- a/doc/src/Eqs/pair_mdf-4.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E(r) = 4\epsilon\Big[\Big(\frac{\sigma}{r}\Big)^{12} - \Big(\frac{\sigma}{r}\Big)^6\Big] -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_mdf-5.jpg b/doc/src/Eqs/pair_mdf-5.jpg deleted file mode 100644 index 9e047a50a8..0000000000 Binary files a/doc/src/Eqs/pair_mdf-5.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_mdf-5.tex b/doc/src/Eqs/pair_mdf-5.tex deleted file mode 100644 index 9b6a28c9d9..0000000000 --- a/doc/src/Eqs/pair_mdf-5.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E(r) = A e^{(-r/\rho)} -\frac{C}{r^6} -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_mdf-6.jpg b/doc/src/Eqs/pair_mdf-6.jpg deleted file mode 100644 index 54a08b25d6..0000000000 Binary files a/doc/src/Eqs/pair_mdf-6.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_mdf-6.tex b/doc/src/Eqs/pair_mdf-6.tex deleted file mode 100644 index 9f25e09bc7..0000000000 --- a/doc/src/Eqs/pair_mdf-6.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E(r) = \frac{A}{r^{12}} - \frac{A}{r^{6}} -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_meam.jpg b/doc/src/Eqs/pair_meam.jpg deleted file mode 100644 index f6de50a998..0000000000 Binary files a/doc/src/Eqs/pair_meam.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_meam.tex b/doc/src/Eqs/pair_meam.tex deleted file mode 100644 index cb9bb1702e..0000000000 --- a/doc/src/Eqs/pair_meam.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \sum_i \left\{ F_i(\bar{\rho}_i) - + \frac{1}{2} \sum_{i \neq j} \phi_{ij} (r_{ij}) \right\} -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_meam_spline.jpg b/doc/src/Eqs/pair_meam_spline.jpg deleted file mode 100644 index 29f1c72543..0000000000 Binary files a/doc/src/Eqs/pair_meam_spline.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_meam_spline.tex b/doc/src/Eqs/pair_meam_spline.tex deleted file mode 100644 index 55d42f801c..0000000000 --- a/doc/src/Eqs/pair_meam_spline.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E=\sum_{ij}\phi(r_{ij})+\sum_{i}U(\rho_{i}), -$$ - -$$ - \rho_{i}=\sum_{j}\rho(r_{ij})+\sum_{jk}f(r_{ij})f(r_{ik})g[\cos(\theta_{jik})] -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_meam_sw_spline.jpg b/doc/src/Eqs/pair_meam_sw_spline.jpg deleted file mode 100644 index 80078999d7..0000000000 Binary files a/doc/src/Eqs/pair_meam_sw_spline.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_meam_sw_spline.tex b/doc/src/Eqs/pair_meam_sw_spline.tex deleted file mode 100644 index 28abc433b5..0000000000 --- a/doc/src/Eqs/pair_meam_sw_spline.tex +++ /dev/null @@ -1,23 +0,0 @@ -\documentclass[showpacs,amsmath,amssymb,prb]{revtex4} - - -\usepackage{graphicx} -\usepackage{dcolumn} -\usepackage{bm} - -\newcommand{\etal}{{\em et al.}} -\newcommand{\OO}{{\mathcal{O}}} -\newtheorem{theorem}{Theorem} - -\begin{document} - -\begin{eqnarray} -E & = & E_{MEAM} + E_{SW} \nonumber \\ -E_{MEAM} & = & \sum _{IJ} \phi (r_{IJ}) + \sum _{I} U(\rho _I) \nonumber \\ -E_{SW} & = & \sum _{I} \sum _{JK} F(r_{IJ}) \, F(r_{IK}) \, G(\cos(\theta _{JIK})) \nonumber \\ -\rho _I & = & \sum _J \rho(r_{IJ}) + \sum _{JK} f(r_{IJ}) \, f(r_{IK}) \, g(\cos(\theta _{JIK})) \nonumber -\end{eqnarray} - -\end{document} - - diff --git a/doc/src/Eqs/pair_mgpt.jpg b/doc/src/Eqs/pair_mgpt.jpg deleted file mode 100644 index 2bede7f90f..0000000000 Binary files a/doc/src/Eqs/pair_mgpt.