integrate dynamical_matrix command into LAMMPS manual

doc/src/Commands_all.txt

@@ -54,6 +54,7 @@ An alphabetic list of all general LAMMPS commands.
 "dump netcdf"_dump_netcdf.html,
 "dump netcdf/mpiio"_dump_netcdf.html,
 "dump vtk"_dump_vtk.html,
+"dynamical_matrix"_dynamical_matrix.html,
 "echo"_echo.html,
 "fix"_fix.html,
 "fix_modify"_fix_modify.html,

doc/src/commands_list.txt

@@ -39,6 +39,7 @@ Commands :h1
    dump_molfile
    dump_netcdf
    dump_vtk
+   dynamical_matrix
    echo
    fix
    fix_modify

doc/src/dynamical_matrix.txt

@@ -0,0 +1,52 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+dynamical_matrix command :h3
+
+[Syntax:]
+
+dynamical_matrix group-ID style gamma args keyword value ... :pre
+
+group-ID = ID of group of atoms to displace :ulb,l
+style = {regular} or {eskm} :l
+gamma = finite different displacement length (distance units) :l
+one or more keyword/arg pairs may be appended :l
+  keyword = {file} or {binary}
+    {file} name = name of output file for the dynamical matrix
+    {binary} arg = {yes} or {no} or {gzip} :pre
+:ule
+
+[Examples:]
+
+dynamical_matrix 1 regular 0.000001
+dynamical_matrix 1 eskm 0.000001
+dynamical_matrix 3 regular 0.00004 file dynmat.dat
+dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre
+
+[Description:]
+
+Calculate the dynamical matrix of the selected group.
+
+[Restrictions:]
+
+The command collects the entire dynamical matrix a single MPI rank,
+so the memory requirements can be very significant for large systems.
+
+This command assumes a periodic system.
+
+This command is part of the USER-PHONON package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"fix phonon"_fix_phonon.html
+
+[Default:]
+
+The default settings are file = "dynmat.dyn", binary = no  

doc/src/lammps.book

@@ -157,6 +157,7 @@ dump_molfile.html
 dump_netcdf.html
 dump_vtk.html
 dump_cfg_uef.html
+dynamical_matrix.html
 echo.html
 group.html
 group2ndx.html

doc/utils/sphinx-config/false_positives.txt

@@ -625,8 +625,10 @@ dVx
 dW
 dx
 dy
+dyn
 dyne
 dynes
+dynmat
 Dyre
 Dzyaloshinskii
 Eaa

src/USER-PHONON/README

@@ -1,19 +1,24 @@
 This package contains a fix phonon command that calculates dynamical
-matrices, which can then be used to compute phonon dispersion
-relations, directly from molecular dynamics simulations.
+matrices from finite temperature MD simulations, which can then be
+used to compute phonon dispersion relations, directly from molecular
+dynamics simulations.
 
-See the doc page for the fix phonon command for detailed usage
-instructions.
+It also contains two commands to compute the dynamical matrix and
+the corresponding third order matrix at pre-optimized positions
+through finite differences.
+
+See the doc page for the fix phonon command or the dynamical_matrix
+third_order commands for detailed usage instructions.
 
 Use of this package requires building LAMMPS with FFT suppport, as
 described in doc/Section_start.html.
 
-There are example scripts for using this package in
+There are example scripts for using commands in this package in
 examples/USER/phonon.
 
 There is an auxiliary post-processing tool in tools/phonon that will
 compute phonon frequencies and dispersion relations from the dynamical
-matrices output by this command.
+matrices output by the fix phonon command.
 
 There is also an alternative code, dump2phonon, available which enables
 one to use the functions of fix-phonon by reading in atom-style dump
@@ -21,6 +26,9 @@ files of lammps (which can be converted from the trajectories of any
 other MD code):
    https://github.com/lingtikong/dump2phonon
 
-The person who created this package is Ling-Ti Kong (konglt at
+The person who created fix phonon is Ling-Ti Kong (konglt at
 sjtu.edu.cn) at Shanghai Jiao Tong University.  Contact him directly
 if you have questions.
+
+The person who created dynamical_matrix and third_order is
+Charlie Sievers at UC Davis.