From cdf2f66c0a75a82953cb38b509726d455742f431 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 31 Jan 2020 14:03:52 -0500 Subject: [PATCH] delete empty lines at the end of files --- doc/src/Build.rst | 2 -- doc/src/Build_basics.rst | 2 -- doc/src/Build_cmake.rst | 2 -- doc/src/Build_development.rst | 3 --- doc/src/Build_extras.rst | 2 -- doc/src/Build_link.rst | 2 -- doc/src/Build_make.rst | 2 -- doc/src/Build_package.rst | 2 -- doc/src/Build_settings.rst | 2 -- doc/src/Build_windows.rst | 2 -- doc/src/Commands_all.rst | 1 - doc/src/Commands_compute.rst | 1 - doc/src/Commands_removed.rst | 2 -- doc/src/Errors.rst | 2 -- doc/src/Errors_bugs.rst | 2 -- doc/src/Errors_common.rst | 2 -- doc/src/Errors_messages.rst | 4 ---- doc/src/Errors_warnings.rst | 4 ---- doc/src/Examples.rst | 4 ---- doc/src/Howto.rst | 2 -- doc/src/Howto_2d.rst | 2 -- doc/src/Howto_barostat.rst | 2 -- doc/src/Howto_bash.rst | 2 -- doc/src/Howto_bioFF.rst | 2 -- doc/src/Howto_body.rst | 2 -- 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doc/src/pair_lj96.rst | 2 -- doc/src/pair_lj_cubic.rst | 2 -- doc/src/pair_lj_expand.rst | 2 -- doc/src/pair_lj_long.rst | 2 -- doc/src/pair_lj_smooth.rst | 2 -- doc/src/pair_lj_smooth_linear.rst | 2 -- doc/src/pair_lj_switch3_coulgauss_long.rst | 2 -- doc/src/pair_local_density.rst | 2 -- doc/src/pair_lubricate.rst | 2 -- doc/src/pair_lubricateU.rst | 2 -- doc/src/pair_mdf.rst | 2 -- doc/src/pair_meam_spline.rst | 2 -- doc/src/pair_meam_sw_spline.rst | 2 -- doc/src/pair_meamc.rst | 2 -- doc/src/pair_meso.rst | 2 -- doc/src/pair_mesocnt.rst | 2 -- doc/src/pair_mgpt.rst | 2 -- doc/src/pair_mie.rst | 2 -- doc/src/pair_mm3_switch3_coulgauss_long.rst | 2 -- doc/src/pair_modify.rst | 2 -- doc/src/pair_momb.rst | 2 -- doc/src/pair_morse.rst | 2 -- doc/src/pair_multi_lucy.rst | 2 -- doc/src/pair_multi_lucy_rx.rst | 2 -- doc/src/pair_nb3b_harmonic.rst | 2 -- doc/src/pair_nm.rst | 2 -- doc/src/pair_none.rst | 2 -- doc/src/pair_oxdna.rst | 2 -- doc/src/pair_oxdna2.rst | 2 -- doc/src/pair_peri.rst | 2 -- doc/src/pair_polymorphic.rst | 2 -- doc/src/pair_python.rst | 2 -- doc/src/pair_quip.rst | 2 -- doc/src/pair_reaxc.rst | 2 -- doc/src/pair_resquared.rst | 2 -- doc/src/pair_sdk.rst | 2 -- doc/src/pair_sdpd_taitwater_isothermal.rst | 2 -- doc/src/pair_smd_hertz.rst | 3 --- doc/src/pair_smd_tlsph.rst | 3 --- doc/src/pair_smd_triangulated_surface.rst | 3 --- doc/src/pair_smd_ulsph.rst | 3 --- doc/src/pair_smtbq.rst | 2 -- doc/src/pair_snap.rst | 2 -- doc/src/pair_soft.rst | 2 -- doc/src/pair_sph_heatconduction.rst | 2 -- doc/src/pair_sph_idealgas.rst | 2 -- doc/src/pair_sph_lj.rst | 2 -- doc/src/pair_sph_rhosum.rst | 2 -- doc/src/pair_sph_taitwater.rst | 2 -- doc/src/pair_sph_taitwater_morris.rst | 2 -- doc/src/pair_spin_dipole.rst | 2 -- doc/src/pair_spin_dmi.rst | 2 -- doc/src/pair_spin_magelec.rst | 2 -- doc/src/pair_srp.rst | 2 -- doc/src/pair_style.rst | 2 -- doc/src/pair_sw.rst | 2 -- doc/src/pair_table.rst | 2 -- doc/src/pair_table_rx.rst | 2 -- doc/src/pair_tersoff.rst | 2 -- doc/src/pair_tersoff_mod.rst | 2 -- doc/src/pair_tersoff_zbl.rst | 2 -- doc/src/pair_thole.rst | 2 -- doc/src/pair_tri_lj.rst | 2 -- doc/src/pair_ufm.rst | 2 -- doc/src/pair_vashishta.rst | 2 -- doc/src/pair_write.rst | 2 -- doc/src/pair_yukawa.rst | 2 -- doc/src/pair_yukawa_colloid.rst | 2 -- doc/src/pair_zbl.rst | 2 -- doc/src/pair_zero.rst | 2 -- doc/src/partition.rst | 2 -- doc/src/prd.rst | 2 -- doc/src/print.rst | 2 -- doc/src/processors.rst | 2 -- doc/src/python.rst | 2 -- doc/src/quit.rst | 2 -- doc/src/read_data.rst | 2 -- doc/src/read_dump.rst | 4 ---- doc/src/read_restart.rst | 2 -- doc/src/region.rst | 2 -- doc/src/replicate.rst | 2 -- doc/src/rerun.rst | 2 -- doc/src/reset_ids.rst | 2 -- doc/src/reset_timestep.rst | 2 -- doc/src/restart.rst | 2 -- doc/src/run.rst | 2 -- doc/src/run_style.rst | 2 -- doc/src/server.rst | 2 -- doc/src/server_mc.rst | 2 -- doc/src/server_md.rst | 2 -- doc/src/set.rst | 2 -- doc/src/shell.rst | 2 -- doc/src/special_bonds.rst | 2 -- doc/src/suffix.rst | 2 -- doc/src/tad.rst | 2 -- doc/src/temper.rst | 2 -- doc/src/temper_grem.rst | 2 -- doc/src/temper_npt.rst | 2 -- doc/src/thermo.rst | 2 -- doc/src/thermo_modify.rst | 2 -- doc/src/thermo_style.rst | 2 -- doc/src/third_order.rst | 2 -- doc/src/timer.rst | 2 -- doc/src/timestep.rst | 2 -- doc/src/uncompute.rst | 2 -- doc/src/undump.rst | 2 -- doc/src/unfix.rst | 2 -- doc/src/units.rst | 2 -- doc/src/variable.rst | 2 -- doc/src/velocity.rst | 2 -- doc/src/write_coeff.rst | 2 -- doc/src/write_data.rst | 2 -- doc/src/write_dump.rst | 2 -- 693 files changed, 1406 deletions(-) diff --git a/doc/src/Build.rst b/doc/src/Build.rst index 750f6df68e..bd218c8165 100644 --- a/doc/src/Build.rst +++ b/doc/src/Build.rst @@ -21,5 +21,3 @@ as described on the :doc:`Install ` doc page. Build_extras Build_windows Build_development - - diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index bb2c522c45..832b6c3f02 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -430,5 +430,3 @@ you want to copy files to is protected. There is no "install" option in the src/Makefile for LAMMPS. If you wish to do this you will need to first build LAMMPS, then manually copy the desired LAMMPS files to the appropriate system directories. - - diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index 394ed2c130..ce103d978a 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -238,5 +238,3 @@ enough version, you can download the latest version at `https://cmake.org/download/ `_. Instructions on how to install it on various platforms can be found `on this page `_. - - diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index 61ca21b188..ef06a27035 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -112,6 +112,3 @@ These reports require GCOVR to be installed. The easiest way to do this to insta .. parsed-literal:: pip install git+https://github.com/gcovr/gcovr.git - - - diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index e59d05d25c..d2d47f694c 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1414,5 +1414,3 @@ the settings are not valid for your system, check if one of the other lib/vtk/Makefile.lammps.\* files is compatible and copy it to Makefile.lammps. If none of the provided files work, you will need to edit the Makefile.lammps file. See lib/vtk/README for details. - - diff --git a/doc/src/Build_link.rst b/doc/src/Build_link.rst index c79536e041..1478eceaf8 100644 --- a/doc/src/Build_link.rst +++ b/doc/src/Build_link.rst @@ -84,5 +84,3 @@ See the sample codes in examples/COUPLE/simple for examples of C++ and C and Fortran codes that invoke LAMMPS through its library interface. Other examples in the COUPLE directory use coupling ideas discussed on the :doc:`Howto couple ` doc page. - - diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst index 62ed156eeb..c7db5dbb52 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -87,5 +87,3 @@ settings may become outdated: make kokkos_omp # build with the KOKKOS package for OpenMP make kokkos_cuda_mpi # build with the KOKKOS package for GPUs make kokkos_phi # build with the KOKKOS package for KNLs - - diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index 22ae9ba82c..7f2fe7f8ef 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -258,5 +258,3 @@ sub-directories with src files. Type "make package-diff" to list all differences between pairs of files in both the src dir and a package dir. - - diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index a4cc65db65..6cc849803e 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -488,5 +488,3 @@ e.g. to Python. .. parsed-literal:: LMP_INC = -DLAMMPS_EXCEPTIONS - - diff --git a/doc/src/Build_windows.rst b/doc/src/Build_windows.rst index 190bcf00f8..fd76f3ac80 100644 --- a/doc/src/Build_windows.rst +++ b/doc/src/Build_windows.rst @@ -104,5 +104,3 @@ Support for the Visual C++ compilers is currently not available. The CMake build system is capable of creating suitable a Visual Studio style build environment, but the LAMMPS code itself is not fully ported to support Visual C++. Volunteers to take on this task are welcome. - - diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index 6e87ffbad6..721c5ece37 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -136,4 +136,3 @@ An alphabetic list of all general LAMMPS commands. * :doc:`write_data ` * :doc:`write_dump ` * :doc:`write_restart ` - diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index 79f0e8d83f..ad5e4f10bf 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -163,4 +163,3 @@ KOKKOS, o = USER-OMP, t = OPT. * :doc:`vcm/chunk ` * :doc:`voronoi/atom ` * :doc:`xrd ` - diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index e40869294e..b749467d13 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -60,5 +60,3 @@ LAMMPS executable directly instead of having a separate tool. A combination of the commands :doc:`read_restart ` and :doc:`write_data ` can be used to the same effect. For added convenience this conversion can also be triggered by :doc:`command line flags ` - - diff --git a/doc/src/Errors.rst b/doc/src/Errors.rst index 32f0a849b1..9c53467719 100644 --- a/doc/src/Errors.rst +++ b/doc/src/Errors.rst @@ -15,5 +15,3 @@ additional details for many of them. Errors_bugs Errors_messages Errors_warnings - - diff --git a/doc/src/Errors_bugs.rst b/doc/src/Errors_bugs.rst index 83f101fa89..9822b7e60f 100644 --- a/doc/src/Errors_bugs.rst +++ b/doc/src/Errors_bugs.rst @@ -25,5 +25,3 @@ causing the problem. .. note:: this page needs to have GitHub issues info added - - diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index 835dcdd8fa..b8832d8f34 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -121,5 +121,3 @@ implementations handle buffering of messages. If the code hangs without an error message, it may be that you need to specify an MPI setting or two (usually via an environment variable) to enable buffering or boost the sizes of messages that can be buffered. - - diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index e4b438e421..bbe84de065 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -8415,7 +8415,3 @@ keyword to allow for additional bonds to be formed *Zero-length lattice orient vector* Self-explanatory. - - - - diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index 4d1681d889..4a0b21356a 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -796,7 +796,3 @@ This will most likely cause errors in kinetic fluctuations. *pair style reax is now deprecated and will soon be retired. Users should switch to pair\_style reax/c* Self-explanatory. - - - - diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 8916b3b4fe..cd4937ab03 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -228,7 +228,3 @@ instructions. See the :doc:`Packages\_details ` doc page for more info on specific USER packages. .. _openkim: https://openkim.org - - - - diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index 4b9fd76760..3a36c82674 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -99,5 +99,3 @@ Packages howto Howto_drude2 Howto_manifold Howto_spins - - diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index a003c1d8c1..302ac78074 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -41,5 +41,3 @@ are for 2d models. and the *disc* option for the :doc:`fix nve/sphere `, :doc:`fix nvt/sphere `, :doc:`fix nph/sphere `, :doc:`fix npt/sphere ` commands. - - diff --git a/doc/src/Howto_barostat.rst b/doc/src/Howto_barostat.rst index 2c6949d9b9..87dab8dd95 100644 --- a/doc/src/Howto_barostat.rst +++ b/doc/src/Howto_barostat.rst @@ -61,5 +61,3 @@ explicitly via the :doc:`thermo_style custom ` command. Or you can use the :doc:`thermo_modify ` command to re-define what pressure compute is used for default thermodynamic output. - - diff --git a/doc/src/Howto_bash.rst b/doc/src/Howto_bash.rst index 0b26b34cdf..a77289317e 100644 --- a/doc/src/Howto_bash.rst +++ b/doc/src/Howto_bash.rst @@ -284,5 +284,3 @@ the PATH variable should be This should give you a jump start when trying to run LAMMPS on Windows. To become effective in this environment I encourage you to look into Linux tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey `_) - - diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index 9ae459230d..4d31d1ee47 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -144,5 +144,3 @@ Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990). - - diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index ee1805f0fa..f60a608eae 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -512,5 +512,3 @@ Particuology, 6, 455 (2008). **(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011). - - diff --git a/doc/src/Howto_chunk.rst b/doc/src/Howto_chunk.rst index 53dff2a723..379225b13c 100644 --- a/doc/src/Howto_chunk.rst +++ b/doc/src/Howto_chunk.rst @@ -212,5 +212,3 @@ using the :doc:`fix ave/chunk ` command to calculate an average dipole moment vector for each bin. This example is explained on the :doc:`compute chunk/spread/atom ` command doc page. - - diff --git a/doc/src/Howto_client_server.rst b/doc/src/Howto_client_server.rst index a969a33341..c7acde5474 100644 --- a/doc/src/Howto_client_server.rst +++ b/doc/src/Howto_client_server.rst @@ -157,5 +157,3 @@ command-line option as their its option, where color is an integer label that will be used to distinguish one executable from another in the multiple executables that the mpirun command launches. In this example the client was colored with a 0, and the server with a 1. - - diff --git a/doc/src/Howto_coreshell.rst b/doc/src/Howto_coreshell.rst index aae83f983b..aae0dc77d6 100644 --- a/doc/src/Howto_coreshell.rst +++ b/doc/src/Howto_coreshell.rst @@ -264,5 +264,3 @@ The additional section in the date file would be formatted like this: **(Fincham)** Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, 6, 393-404 (1994). - - diff --git a/doc/src/Howto_couple.rst b/doc/src/Howto_couple.rst index d415b7740f..849415a0e3 100644 --- a/doc/src/Howto_couple.rst +++ b/doc/src/Howto_couple.rst @@ -118,5 +118,3 @@ instances of LAMMPS to perform different calculations. (4) Couple LAMMPS with another code in a client/server mode. This is described on the :doc:`Howto client/server ` doc page. - - diff --git a/doc/src/Howto_diffusion.rst b/doc/src/Howto_diffusion.rst index ebf0d0c2f6..b3cf62e620 100644 --- a/doc/src/Howto_diffusion.rst +++ b/doc/src/Howto_diffusion.rst @@ -24,6 +24,3 @@ and thus extract D. ---------- - - - diff --git a/doc/src/Howto_dispersion.rst b/doc/src/Howto_dispersion.rst index 6aea99b0c5..f1c818162b 100644 --- a/doc/src/Howto_dispersion.rst +++ b/doc/src/Howto_dispersion.rst @@ -98,5 +98,3 @@ This can be achieved using the *kspace\_modify mix/disp none* command. Note that the code does not check automatically whether any mixing rule is fulfilled. If mixing rules do not apply, the user will have to specify this command explicitly. - - diff --git a/doc/src/Howto_drude.rst b/doc/src/Howto_drude.rst index 425575fd80..b6292ca622 100644 --- a/doc/src/Howto_drude.rst +++ b/doc/src/Howto_drude.rst @@ -65,5 +65,3 @@ too close, which can cause numerical issues. **(Lamoureux and Roux)** G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) - - diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index 3d22d6030d..0c2e08a431 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -535,5 +535,3 @@ NPT ensemble using Nose-Hoover thermostat: **(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys Let, 418, 245-249 (2006) - - diff --git a/doc/src/Howto_elastic.rst b/doc/src/Howto_elastic.rst index 4d4f01f5f0..001eb4886b 100644 --- a/doc/src/Howto_elastic.rst +++ b/doc/src/Howto_elastic.rst @@ -42,5 +42,3 @@ converge and requires careful post-processing :ref:`(Shinoda) ` **(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). - - diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 299b36fb71..9b9959d202 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -492,5 +492,3 @@ and code checks to make sure they at the very least compile. A discussion of the LAMMPS developer GitHub workflow can be found in the file `doc/github-development-workflow.md `_ - - diff --git a/doc/src/Howto_granular.rst b/doc/src/Howto_granular.rst index 8e387bea3a..25fc9869ea 100644 --- a/doc/src/Howto_granular.rst +++ b/doc/src/Howto_granular.rst @@ -48,5 +48,3 @@ computations between frozen atoms by using this command: will be the same as in 3d. If you wish to model granular particles in 2d as 2d discs, see the note on this topic on the :doc:`Howto 2d ` doc page, where 2d simulations are discussed. - - diff --git a/doc/src/Howto_kappa.rst b/doc/src/Howto_kappa.rst index fe2dd99bf3..b737f8317d 100644 --- a/doc/src/Howto_kappa.rst +++ b/doc/src/Howto_kappa.rst @@ -79,5 +79,3 @@ formalism. **(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015). - - diff --git a/doc/src/Howto_library.rst b/doc/src/Howto_library.rst index fe8d4f5ad6..3a859f697c 100644 --- a/doc/src/Howto_library.rst +++ b/doc/src/Howto_library.rst @@ -245,5 +245,3 @@ lammps\_reset\_box()) to restore a previously extracted and saved state of a simulation. Additional properties for the new atoms can then be assigned via the lammps\_scatter\_atoms() or lammps\_extract\_atom() functions. - - diff --git a/doc/src/Howto_manifold.rst b/doc/src/Howto_manifold.rst index dc1b69455b..8d60a0d36d 100644 --- a/doc/src/Howto_manifold.rst +++ b/doc/src/Howto_manifold.rst @@ -50,5 +50,3 @@ to the relevant fixes. **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 `_. - - diff --git a/doc/src/Howto_multiple.rst b/doc/src/Howto_multiple.rst index b1d3dca024..72787e6c29 100644 --- a/doc/src/Howto_multiple.rst +++ b/doc/src/Howto_multiple.rst @@ -96,5 +96,3 @@ on the 3 partitions one after the other until all were finished. Initially, 3 simulations would be started simultaneously, one on each partition. When one finished, that partition would then start the 4th simulation, and so forth, until all 8 were completed. - - diff --git a/doc/src/Howto_nemd.rst b/doc/src/Howto_nemd.rst index 97529eafd2..1138315c1e 100644 --- a/doc/src/Howto_nemd.rst +++ b/doc/src/Howto_nemd.rst @@ -53,5 +53,3 @@ using the :doc:`fix flow/gauss ` command. **(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). - - diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index 9eda1987a6..9030e6edf8 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -342,5 +342,3 @@ vector input could be a column of an array. +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ | :doc:`fix store/state ` | per-atom vectors | per-atom vector/array | +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ - - diff --git a/doc/src/Howto_polarizable.rst b/doc/src/Howto_polarizable.rst index b60cc4c2d9..c1c6e1fc76 100644 --- a/doc/src/Howto_polarizable.rst +++ b/doc/src/Howto_polarizable.rst @@ -71,5 +71,3 @@ temperature is regulated using the velocities of the center of mass of core+shell (or Drude) pairs, but in the Drude model the actual relative core-Drude particle motion is thermostatted separately as well. - - diff --git