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_mgpt.tex b/doc/src/Eqs/pair_mgpt.tex deleted file mode 100644 index 9c314df916..0000000000 --- a/doc/src/Eqs/pair_mgpt.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega ) - + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega ) - + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega ) - + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega ) -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_mie.jpg b/doc/src/Eqs/pair_mie.jpg deleted file mode 100644 index 05a8221a93..0000000000 Binary files a/doc/src/Eqs/pair_mie.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_mie.tex b/doc/src/Eqs/pair_mie.tex deleted file mode 100644 index 2702ce9bcf..0000000000 --- a/doc/src/Eqs/pair_mie.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right] - \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_mie2.jpg b/doc/src/Eqs/pair_mie2.jpg deleted file mode 100644 index 216ca1554a..0000000000 Binary files a/doc/src/Eqs/pair_mie2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_mie2.tex b/doc/src/Eqs/pair_mie2.tex deleted file mode 100644 index 2ee9e9b34e..0000000000 --- a/doc/src/Eqs/pair_mie2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - C = \left(\frac{\gamma_{rep}}{\gamma_{rep}-\gamma_{att}}\right) \left(\frac{\gamma_{rep}}{\gamma_{att}}\right)^{\left(\frac{\gamma_{att}}{\gamma_{rep}-\gamma_{att}}\right)} -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_morse.jpg b/doc/src/Eqs/pair_morse.jpg deleted file mode 100644 index 5ebcdb2e1d..0000000000 Binary files a/doc/src/Eqs/pair_morse.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_morse.tex b/doc/src/Eqs/pair_morse.tex deleted file mode 100644 index 21204daa20..0000000000 --- a/doc/src/Eqs/pair_morse.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] - \qquad r < r_c -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_morse_smooth_linear.jpg b/doc/src/Eqs/pair_morse_smooth_linear.jpg deleted file mode 100644 index b951023609..0000000000 Binary files a/doc/src/Eqs/pair_morse_smooth_linear.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_morse_smooth_linear.tex b/doc/src/Eqs/pair_morse_smooth_linear.tex deleted file mode 100644 index f021d018f5..0000000000 --- a/doc/src/Eqs/pair_morse_smooth_linear.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} -\pagestyle{empty} - -\begin{document} - -\begin{eqnarray*} -\phi\left(r\right) & = & D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c \\ -E\left(r\right) & = & \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c -\end{eqnarray*} - -\end{document} - - diff --git a/doc/src/Eqs/pair_nb3b_harmonic.jpg b/doc/src/Eqs/pair_nb3b_harmonic.jpg deleted file mode 100644 index c8d23da042..0000000000 Binary files a/doc/src/Eqs/pair_nb3b_harmonic.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_nb3b_harmonic.tex b/doc/src/Eqs/pair_nb3b_harmonic.tex deleted file mode 100644 index 7f7aa8078e..0000000000 --- a/doc/src/Eqs/pair_nb3b_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\theta - \theta_0)^2 -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_nm.jpg b/doc/src/Eqs/pair_nm.jpg deleted file mode 100644 index 1e7fe0981c..0000000000 Binary files a/doc/src/Eqs/pair_nm.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_nm.tex b/doc/src/Eqs/pair_nm.tex deleted file mode 100644 index 4adf9331cc..0000000000 --- a/doc/src/Eqs/pair_nm.