diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index f137ccffd9..ff86cd842a 100644 --- a/doc/src/Commands_all.txt +++ b/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, diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index 78fa9fbf87..81f088d3d3 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -39,6 +39,7 @@ Commands :h1 dump_molfile dump_netcdf dump_vtk + dynamical_matrix echo fix fix_modify diff --git a/doc/src/dynamical_matrix.txt b/doc/src/dynamical_matrix.txt new file mode 100644 index 0000000000..a7dc4e442e --- /dev/null +++ b/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 diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 5ae3456ad4..827cafed75 100644 --- a/doc/src/lammps.book +++ b/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 diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 8807b2d680..bbfdf946f4 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -625,8 +625,10 @@ dVx dW dx dy +dyn dyne dynes +dynmat Dyre Dzyaloshinskii Eaa diff --git a/src/USER-PHONON/README b/src/USER-PHONON/README index 2212eaaebd..b1ffcb9b09 100644 --- a/src/USER-PHONON/README +++ b/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.