a/doc/src/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst index cb323d647c..5ee9892db9 100644 --- a/doc/src/Howto_pylammps.rst +++ b/doc/src/Howto_pylammps.rst @@ -577,5 +577,3 @@ If you find this Python interface useful, please feel free to provide feedback and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage and maybe their latest research results. - - diff --git a/doc/src/Howto_replica.rst b/doc/src/Howto_replica.rst index aa5dae840e..92d2455dd1 100644 --- a/doc/src/Howto_replica.rst +++ b/doc/src/Howto_replica.rst @@ -53,5 +53,3 @@ processors. Thus the above commands could be run on a single-processor (or few-processor) desktop so that you can run a multi-replica simulation on more replicas than you have physical processors. - - diff --git a/doc/src/Howto_restart.rst b/doc/src/Howto_restart.rst index 79b0c30221..1459ed868f 100644 --- a/doc/src/Howto_restart.rst +++ b/doc/src/Howto_restart.rst @@ -98,5 +98,3 @@ commands since the new data file lists the force field coefficients. Also, the :doc:`reset_timestep ` command is used to tell LAMMPS the current timestep. This value is stored in restart files, but not in data files. - - diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst index c0f255ce84..e9b0863a6a 100644 --- a/doc/src/Howto_spc.rst +++ b/doc/src/Howto_spc.rst @@ -50,5 +50,3 @@ Wikipedia also has a nice article on `water models `. Interactions between pairs of body particles are computed via a command like :doc:`pair_style body/nparticle `. - - diff --git a/doc/src/Howto_spins.rst b/doc/src/Howto_spins.rst index 87763d9405..08939576e3 100644 --- a/doc/src/Howto_spins.rst +++ b/doc/src/Howto_spins.rst @@ -66,5 +66,3 @@ magnetic spin, or the magnetic force acting on this spin. **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). - - diff --git a/doc/src/Howto_temperature.rst b/doc/src/Howto_temperature.rst index dce83534ac..3082f3cded 100644 --- a/doc/src/Howto_temperature.rst +++ b/doc/src/Howto_temperature.rst @@ -31,5 +31,3 @@ They both allow for velocity biases indirectly, via an optional extra argument which is another temperature compute that subtracts a velocity bias. This allows the translational velocity of spherical or aspherical particles to be adjusted in prescribed ways. - - diff --git a/doc/src/Howto_thermostat.rst b/doc/src/Howto_thermostat.rst index 5a87356893..e953b28d49 100644 --- a/doc/src/Howto_thermostat.rst +++ b/doc/src/Howto_thermostat.rst @@ -92,5 +92,3 @@ temperature compute is used for default thermodynamic output. **(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). - - diff --git a/doc/src/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst index 4c03c719ec..921dface17 100644 --- a/doc/src/Howto_tip3p.rst +++ b/doc/src/Howto_tip3p.rst @@ -74,5 +74,3 @@ Phys, 79, 926 (1983). **(Price)** Price and Brooks, J Chem Phys, 121, 10096 (2004). - - diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index c527f5642c..480ddc3bc6 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -109,5 +109,3 @@ Wikipedia also has a nice article on `water models ` command can be used for this purpose. It allows dynamic control of the xy, xz, yz tilt factors as a simulation runs. This is discussed in the next section on non-equilibrium MD (NEMD) simulations. - diff --git a/doc/src/Howto_viscosity.rst b/doc/src/Howto_viscosity.rst index 748e9af910..ce738734f8 100644 --- a/doc/src/Howto_viscosity.rst +++ b/doc/src/Howto_viscosity.rst @@ -141,5 +141,3 @@ with time at sufficiently long times. **(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). - - diff --git a/doc/src/Howto_viz.rst b/doc/src/Howto_viz.rst index 8b0316c216..a5e83ce2c3 100644 --- a/doc/src/Howto_viz.rst +++ b/doc/src/Howto_viz.rst @@ -34,7 +34,3 @@ snapshots. .. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A - - - - diff --git a/doc/src/Howto_walls.rst b/doc/src/Howto_walls.rst index 4f53b8e92a..4d35cd66b3 100644 --- a/doc/src/Howto_walls.rst +++ b/doc/src/Howto_walls.rst @@ -69,5 +69,3 @@ The only frictional idealized walls currently in LAMMPS are flat or curved surfaces specified by the :doc:`fix wall/gran ` command. At some point we plan to allow regoin surfaces to be used as frictional walls, as well as triangulated surfaces. - - diff --git a/doc/src/Install.rst b/doc/src/Install.rst index 3b2eba9be4..9f744ff05f 100644 --- a/doc/src/Install.rst +++ b/doc/src/Install.rst @@ -51,5 +51,3 @@ These are the files and sub-directories in the LAMMPS distribution: You will have all of these if you download source. You will only have some of them if you download executables, as explained on the pages listed above. - - diff --git a/doc/src/Install_conda.rst b/doc/src/Install_conda.rst index 547513e42d..7c69dcf745 100644 --- a/doc/src/Install_conda.rst +++ b/doc/src/Install_conda.rst @@ -42,4 +42,3 @@ up the Conda capability. .. _conda: https://docs.conda.io/en/latest/index.html .. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html - diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index 85b919bf38..b1987bcd21 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -121,5 +121,3 @@ The LAMMPS GitHub project is managed by Christoph Junghans (LANL, junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at gmail.com) and Richard Berger (Temple U, richard.berger at temple.edu). - - diff --git a/doc/src/Install_linux.rst b/doc/src/Install_linux.rst index fe3aac24ea..92b0f6a8c8 100644 --- a/doc/src/Install_linux.rst +++ b/doc/src/Install_linux.rst @@ -262,5 +262,3 @@ Alternatively, you may use an AUR helper to install these packages. Note that the AUR provides build-scripts that download the source and the build the package on your machine. - - diff --git a/doc/src/Install_mac.rst b/doc/src/Install_mac.rst index f9a1adcf87..1a3c200f65 100644 --- a/doc/src/Install_mac.rst +++ b/doc/src/Install_mac.rst @@ -46,6 +46,3 @@ up the Homebrew capability. .. _openkim: https://openkim.org - - - diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst index e7e5d36aa8..7569b0b146 100644 --- a/doc/src/Install_patch.rst +++ b/doc/src/Install_patch.rst @@ -61,5 +61,3 @@ up to date. sub-dir of src, then re-install the package. The version in the src dir is merely a copy and will be wiped out if you type "make package-update". - - diff --git a/doc/src/Install_svn.rst b/doc/src/Install_svn.rst index 1310a8d930..42d5d2e855 100644 --- a/doc/src/Install_svn.rst +++ b/doc/src/Install_svn.rst @@ -95,5 +95,3 @@ The LAMMPS GitHub project is managed by Christoph Junghans (LANL, junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at gmail.com) and Richard Berger (Temple U, richard.berger at temple.edu). - - diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst index de874c967f..c02b3052e9 100644 --- a/doc/src/Install_tarball.rst +++ b/doc/src/Install_tarball.rst @@ -77,5 +77,3 @@ The patch files are posted on the `bug and feature page `_ of the website, along with a list of changed files and details about what is in the new patch release. Instructions for applying a patch file are on the :doc:`Install patch ` doc page. - - diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index 17edf1c3f8..32375264db 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -42,5 +42,3 @@ automatically, so this should only be done for debugging purposes. Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting up this Windows capability. - - diff --git a/doc/src/Intro.rst b/doc/src/Intro.rst index 0c6fc3e74e..cc4ae4c48f 100644 --- a/doc/src/Intro.rst +++ b/doc/src/Intro.rst @@ -14,5 +14,3 @@ These pages provide a brief introduction to LAMMPS. Intro_opensource Intro_authors Intro_website - - diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst index e51ea67430..4717800148 100644 --- a/doc/src/Intro_authors.rst +++ b/doc/src/Intro_authors.rst @@ -62,5 +62,3 @@ version of LAMMPS were the following: * Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb) * Steve Lustig (Dupont) * Jim Belak and Roy Pollock (LLNL) - - diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index a3beffafe2..3c3419ce05 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -224,5 +224,3 @@ classical MD options: * :doc:`Lattice Boltzmann fluid ` * :doc:`targeted ` and :doc:`steered ` molecular dynamics * :doc:`two-temperature electron model ` - - diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index 4f44f6e989..53cbe1bdf3 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -80,5 +80,3 @@ Here are suggestions on how to perform these tasks: simulations. It thus provides some functionality for several of the above bullets. Pizza.py is written in `Python `_ and is available for download from `this page `_. - - diff --git a/doc/src/Intro_opensource.rst b/doc/src/Intro_opensource.rst index b481611166..ea06bd4814 100644 --- a/doc/src/Intro_opensource.rst +++ b/doc/src/Intro_opensource.rst @@ -42,5 +42,3 @@ of the GPL. (4) If you give LAMMPS files to someone else, the GPL LICENSE file and source file headers (including the copyright and GPL notices) should remain part of the code. - - diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst index 5379231b9c..045d62cb41 100644 --- a/doc/src/Intro_overview.rst +++ b/doc/src/Intro_overview.rst @@ -47,5 +47,3 @@ partition the simulation domain into small sub-domains of equal computational cost, one of which is assigned to each processor. Processors communicate and store "ghost" atom information for atoms that border their sub-domain. - - diff --git a/doc/src/Intro_website.rst b/doc/src/Intro_website.rst index eb054f2bea..f5d65d1a2b 100644 --- a/doc/src/Intro_website.rst +++ b/doc/src/Intro_website.rst @@ -32,5 +32,3 @@ this Intr are included in this list. * `Authors of LAMMPS `_ * `History of LAMMPS development `_ * `Funding for LAMMPS `_ - - diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index b6a670b6a8..93f43c033a 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -85,5 +85,3 @@ Indices and tables .. raw:: html - - diff --git a/doc/src/Manual_build.rst b/doc/src/Manual_build.rst index 9351356e0a..49f4d18097 100644 --- a/doc/src/Manual_build.rst +++ b/doc/src/Manual_build.rst @@ -134,5 +134,3 @@ For converting the generated ePUB file to a MOBI format file also need to have the 'ebook-convert' tool from the "calibre" software installed. `http://calibre-ebook.com/ `_ You first create the ePUB file and then convert it with 'make mobi' - - diff --git a/doc/src/Manual_version.rst b/doc/src/Manual_version.rst index 167f674dc0..7a76824d0c 100644 --- a/doc/src/Manual_version.rst +++ b/doc/src/Manual_version.rst @@ -21,5 +21,3 @@ first page of the :doc:`manual `. describe the most current patch release of LAMMPS. * If you browse the HTML doc pages included in your tarball, they describe the version you have, which may be older. - - diff --git a/doc/src/Modify.rst b/doc/src/Modify.rst index 312bc9dba4..677e94b026 100644 --- a/doc/src/Modify.rst +++ b/doc/src/Modify.rst @@ -33,5 +33,3 @@ as a pull request on our `GitHub site `_, afte Modify_body Modify_thermo Modify_variable - - diff --git a/doc/src/Modify_atom.rst b/doc/src/Modify_atom.rst index d0cfd3b867..5499a6d7be 100644 --- a/doc/src/Modify_atom.rst +++ b/doc/src/Modify_atom.rst @@ -117,5 +117,3 @@ accessed using the returned index as Ivector or dvector are vectors of length Nlocal = # of owned atoms, which store the attributes of individual atoms. - - diff --git a/doc/src/Modify_body.rst b/doc/src/Modify_body.rst index 82114acbad..e469b8520f 100644 --- a/doc/src/Modify_body.rst +++ b/doc/src/Modify_body.rst @@ -33,5 +33,3 @@ class. See body.h for details. +----------------------+-----------------------------------------------------------+ | unpack\_border\_body | unpacking of those attributes | +----------------------+-----------------------------------------------------------+ - - diff --git a/doc/src/Modify_bond.rst b/doc/src/Modify_bond.rst index 1582e921b6..06db272395 100644 --- a/doc/src/Modify_bond.rst +++ b/doc/src/Modify_bond.rst @@ -34,5 +34,3 @@ for details and specific additional methods. +-----------------------+---------------------------------------------------------------------------+ | memory\_usage | tally memory allocated by the style (optional) | +-----------------------+---------------------------------------------------------------------------+ - - diff --git a/doc/src/Modify_command.rst b/doc/src/Modify_command.rst index 4b6e36b131..37e1b2c490 100644 --- a/doc/src/Modify_command.rst +++ b/doc/src/Modify_command.rst @@ -18,5 +18,3 @@ The single method your new class must define is as follows: Of course, the new class can define other methods and variables as needed. - - diff --git a/doc/src/Modify_compute.rst b/doc/src/Modify_compute.rst index 55d9db88df..b32350e048 100644 --- a/doc/src/Modify_compute.rst +++ b/doc/src/Modify_compute.rst @@ -55,5 +55,3 @@ each pair after force and energy has been computed for this pair. Then the tallied values are retrieved with the standard compute\_scalar or compute\_vector or compute\_peratom methods. The USER-TALLY package provides *examples*\ \_compute\_tally.html for utilizing this mechanism. - - diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index a83a7d830f..92ac9b8744 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -196,5 +196,3 @@ Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature. - - diff --git a/doc/src/Modify_dump.rst b/doc/src/Modify_dump.rst index 275b0417e7..8d98f848d2 100644 --- a/doc/src/Modify_dump.rst +++ b/doc/src/Modify_dump.rst @@ -30,5 +30,3 @@ new quantities to dump. Note that new keywords for atom properties are not typically added to the :doc:`dump custom ` command. Instead they are added to the :doc:`compute property/atom ` command. - - diff --git a/doc/src/Modify_fix.rst b/doc/src/Modify_fix.rst index 4ab8a2065a..9e1705e435 100644 --- a/doc/src/Modify_fix.rst +++ b/doc/src/Modify_fix.rst @@ -151,5 +151,3 @@ command), the initial\_integrate, post\_force\_integrate, and final\_integrate\_respa methods can be implemented. The thermo method enables a fix to contribute values to thermodynamic output, as printed quantities and/or to be summed to the potential energy of the system. - - diff --git a/doc/src/Modify_kspace.rst b/doc/src/Modify_kspace.rst index f7a7fde802..c45c8f94a1 100644 --- a/doc/src/Modify_kspace.rst +++ b/doc/src/Modify_kspace.rst @@ -19,5 +19,3 @@ class. See kspace.h for details. +---------------+----------------------------------------------+ | memory\_usage | tally of memory usage | +---------------+----------------------------------------------+ - - diff --git a/doc/src/Modify_min.rst b/doc/src/Modify_min.rst index f6cf570f03..d8bcd2d3f2 100644 --- a/doc/src/Modify_min.rst +++ b/doc/src/Modify_min.rst @@ -17,5 +17,3 @@ class. See min.h for details. +---------------+------------------------------------------+ | memory\_usage | tally of memory usage | +---------------+------------------------------------------+ - - diff --git a/doc/src/Modify_overview.rst b/doc/src/Modify_overview.rst index 5f54e3f2af..33d8b0e2ff 100644 --- a/doc/src/Modify_overview.rst +++ b/doc/src/Modify_overview.rst @@ -100,5 +100,3 @@ functionality: **(Foo)** Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). - - diff --git a/doc/src/Modify_pair.rst b/doc/src/Modify_pair.rst index 2ea57ccaf4..78ee144d53 100644 --- a/doc/src/Modify_pair.rst +++ b/doc/src/Modify_pair.rst @@ -33,5 +33,3 @@ Here is a brief description of the class methods in pair.h: +---------------------------------+-------------------------------------------------------------------+ The inner/middle/outer routines are optional. - - diff --git a/doc/src/Modify_region.rst b/doc/src/Modify_region.rst index 071840b17e..a9e9c734a4 100644 --- a/doc/src/Modify_region.rst +++ b/doc/src/Modify_region.rst @@ -20,5 +20,3 @@ class. See region.h for details. +-------------------+---------------------------------------------------------------------+ | shape\_update | change region shape if set by time-dependent variable | +-------------------+---------------------------------------------------------------------+ - - diff --git a/doc/src/Modify_thermo.rst b/doc/src/Modify_thermo.rst index 18ddacc3be..564df9ec7a 100644 --- a/doc/src/Modify_thermo.rst +++ b/doc/src/Modify_thermo.rst @@ -25,5 +25,3 @@ for thermo output of quantities calculated by :doc:`fixes `, :doc:`computes `, and :doc:`variables `. Thus, it may be simpler to compute what you wish via one of those constructs, than by adding a new keyword to the thermo command. - - diff --git a/doc/src/Modify_variable.rst b/doc/src/Modify_variable.rst index e746ab363a..c1fe0440ff 100644 --- a/doc/src/Modify_variable.rst +++ b/doc/src/Modify_variable.rst @@ -38,5 +38,3 @@ to find the appropriate location. Adding new :doc:`compute styles ` (whose calculated values can then be accessed by variables) is discussed on the :doc:`Modify compute ` doc page. - - diff --git a/doc/src/Packages.rst b/doc/src/Packages.rst index acc1c3c873..f8f5febaca 100644 --- a/doc/src/Packages.rst +++ b/doc/src/Packages.rst @@ -18,5 +18,3 @@ LAMMPS build process. Packages_standard Packages_user Packages_details - - diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 9e96d80252..3430624090 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -2446,5 +2446,3 @@ which discuss the `QuickFF `_ methodology. * :doc:`pair_style mm3/switch3/coulgauss/long ` * :doc:`pair_style lj/switch3/coulgauss/long ` * examples/USER/yaff - - diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst index e6d953a193..b0b70cb4ee 100644 --- a/doc/src/Packages_standard.rst +++ b/doc/src/Packages_standard.rst @@ -89,5 +89,3 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`VORONOI ` | Voronoi tesselation | :doc:`compute voronoi/atom ` | n/a | ext | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ - - diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 72a8763443..e3f0dba469 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -114,4 +114,3 @@ package: .. _MOFplus: https://www.mofplus.org/content/show/MOF-FF .. _PLUMED: http://www.plumed.org - diff --git a/doc/src/Python_call.rst b/doc/src/Python_call.rst index 561ce30249..155d4e0462 100644 --- a/doc/src/Python_call.rst +++ b/doc/src/Python_call.rst @@ -77,5 +77,3 @@ If you want to write Python code with callbacks to LAMMPS, then you must also follow the steps summarized in the :doc:`Python run ` doc page. I.e. you must build LAMMPS as a shared library and insure that Python can find the python/lammps.py file and the shared library. - - diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst index 38f24d36e2..59525d57be 100644 --- a/doc/src/Python_examples.rst +++ b/doc/src/Python_examples.rst @@ -109,5 +109,3 @@ different visualization package options. Click to see larger images: .. image:: JPG/screenshot_vmd_small.jpg :target: JPG/screenshot_vmd.jpg - - diff --git a/doc/src/Python_head.rst b/doc/src/Python_head.rst index 1f3ffda389..ce514629ae 100644 --- a/doc/src/Python_head.rst +++ b/doc/src/Python_head.rst @@ -42,5 +42,3 @@ interesting Python functions that can be called from a LAMMPS input script, that you