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ - E = \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - - n \left(\frac{r_0}{r}\right)^m \right] \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_resquared.jpg b/doc/src/Eqs/pair_resquared.jpg deleted file mode 100644 index c290c68dfd..0000000000 Binary files a/doc/src/Eqs/pair_resquared.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_resquared.tex b/doc/src/Eqs/pair_resquared.tex deleted file mode 100755 index e5c758aec0..0000000000 --- a/doc/src/Eqs/pair_resquared.tex +++ /dev/null @@ -1,7 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ A_{12} = 4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3)^2 $$ - -\end{document} diff --git a/doc/src/Eqs/pair_resquared2.jpg b/doc/src/Eqs/pair_resquared2.jpg deleted file mode 100644 index d2ed21a62a..0000000000 Binary files a/doc/src/Eqs/pair_resquared2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_resquared2.tex b/doc/src/Eqs/pair_resquared2.tex deleted file mode 100755 index ff2c3ca749..0000000000 --- a/doc/src/Eqs/pair_resquared2.tex +++ /dev/null @@ -1,7 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ A_{12} = 4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3) $$ - -\end{document} diff --git a/doc/src/Eqs/pair_resquared3.jpg b/doc/src/Eqs/pair_resquared3.jpg deleted file mode 100644 index 3916062a1c..0000000000 Binary files a/doc/src/Eqs/pair_resquared3.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_resquared3.tex b/doc/src/Eqs/pair_resquared3.tex deleted file mode 100755 index 136bcf73dc..0000000000 --- a/doc/src/Eqs/pair_resquared3.tex +++ /dev/null @@ -1,7 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ A_{12} = \epsilon_{\mathrm{LJ}} $$ - -\end{document} diff --git a/doc/src/Eqs/pair_resquared4.jpg b/doc/src/Eqs/pair_resquared4.jpg deleted file mode 100644 index 79ad067fa7..0000000000 Binary files a/doc/src/Eqs/pair_resquared4.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_resquared4.tex b/doc/src/Eqs/pair_resquared4.tex deleted file mode 100755 index 6efb755774..0000000000 --- a/doc/src/Eqs/pair_resquared4.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ \epsilon_a = \sigma \cdot { \frac{a}{ b \cdot c } }; \epsilon_b = -\sigma \cdot { \frac{b}{ a \cdot c } }; \epsilon_c = \sigma \cdot { -\frac{c}{ a \cdot b } } $$ - -\end{document} diff --git a/doc/src/Eqs/pair_smtbq1.jpg b/doc/src/Eqs/pair_smtbq1.jpg deleted file mode 100644 index 6bfb07b778..0000000000 Binary files a/doc/src/Eqs/pair_smtbq1.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_smtbq1.tex b/doc/src/Eqs/pair_smtbq1.tex deleted file mode 100755 index 21ae0e9a49..0000000000 --- a/doc/src/Eqs/pair_smtbq1.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -E_{tot} & = & E_{ES} + E_{OO} + E_{MO} \\ -E_{ES} & = & \sum_i{\Big[ \chi_{i}^{0}Q_i + \frac{1}{2}J_{i}^{0}Q_{i}^{2} + - \frac{1}{2} \sum_{j\neq i}{ J_{ij}(r_{ij})f_{cut}^{R_{coul}}(r_{ij})Q_i Q_j } \Big] } \\ -E_{OO} & = & \sum_{i,j}^{i,j = O}{\Bigg[Cexp( -\frac{r_{ij}}{\rho} ) - Df_{cut}^{r_1^{OO}r_2^{OO}}(r_{ij}) exp(Br_{ij})\Bigg]} \\ -E_{MO} & = & \sum_i{E_{cov}^{i} + \sum_{j\neq i}{ Af_{cut}^{r_{c1}r_{c2}}(r_{ij})exp\Big[-p(\frac{r_{ij}}{r_0} -1) \Big] } } \\ -\end{eqnarray*} - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_smtbq2.jpg b/doc/src/Eqs/pair_smtbq2.jpg deleted file mode 100644 index 0e20248788..0000000000 Binary files a/doc/src/Eqs/pair_smtbq2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_smtbq2.tex b/doc/src/Eqs/pair_smtbq2.tex deleted file mode 100755 index 8524c2586c..0000000000 --- a/doc/src/Eqs/pair_smtbq2.