Merge pull request #1525 from akohlmey/collected-small-changes

Collected small changes and fixes for the next patch

doc/src/Commands_all.txt

@@ -50,11 +50,11 @@ An alphabetic list of all general LAMMPS commands.
 "dump"_dump.html,
 "dump adios"_dump_adios.html,
 "dump image"_dump_image.html,
-"dump_modify"_dump_modify.html,
 "dump movie"_dump_image.html,
 "dump netcdf"_dump_netcdf.html,
 "dump netcdf/mpiio"_dump_netcdf.html,
 "dump vtk"_dump_vtk.html,
+"dump_modify"_dump_modify.html,
 "dynamical_matrix"_dynamical_matrix.html,
 "echo"_echo.html,
 "fix"_fix.html,

doc/src/Commands_pair.txt

@@ -222,6 +222,8 @@ OPT.
 "sph/rhosum"_pair_sph_rhosum.html,
 "sph/taitwater"_pair_sph_taitwater.html,
 "sph/taitwater/morris"_pair_sph_taitwater_morris.html,
+"spin/dipole/cut"_pair_spin_dipole.html,
+"spin/dipole/long"_pair_spin_dipole.html,
 "spin/dmi"_pair_spin_dmi.html,
 "spin/exchange"_pair_spin_exchange.html,
 "spin/magelec"_pair_spin_magelec.html,

doc/src/Eqs/angle_class2_p6.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/angle_cosine_buck6d.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/improper_inversion_harmonic.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E = K \left(\theta - \theta_0\right)^2
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/pair_agni.tex

@@ -0,0 +1,18 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+  F_i^u & = & \sum_t^{N_t}\alpha_t \cdot \exp\left[-\frac{\left(d_{i,t}^u\right)^2}{2l^2}\right] \\
+  d_{i,t}^u & = & \left|\left| V_i^u(\eta) - V_t^u(\eta) \right|\right| \\
+  V_i^u(\eta) & = & \sum_{j \neq i}\frac{r^u_{ij}}{r_{ij}} \cdot e^{-\left(\frac{r_{ij}}{\eta} \right)^2} \cdot f_d\left(r_{ij}\right) \\
+  f_d\left(r_{ij}\right) & = & \frac{1}{2} \left[\cos\left(\frac{\pi r_{ij}}{R_c}\right) + 1 \right]
+\end{eqnarray*}
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/pair_buck6d.tex

@@ -1,6 +1,7 @@
 \documentclass[12pt]{article}
 
 \begin{document}
+\pagestyle{empty}
 
 \begin{eqnarray*}
   E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\

doc/src/Eqs/pair_coul_gauss.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Packages_details.txt

@@ -911,6 +911,8 @@ the usual manner via MD.  Various pair, fix, and compute styles.
 
 src/SPIN: filenames -> commands
 "Howto spins"_Howto_spins.html
+"pair_style spin/dipole/cut"_pair_spin_dipole.html
+"pair_style spin/dipole/long"_pair_spin_dipole.html
 "pair_style spin/dmi"_pair_spin_dmi.html
 "pair_style spin/exchange"_pair_spin_exchange.html
 "pair_style spin/magelec"_pair_spin_magelec.html

doc/src/lammps.book

@@ -647,6 +647,7 @@ pair_sph_lj.html
 pair_sph_rhosum.html
 pair_sph_taitwater.html
 pair_sph_taitwater_morris.html
+pair_spin_dipole.html
 pair_spin_dmi.html
 pair_spin_exchange.html
 pair_spin_magelec.html

doc/src/pair_modify.txt

@@ -13,7 +13,8 @@ pair_modify command :h3
 pair_modify keyword values ... :pre
 
 one or more keyword/value pairs may be listed :ulb,l
-keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l
+keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner}
+or {tabinner/disp} or {tail} or {compute} or {nofdotr} :l
   {pair} values = sub-style N {special} which wt1 wt2 wt3
                or sub-style N {compute/tally} flag
     sub-style = sub-style of "pair hybrid"_pair_hybrid.html
@@ -33,7 +34,8 @@ keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or
   {tabinner/disp} value = cutoff
     cutoff = inner cutoff at which to begin table (distance units)
   {tail} value = {yes} or {no}
-  {compute} value = {yes} or {no} :pre
+  {compute} value = {yes} or {no}
+  {nofdotr} :pre
 :ule
 
 [Examples:]
@@ -212,6 +214,10 @@ a pair style will not work, because the
 "kspace_style"_kspace_style.html command requires a Kspace-compatible
 pair style be defined.
 
+The {nofdotr} keyword allows to disable an optimization that computes
+the global stress tensor from the total forces and atom positions rather
+than from summing forces between individual pairs of atoms.
+
 :line
 
 The {special} keyword allows to override the 1-2, 1-3, and 1-4

doc/src/pair_style.txt

@@ -284,6 +284,8 @@ accelerated styles exist.
 "sph/rhosum"_pair_sph_rhosum.html -
 "sph/taitwater"_pair_sph_taitwater.html -
 "sph/taitwater/morris"_pair_sph_taitwater_morris.html -
+"spin/dipole/cut"_pair_spin_dipole.html -
+"spin/dipole/long"_pair_spin_dipole.html -
 "spin/dmi"_pair_spin_dmi.html -
 "spin/exchange"_pair_spin_exchange.html -
 "spin/magelec"_pair_spin_magelec.html -

doc/src/pairs.txt

@@ -105,6 +105,7 @@ Pair Styles :h1
    pair_sph_rhosum
    pair_sph_taitwater
    pair_sph_taitwater_morris
+   pair_spin_dipole
    pair_spin_dmi
    pair_spin_exchange
    pair_spin_magelec