think would be generally useful, please post them as a pull request to our `GitHub site `_, and they can be added to the LAMMPS distribution or webpage. - - diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst index 1171f70ae3..8a03dd7249 100644 --- a/doc/src/Python_install.rst +++ b/doc/src/Python_install.rst @@ -68,5 +68,3 @@ the LAMMPS shared library (see :doc:`this section `), you will need to manually copy files like liblammps\_g++.so into the appropriate system directory. This is not needed if you set the LD\_LIBRARY\_PATH environment variable as described above. - - diff --git a/doc/src/Python_library.rst b/doc/src/Python_library.rst index 7500de4399..d4acd07257 100644 --- a/doc/src/Python_library.rst +++ b/doc/src/Python_library.rst @@ -274,4 +274,3 @@ following steps: .. autoclass:: lammps.NeighList :members: :no-undoc-members: - diff --git a/doc/src/Python_mpi.rst b/doc/src/Python_mpi.rst index cf8975649c..9ecd876bcf 100644 --- a/doc/src/Python_mpi.rst +++ b/doc/src/Python_mpi.rst @@ -74,5 +74,3 @@ and see one line of output for each processor you run on. both mpi4py and LAMMPS together, this is an issue you may need to address, e.g. by moving other MPI installations so that mpi4py finds the right one. - - diff --git a/doc/src/Python_overview.rst b/doc/src/Python_overview.rst index a73d78094a..a41de5d444 100644 --- a/doc/src/Python_overview.rst +++ b/doc/src/Python_overview.rst @@ -23,5 +23,3 @@ to query or change its attributes through the LAMMPS Python module mentioned above. In Python lingo, this is "embedding" Python in LAMMPS. When used in this mode, Python can perform script operations that the simple LAMMPS input script syntax can not. - - diff --git a/doc/src/Python_pylammps.rst b/doc/src/Python_pylammps.rst index 63c49d4007..ad34706f50 100644 --- a/doc/src/Python_pylammps.rst +++ b/doc/src/Python_pylammps.rst @@ -3,5 +3,3 @@ PyLammps interface PyLammps is a Python wrapper class which can be created on its own or use an existing lammps Python object. It has its own :doc:`Howto pylammps ` doc page. - - diff --git a/doc/src/Python_run.rst b/doc/src/Python_run.rst index 164ea9fade..9aab6da9c6 100644 --- a/doc/src/Python_run.rst +++ b/doc/src/Python_run.rst @@ -30,5 +30,3 @@ which auto-generates the interface code needed between Python and a set of C-style library functions. Ctypes is part of standard Python for versions 2.5 and later. You can check which version of Python you have by simply typing "python" at a shell prompt. - - diff --git a/doc/src/Python_shlib.rst b/doc/src/Python_shlib.rst index 5be6002da2..0289b7acc4 100644 --- a/doc/src/Python_shlib.rst +++ b/doc/src/Python_shlib.rst @@ -79,5 +79,3 @@ it, which contains the installed liblammps.so. Starting Python outside (!) of your build directory, but with the virtualenv enabled and with the LD\_LIBRARY\_PATH set gives you access to LAMMPS via Python. - - diff --git a/doc/src/Python_test.rst b/doc/src/Python_test.rst index e840445a20..3368041935 100644 --- a/doc/src/Python_test.rst +++ b/doc/src/Python_test.rst @@ -163,5 +163,3 @@ With the "-i" flag, you will be left in the Python interpreter when the script finishes, so you can type subsequent commands. As mentioned above, you can only run Python interactively when running Python on a single processor, not in parallel. - - diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index 029fbdd95a..72b966c832 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -89,5 +89,3 @@ processors it was run on. Some of the examples or benchmarks require LAMMPS to be built with optional packages. - - diff --git a/doc/src/Run_head.rst b/doc/src/Run_head.rst index 18aa49d3c2..bdc122e3f7 100644 --- a/doc/src/Run_head.rst +++ b/doc/src/Run_head.rst @@ -14,5 +14,3 @@ they can contain. Run_options Run_output Run_windows - - diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 8992f6c5f5..14bddd58fc 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -639,5 +639,3 @@ input scripts. multiple variable values if any of them start with a "-", e.g. a negative numeric value. It is OK if the first value1 starts with a "-", since it is automatically skipped. - - diff --git a/doc/src/Run_output.rst b/doc/src/Run_output.rst index c1170800f3..a75513b2c5 100644 --- a/doc/src/Run_output.rst +++ b/doc/src/Run_output.rst @@ -190,5 +190,3 @@ with and without the communication and a Gflop rate is computed. The 3d rate is with communication; the 1d rate is without (just the 1d FFTs). Thus you can estimate what fraction of your FFT time was spent in communication, roughly 75% in the example above. - - diff --git a/doc/src/Run_windows.rst b/doc/src/Run_windows.rst index 5c97d37887..af7ade1ac7 100644 --- a/doc/src/Run_windows.rst +++ b/doc/src/Run_windows.rst @@ -74,5 +74,3 @@ multi-threading, which can be combined with MPI using something like: .. parsed-literal:: mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp - - diff --git a/doc/src/Speed.rst b/doc/src/Speed.rst index 9c3ca0aeaa..a5b3d36a25 100644 --- a/doc/src/Speed.rst +++ b/doc/src/Speed.rst @@ -28,5 +28,3 @@ hardware platforms. Speed_tips Speed_packages Speed_compare - - diff --git a/doc/src/Speed_bench.rst b/doc/src/Speed_bench.rst index de781c4d72..076e74fdbd 100644 --- a/doc/src/Speed_bench.rst +++ b/doc/src/Speed_bench.rst @@ -75,5 +75,3 @@ Phi), you should first measure single node performance. Then you can estimate parallel performance for multi-node runs using the same logic as for all-MPI mode, except that now you will typically need many more atoms/node to achieve good scalability. - - diff --git a/doc/src/Speed_compare.rst b/doc/src/Speed_compare.rst index d8a80cb620..f6795e202a 100644 --- a/doc/src/Speed_compare.rst +++ b/doc/src/Speed_compare.rst @@ -93,6 +93,3 @@ section below for examples where this has been done. * OpenCL in the GPU package does theoretically also support Intel CPUs or Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL) is superior. - - - diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index c5622336f3..9492d1466a 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -178,5 +178,3 @@ Restrictions None. - - diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index feb4b849d1..86afd8d2ed 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -545,6 +545,3 @@ supported. * Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. * Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. `_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). * Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. - - - diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 051e1eba23..700ef91998 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -444,5 +444,3 @@ Restrictions Currently, there are no precision options with the KOKKOS package. All compilation and computation is performed in double precision. - - diff --git a/doc/src/Speed_measure.rst b/doc/src/Speed_measure.rst index 90fe5246e1..2f86aa18f2 100644 --- a/doc/src/Speed_measure.rst +++ b/doc/src/Speed_measure.rst @@ -44,5 +44,3 @@ reported times for "Communication" or "Other" may be higher than they really are, due to load-imbalance. If this is an issue, you can uncomment the MPI\_Barrier() lines in src/timer.cpp, and re-compile LAMMPS, to obtain synchronized timings. - - diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index 364db907ec..44233902a7 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -160,5 +160,3 @@ Restrictions None. - - diff --git a/doc/src/Speed_opt.rst b/doc/src/Speed_opt.rst index 6c9e74e2bf..f684720905 100644 --- a/doc/src/Speed_opt.rst +++ b/doc/src/Speed_opt.rst @@ -51,5 +51,3 @@ Restrictions None. - - diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index 2948ffcd7b..90b2c236ab 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -188,5 +188,3 @@ The individual accelerator package doc pages explain: * speed-ups to expect * guidelines for best performance * restrictions - - diff --git a/doc/src/Speed_tips.rst b/doc/src/Speed_tips.rst index 55ee0ae7e7..8798cce245 100644 --- a/doc/src/Speed_tips.rst +++ b/doc/src/Speed_tips.rst @@ -54,5 +54,3 @@ relative accuracy of slightly greater than 1e-5 and above. of energy and pressure as it does in forces, so some caution must be used if energy and/or pressure are quantities of interest, such as when using a barostat. - - diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index e404f30c9f..5e90fcd268 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -741,5 +741,3 @@ simulation. See the README file for details. These files were provided by Vikas Varshney (vv0210 at gmail.com) - - diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 0282f74149..1c667781af 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -566,6 +566,3 @@ Related commands .. _pizza: http://pizza.sandia.gov **Default:** none - - - diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index bdc0d52075..baf843426e 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -119,5 +119,3 @@ Default .. parsed-literal:: boundary p p p - - diff --git a/doc/src/box.rst b/doc/src/box.rst index ceaad02e89..052057bb90 100644 --- a/doc/src/box.rst +++ b/doc/src/box.rst @@ -69,5 +69,3 @@ Default """"""" The default value is tilt = small. - - diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst index 0bd61c435d..02f06ac681 100644 --- a/doc/src/change_box.rst +++ b/doc/src/change_box.rst @@ -380,5 +380,3 @@ Default """"""" The option default is units = lattice. - - diff --git a/doc/src/clear.rst b/doc/src/clear.rst index 62696d1529..b8cb8b7410 100644 --- a/doc/src/clear.rst +++ b/doc/src/clear.rst @@ -42,5 +42,3 @@ Restrictions **Related commands:** none **Default:** none - - diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 9174a03f7c..67ce65e2a9 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -180,5 +180,3 @@ Default The option defaults are mode = single, group = all, cutoff = 0.0, vel = no. The cutoff default of 0.0 means that ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. - - diff --git a/doc/src/comm_style.rst b/doc/src/comm_style.rst index 0e2758d55f..bbafa21d62 100644 --- a/doc/src/comm_style.rst +++ b/doc/src/comm_style.rst @@ -71,5 +71,3 @@ Default """"""" The default style is brick. - - diff --git a/doc/src/commands_list.rst b/doc/src/commands_list.rst index 2eaa78d59c..1b1691cefd 100644 --- a/doc/src/commands_list.rst +++ b/doc/src/commands_list.rst @@ -121,4 +121,3 @@ Commands write_data write_dump write_restart - diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 10e47d8c73..fd3c08c626 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -332,5 +332,3 @@ Related commands :doc:`uncompute `, :doc:`compute_modify `, :doc:`fix ave/atom `, :doc:`fix ave/time `, :doc:`fix ave/histo ` **Default:** none - - diff --git a/doc/src/compute_ackland_atom.rst b/doc/src/compute_ackland_atom.rst index c2d919b652..f1cabdc3a3 100644 --- a/doc/src/compute_ackland_atom.rst +++ b/doc/src/compute_ackland_atom.rst @@ -97,5 +97,3 @@ The keyword *legacy* defaults to *no*\ . **(Ackland)** Ackland, Jones, Phys Rev B, 73, 054104 (2006). - - diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index e92f9e43a9..f403f5e5bf 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -227,5 +227,3 @@ Default """"""" The keyword default is ordinate = degree. - - diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst index c165aa2943..155b387d4e 100644 --- a/doc/src/compute_angle.rst +++ b/doc/src/compute_angle.rst @@ -55,5 +55,3 @@ Related commands :doc:`compute pe `, :doc:`compute pair ` **Default:** none - - diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index 3a61f68388..923233fcfc 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -151,5 +151,3 @@ Related commands :doc:`dump local `, :doc:`compute property/local ` **Default:** none - - diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index 0b8f896e5e..b800c91303 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -93,5 +93,3 @@ Related commands :doc:`variable angmom() function ` **Default:** none - - diff --git a/doc/src/compute_basal_atom.rst b/doc/src/compute_basal_atom.rst index 8dd55b8ad2..ed10a2ffd5 100644 --- a/doc/src/compute_basal_atom.rst +++ b/doc/src/compute_basal_atom.rst @@ -83,5 +83,3 @@ Related commands **(Barrett)** Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012). - - diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index 52ded3ff60..47fe6de85b 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -103,5 +103,3 @@ Related commands :doc:`dump local ` **Default:** none - - diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst index 2ba5fc27a1..ee95e29de8 100644 --- a/doc/src/compute_bond.rst +++ b/doc/src/compute_bond.rst @@ -55,5 +55,3 @@ Related commands :doc:`compute pe `, :doc:`compute pair ` **Default:** none - - diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index b7723f2a12..cc2f929af9 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -207,5 +207,3 @@ Related commands :doc:`dump local `, :doc:`compute property/local ` **Default:** none - - diff --git a/doc/src/compute_centro_atom.rst b/doc/src/compute_centro_atom.rst index 0d31a292a7..f00cc179f8 100644 --- a/doc/src/compute_centro_atom.rst +++ b/doc/src/compute_centro_atom.rst @@ -173,5 +173,3 @@ The default value for the optional keyword is axes = no. **(Kelchner)** Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998). - - diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index 1d75905e96..354aa44d5b 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -700,5 +700,3 @@ The option defaults are as follows: * bound = lower and upper in all dimensions * pbc = no * units = lattice - - diff --git a/doc/src/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst index 7e71e71840..a1b5cf45e5 100644 --- a/doc/src/compute_chunk_spread_atom.rst +++ b/doc/src/compute_chunk_spread_atom.rst @@ -230,5 +230,3 @@ Related commands :doc:`compute chunk/atom `, :doc:`fix ave/chunk `, :doc:`compute reduce/chunk ` **Default:** none - - diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index ea442202b9..908974de38 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -110,5 +110,3 @@ Related commands :doc:`compute coord/atom ` **Default:** none - - diff --git a/doc/src/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst index 61b2dc8626..16ce67d7af 100644 --- a/doc/src/compute_cna_atom.rst +++ b/doc/src/compute_cna_atom.rst @@ -112,5 +112,3 @@ Related commands **(Tsuzuki)** Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). - - diff --git a/doc/src/compute_cnp_atom.rst b/doc/src/compute_cnp_atom.rst index 021360a087..3290f67508 100644 --- a/doc/src/compute_cnp_atom.rst +++ b/doc/src/compute_cnp_atom.rst @@ -126,5 +126,3 @@ Related commands **(Tsuzuki)** Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). - - diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst index 5ad94d4f51..a77d00a004 100644 --- a/doc/src/compute_com.rst +++ b/doc/src/compute_com.rst @@ -62,5 +62,3 @@ Related commands :doc:`compute com/chunk ` **Default:** none - - diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst index b7732ab488..0d210fb113 100644 --- a/doc/src/compute_com_chunk.rst +++ b/doc/src/compute_com_chunk.rst @@ -91,5 +91,3 @@ Related commands :doc:`compute com ` **Default:** none - - diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst index ab2678c909..3c88f66ea5 100644 --- a/doc/src/compute_contact_atom.rst +++ b/doc/src/compute_contact_atom.rst @@ -59,5 +59,3 @@ Related commands :doc:`compute coord/atom ` **Default:** none - - diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index b83c9100ef..b46af08d63 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -155,5 +155,3 @@ group = all **(tenWolde)** P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996). - - diff --git a/doc/src/compute_damage_atom.rst b/doc/src/compute_damage_atom.rst index 6718922545..b39076c17d 100644 --- a/doc/src/compute_damage_atom.rst +++ b/doc/src/compute_damage_atom.rst @@ -65,5 +65,3 @@ Related commands :doc:`compute plasticity/atom ` **Default:** none - - diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst index faf0d650e5..c8d4e14d7e 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -54,5 +54,3 @@ Related commands :doc:`compute pe `, :doc:`compute pair ` **Default:** none - - diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 302e496c33..a1dab677ee 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -144,5 +144,3 @@ Related commands :doc:`dump local `, :doc:`compute property/local ` **Default:** none - - diff --git a/doc/src/compute_dilatation_atom.rst b/doc/src/compute_dilatation_atom.rst index 67cefb82c2..cc64634397 100644 --- a/doc/src/compute_dilatation_atom.rst +++ b/doc/src/compute_dilatation_atom.rst @@ -68,5 +68,3 @@ Related commands :doc:`compute plasticity/atom ` **Default:** none - - diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index 213df9aebd..44875e48d8 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -96,5 +96,3 @@ Related commands :doc:`compute com/chunk ` **Default:** none - - diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index 2ece320606..2d7cdfed3f 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -153,5 +153,3 @@ Related commands :doc:`compute msd `, :doc:`dump custom `, :doc:`fix store/state ` **Default:** none - - diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index 5aaf6ae139..bca72efdcd 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -83,5 +83,3 @@ Related commands W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014). - - diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst index 3fae8502ea..12956cc5d6 100644 --- a/doc/src/compute_dpd_atom.rst +++ b/doc/src/compute_dpd_atom.rst @@ -72,5 +72,3 @@ Related commands W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014). - - diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index 38609878e0..e51e70e7f6 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -73,5 +73,3 @@ Related commands **(Li2014)** Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003. - - diff --git a/doc/src/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst index e095a07358..96d55bbb0d 100644 --- a/doc/src/compute_entropy_atom.rst +++ b/doc/src/compute_entropy_atom.rst @@ -157,5 +157,3 @@ The default values for the optional keywords are avg = no and local = no. **(Nettleton)** Nettleton and Green, J Chem Phys, 29, 6 (1958). - - diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index 01ed3193bb..9ba2edb1a6 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -75,5 +75,3 @@ particles. :doc:`compute erotate/sphere ` **Default:** none - - diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst index 316712a6d3..9fbea18529 100644 --- a/doc/src/compute_erotate_rigid.rst +++ b/doc/src/compute_erotate_rigid.rst @@ -63,5 +63,3 @@ Related commands :doc:`compute ke/rigid ` **Default:** none - - diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index 79db7fda02..61e3b5c1dc 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -64,5 +64,3 @@ Related commands :doc:`compute erotate/asphere ` **Default:** none - - diff --git