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -E_{cov}^{i(i=M,O)} & = & - \Bigg\{\eta_i(\mu \xi^{0})^2 f_{cut}^{r_{c1}r_{c2}}(r_{ij}) -\Bigg( \sum_{j(j=O,M)}{ exp[ -2q(\frac{r_{ij}}{r_0} - 1)] } \Bigg) -\delta Q_i \Big( 2\frac{n_0}{\eta_i} - \delta Q_i \Big) \Bigg\}^{1/2} \\ -\delta Q_i & = & | Q_i^{F} | - | Q_i | -\end{eqnarray*} - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_smtbq3.jpg b/doc/src/Eqs/pair_smtbq3.jpg deleted file mode 100644 index 1d60459165..0000000000 Binary files a/doc/src/Eqs/pair_smtbq3.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_smtbq3.tex b/doc/src/Eqs/pair_smtbq3.tex deleted file mode 100755 index 5bc6e465d1..0000000000 --- a/doc/src/Eqs/pair_smtbq3.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -\xi^0 & = & \frac{\xi_O}{m} = \frac{\xi_C}{n} \\ -\frac{\beta_O}{\sqrt{m}} & = & \frac{\beta_C}{\sqrt{n}} = \xi^0 \frac{\sqrt{m}+\sqrt{n}}{2}\\ -\end{eqnarray*} - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_snap.jpg b/doc/src/Eqs/pair_snap.jpg deleted file mode 100644 index af48357b5e..0000000000 Binary files a/doc/src/Eqs/pair_snap.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_snap.tex b/doc/src/Eqs/pair_snap.tex deleted file mode 100644 index d0a17de1fb..0000000000 --- a/doc/src/Eqs/pair_snap.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\alpha_i}_0 + \sum_{k=1}^K \beta_k^{\alpha_i} B_k^i -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_soft.jpg b/doc/src/Eqs/pair_soft.jpg deleted file mode 100644 index e8a654e1ed..0000000000 Binary files a/doc/src/Eqs/pair_soft.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_soft.tex b/doc/src/Eqs/pair_soft.tex deleted file mode 100644 index c2db15c2ee..0000000000 --- a/doc/src/Eqs/pair_soft.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = A \left[ 1 + \cos\left(\frac{\pi r}{r_c}\right) \right] - \qquad r < r_c -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_sph_ideal.jpg b/doc/src/Eqs/pair_sph_ideal.jpg deleted file mode 100644 index 370b75fe94..0000000000 Binary files a/doc/src/Eqs/pair_sph_ideal.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_sph_ideal.tex b/doc/src/Eqs/pair_sph_ideal.tex deleted file mode 100644 index 91c64f00bc..0000000000 --- a/doc/src/Eqs/pair_sph_ideal.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - p = (\gamma - 1) \rho e -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_sph_tait.jpg b/doc/src/Eqs/pair_sph_tait.jpg deleted file mode 100644 index 8bbfe80512..0000000000 Binary files a/doc/src/Eqs/pair_sph_tait.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_sph_tait.tex b/doc/src/Eqs/pair_sph_tait.tex deleted file mode 100644 index 4e1fa9cfed..0000000000 --- a/doc/src/Eqs/pair_sph_tait.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - p = B [(\frac{\rho}{\rho_0})^{\gamma} - 1] -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_srp1.jpg b/doc/src/Eqs/pair_srp1.jpg deleted file mode 100644 index bbbdc43e05..0000000000 Binary files a/doc/src/Eqs/pair_srp1.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_srp1.tex b/doc/src/Eqs/pair_srp1.tex deleted file mode 100644 index 45aa005d86..0000000000 --- a/doc/src/Eqs/pair_srp1.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - F^{SRP}_{ij} & = & C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c \\ -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_srp2.jpg b/doc/src/Eqs/pair_srp2.jpg deleted file mode 100644 index c5d20dc212..0000000000 Binary files a/doc/src/Eqs/pair_srp2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_srp2.tex b/doc/src/Eqs/pair_srp2.tex deleted file mode 100644 index 19cb19ae72..0000000000 --- a/doc/src/Eqs/pair_srp2.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - F_{i1}^{SRP} & = & F^{SRP}_{ij}(L) \\ - F_{i2}^{SRP} & = & F^{SRP}_{ij}(1-L) -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_sw.jpg b/doc/src/Eqs/pair_sw.jpg deleted file mode 100644 index f60f07fd27..0000000000 Binary files a/doc/src/Eqs/pair_sw.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_sw.tex b/doc/src/Eqs/pair_sw.tex deleted file mode 100644 index ebcc39d77b..0000000000 --- a/doc/src/Eqs/pair_sw.tex +++ /dev/null @@ -1,18 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E & = & \sum_i \sum_{j > i} \phi_2 (r_{ij}) + - \sum_i \sum_{j \neq i} \sum_{k > j} - \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) \\ - \phi_2(r_{ij}) & = & A_{ij} \epsilon_{ij} \left[ B_{ij} (\frac{\sigma_{ij}}{r_{ij}})^{p_{ij}} - - (\frac{\sigma_{ij}}{r_{ij}})^{q_{ij}} \right] - \exp \left( \frac{\sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) \\ - \phi_3(r_{ij},r_{ik},\theta_{ijk}) & = & \lambda_{ijk} \epsilon_{ijk} \left[ \cos \theta_{ijk} - - \cos \theta_{0ijk} \right]^2 - \exp \left( \frac{\gamma_{ij} \sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) - \exp \left( \frac{\gamma_{ik} \sigma_{ik}}{r_{ik} - a_{ik} \sigma_{ik}} \right) -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_tersoff.jpg b/doc/src/Eqs/pair_tersoff.jpg deleted file mode 100644 index bd3e147192..0000000000 Binary files a/doc/src/Eqs/pair_tersoff.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_tersoff_1.jpg b/doc/src/Eqs/pair_tersoff_1.jpg deleted file mode 100644 index 79600b499c..0000000000 Binary files a/doc/src/Eqs/pair_tersoff_1.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_tersoff_1.tex b/doc/src/Eqs/pair_tersoff_1.tex deleted file mode 100644 index 7d34712491..0000000000 --- a/doc/src/Eqs/pair_tersoff_1.tex +++ /dev/null @@ -1,24 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\ - f_C(r) & = & \left\{ \begin{array} {r@{\quad:\quad}l} - 1 & r < R - D \\ - \frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) & - R-D < r < R + D \\ - 0 & r > R + D - \end{array} \right. \\ - f_R(r) & = & A \exp (-\lambda_1 r) \\ - f_A(r) & = & -B \exp (-\lambda_2 r) \\ - b_{ij} & = & \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\ - \zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk}) - \exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\ - g(\theta) & = & \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} - - \frac{c^2}{\left[ d^2 + - (\cos \theta - \cos \theta_0)^2\right]} \right) -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_tersoff_2.jpg b/doc/src/Eqs/pair_tersoff_2.jpg deleted file mode 100644 index 6cb8778a09..0000000000 Binary files a/doc/src/Eqs/pair_tersoff_2.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_tersoff_2.tex b/doc/src/Eqs/pair_tersoff_2.tex deleted file mode 100644 index 7b5beb8ef3..0000000000 --- a/doc/src/Eqs/pair_tersoff_2.tex +++ /dev/null @@ -1,14 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -\lambda_1^{i,j} &=& \frac{1}{2}(\lambda_1^i + \lambda_1^j)\\ -\lambda_2^{i,j} &=& \frac{1}{2}(\lambda_2^i + \lambda_2^j)\\ -A_{i,j} &=& (A_{i}A_{j})^{1/2}\\ -B_{i,j} &=& \chi_{ij}(B_{i}B_{j})^{1/2}\\ -R_{i,j} &=& (R_{i}R_{j})^{1/2}\\ -S_{i,j} &=& (S_{i}S_{j})^{1/2}\\ -\end{eqnarray*} - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/pair_tersoff_mod.jpg b/doc/src/Eqs/pair_tersoff_mod.jpg deleted file mode 100644 index 2618943d85..0000000000 Binary files a/doc/src/Eqs/pair_tersoff_mod.