a/doc/src/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst index e18bfb0aca..94cc5948e7 100644 --- a/doc/src/compute_erotate_sphere_atom.rst +++ b/doc/src/compute_erotate_sphere_atom.rst @@ -60,5 +60,3 @@ Related commands :doc:`dump custom ` **Default:** none - - diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst index 1b88184d73..a99f77ec52 100644 --- a/doc/src/compute_event_displace.rst +++ b/doc/src/compute_event_displace.rst @@ -69,5 +69,3 @@ Related commands :doc:`prd `, :doc:`tad ` **Default:** none - - diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index dcf827d383..1cbabef023 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -342,5 +342,3 @@ The option defaults are *tail* = *no*\ , *volume* = *no*\ . **(AllenTildesley)** Allen and Tildesley, Computer Simulation of Liquids, Oxford University Press (1987) - - diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index 5b929ff706..01e1d8650a 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -243,5 +243,3 @@ Related commands :doc:`compute chunk/atom `, :doc:`compute reduce ` **Default:** none - - diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index 232f9a3d73..76766ce755 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -180,5 +180,3 @@ molecule = off. Bogusz et al, J Chem Phys, 108, 7070 (1998) - - diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index c0da59495e..6eb629c85b 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -79,5 +79,3 @@ Related commands :doc:`compute gyration/shape ` **Default:** none - - diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index 403fa7c922..4cdb6fa4d6 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -119,5 +119,3 @@ Restrictions :doc:`compute gyration ` **Default:** none - - diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index 043d31e619..590aca59a2 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -104,5 +104,3 @@ Related commands **(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985). - - diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index ceb6f23871..309b9d7b6d 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -106,5 +106,3 @@ Related commands **(Theodorou)** Theodorou, Suter, Macromolecules, 18, 1206 (1985). - - diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index e780eeaf77..2122c3acd0 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -251,5 +251,3 @@ Related commands **(Boone)** Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019). - - diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index 72960cd845..66cbcf2409 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -132,5 +132,3 @@ The option defaults are *cutoff* = pair style cutoff, *nnn* = 6, *degree* = 6 **(Nelson)** Nelson, Halperin, Phys Rev B, 19, 2457 (1979). - - diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index b9aaa34d6e..c66c1d1650 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -205,5 +205,3 @@ this compute. **(Moustafa)** Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , `Phys. Rev. E [92], 043303 (2015) `_ - - diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index 27b4a8426f..e7fb761958 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -54,5 +54,3 @@ Related commands :doc:`compute pe `, :doc:`compute pair ` **Default:** none - - diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index 0b085bc85c..71286d5c9d 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -88,5 +88,3 @@ Related commands :doc:`dump local `, :doc:`compute property/local ` **Default:** none - - diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index c5c89dc477..b592fe828f 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -92,5 +92,3 @@ Related commands :doc:`variable inertia() function ` **Default:** none - - diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst index 026e701f3d..8ec1e8e817 100644 --- a/doc/src/compute_ke.rst +++ b/doc/src/compute_ke.rst @@ -64,5 +64,3 @@ Related commands :doc:`compute erotate/sphere ` **Default:** none - - diff --git a/doc/src/compute_ke_atom.rst b/doc/src/compute_ke_atom.rst index ec0767068a..37f08e83d8 100644 --- a/doc/src/compute_ke_atom.rst +++ b/doc/src/compute_ke_atom.rst @@ -53,5 +53,3 @@ Related commands :doc:`dump custom ` **Default:** none - - diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst index 23e389d890..85b5756182 100644 --- a/doc/src/compute_ke_atom_eff.rst +++ b/doc/src/compute_ke_atom_eff.rst @@ -84,5 +84,3 @@ Related commands :doc:`dump custom ` **Default:** none - - diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst index 15f1ab5ad1..5819bb6220 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -83,5 +83,3 @@ LAMMPS was built with that package. See the :doc:`Build package **Related commands:** none **Default:** none - - diff --git a/doc/src/compute_ke_rigid.rst b/doc/src/compute_ke_rigid.rst index be177f9cb2..3edb69f2a1 100644 --- a/doc/src/compute_ke_rigid.rst +++ b/doc/src/compute_ke_rigid.rst @@ -62,5 +62,3 @@ Related commands :doc:`compute erotate/rigid ` **Default:** none - - diff --git a/doc/src/compute_meso_e_atom.rst b/doc/src/compute_meso_e_atom.rst index 02d4543d43..b805121b20 100644 --- a/doc/src/compute_meso_e_atom.rst +++ b/doc/src/compute_meso_e_atom.rst @@ -60,5 +60,3 @@ Related commands :doc:`dump custom ` **Default:** none - - diff --git a/doc/src/compute_meso_rho_atom.rst b/doc/src/compute_meso_rho_atom.rst index 232b83e6c5..1f525c1d25 100644 --- a/doc/src/compute_meso_rho_atom.rst +++ b/doc/src/compute_meso_rho_atom.rst @@ -60,5 +60,3 @@ Related commands :doc:`dump custom ` **Default:** none - - diff --git a/doc/src/compute_meso_t_atom.rst b/doc/src/compute_meso_t_atom.rst index 01b0dcb570..7969953128 100644 --- a/doc/src/compute_meso_t_atom.rst +++ b/doc/src/compute_meso_t_atom.rst @@ -62,5 +62,3 @@ Related commands :doc:`dump custom ` **Default:** none - - diff --git a/doc/src/compute_modify.rst b/doc/src/compute_modify.rst index 82a75269d9..723f78df9f 100644 --- a/doc/src/compute_modify.rst +++ b/doc/src/compute_modify.rst @@ -80,5 +80,3 @@ Default The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and dynamic/dof = no. - - diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst index f90b6e7611..32e325a103 100644 --- a/doc/src/compute_momentum.rst +++ b/doc/src/compute_momentum.rst @@ -52,5 +52,3 @@ Related commands """""""""""""""" **Default:** none - - diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst index 08a7fcf02e..8ced34f66d 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -122,5 +122,3 @@ Default """"""" The option default are com = no, average = no. - - diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index 615d2bf123..9cf2b0bc8a 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -130,5 +130,3 @@ Related commands :doc:`compute msd ` **Default:** none - - diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst index 5a0190a569..180b922097 100644 --- a/doc/src/compute_msd_nongauss.rst +++ b/doc/src/compute_msd_nongauss.rst @@ -89,5 +89,3 @@ Default """"""" The option default is com = no. - - diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index 75feaeba21..66e21a2ae4 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -93,5 +93,3 @@ Related commands :doc:`variable omega() function ` **Default:** none - - diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index 504b9d70d3..401f6b46a2 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -190,5 +190,3 @@ J. Chem. Phys. 138, 044501 (2013). **(tenWolde)** P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996). - - diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst index 59804ad090..87ea8bda58 100644 --- a/doc/src/compute_pair.rst +++ b/doc/src/compute_pair.rst @@ -100,5 +100,3 @@ Default """"""" The keyword defaults are *evalue* = *epair*\ , nsub = 0. - - diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index 5d9e962a00..7808253576 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -172,5 +172,3 @@ Default """"""" The keyword default is cutoff = type. - - diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index 884a1b4dd0..e8075a361a 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -90,5 +90,3 @@ Related commands :doc:`compute pe/atom ` **Default:** none - - diff --git a/doc/src/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst index 13df88c915..abc504a56b 100644 --- a/doc/src/compute_pe_atom.rst +++ b/doc/src/compute_pe_atom.rst @@ -116,5 +116,3 @@ Related commands **(Heyes)** Heyes, Phys Rev B 49, 755 (1994), - - diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst index 95309200c9..8c9515941f 100644 --- a/doc/src/compute_plasticity_atom.rst +++ b/doc/src/compute_plasticity_atom.rst @@ -75,5 +75,3 @@ Related commands **(Mitchell)** Mitchell, "A non-local, ordinary-state-based viscoelasticity model for peridynamics", Sandia National Lab Report, 8064:1-28 (2011). - - diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 389b2b2fae..c6530ed11e 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -169,5 +169,3 @@ Related commands **(Thompson)** Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). - - diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst index 48f41c4604..9c20e55a39 100644 --- a/doc/src/compute_pressure_cylinder.rst +++ b/doc/src/compute_pressure_cylinder.rst @@ -89,5 +89,3 @@ Related commands **(Addington)** Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018). - - diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst index 4eaae2e2bf..e674950c32 100644 --- a/doc/src/compute_pressure_uef.rst +++ b/doc/src/compute_pressure_uef.rst @@ -63,5 +63,3 @@ Related commands :doc:`compute temp/uef ` **Default:** none - - diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index 5a8fdd0000..5aa9ead974 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -191,5 +191,3 @@ Related commands :doc:`fix property/atom ` **Default:** none - - diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index c2d9d5ec41..cd9750f96e 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -122,5 +122,3 @@ Related commands :doc:`fix ave/chunk ` **Default:** none - - diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index d230360c45..2e01958194 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -172,5 +172,3 @@ Default """"""" The keyword default is cutoff = type. - - diff --git a/doc/src/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst index 546cf38c9e..e7667adae9 100644 --- a/doc/src/compute_ptm_atom.rst +++ b/doc/src/compute_ptm_atom.rst @@ -128,5 +128,3 @@ Related commands **(Larsen)** Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016). - - diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index 75908b4406..b35aa54e09 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -217,5 +217,3 @@ Default """"""" The keyword defaults are cutoff = 0.0 (use the pairwise force cutoff). - - diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index 0b8c1cc922..cfd7b27614 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -237,5 +237,3 @@ Related commands :doc:`compute `, :doc:`fix `, :doc:`variable ` **Default:** none - - diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index ae0cff42b3..8f850a32c2 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -198,5 +198,3 @@ Related commands :doc:`compute chunk/atom `, :doc:`compute reduce `, :doc:`compute chunk/spread/atom ` **Default:** none - - diff --git a/doc/src/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst index f5657f6776..d7e9d4dcdd 100644 --- a/doc/src/compute_rigid_local.rst +++ b/doc/src/compute_rigid_local.rst @@ -198,5 +198,3 @@ Related commands :doc:`dump local `, :doc:`compute reduce ` **Default:** none - - diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index 87172213e6..9b4067043f 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -207,5 +207,3 @@ Volume C: Mathematical and Chemical Tables, 554-95 (2004). **(Fox)** Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93 (1989). - - diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index 6e3d4af532..4ed35eb0ff 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -130,5 +130,3 @@ Related commands :doc:`compute `, :doc:`fix `, :doc:`compute reduce ` **Default:** none - - diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst index e31b037310..5ac0cc1de7 100644 --- a/doc/src/compute_smd_contact_radius.rst +++ b/doc/src/compute_smd_contact_radius.rst @@ -59,5 +59,3 @@ Related commands :doc:`dump custom ` smd/hertz smd/tri\_surface **Default:** none - - diff --git a/doc/src/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst index 19e2b2114e..235f6f63cc 100644 --- a/doc/src/compute_smd_damage.rst +++ b/doc/src/compute_smd_damage.rst @@ -52,5 +52,3 @@ Related commands :doc:`smd/plastic\_strain `, :doc:`smd/tlsph\_stress ` **Default:** none - - diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst index 9068202e9a..d7c3764088 100644 --- a/doc/src/compute_smd_hourglass_error.rst +++ b/doc/src/compute_smd_hourglass_error.rst @@ -65,5 +65,3 @@ tlsph pair style. Default """"""" - - diff --git a/doc/src/compute_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst index 8825bf1aa0..5aa618a031 100644 --- a/doc/src/compute_smd_internal_energy.rst +++ b/doc/src/compute_smd_internal_energy.rst @@ -53,5 +53,3 @@ or total Lagrangian SPH pair styles. Default """"""" - - diff --git a/doc/src/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst index 8bfb6d4d55..3330a34dd0 100644 --- a/doc/src/compute_smd_plastic_strain.rst +++ b/doc/src/compute_smd_plastic_strain.rst @@ -58,5 +58,3 @@ Related commands :doc:`smd/tlsph/strain ` **Default:** none - - diff --git a/doc/src/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst index a2a8633a47..b3157bec12 100644 --- a/doc/src/compute_smd_plastic_strain_rate.rst +++ b/doc/src/compute_smd_plastic_strain_rate.rst @@ -58,5 +58,3 @@ Related commands :doc:`smd/tlsph/strain ` **Default:** none - - diff --git a/doc/src/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst index bc3d38909c..f6e4c9b764 100644 --- a/doc/src/compute_smd_rho.rst +++ b/doc/src/compute_smd_rho.rst @@ -55,5 +55,3 @@ Related commands :doc:`compute smd/vol ` **Default:** none - - diff --git a/doc/src/compute_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst index 72027f02f0..7ef38db492 100644 --- a/doc/src/compute_smd_tlsph_defgrad.rst +++ b/doc/src/compute_smd_tlsph_defgrad.rst @@ -60,5 +60,3 @@ Related commands :doc:`smd/hourglass/error ` **Default:** none - - diff --git a/doc/src/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst index 94d5322f88..4213448101 100644 --- a/doc/src/compute_smd_tlsph_dt.rst +++ b/doc/src/compute_smd_tlsph_dt.rst @@ -62,5 +62,3 @@ Related commands :doc:`smd/adjust/dt ` **Default:** none - - diff --git a/doc/src/compute_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst index 75481cd226..afd398e8a2 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.rst +++ b/doc/src/compute_smd_tlsph_num_neighs.rst @@ -57,5 +57,3 @@ Related commands :doc:`smd/ulsph/num/neighs ` **Default:** none - - diff --git a/doc/src/compute_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst index bfb662bf3a..9787d8304c 100644 --- a/doc/src/compute_smd_tlsph_shape.rst +++ b/doc/src/compute_smd_tlsph_shape.rst @@ -64,5 +64,3 @@ Related commands :doc:`smd/contact/radius ` **Default:** none - - diff --git a/doc/src/compute_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst index 1719b8c5a6..5382382773 100644 --- a/doc/src/compute_smd_tlsph_strain.rst +++ b/doc/src/compute_smd_tlsph_strain.rst @@ -61,5 +61,3 @@ Related commands :doc:`smd/tlsph/stress ` **Default:** none - - diff --git a/doc/src/compute_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst index 5e88ddbb8c..fd489d4f29 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.rst +++ b/doc/src/compute_smd_tlsph_strain_rate.rst @@ -59,5 +59,3 @@ Related commands :doc:`compute smd/tlsph/strain `, :doc:`compute smd/tlsph/stress ` **Default:** none - - diff --git a/doc/src/compute_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst index 740964e4eb..7060144cfd 100644 --- a/doc/src/compute_smd_tlsph_stress.rst +++ b/doc/src/compute_smd_tlsph_stress.rst @@ -61,5 +61,3 @@ Related commands :doc:`compute smd/tlsph/strain `, :doc:`cmopute smd/tlsph/strain/rate ` **Default:** none - - diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst index 4b042a4299..9b92a896cb 100644 --- a/doc/src/compute_smd_triangle_vertices.rst +++ b/doc/src/compute_smd_triangle_vertices.rst @@ -65,5 +65,3 @@ Related commands :doc:`fix smd/wall\_surface ` **Default:** none - - diff --git a/doc/src/compute_smd_ulsph_num_neighs.rst b/doc/src/compute_smd_ulsph_num_neighs.rst index 605574a93c..7652d53915 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.rst +++ b/doc/src/compute_smd_ulsph_num_neighs.rst @@ -56,5 +56,3 @@ Related commands :doc:`compute smd/tlsph/num/neighs ` **Default:** none - - diff --git a/doc/src/compute_smd_ulsph_strain.rst b/doc/src/compute_smd_ulsph_strain.rst index 3d293deb5f..a335c7add9 100644 --- a/doc/src/compute_smd_ulsph_strain.rst +++ b/doc/src/compute_smd_ulsph_strain.rst @@ -59,5 +59,3 @@ Related commands :doc:`compute smd/tlsph/strain ` **Default:** none - - diff --git a/doc/src/compute_smd_ulsph_strain_rate.rst b/doc/src/compute_smd_ulsph_strain_rate.rst index 36b3f1c73f..b4485253b2 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.rst +++ b/doc/src/compute_smd_ulsph_strain_rate.rst @@ -60,5 +60,3 @@ Related commands :doc:`compute smd/tlsph/strain/rate ` **Default:** none - - diff --git a/doc/src/compute_smd_ulsph_stress.rst b/doc/src/compute_smd_ulsph_stress.rst index 8f929c9c97..52d3e69ec4 100644 --- a/doc/src/compute_smd_ulsph_stress.rst +++ b/doc/src/compute_smd_ulsph_stress.rst @@ -59,5 +59,3 @@ Related commands :doc:`compute smd/ulsph/strain `, :doc:`compute smd/ulsph/strain/rate ` :doc:`compute smd/tlsph/stress ` **Default:** none - - diff --git a/doc/src/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst index 6068c8a8ca..caae817ff1 100644 --- a/doc/src/compute_smd_vol.rst +++ b/doc/src/compute_smd_vol.rst @@ -57,5 +57,3 @@ Related commands :doc:`compute smd/rho ` **Default:** none - - diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 03188e19fc..be3deaf36a 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -357,5 +357,3 @@ available at `arXiv:1409.3880 `_ **(Varshalovich)** Varshalovich, Moskalev, Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore (1987). - - diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index 88b3211612..e87b49428e 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -272,5 +272,3 @@ Related commands **(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019). - - diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index eaa4ed86ff..0d721db3fe 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -120,5 +120,3 @@ Related commands **(Todd)** B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995). - - diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index f391bd288a..a5973a038a 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -113,5 +113,3 @@ Related commands