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_tersoff_mod.tex b/doc/src/Eqs/pair_tersoff_mod.tex deleted file mode 100644 index eafc4fdeeb..0000000000 --- a/doc/src/Eqs/pair_tersoff_mod.tex +++ /dev/null @@ -1,24 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\ - f_C(r) & = & \left\{ \begin{array} {r@{\quad:\quad}l} - 1 & r < R - D \\ - \frac{1}{2} - \frac{9}{16} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) - \frac{1}{16} \sin \left( \frac{3\pi}{2} \frac{r-R}{D} \right) & - R-D < r < R + D \\ - 0 & r > R + D - \end{array} \right. \\ - f_R(r) & = & A \exp (-\lambda_1 r) \\ - f_A(r) & = & -B \exp (-\lambda_2 r) \\ - b_{ij} & = & \left( 1 + {\zeta_{ij}}^\eta \right)^{-\frac{1}{2n}} \\ - \zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk}) - \exp \left[ \alpha (r_{ij} - r_{ik})^\beta \right] \\ - g(\theta) & = & c_1 + g_o(\theta) g_a(\theta) \\ - g_o(\theta) & = & \frac{c_2 (h - \cos \theta)^2}{c_3 + (h - \cos \theta)^2} \\ - g_a(\theta) & = & 1 + c_4 \exp \left[ -c_5 (h - \cos \theta)^2 \right] \\ -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_tersoff_zbl.jpg b/doc/src/Eqs/pair_tersoff_zbl.jpg deleted file mode 100644 index 20d60d2256..0000000000 Binary files a/doc/src/Eqs/pair_tersoff_zbl.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_tersoff_zbl.tex b/doc/src/Eqs/pair_tersoff_zbl.tex deleted file mode 100644 index 902819aa1b..0000000000 --- a/doc/src/Eqs/pair_tersoff_zbl.tex +++ /dev/null @@ -1,33 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} & = & (1 - f_F(r_{ij})) V^{ZBL}_{ij} + f_F(r_{ij}) V^{Tersoff}_{ij} \\ -f_F(r_{ij}) & = & \frac{1}{1 + e^{-A_F(r_{ij} - r_C)}}\\ - \\ - \\ - V^{ZBL}_{ij} & = & \frac{1}{4\pi\epsilon_0} \frac{Z_1 Z_2 \,e^2}{r_{ij}} \phi(r_{ij}/a) \\ - a & = & \frac{0.8854\,a_0}{Z_{1}^{0.23} + Z_{2}^{0.23}}\\ - \phi(x) & = & 0.1818e^{-3.2x} + 0.5099e^{-0.9423x} + 0.2802e^{-0.4029x} + 0.02817e^{-0.2016x}\\ - \\ - \\ - V^{Tersoff}_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\ - f_C(r) & = & \left\{ \begin{array} {r@{\quad:\quad}l} - 1 & r < R - D \\ - \frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) & - R-D < r < R + D \\ - 0 & r > R + D - \end{array} \right. \\ - f_R(r) & = & A \exp (-\lambda_1 r) \\ - f_A(r) & = & -B \exp (-\lambda_2 r) \\ - b_{ij} & = & \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\ - \zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk}) - \exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\ - g(\theta) & = & \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} - - \frac{c^2}{\left[ d^2 + - (\cos \theta - \cos \theta_0)^2\right]} \right) -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_vashishta.jpg b/doc/src/Eqs/pair_vashishta.jpg deleted file mode 100644 index ca5f118a87..0000000000 Binary files a/doc/src/Eqs/pair_vashishta.