heat/flux*\ \_compute\_heat\_flux.html **Default:** none - - diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index 2412ffc4af..bd3c5df074 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -68,5 +68,3 @@ Related commands **(Li2015)** Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI: 10.1063/1.4923254 - - diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index d6f919d65c..e485b982f2 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -120,5 +120,3 @@ Related commands :doc:`compute temp/partial `, :doc:`compute temp/region `, :doc:`compute pressure ` **Default:** none - - diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index c770a50230..eef88ebe86 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -166,5 +166,3 @@ Related commands :doc:`compute temp ` **Default:** none - - diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index c4a6839528..df9ff29f2d 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -142,5 +142,3 @@ Related commands :doc:`compute temp ` **Default:** none - - diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index 9a9ba1eaeb..a23ddd0c6d 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -253,5 +253,3 @@ Default The option defaults are com no, no bias, adof = dimensionality of the system (2 or 3), and cdof = 0.0. - - diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index b6271cfe00..edc7adb3bf 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -93,5 +93,3 @@ Related commands :doc:`compute temp ` **Default:** none - - diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 943be37c6b..fa4949fa78 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -124,5 +124,3 @@ Related commands **(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993). - - diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index e093e8e562..d470b24bdc 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -135,5 +135,3 @@ Related commands :doc:`fix nvt/sllod ` **Default:** none - - diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index 2597abba86..46292fcfc1 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -73,5 +73,3 @@ Related commands :doc:`fix nvt/sllod/eff ` **Default:** none - - diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index 85df7d985e..706ee32beb 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -80,5 +80,3 @@ Related commands :doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`pair_style thole `, :doc:`compute temp ` **Default:** none - - diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index e76fb1bdd8..06cdfbb8f0 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -101,5 +101,3 @@ Related commands :doc:`compute temp/partial `, :doc:`compute temp/region `, :doc:`compute pressure ` **Default:** none - - diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index 41127e848b..a01abd49a0 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -119,5 +119,3 @@ Related commands :doc:`compute temp `, :doc:`compute temp/region `, :doc:`compute pressure ` **Default:** none - - diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index fc1d9b3f2a..9ecf985596 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -195,5 +195,3 @@ The option default is out = tensor. **(Evans)** Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986). - - diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 915cb30572..1fae6bb419 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -118,5 +118,3 @@ Default """"""" The option default is units = lattice. - - diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index 0aae53a177..b896863756 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -107,5 +107,3 @@ Related commands :doc:`compute temp `, :doc:`compute pressure ` **Default:** none - - diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index 09d8a39279..9026d15d67 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -64,5 +64,3 @@ Related commands :doc:`compute temp/region `, :doc:`compute temp/eff `, :doc:`compute pressure ` **Default:** none - - diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index 371372b03d..697444c6ed 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -95,5 +95,3 @@ Related commands :doc:`compute temp ` **Default:** none - - diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index a0573b8c83..64fc371b50 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -152,5 +152,3 @@ Default """"""" The option defaults are no bias and dof = all. - - diff --git a/doc/src/compute_temp_uef.rst b/doc/src/compute_temp_uef.rst index 5f487d365b..ca554c2314 100644 --- a/doc/src/compute_temp_uef.rst +++ b/doc/src/compute_temp_uef.rst @@ -55,5 +55,3 @@ Related commands :doc:`compute pressure/uef ` **Default:** none - - diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index 3b15e51f1f..9ac5cc5bc3 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -155,5 +155,3 @@ Related commands **(Eike)** Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006). - - diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst index bed2673b2b..ae4d5f120c 100644 --- a/doc/src/compute_torque_chunk.rst +++ b/doc/src/compute_torque_chunk.rst @@ -92,5 +92,3 @@ Related commands :doc:`variable torque() function ` **Default:** none - - diff --git a/doc/src/compute_vacf.rst b/doc/src/compute_vacf.rst index fef5d6b028..a10299d5e1 100644 --- a/doc/src/compute_vacf.rst +++ b/doc/src/compute_vacf.rst @@ -80,5 +80,3 @@ Related commands :doc:`compute msd ` **Default:** none - - diff --git a/doc/src/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst index c08f831826..338265374b 100644 --- a/doc/src/compute_vcm_chunk.rst +++ b/doc/src/compute_vcm_chunk.rst @@ -79,5 +79,3 @@ Restrictions **Related commands:** none **Default:** none - - diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 4d43126fa4..0e75db4999 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -249,5 +249,3 @@ Related commands :doc:`dump custom `, :doc:`dump local ` **Default:** *neighbors* no, *peratom* yes - - diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index dd1c4d558d..b7ed547572 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -271,5 +271,3 @@ Volume C: Mathematical and Chemical Tables, 249-429 (2004). **(Peng)** Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 (1996). - - diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index c554e6984d..c54fd675dc 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -385,5 +385,3 @@ The default for the *basis* keyword is that all created atoms are assigned the argument *type* as their atom type (when single atoms are being created). The other defaults are *remap* = no, *rotate* = random, and *units* = lattice. - - diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index 4fcc178e11..332b0ad0df 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -232,5 +232,3 @@ Default """"""" The keyword default is special = yes. - - diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index fe1edfc629..67690207f9 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -163,5 +163,3 @@ Related commands :doc:`region ` **Default:** none - - diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 7ed9cfed9a..97f4700612 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -168,5 +168,3 @@ Default """"""" The option defaults are compress = yes, bond = no, mol = no. - - diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index c6dcd362e6..11d9954647 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -161,5 +161,3 @@ Related commands :doc:`special_bonds `, :doc:`fix shake ` **Default:** none - - diff --git a/doc/src/dielectric.rst b/doc/src/dielectric.rst index 4eb25f0439..f5cbf56a0f 100644 --- a/doc/src/dielectric.rst +++ b/doc/src/dielectric.rst @@ -48,5 +48,3 @@ Default .. parsed-literal:: dielectric 1.0 - - diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index ce91bee44d..c5475b97d1 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -190,5 +190,3 @@ Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998). - - diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst index 39f45e1afc..3263671f34 100644 --- a/doc/src/dihedral_class2.rst +++ b/doc/src/dihedral_class2.rst @@ -195,5 +195,3 @@ Related commands **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). - - diff --git a/doc/src/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst index fcd9955ad9..be455b384b 100644 --- a/doc/src/dihedral_coeff.rst +++ b/doc/src/dihedral_coeff.rst @@ -112,5 +112,3 @@ Related commands :doc:`dihedral_style ` **Default:** none - - diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index 8f54f2b4ee..09413622ef 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -95,5 +95,3 @@ Related commands :doc:`angle_style cosine/shift/exp ` **Default:** none - - diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index 6b306a4e15..5fd00bbb8d 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -88,5 +88,3 @@ Related commands :doc:`dihedral_coeff ` **Default:** none - - diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst index 374291ce9e..82de0499db 100644 --- a/doc/src/dihedral_harmonic.rst +++ b/doc/src/dihedral_harmonic.rst @@ -100,5 +100,3 @@ Related commands :doc:`dihedral_coeff ` **Default:** none - - diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 44dac56e07..9a2b7f2846 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -98,5 +98,3 @@ Related commands **(Guo)** Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996). - - diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst index ff3c6a9fe0..0aecb24d20 100644 --- a/doc/src/dihedral_hybrid.rst +++ b/doc/src/dihedral_hybrid.rst @@ -104,5 +104,3 @@ Related commands :doc:`dihedral_coeff ` **Default:** none - - diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index f5a0999595..8833d7b544 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -82,5 +82,3 @@ Related commands :doc:`dihedral_coeff ` **Default:** none - - diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index ca4de96101..0623f71531 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -82,5 +82,3 @@ Related commands :doc:`dihedral_coeff ` **Default:** none - - diff --git a/doc/src/dihedral_none.rst b/doc/src/dihedral_none.rst index 86451451fa..1edba31372 100644 --- a/doc/src/dihedral_none.rst +++ b/doc/src/dihedral_none.rst @@ -39,5 +39,3 @@ Related commands :doc:`dihedral_style zero ` **Default:** none - - diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst index bd5c9e63a5..cbe5e596af 100644 --- a/doc/src/dihedral_opls.rst +++ b/doc/src/dihedral_opls.rst @@ -104,5 +104,3 @@ Related commands **(Watkins)** Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001). - - diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index 36906abd7e..25048fadb6 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -83,5 +83,3 @@ Related commands :doc:`dihedral_coeff ` **Default:** none - - diff --git a/doc/src/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst index 90ba6f8ae5..fdb5938270 100644 --- a/doc/src/dihedral_spherical.rst +++ b/doc/src/dihedral_spherical.rst @@ -97,5 +97,3 @@ Related commands :doc:`dihedral_coeff ` **Default:** none - - diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index 103ea44297..9091008340 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -143,5 +143,3 @@ Default """"""" dihedral\_style none - - diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index 60fd465729..02a618b23b 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -226,5 +226,3 @@ Related commands :doc:`dihedral_coeff ` **Default:** none - - diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst index 0a069b37a5..5af64b06e7 100644 --- a/doc/src/dihedral_table_cut.rst +++ b/doc/src/dihedral_table_cut.rst @@ -229,5 +229,3 @@ Related commands **(Salerno)** Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018). - - diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 6ec39e319e..38712957e8 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -51,5 +51,3 @@ Restrictions :doc:`dihedral_style none ` **Default:** none - - diff --git a/doc/src/dimension.rst b/doc/src/dimension.rst index a3c9c44905..0f4fc329d6 100644 --- a/doc/src/dimension.rst +++ b/doc/src/dimension.rst @@ -59,5 +59,3 @@ Default .. parsed-literal:: dimension 3 - - diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index 1e63fc9954..5d714c9625 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -160,5 +160,3 @@ Default """"""" The option defaults are units = lattice. - - diff --git a/doc/src/dump.rst b/doc/src/dump.rst index f15d352c9b..89a0c53e30 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -726,5 +726,3 @@ Default The defaults for the *image* and *movie* styles are listed on the :doc:`dump image ` doc page. - - diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index 4e01ef76d4..b885a7cb85 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -88,6 +88,3 @@ Related commands ---------- - - - diff --git a/doc/src/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst index 5bd0fd41d4..02e40b7b67 100644 --- a/doc/src/dump_cfg_uef.rst +++ b/doc/src/dump_cfg_uef.rst @@ -60,5 +60,3 @@ Related commands :doc:`fix nvt/uef ` **Default:** none - - diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index 4317ae7fed..ee42cc54a6 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -151,5 +151,3 @@ Related commands efficient, and portable file format for molecular data, Comp. Phys. Comm. 185(6), 1546-1553 (2014) - `[arXiv:1308.6382] `_. - - diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 923fcea56c..60e6bf52ea 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -746,5 +746,3 @@ The defaults for the keywords are as follows: * subbox no 0.0 * shiny = 1.0 * ssao = no - - diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 8c18814242..259a30d1cc 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -1193,5 +1193,3 @@ Divide each value by 255 to get the equivalent 0.0 to 1.0 value. +-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ | wheat = 245, 222, 179 | white = 255, 255, 255 | whitesmoke = 245, 245, 245 | yellow = 255, 255, 0 | yellowgreen = 154, 205, 50 | +-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ - - diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst index 4037772a59..fa9eb106c9 100644 --- a/doc/src/dump_molfile.rst +++ b/doc/src/dump_molfile.rst @@ -138,5 +138,3 @@ Default """"""" The default path is ".". All other properties have to be specified. - - diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst index 5a9fc52481..c03ea4ef1e 100644 --- a/doc/src/dump_netcdf.rst +++ b/doc/src/dump_netcdf.rst @@ -90,5 +90,3 @@ Related commands """""""""""""""" :doc:`dump `, :doc:`dump_modify `, :doc:`undump ` - - diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index b4c2633437..aab7d7809d 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -192,5 +192,3 @@ Default By default, files are written in ASCII format. If the file extension is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used. - - diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst index 2aaaafbe75..0f5b2093fc 100644 --- a/doc/src/dynamical_matrix.rst +++ b/doc/src/dynamical_matrix.rst @@ -81,5 +81,3 @@ Default """"""" The default settings are file = "dynmat.dyn", binary = no - - diff --git a/doc/src/echo.rst b/doc/src/echo.rst index 1251633733..6ed4911b2c 100644 --- a/doc/src/echo.rst +++ b/doc/src/echo.rst @@ -46,5 +46,3 @@ Default .. parsed-literal:: echo log - - diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 2baeb3a2c8..57a1b706b3 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -407,5 +407,3 @@ Related commands :doc:`unfix `, :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 04289c3614..0e57ec98c1 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -383,5 +383,3 @@ Default """"""" The option defaults are scale = no, reset = no. - - diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index b86aaee7e3..2ec43eb5fc 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -325,5 +325,3 @@ Default """"""" The option defaults are scale = no, reset = no, after = no. - - diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 50001a03d9..f85c3f4925 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -199,5 +199,3 @@ Default """"""" The option default for the every keyword is every = 1. - - diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst index 80ff444a37..f9a17cc3ef 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -101,5 +101,3 @@ Related commands :doc:`fix addforce ` **Default:** none - - diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst index 7d1fea03a5..ff3fea459f 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -121,5 +121,3 @@ Default The keyword defaults are size = 0.0, freq = 0, units = lattice. All added atoms are of type 1 unless the basis keyword is used. - - diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index f5d2f8269e..48ee5cb243 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -290,5 +290,3 @@ For detailed exposition of the theory and algorithms please see: **(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115. Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation. - - diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index 7965176d9e..ce6190a58c 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -206,5 +206,3 @@ all atom types. **(Sadigh)** B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012). - - diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 433e90d1e1..4a33a5e85c 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -187,5 +187,3 @@ Related commands :doc:`variable `, **Default:** none - - diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index 4515f3e997..f757894c02 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -513,5 +513,3 @@ Default The option defaults are norm = all, ave = one, bias = none, no file output, and title 1,2,3 = strings as described above. - - diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 8b3ced4cc9..277a7ac25c 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -386,5 +386,3 @@ Related commands The option defaults are ave = one, type = auto, start = 0, no file output, title 1,2,3 = strings as described above, and prefactor = 1.0. - - diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst index 3450b017a5..6c9d7c076b 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -155,5 +155,3 @@ follows: ncorr=20, nlen=16, ncount=2. **(Ramirez)** J. Ramirez, S.K. Sukumaran, B. Vorselaars and A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010). - - diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 0bfcba9fa2..2987c25731 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -388,5 +388,3 @@ Related commands The option defaults are mode = scalar, kind = figured out from input arguments, ave = one, start = 0, no file output, beyond = ignore, and title 1,2,3 = strings as described above. - - diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index ea2c21fcf7..20bd4382c7 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -368,5 +368,3 @@ Default The option defaults are mode = scalar, ave = one, start = 0, no file output, format = %g, title 1,2,3 = strings as described above, and no off settings for any input values. - - diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index 78266a7758..d6f67d14c7 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -132,5 +132,3 @@ Related commands :doc:`fix setforce `, :doc:`fix addforce ` **Default:** none - - diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 2a5d18bca1..6ba6605377 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -422,6 +422,3 @@ Related commands .. _pizza: http://pizza.sandia.gov **Default:** none - - - diff --git a/doc/src/fix_bocs.rst b/doc/src/fix_bocs.rst index f699762e50..5ee6ba2f83 100644 --- a/doc/src/fix_bocs.rst +++ b/doc/src/fix_bocs.rst @@ -133,5 +133,3 @@ paper by Dunn et. al. :ref:`(Dunn2) ` . **(Dunn2)** Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018). - - diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index ea7e2c5acc..ce06447f07 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -156,5 +156,3 @@ Default """"""" The option defaults are prob = 1.0. - - diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index b1d1ff269c..5ed22bcd58 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -258,5 +258,3 @@ Default The option defaults are iparam = (0,itype), jparam = (0,jtype), and prob = 1.0. - - diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index cd3e737b0b..ec431168b8 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -541,5 +541,3 @@ update\_edges = none **(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211 (2017). - - diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst index 96fd8717dc..296cf986cf 100644 --- a/doc/src/fix_bond_swap.rst +++ b/doc/src/fix_bond_swap.rst @@ -209,5 +209,3 @@ Related commands **(Sides)** Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, 199-208 (2004). - - diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst index 4a52fbd6ce..d915d1a2a0 100644 --- a/doc/src/fix_box_relax.rst +++ b/doc/src/fix_box_relax.rst @@ -415,5 +415,3 @@ The keyword defaults are dilate = all, vmax = 0.0001, nreset = 0. **(Parrinello1981)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). - - diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst index 3a9ef1a8af..85b0762d21 100644 --- a/doc/src/fix_client_md.rst +++ b/doc/src/fix_client_md.rst @@ -108,5 +108,3 @@ Related commands :doc:`message `, :doc:`server ` **Default:** none - - diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index 61c0e60860..00a1851e88 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -165,5 +165,3 @@ Related commands **(Brooks)** Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009). - - diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index 15199761c5..dd4057a346 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -155,5 +155,3 @@ and tstat = NULL. **(Fiorin)** Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 - - diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 71040fd473..7561df6856 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -224,5 +224,3 @@ Related commands :doc:`fix adapt ` **Default:** none - - diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index c3b332543f..1ddeff6953 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -636,5 +636,3 @@ Default """"""" The option defaults are remap = x, flip = yes, and units = lattice. - - diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 1e58d0ca89..573e9bdf2b 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -320,5 +320,3 @@ is an equal probabilities for all molecules in the template. Additional option defaults are id = max, delta = 0.0, near = 0.0, attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0, and units = lattice. - - diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index 817b24862e..ce370a90f6 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -120,5 +120,3 @@ J. Chem. Phys., 135, 204105 (2011). W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014). - - diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 40efdf3e29..368971b1c7 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -117,5 +117,3 @@ temperature-dependent properties", J. Comput. Phys., 265: 113-127 "Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems", J. Chem. Phys., 143: 014101 (2015). DOI: 10.1063/1.4923254 - - diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst index 7b2a55b57a..38f86ff8f8 100644 --- a/doc/src/fix_drag.rst +++ b/doc/src/fix_drag.rst @@ -67,5 +67,3 @@ Related commands :doc:`fix spring/rg `, :doc:`fix smd ` **Default:** none - - diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst index 9fae8aa926..2bf34ce90f 100644 --- a/doc/src/fix_drude.rst +++ b/doc/src/fix_drude.rst @@ -52,5 +52,3 @@ Related commands :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair_style thole ` **Default:** None - - diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 8ed0ff41d7..4ee850c617 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -224,5 +224,3 @@ Related commands **(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003). - - diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index cc000f04a5..ca95e576b7 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -111,5 +111,3 @@ Default The option defaults are units = lattice, and no emax kinetic energy limit. - - diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index 771e9e1598..a530ccb689 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -179,5 +179,3 @@ Related commands :doc:`fix addforce ` **Default:** none - - diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst index 55aeaa2e72..34445fd284 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -202,5 +202,3 @@ Related commands **(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015). - - diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index d7daeada50..d617eb9a45 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -203,5 +203,3 @@ The default is no limitation by region, and minneigh = 1. **(PASS)** PASS webpage: https://www.sdu.dk/en/DPASS - - diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index 3404afe9bc..7605c3cd5a 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -76,5 +76,3 @@ Restrictions **Related commands:** none **Default:** none - - diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst index 86b0e00b43..b871429ffa 100644 --- a/doc/src/fix_eos_cv.rst +++ b/doc/src/fix_eos_cv.rst @@ -72,5 +72,3 @@ Related commands W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014). - - diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst index ee5654cf50..1f8ec7ba9b 100644 --- a/doc/src/fix_eos_table.rst +++ b/doc/src/fix_eos_table.rst @@ -127,5 +127,3 @@ Related commands :doc:`fix shardlow `, :doc:`pair dpd/fdt ` **Default:** none - - diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index 9d771ea02d..467c4118c2 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -224,6 +224,3 @@ Related commands ---------- - - - diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst index 0647fb436e..c24cb51738 100644 --- a/doc/src/fix_evaporate.rst +++ b/doc/src/fix_evaporate.rst @@ -105,5 +105,3 @@ Default """"""" The option defaults are molecule = no. - - diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index e108469999..c20b591906 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -180,5 +180,3 @@ Restrictions **Related commands:** none **Default:** none - - diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst index 5faddf0a18..07a483039f 100644 --- a/doc/src/fix_ffl.rst +++ b/doc/src/fix_ffl.rst @@ -135,5 +135,3 @@ Related commands **(Bussi)** G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007) - - diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst index 362d7cc8ae..8812398bbe 100644 --- a/doc/src/fix_filter_corotate.rst +++ b/doc/src/fix_filter_corotate.rst @@ -97,5 +97,3 @@ Related commands **(Fath)** Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017). - - diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index 22b92bd3c0..4077d45e01 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -183,5 +183,3 @@ The option default for the *energy* keyword is energy = no. **(Zhu)** Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002). - - diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index 03639a0a48..3aa7512bad 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -94,5 +94,3 @@ Related commands :doc:`atom_style sphere `, :doc:`fix setforce ` **Default:** none - - diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index 77f5a59fd4..a0717dd6ae 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -493,5 +493,3 @@ listed above. **(Frenkel)** Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002. - - diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index d25d06f042..fdc1bd3c6a 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -174,5 +174,3 @@ The option defaults are frozen = no, zero = no. **(Baczewski)** A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013). - - diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index 1eef32d68c..e4aadfa401 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -175,5 +175,3 @@ Related commands **(Ceriotti2)** Ceriotti, Bussi and Parrinello, Phys Rev Lett 103, 030603 (2009) - - diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index 38f61f532b..6fbf9a80c5 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -156,5 +156,3 @@ Related commands :doc:`atom_style sphere `, :doc:`fix addforce ` **Default:** none - - diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index 3e6309d5f6..4c2054e0c0 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -124,5 +124,3 @@ Related commands **(Malolepsza)** Malolepsza, Secor, Keyes, J Phys Chem B 119 (42), 13379-13384 (2015). - - diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index d85eddfc53..296be3aa10 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -167,5 +167,3 @@ Default """"""" The option defaults are error = hard and message = yes. - - diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst index 7fb7c87733..86850a2db7 100644 --- a/doc/src/fix_heat.rst +++ b/doc/src/fix_heat.rst @@ -137,5 +137,3 @@ Related commands :doc:`fix ehex `, :doc:`compute temp `, :doc:`compute temp/region ` **Default:** none - - diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index 62796c2ca2..809bd37981 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -294,5 +294,3 @@ Related commands **(Miron)** R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003). - - diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index e278a29d5d..335cd10f69 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -570,5 +570,3 @@ default. **(Miron)** R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003). - - diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index d224aca553..d7931e1666 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -175,5 +175,3 @@ needs to use a different port number. **Related commands:** none **Default:** none - - diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index 203874cf97..51a90bc3cc 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -227,5 +227,3 @@ Default """"""" The option defaults are side = out and units = lattice. - - diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index 3be859c108..d0e1903689 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -110,5 +110,3 @@ Related commands **(IPI)** `http://epfl-cosmo.github.io/gle4md/index.html?page=ipi `_ - - diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index b776ca015b..45b900b298 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -379,5 +379,3 @@ types, tally = no, zero = no, gjf = no. **(Gronbech-Jensen)** Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506 - - diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index 29dd71e12e..712847ba5d 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -319,5 +319,3 @@ The option defaults are zero = no. **(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011). - - diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index 572019f9f1..2fa055e380 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -133,5 +133,3 @@ The option defaults are scale = 1.0 for all types and tally = no. **(Schneider)** Schneider and Stoll, Phys Rev B, 17, 1302 (1978). - - diff --git a/doc/src/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst index 2a5b235964..bccedc8520 100644 --- a/doc/src/fix_langevin_spin.rst +++ b/doc/src/fix_langevin_spin.rst @@ -119,5 +119,3 @@ Related commands **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). - - diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index adcb7fb5b6..ddea5a809f 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -252,5 +252,3 @@ J. Sci. Comput. 36 (2), 147-170, (2014). **(Negre2016)** C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016). - - diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index a7d05f33f4..b7ce7ffdc8 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -405,5 +405,3 @@ If walls are present, they are assumed to be stationary. **(Adhikari et al.)** Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479. - - diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index 9d85e76c6b..8eb4fa094b 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -82,5 +82,3 @@ Default """"""" Zeros the total system linear momentum in each dimension. - - diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst index d689489a4e..44a86047fb 100644 --- a/doc/src/fix_lb_pc.rst +++ b/doc/src/fix_lb_pc.rst @@ -66,5 +66,3 @@ Related commands **(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. - - diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst index 5f1c5e3a9e..34336f0940 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.rst +++ b/doc/src/fix_lb_rigid_pc_sphere.rst @@ -166,5 +166,3 @@ The defaults are force \* on on on, and torque \* on on on. **(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. - - diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst index 821ea54ad2..d20e969f80 100644 --- a/doc/src/fix_lb_viscous.rst +++ b/doc/src/fix_lb_viscous.rst @@ -101,5 +101,3 @@ Related commands **(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. - - diff --git a/doc/src/fix_lineforce.rst b/doc/src/fix_lineforce.rst index d365a63554..b97936fead 100644 --- a/doc/src/fix_lineforce.rst +++ b/doc/src/fix_lineforce.rst @@ -55,5 +55,3 @@ Related commands :doc:`fix planeforce ` **Default:** none - - diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst index dc17f0f706..63a90c626e 100644 --- a/doc/src/fix_manifoldforce.rst +++ b/doc/src/fix_manifoldforce.rst @@ -67,5 +67,3 @@ Related commands """""""""""""""" :doc:`fix nve/manifold/rattle `, :doc:`fix nvt/manifold/rattle ` - - diff --git a/doc/src/fix_meso.rst b/doc/src/fix_meso.rst index 2db76d7b4d..8eb6b4831d 100644 --- a/doc/src/fix_meso.rst +++ b/doc/src/fix_meso.rst @@ -54,5 +54,3 @@ Related commands "fix meso/stationary" **Default:** none - - diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst index 22319b2600..eb60f18146 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -266,5 +266,3 @@ Default """"""" The option default is units = lattice. - - diff --git a/doc/src/fix_meso_stationary.rst b/doc/src/fix_meso_stationary.rst index 140649f1ef..6d8eebfdd7 100644 --- a/doc/src/fix_meso_stationary.rst +++ b/doc/src/fix_meso_stationary.rst @@ -55,5 +55,3 @@ Related commands "fix meso" **Default:** none - - diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index 0cb0ac98b2..4ac460952f 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -167,5 +167,3 @@ Default The option defaults are temp = ID defined by fix, press = ID defined by fix, energy = no, virial = different for each fix style, respa = 0, bodyforce = late. - - diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index e14d16c91e..f2730e54e4 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -110,5 +110,3 @@ Related commands :doc:`fix recenter `, :doc:`velocity ` **Default:** none - - diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index 1e79d7ce8e..82b5b585a0 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -256,5 +256,3 @@ Related commands **Default:** none The option default is units = lattice. - - diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst index 0484a6c973..e6b09d9cc6 100644 --- a/doc/src/fix_mscg.rst +++ b/doc/src/fix_mscg.rst @@ -148,5 +148,3 @@ The default keyword settings are range off, max 4 12 36. **(Noid)** Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys 128, 134105 (2008). - - diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst index 5270248ea9..36f2bd2ae0 100644 --- a/doc/src/fix_msst.rst +++ b/doc/src/fix_msst.rst @@ -221,5 +221,3 @@ timestep. **(Goldman)** Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner, J. Phys. Chem. C, 117, 7885 (2013). - - diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index 4cae1776e7..55066c8ce4 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -112,5 +112,3 @@ The default value for the optional *lambda* parameter is 0.5. **(Groot)** Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI: 10.1063/1.474784 - - diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 7abbbf5986..2b79185551 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -285,5 +285,3 @@ and Coker World Scientific, Singapore, 1998, p 385. **(Maras)** Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016). - - diff --git a/doc/src/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst index 1afcf0624e..ffef23873c 100644 --- a/doc/src/fix_neb_spin.rst +++ b/doc/src/fix_neb_spin.rst @@ -86,5 +86,3 @@ none **(BessarabB)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015). - - diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index ac9bef40c6..36f2d6c8f3 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -736,5 +736,3 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006). **(Dullweber)** Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997). - - diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 07cd487ced..1f07d13625 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -174,5 +174,3 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006). **(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). - - diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 124ca188aa..2732087800 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -272,5 +272,3 @@ given in :doc:`fix nvt/sllod `. **(Nicholson and Rutledge)** Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016). - - diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index 8500184eac..8f4a4ad39b 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -157,5 +157,3 @@ Related commands :doc:`fix nph `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_nph_body.rst b/doc/src/fix_nph_body.rst index d1e51e56b6..bae12f2b86 100644 --- a/doc/src/fix_nph_body.rst +++ b/doc/src/fix_nph_body.rst @@ -150,5 +150,3 @@ Related commands :doc:`fix nph `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix npt\_body `, :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index 14c7b38791..d7322aa46d 