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_vashishta.tex b/doc/src/Eqs/pair_vashishta.tex deleted file mode 100644 index b65056a254..0000000000 --- a/doc/src/Eqs/pair_vashishta.tex +++ /dev/null @@ -1,22 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - U & = & \sum_i^N \sum_{j > i}^N U_{ij}^{(2)} (r_{ij}) + - \sum_i^N \sum_{j \neq i}^N \sum_{k > j, k \neq i}^N - U_{ijk}^{(3)} (r_{ij}, r_{ik}, \theta_{ijk}) - \\ - U_{ij}^{(2)} (r) & = & \frac{H_{ij}}{r^{\eta_{ij}}} - + \frac{Z_i Z_j}{r}\exp(-r/\lambda_{1,ij}) - - \frac{D_{ij}}{r^4}\exp(-r/\lambda_{4,ij}) - - \frac{W_{ij}}{r^6}, r < r_{c,{ij}} - \\ - U_{ijk}^{(3)}(r_{ij},r_{ik},\theta_{ijk}) & = & B_{ijk} - \frac{\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} - {1+C_{ijk}\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} \times \\ -& & \exp \left( \frac{\gamma_{ij}}{r_{ij} - r_{0,ij}} \right) - \exp \left( \frac{\gamma_{ik}}{r_{ik} - r_{0,ik}} \right), r_{ij} < r_{0,ij}, r_{ik} < r_{0,ik} -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/pair_yukawa.jpg b/doc/src/Eqs/pair_yukawa.jpg deleted file mode 100644 index 103edc6043..0000000000 Binary files a/doc/src/Eqs/pair_yukawa.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_yukawa.tex b/doc/src/Eqs/pair_yukawa.tex deleted file mode 100644 index 382cf249a8..0000000000 --- a/doc/src/Eqs/pair_yukawa.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = A \frac{e^{- \kappa r}}{r} \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_yukawa_colloid.jpg b/doc/src/Eqs/pair_yukawa_colloid.jpg deleted file mode 100644 index 1d83624757..0000000000 Binary files a/doc/src/Eqs/pair_yukawa_colloid.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_yukawa_colloid.tex b/doc/src/Eqs/pair_yukawa_colloid.tex deleted file mode 100644 index dbdbbcd140..0000000000 --- a/doc/src/Eqs/pair_yukawa_colloid.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = \frac{A}{\kappa} e^{- \kappa (r - (r_i + r_j))} \qquad r < r_c -$$ - -\end{document} diff --git a/doc/src/Eqs/pair_zbl.jpg b/doc/src/Eqs/pair_zbl.jpg deleted file mode 100644 index 88656af5eb..0000000000 Binary files a/doc/src/Eqs/pair_zbl.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_zbl.tex b/doc/src/Eqs/pair_zbl.tex deleted file mode 100644 index 3d68dbed23..0000000000 --- a/doc/src/Eqs/pair_zbl.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E^{ZBL}_{ij} & = & \frac{1}{4\pi\epsilon_0} \frac{Z_i Z_j \,e^2}{r_{ij}} \phi(r_{ij}/a)+ S(r_{ij})\\ - a & = & \frac{0.46850}{Z_{i}^{0.23} + Z_{j}^{0.23}}\\ - \phi(x) & = & 0.18175e^{-3.19980x} + 0.50986e^{-0.94229x} + 0.28022e^{-0.40290x} + 0.02817e^{-0.20162x}\\ - \end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/polymorphic1.jpg b/doc/src/Eqs/polymorphic1.jpg deleted file mode 100644 index 4757cb7ad8..0000000000 Binary files a/doc/src/Eqs/polymorphic1.jpg and /dev/null differ diff --git a/doc/src/Eqs/polymorphic1.tex b/doc/src/Eqs/polymorphic1.tex deleted file mode 100644 index b4b925ccf8..0000000000 --- a/doc/src/Eqs/polymorphic1.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -E=\frac{1}{2}\sum_{i=1}^{i=N}\sum_{j=1}^{j=N}\left[\left(1-\delta_{ij}\right)\cdot U_{IJ}\left(r_{ij}\right)-\left(1-\eta_{ij}\right)\cdot F_{IJ}\left(r_{ij}\right)\cdot V_{IJ}\left(r_{ij}\right)\right] -$$ - -\end{document} diff --git a/doc/src/Eqs/polymorphic2.jpg b/doc/src/Eqs/polymorphic2.jpg deleted file mode 100644 index 05133f4849..0000000000 Binary files a/doc/src/Eqs/polymorphic2.jpg and /dev/null differ diff --git a/doc/src/Eqs/polymorphic2.tex b/doc/src/Eqs/polymorphic2.tex deleted file mode 100644 index 80b1c93821..0000000000 --- a/doc/src/Eqs/polymorphic2.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -X_{ij}=\sum_{k=i_1,k\neq i,j}^{i_N}W_{IK}\left(r_{ik}\right)\cdot G_{JIK}\left(\theta_{jik}\right)\cdot P_{IK}\left(\Delta r_{jik}\right) -\label{X_eq2} -$$ - -\end{document} diff --git a/doc/src/Eqs/polymorphic3.jpg b/doc/src/Eqs/polymorphic3.jpg deleted file mode 100644 index ba748e63c5..0000000000 Binary files a/doc/src/Eqs/polymorphic3.jpg and /dev/null differ diff --git a/doc/src/Eqs/polymorphic3.tex b/doc/src/Eqs/polymorphic3.tex deleted file mode 100644 index 71db8d81b0..0000000000 --- a/doc/src/Eqs/polymorphic3.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -\Delta r_{jik}=r_{ij}-\xi_{IJ}\cdot r_{ik} -\label{Dr_eq3} -$$ - -\end{document} diff --git a/doc/src/Eqs/polymorphic4.jpg b/doc/src/Eqs/polymorphic4.jpg deleted file mode 100644 index 7a094d6a21..0000000000 Binary files a/doc/src/Eqs/polymorphic4.jpg and /dev/null differ diff --git a/doc/src/Eqs/polymorphic4.tex b/doc/src/Eqs/polymorphic4.tex deleted file mode 100644 index b792df82a0..0000000000 --- a/doc/src/Eqs/polymorphic4.tex +++ /dev/null @@ -1,17 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -\left\{\begin{array}{l} -\eta_{ij}=\delta_{ij},\xi_{IJ}=0 \\ -U_{IJ}\left(r\right)=A_{IJ}\cdot\epsilon_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^q\cdot \left[B_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^{p-q}-1\right]\cdot exp\left(\frac{\sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ -V_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ -F_{IJ}\left(X\right)=-X \\ -P_{IJ}\left(\Delta r\right)=1 \\ -W_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ -G_{JIK}\left(\theta\right)=\left(cos\theta+\frac{1}{3}\right)^2 -\end{array}\right. -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/polymorphic5.jpg b/doc/src/Eqs/polymorphic5.jpg deleted file mode 100644 index 500238b2a9..0000000000 Binary files a/doc/src/Eqs/polymorphic5.jpg and /dev/null differ diff --git a/doc/src/Eqs/polymorphic5.tex b/doc/src/Eqs/polymorphic5.tex deleted file mode 100644 index a5451b98d6..0000000000 --- a/doc/src/Eqs/polymorphic5.tex +++ /dev/null @@ -1,17 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -\left\{\begin{array}{l} -\eta_{ij}=\delta_{ij},\xi_{IJ}=1 \\ -U_{IJ}\left(r\right)=\frac{D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{2S_{IJ}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\ -V_{IJ}\left(r\right)=\frac{S_{IJ}\cdot D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{\frac{2}{S_{IJ}}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\ -F_{IJ}\left(X\right)=\left(1+X\right)^{-\frac{1}{2}} \\ -P_{IJ}\left(\Delta r\right)=exp\left(2\mu_{IK}\cdot \Delta r\right) \\ -W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\ -G_{JIK}\left(\theta\right)=\gamma_{IK}\left[1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}\right] -\end{array}\right. -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/polymorphic6.jpg b/doc/src/Eqs/polymorphic6.jpg deleted file mode 100644 index 65ea78bf21..0000000000 Binary files a/doc/src/Eqs/polymorphic6.jpg and /dev/null differ diff --git a/doc/src/Eqs/polymorphic6.tex b/doc/src/Eqs/polymorphic6.tex deleted file mode 100644 index c8f9f2f25b..0000000000 --- a/doc/src/Eqs/polymorphic6.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} -f_{c,IJ}=\left\{\begin{array}{lr} -1, & r\leq r_{s,IJ} \\ -\frac{1}{2}+\frac{1}{2} cos \left[\frac{\pi \left(r-r_{s,IJ}\right)}{r_{c,IJ}-r_{s,IJ}}\right], & r_{s,IJ}