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -170,5 +170,3 @@ Related commands :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index 25483556a9..2261600f93 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -252,5 +252,3 @@ The keyword defaults are the same as those for :doc:`fix npt ` **(Ravelo)** Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). - - diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index 261dc4a333..2b84011cc8 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -182,5 +182,3 @@ Related commands :doc:`fix npt `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_npt_body.rst b/doc/src/fix_npt_body.rst index 33303b3ed8..4eecd404ff 100644 --- a/doc/src/fix_npt_body.rst +++ b/doc/src/fix_npt_body.rst @@ -175,5 +175,3 @@ Related commands :doc:`fix npt `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index cd6b13d89e..133305f13c 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -672,5 +672,3 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006). **(Miller)** Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, 144, 184107 (2016). - - diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index daba4c3b9b..d82e4e26cb 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -194,5 +194,3 @@ Related commands :doc:`fix npt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_sphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index deff980bba..b3928e6389 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -83,5 +83,3 @@ Related commands :doc:`fix nvt `, :doc:`fix npt ` **Default:** none - - diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index f7e6ea7fae..ea311d3f69 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -91,5 +91,3 @@ Related commands :doc:`fix nve `, :doc:`fix nve/sphere ` **Default:** none - - diff --git a/doc/src/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst index 4f41ffc21d..ed2897c978 100644 --- a/doc/src/fix_nve_asphere_noforce.rst +++ b/doc/src/fix_nve_asphere_noforce.rst @@ -65,5 +65,3 @@ Related commands :doc:`fix nve/noforce `, :doc:`fix nve/asphere ` **Default:** none - - diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst index aa4c4c1cfc..c29de946d8 100644 --- a/doc/src/fix_nve_awpmd.rst +++ b/doc/src/fix_nve_awpmd.rst @@ -58,5 +58,3 @@ Related commands :doc:`fix nve ` **Default:** none - - diff --git a/doc/src/fix_nve_body.rst b/doc/src/fix_nve_body.rst index 20231fe5e6..36a9a426ec 100644 --- a/doc/src/fix_nve_body.rst +++ b/doc/src/fix_nve_body.rst @@ -62,5 +62,3 @@ Related commands :doc:`fix nve `, :doc:`fix nve/sphere `, :doc:`fix nve/asphere ` **Default:** none - - diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst index 7f7dd51720..5f3ede0386 100644 --- a/doc/src/fix_nve_dot.rst +++ b/doc/src/fix_nve_dot.rst @@ -77,5 +77,3 @@ Related commands .. _Henrich4: **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). - - diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index 2bbe8d6f45..5704966827 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -169,5 +169,3 @@ Related commands .. _Henrich5: **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). - - diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst index eab8e423c8..88bc6a3607 100644 --- a/doc/src/fix_nve_eff.rst +++ b/doc/src/fix_nve_eff.rst @@ -53,5 +53,3 @@ Related commands :doc:`fix nve `, :doc:`fix nvt/eff `, :doc:`fix npt/eff ` **Default:** none - - diff --git a/doc/src/fix_nve_limit.rst b/doc/src/fix_nve_limit.rst index 9965688639..07746e71a2 100644 --- a/doc/src/fix_nve_limit.rst +++ b/doc/src/fix_nve_limit.rst @@ -91,5 +91,3 @@ Related commands :doc:`pair_style soft ` **Default:** none - - diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst index f7193b057b..ec971bc41e 100644 --- a/doc/src/fix_nve_line.rst +++ b/doc/src/fix_nve_line.rst @@ -58,5 +58,3 @@ Related commands :doc:`fix nve `, :doc:`fix nve/asphere ` **Default:** none - - diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index ac1f0799b8..68c2d7b574 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -122,5 +122,3 @@ Related commands **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 `_. - - diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst index ebf0a0dd87..568be83bdc 100644 --- a/doc/src/fix_nve_noforce.rst +++ b/doc/src/fix_nve_noforce.rst @@ -57,5 +57,3 @@ Related commands :doc:`fix nve ` **Default:** none - - diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index dc3d27d24d..b5460fa1e0 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -139,5 +139,3 @@ Related commands **(Dullweber)** Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997). - - diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst index 7041cd256d..6caa7cc8a6 100644 --- a/doc/src/fix_nve_spin.rst +++ b/doc/src/fix_nve_spin.rst @@ -106,5 +106,3 @@ The option default is lattice = moving. **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). - - diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst index 76e1614797..6c4bb882e6 100644 --- a/doc/src/fix_nve_tri.rst +++ b/doc/src/fix_nve_tri.rst @@ -59,5 +59,3 @@ Related commands :doc:`fix nve `, :doc:`fix nve/asphere ` **Default:** none - - diff --git a/doc/src/fix_nvk.rst b/doc/src/fix_nvk.rst index c6836f4531..3eb1755411 100644 --- a/doc/src/fix_nvk.rst +++ b/doc/src/fix_nvk.rst @@ -82,5 +82,3 @@ LAMMPS was built with that package. See the :doc:`Build package **(Zhang)** Zhang, J Chem Phys, 106, 6102 (1997). - - diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index 3c0cea29e3..35a18a205c 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -156,5 +156,3 @@ Related commands :doc:`fix nvt `, :doc:`fix nve\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst index 22e926da1a..e564092d35 100644 --- a/doc/src/fix_nvt_body.rst +++ b/doc/src/fix_nvt_body.rst @@ -149,5 +149,3 @@ Related commands :doc:`fix nvt `, :doc:`fix nve\_body `, :doc:`fix npt\_body `, :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index 1cb10b8417..6fb9d8de3a 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -96,5 +96,3 @@ Related commands **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 `_. - - diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst index 7b8274ed60..e195121c9a 100644 --- a/doc/src/fix_nvt_sllod.rst +++ b/doc/src/fix_nvt_sllod.rst @@ -208,5 +208,3 @@ Same as :doc:`fix nvt `, except tchain = 1. **(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). - - diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst index 1df8d45f37..58836f17d6 100644 --- a/doc/src/fix_nvt_sllod_eff.rst +++ b/doc/src/fix_nvt_sllod_eff.rst @@ -96,5 +96,3 @@ Same as :doc:`fix nvt/eff `, except tchain = 1. **(Tuckerman)** Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997). - - diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index c2f9ccfeef..7bf80307ae 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -169,5 +169,3 @@ Related commands :doc:`fix nvt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_sphere `, :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst index 660f263d57..a1a11970a6 100644 --- a/doc/src/fix_oneway.rst +++ b/doc/src/fix_oneway.rst @@ -65,6 +65,3 @@ Related commands ---------- - - - diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index ef0d2d2bdc..7100efc4e5 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -224,5 +224,3 @@ file1: 2.395231296138225 0.000000000000000 -0.798410432046075 1.596820864092150 1.785300000000000 0.798410432046075 1.596820864092150 -1.785300000000000 0.798410432046075 - - diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index 819833f0b6..93572b27c6 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -238,5 +238,3 @@ method*\ , `Computer Physics Communications [182](2):540-541 (2011). `_ - - diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index d3f903e9c1..436b13d9bc 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -221,5 +221,3 @@ Path Integrals, McGraw-Hill, New York (1965). **(Calhoun)** A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996). - - diff --git a/doc/src/fix_planeforce.rst b/doc/src/fix_planeforce.rst index ea87640f83..ed830e7135 100644 --- a/doc/src/fix_planeforce.rst +++ b/doc/src/fix_planeforce.rst @@ -55,5 +55,3 @@ Related commands :doc:`fix lineforce ` **Default:** none - - diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index 23068c979b..0f6ccf4d31 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -133,7 +133,3 @@ The default options are plumedfile = NULL and outfile = NULL .. _plumedhome: http://www.plumed.org/ - - - - diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index 8eec68813d..38b4794237 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -152,5 +152,3 @@ Related commands **(Anderson)** Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", Engineering With Computers (2006). (`link to paper `_) - - diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index 1cb98b3ac0..d5933ba296 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -284,5 +284,3 @@ setting is defined. If the *mol* keyword is used, the default for Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol = 0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0 (for 3d), vel = 0.0 0.0 0.0 (for 2d), and id = max. - - diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst index 0b0bbae54d..fd45553713 100644 --- a/doc/src/fix_press_berendsen.rst +++ b/doc/src/fix_press_berendsen.rst @@ -255,5 +255,3 @@ pressure for whatever :doc:`units ` are defined. **(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984). - - diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst index f79f465334..1b97a3f879 100644 --- a/doc/src/fix_print.rst +++ b/doc/src/fix_print.rst @@ -117,5 +117,3 @@ Default The option defaults are no file output, screen = yes, and title string as described above. - - diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index 7189fdac88..d225acc0e5 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -106,5 +106,3 @@ Eur. Phys. J. B 15, 105-113, 2000. **(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012. **Default:** types - - diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 42c755e8af..799d62a0aa 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -336,5 +336,3 @@ Default """"""" The default keyword values are ghost = no. - - diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index 097954db3d..f45f3f8f5b 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -86,5 +86,3 @@ Related commands """""""""""""""" :doc:`python command ` - - diff --git a/doc/src/fix_python_move.rst b/doc/src/fix_python_move.rst index 2be9d95437..44fd76040a 100644 --- a/doc/src/fix_python_move.rst +++ b/doc/src/fix_python_move.rst @@ -110,5 +110,3 @@ Related commands :doc:`fix nve `, :doc:`fix python/invoke ` **Default:** none - - diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index 828312eecf..94a4294e8b 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -249,5 +249,3 @@ T\_init=300.0. e0, p0, and v0 are calculated on the first step. **(Qi)** Qi and Reed, J. Phys. Chem. A 116, 10451 (2012). - - diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 1c84764e4e..6ac647dad9 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -263,5 +263,3 @@ Physical Chemistry, 105, 9396-9049 (2001) **(QEq/Fire)** T.-R. Shan, A. P. Thompson, S. J. Plimpton, in preparation - - diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index c3b336e13d..dcd0950bf2 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -158,5 +158,3 @@ Phillpot, Phys Rev B, 81, 125328 (2010). **(Rick\_and\_Stuart)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141 (1994). - - diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst index f3013d712f..ab26c27bde 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -149,5 +149,3 @@ Related commands **(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012). - - diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index 17d882e0e3..d3aaa4b6f3 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -66,5 +66,3 @@ executable. See the lib/qmmm/README file for details. **Related commands:** none **Default:** none - - diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst index 63897cff90..235c28ca19 100644 --- a/doc/src/fix_qtb.rst +++ b/doc/src/fix_qtb.rst @@ -211,5 +211,3 @@ Lett, 103, 190601 (2009). **(Barrat)** Barrat and Rodney, J. Stat. Phys, 144, 679 (2011). - - diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index 9c542c5194..dd5c9e6634 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -115,5 +115,3 @@ Related commands :doc:`pair_style reax/c `, :doc:`fix reax/c/species ` **Default:** none - - diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index 464f943997..a709ddaa35 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -197,5 +197,3 @@ Default The default values for bond-order cutoffs are 0.3 for all I-J pairs. The default element symbols are C, H, O, N. Position files are not written by default. - - diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst index df5805059e..6c63ead911 100644 --- a/doc/src/fix_recenter.rst +++ b/doc/src/fix_recenter.rst @@ -136,5 +136,3 @@ Default """"""" The option defaults are shift = fix group-ID, and units = lattice. - - diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst index fa452f8e78..ba381a37d3 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -64,5 +64,3 @@ Related commands **(Pedersen)** Pedersen, J. Chem. Phys., 139, 104102 (2013). - - diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index b1ad30a875..15f7c41b60 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -951,5 +951,3 @@ J Chem Phys, 116, 8649 (2002). **(Zhang)** Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004). - - diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index d5d3c7cf2d..3f6796c4c6 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -389,5 +389,3 @@ torque. Also reinit = yes. **(Miller)** Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, J Chem Phys, 116, 8649 (2002). - - diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index 2658afc1ac..ce40a58524 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -246,5 +246,3 @@ Related commands :doc:`pair dpd/fdt/energy ` **Default:** none - - diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst index 2ff6aa145c..c2f57618ed 100644 --- a/doc/src/fix_saed_vtk.rst +++ b/doc/src/fix_saed_vtk.rst @@ -212,5 +212,3 @@ The option defaults are ave = one, start = 0, no file output. **(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013). - - diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index 88cfa12f53..3e358aef31 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -160,5 +160,3 @@ Related commands :doc:`fix addforce `, :doc:`fix aveforce ` **Default:** none - - diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index e9b4892af3..bca1a55d16 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -263,5 +263,3 @@ J of Comp Phys, 23, 327-341 (1977). **(Andersen)** H. Andersen, J of Comp Phys, 52, 24-34 (1983). - - diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index ed8b792f7b..771b6bf7e3 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -134,5 +134,3 @@ Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014). W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014). - - diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index fd5abade82..5c8496c2a8 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -177,5 +177,3 @@ Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998. **(Jarzynski)** Jarzynski, Phys. Rev. Lett. 78, 2690 (1997) - - diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst index ad3322e4f0..4677c455f3 100644 --- a/doc/src/fix_smd_adjust_dt.rst +++ b/doc/src/fix_smd_adjust_dt.rst @@ -67,5 +67,3 @@ Related commands :doc:`smd/tlsph\_dt ` **Default:** none - - diff --git a/doc/src/fix_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst index 8bd879108d..e153fec089 100644 --- a/doc/src/fix_smd_integrate_tlsph.rst +++ b/doc/src/fix_smd_integrate_tlsph.rst @@ -62,5 +62,3 @@ Related commands :doc:`smd/integrate\_ulsph ` **Default:** none - - diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index 9be6ff3414..d0fe508e4e 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -66,5 +66,3 @@ LAMMPS was built with that package. See the :doc:`Build package **Related commands:** none **Default:** none - - diff --git a/doc/src/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst index 912492b7f1..56fbccf2a6 100644 --- a/doc/src/fix_smd_move_triangulated_surface.rst +++ b/doc/src/fix_smd_move_triangulated_surface.rst @@ -86,5 +86,3 @@ Related commands :doc:`smd/wall\_surface ` **Default:** none - - diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index 1df6010bb6..9c860f2766 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -93,5 +93,3 @@ LAMMPS was built with that package. See the :doc:`Build package **Related commands:** none **Default:** none - - diff --git a/doc/src/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst index 810feab803..713569b372 100644 --- a/doc/src/fix_smd_wall_surface.rst +++ b/doc/src/fix_smd_wall_surface.rst @@ -79,5 +79,3 @@ Related commands :doc:`smd/tri\_surface ` **Default:** none - - diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst index 676b047297..e7db053d57 100644 --- a/doc/src/fix_spring.rst +++ b/doc/src/fix_spring.rst @@ -154,5 +154,3 @@ Related commands :doc:`fix spring/rg `, :doc:`fix smd ` **Default:** none - - diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst index a89c15c3d8..8cd05d98aa 100644 --- a/doc/src/fix_spring_chunk.rst +++ b/doc/src/fix_spring_chunk.rst @@ -92,5 +92,3 @@ Related commands :doc:`fix spring/rg ` **Default:** none - - diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst index 17637f0b22..e1463dc4e3 100644 --- a/doc/src/fix_spring_rg.rst +++ b/doc/src/fix_spring_rg.rst @@ -78,5 +78,3 @@ Related commands :doc:`fix drag `, :doc:`fix smd ` **Default:** none - - diff --git a/doc/src/fix_spring_self.rst b/doc/src/fix_spring_self.rst index 60d72f9f99..e74e515631 100644 --- a/doc/src/fix_spring_self.rst +++ b/doc/src/fix_spring_self.rst @@ -89,5 +89,3 @@ Related commands :doc:`fix smd `, :doc:`fix spring/rg ` **Default:** none - - diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 2f6529d079..92ae085ff1 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -425,5 +425,3 @@ Chem Phys, 132, 174106 (2010). **(Lechman)** Lechman, et al, in preparation (2010). - - diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst index aa91c469a5..1a9dbf5849 100644 --- a/doc/src/fix_store_force.rst +++ b/doc/src/fix_store_force.rst @@ -74,5 +74,3 @@ Related commands :doc:`fix store\_state ` **Default:** none - - diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index 7977a81792..d480a45d60 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -141,5 +141,3 @@ Default """"""" The option default is com = no. - - diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index 4c6820b1b6..6351bb947b 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/doc/src/fix_temp_berendsen.rst @@ -179,5 +179,3 @@ Related commands **(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984). - - diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index a6434353c8..d57c0e2583 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -191,5 +191,3 @@ Related commands **(Bussi2)** Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007) - - diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index 76b25ee517..b8713d6c85 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -166,5 +166,3 @@ Related commands :doc:`fix_modify ` **Default:** none - - diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst index de9c085b9e..6a13b4e922 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/doc/src/fix_temp_rescale_eff.rst @@ -76,5 +76,3 @@ Related commands :doc:`fix temp rescale `, **Default:** none - - diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst index b24481a493..2b111a4288 100644 --- a/doc/src/fix_tfmc.rst +++ b/doc/src/fix_tfmc.rst @@ -174,5 +174,3 @@ A. Stesmans, Phys. Rev. B 85, 134301 (2012). **(Neyts)** E. C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 (2013). - - diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index 5d309f5b78..4c62ccd9be 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/doc/src/fix_thermal_conductivity.rst @@ -181,5 +181,3 @@ The option defaults are swap = 1. **(Zhang)** Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, 109, 15060-15067 (2005). - - diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst index db6ddbf146..ec4599b519 100644 --- a/doc/src/fix_ti_spring.rst +++ b/doc/src/fix_ti_spring.rst @@ -182,5 +182,3 @@ Science, 112, 333 (2016). **(de Koning)** de Koning and Antonelli, Phys Rev E, 53, 465 (1996). - - diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst index 65bb697b53..30a927c7e7 100644 --- a/doc/src/fix_tmd.rst +++ b/doc/src/fix_tmd.rst @@ -144,5 +144,3 @@ coordinates for modelling activated processes", J Molecular Modeling, **(Schlitter2)** Schlitter and Klahn, "The free energy of a reaction coordinate at multiple constraints: a concise formulation", Molecular Physics, 101, 3439-3443 (2003). - - diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 49e5ddc0b0..eeafd8bfe0 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -376,5 +376,3 @@ Plasma Phys., 53, 129-139 (2013). **(Pisarev)** V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, 475401 (2014). - - diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index 9ec4c920e2..42040af013 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -102,5 +102,3 @@ Related commands Default """"""" - - diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 13428d45ad..92ebffba1e 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -174,5 +174,3 @@ Related commands :doc:`compute `, :doc:`variable ` **Default:** none - - diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index 4be98f6d25..9dd1cf3557 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -184,5 +184,3 @@ The option defaults are swap = 1 and vtarget = INF. **(Maginn)** Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, 260, 218-231 (2007). - - diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst index 982c07c8a4..026a850b46 100644 --- a/doc/src/fix_viscous.rst +++ b/doc/src/fix_viscous.rst @@ -115,5 +115,3 @@ Related commands :doc:`fix langevin ` **Default:** none - - diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 6126bf4274..ba37b19205 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -408,5 +408,3 @@ The option defaults units = lattice, fld = no, and pbc = no. **(Magda)** Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985); erratum in JCP 84, 2901 (1986). - - diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 17364bc5f5..6b0ba4b130 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -112,5 +112,3 @@ Related commands :doc:`atom_style body `, :doc:`pair_style body/rounded/polygon ` **Default:** none - - diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index d6ccfb5073..38e75de13a 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -111,5 +111,3 @@ Related commands :doc:`atom_style body `, :doc:`pair_style body/rounded/polyhedron ` **Default:** none - - diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index c9411e40c4..6374109cc6 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -138,5 +138,3 @@ none **(Babadi)** Babadi and Ejtehadi, EPL, 77 (2007) 23002. - - diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 1e4883927c..dde9af0f94 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -210,5 +210,3 @@ Related commands :doc:`pair_style granular ` **Default:** none - - diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 929982f3bf..6f82bfd85a 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -243,5 +243,3 @@ Related commands :doc:`region ` **Default:** none - - diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index e26381b66f..cb5c611f61 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -128,5 +128,3 @@ Default """"""" The keyword defaults are pos = 0, vel = 0, units = lattice. - - diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 612ffdfb1f..7a7cc6425b 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -214,5 +214,3 @@ The default for the units keyword is lattice. **(Bond)** Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007). - - diff --git a/doc/src/fix_wall_reflect_stochastic.rst b/doc/src/fix_wall_reflect_stochastic.rst index 9cfb98a0ee..bf254945a1 100644 --- a/doc/src/fix_wall_reflect_stochastic.rst +++ b/doc/src/fix_wall_reflect_stochastic.rst @@ -150,5 +150,3 @@ Stat. Phys. 1, 2, 101 (1971). **(To)** Q.D. To, V.H. Vu, G. Lauriat, and C. Leonard. J. Math. Phys. 56, 103101 (2015). - - diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index b7c68a8003..162b9d6994 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -225,5 +225,3 @@ Related commands :doc:`fix wall/gran ` **Default:** none - - diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index a0935bd99e..8685b39fff 100644 --- a/doc/src/fix_wall_srd.rst +++ b/doc/src/fix_wall_srd.rst @@ -218,5 +218,3 @@ Related commands :doc:`fix srd ` **Default:** none - - diff --git a/doc/src/group.rst b/doc/src/group.rst index fc72cdc713..9246f432c8 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -321,5 +321,3 @@ Default """"""" All atoms belong to the "all" group. - - diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst index 1b031224fa..59528ac7bb 100644 --- a/doc/src/group2ndx.rst +++ b/doc/src/group2ndx.rst @@ -72,5 +72,3 @@ Related commands :doc:`group `, :doc:`dump `, :doc:`fix colvars ` **Default:** none - - diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst index 36eb83cb59..eab9cf8973 100644 --- a/doc/src/hyper.rst +++ b/doc/src/hyper.rst @@ -212,5 +212,3 @@ The option defaults are min = 0.1 0.1 40 50 and time = steps. **(Voter2002)** Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002). - - diff --git a/doc/src/if.rst b/doc/src/if.rst index ce9cdc44c7..f7d09c8f50 100644 --- a/doc/src/if.rst +++ b/doc/src/if.rst @@ -216,5 +216,3 @@ Related commands :doc:`variable `, :doc:`print ` **Default:** none - - diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst index 59af9e3959..9bb5c88618 100644 --- a/doc/src/improper_class2.rst +++ b/doc/src/improper_class2.rst @@ -141,5 +141,3 @@ Related commands **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). - - diff --git a/doc/src/improper_coeff.rst b/doc/src/improper_coeff.rst index 05506e9743..6415d9d3f4 100644 --- a/doc/src/improper_coeff.rst +++ b/doc/src/improper_coeff.rst @@ -103,5 +103,3 @@ Related commands :doc:`improper_style ` **Default:** none - - diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index ce1451a48a..7428a7f02e 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -95,5 +95,3 @@ Related commands :doc:`improper_coeff ` **Default:** none - - diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index 7b84b86f28..a6938c7a12 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -98,5 +98,3 @@ Related commands :doc:`improper_coeff ` **Default:** none - - diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst index b6be5ec0c6..c170be50f2 100644 --- a/doc/src/improper_distance.rst +++ b/doc/src/improper_distance.rst @@ -64,5 +64,3 @@ Related commands :doc:`improper_coeff ` **Default:** none - - diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst index d7e6eeb914..09f835f575 100644 --- a/doc/src/improper_distharm.rst +++ b/doc/src/improper_distharm.rst @@ -58,5 +58,3 @@ Related commands :doc:`improper_coeff ` **Default:** none - - diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index d104e3aa7f..1cc72c7319 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -91,5 +91,3 @@ Related commands :doc:`improper_coeff ` **Default:** none - - diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index 8f62dcc433..6c9496dc42 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -104,5 +104,3 @@ Related commands :doc:`improper_coeff ` **Default:** none - - diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst index 87bce2137e..75bc592c68 100644 --- a/doc/src/improper_hybrid.rst +++ b/doc/src/improper_hybrid.rst @@ -76,5 +76,3 @@ Related commands :doc:`improper_coeff ` **Default:** none - - diff --git a/doc/src/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst index 69ce1604d5..e91b6d50c7 100644 --- a/doc/src/improper_inversion_harmonic.rst +++ b/doc/src/improper_inversion_harmonic.rst @@ -74,6 +74,3 @@ Related commands ---------- - - - diff --git a/doc/src/improper_none.rst b/doc/src/improper_none.rst index 626c342b55..c194eebd0f 100644 --- a/doc/src/improper_none.rst +++ b/doc/src/improper_none.rst @@ -39,5 +39,3 @@ Related commands :doc:`improper_style zero ` **Default:** none - - diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index 0fe0b5b4c6..3f6bec718b 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -104,5 +104,3 @@ Related commands **(Destree)** M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, J Chem Phys, 112, 9632 (2000). - - diff --git a/doc/src/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst index 57df51b2ab..ec1e68959a 100644 --- a/doc/src/improper_sqdistharm.rst +++ b/doc/src/improper_sqdistharm.rst @@ -59,5 +59,3 @@ Related commands :doc:`improper_coeff ` **Default:** none - - diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst index 917da9d7de..463e66704b 100644 --- a/doc/src/improper_style.rst +++ b/doc/src/improper_style.rst @@ -121,5 +121,3 @@ Default .. parsed-literal:: improper_style none - - diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst index c002f61ef9..8515a94598 100644 --- a/doc/src/improper_umbrella.rst +++ b/doc/src/improper_umbrella.rst @@ -105,5 +105,3 @@ Related commands **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990), - - diff --git a/doc/src/improper_zero.rst b/doc/src/improper_zero.rst index cfc68e4504..c745b69013 100644 --- a/doc/src/improper_zero.rst +++ b/doc/src/improper_zero.rst @@ -51,5 +51,3 @@ Restrictions :doc:`improper_style none ` **Default:** none - - diff --git a/doc/src/include.rst b/doc/src/include.rst index 8caa683f04..906fe0b16a 100644 --- a/doc/src/include.rst +++ b/doc/src/include.rst @@ -45,5 +45,3 @@ Related commands :doc:`variable `, :doc:`jump ` **Default:** none - - diff --git a/doc/src/info.rst b/doc/src/info.rst index 9bc04f01be..70f9e9bfed 100644 --- a/doc/src/info.rst +++ b/doc/src/info.rst @@ -128,5 +128,3 @@ Default The *out* option has the default *screen*\ . The *styles* option has the default *all*\ . - - diff --git a/doc/src/jump.rst b/doc/src/jump.rst index 30b76c11ec..e7ece020e3 100644 --- a/doc/src/jump.rst +++ b/doc/src/jump.rst @@ -156,5 +156,3 @@ Related commands :doc:`next ` **Default:** none - - diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index 46c1596b57..704657bb68 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -913,5 +913,3 @@ doi: `https://doi.org/10.1007/s11837-011-0102-6 `_ (2011) doi: `https://doi.org/10.25950/FF8F563A `_ - - diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index ed1b17f187..087466a9e1 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -560,5 +560,3 @@ Chem Theory Comput, 9, 5412 (2013). **(Wennberg)** Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013). - - diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index cf9473febf..41a66078ae 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -590,5 +590,3 @@ Illinois at Urbana-Champaign, (2006). **(Who)** Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 (2012). - - diff --git a/doc/src/label.rst b/doc/src/label.rst index b135575ce6..52387f661f 100644 --- a/doc/src/label.rst +++ b/doc/src/label.rst @@ -40,5 +40,3 @@ Restrictions **Related commands:** none **Default:** none - - diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index a9c0a77fde..6969ae8aa5 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -328,5 +328,3 @@ Default For other lattice styles, the option defaults are origin = 0.0 0.0 0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1 0 0, a2 = 0 1 0, and a3 = 0 0 1. - - diff --git a/doc/src/log.rst b/doc/src/log.rst index 35f13fe35b..6c014953f5 100644 --- a/doc/src/log.rst +++ b/doc/src/log.rst @@ -49,5 +49,3 @@ Default """"""" The default LAMMPS log file is named log.lammps - - diff --git a/doc/src/mass.rst b/doc/src/mass.rst index 735301099e..c9c21b5d8d 100644 --- a/doc/src/mass.rst +++ b/doc/src/mass.rst @@ -88,5 +88,3 @@ The mass assigned to any type or atom must be > 0.0. **Related commands:** none **Default:** none - - diff --git a/doc/src/message.rst b/doc/src/message.rst index 901149d707..2552991318 100644 --- a/doc/src/message.rst +++ b/doc/src/message.rst @@ -203,5 +203,3 @@ Related commands :doc:`server `, :doc:`fix client/md ` **Default:** none - - diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index d15dc75e25..0e586e8fe0 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -145,5 +145,3 @@ The option defaults are dmax = 0.1, line = quadratic and norm = two. For the *spin*\ , *spin/cg* and *spin/lbfgs* styles, the option defaults are alpha\_damp = 1.0, discrete\_factor = 10.0, line = spin\_none, and norm = euclidean. - - diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index a88ba97d5a..1c976cc4c9 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -125,5 +125,3 @@ The option defaults are *alpha\_damp* = 1.0, *discrete\_factor* = **(Ivanov)** Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019). - - diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst index 1c403ba779..48dad03567 100644 --- a/doc/src/min_style.rst +++ b/doc/src/min_style.rst @@ -163,5 +163,3 @@ Jonsson, Mills, Jacobsen. **(Bitzek)** Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006). - - diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index 92c23dd8ef..6caf4e0f43 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -337,5 +337,3 @@ Related commands :doc:`run_style ` **Default:** none - - diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index d5b22ae043..ba57aed2ca 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -511,5 +511,3 @@ Default """"""" The default keywords values are offset 0 0 0 0 0 and scale = 1.0. - - diff --git a/doc/src/neb.rst b/doc/src/neb.rst index a8686a8994..5b1e4570bc 100644 --- a/doc/src/neb.rst +++ b/doc/src/neb.rst @@ -471,5 +471,3 @@ none **(Maras)** Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016) - - diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index f05853d7f9..5906bd64e8 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -417,5 +417,3 @@ none **(BessarabA)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015). - - diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index f6d02ed2e0..77d450315a 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -227,5 +227,3 @@ Default The option defaults are delay = 10, every = 1, check = yes, once = no, cluster = no, include = all (same as no include option defined), exclude = none, page = 100000, one = 2000, and binsize = 0.0. - - diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 8543133ab2..a8b70cb731 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -88,5 +88,3 @@ Default | 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm | 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm | - - diff --git a/doc/src/newton.rst b/doc/src/newton.rst index fa5560b47e..38324e8143 100644 --- a/doc/src/newton.rst +++ b/doc/src/newton.rst @@ -71,5 +71,3 @@ Default .. parsed-literal:: newton on - - diff --git a/doc/src/next.rst b/doc/src/next.rst index 7afb1e642d..7a1e2264a1 100644 --- a/doc/src/next.rst +++ b/doc/src/next.rst @@ -156,5 +156,3 @@ Related commands :doc:`variable `, **Default:** none - - diff --git a/doc/src/package.rst b/doc/src/package.rst index b691728505..4a8b3dcdcd 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -682,5 +682,3 @@ defaults are neigh = yes. These settings are made automatically if the "-sf omp" :doc:`command-line switch ` is used. If it is not used, you must invoke the package omp command in your input script or via the "-pk omp" :doc:`command-line switch `. - - diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index c94a8593ff..69051f545e 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -204,5 +204,3 @@ Related commands **(Singh)** Singh and Warner, Acta Mater, 58, 5797-5805 (2010), - - diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index 202016dd36..fc2b47b63d 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -150,5 +150,3 @@ Related commands **(Botu3)** V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016). - - diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index 868f63f90c..0cd2a79fe8 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -286,5 +286,3 @@ Physics: Condensed Matter, 14, 783-802 (2002). **(O'Connor)** O'Connor et al., J. Chem. Phys. 142, 024903 (2015). - - diff --git a/doc/src/pair_atm.rst b/doc/src/pair_atm.rst index 4de322c51e..6118b0943f 100644 --- a/doc/src/pair_atm.rst +++ b/doc/src/pair_atm.rst @@ -190,5 +190,3 @@ Related commands **(Axilrod)** Axilrod and Teller, J Chem Phys, 11, 299 (1943); Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943). - - diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst index 97479e337c..baef5d7209 100644 --- a/doc/src/pair_awpmd.rst +++ b/doc/src/pair_awpmd.rst @@ -133,5 +133,3 @@ Default These are the defaults for the pair\_style keywords: *hartree* for the initial wave function, *free* for the wave packet width. - - diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index d7d6ae9471..6a407e11a9 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -126,5 +126,3 @@ Related commands **(Beck)** Beck, Molecular Physics, 14, 311 (1968). - - diff --git a/doc/src/pair_body_nparticle.rst b/doc/src/pair_body_nparticle.rst index 00ce78ee71..1214890070 100644 --- a/doc/src/pair_body_nparticle.rst +++ b/doc/src/pair_body_nparticle.rst @@ -126,5 +126,3 @@ Related commands :doc:`pair_coeff `, :doc:`fix rigid ` **Default:** none - - diff --git a/doc/src/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst index e0a3f2310b..9a042b5b5a 100644 --- a/doc/src/pair_body_rounded_polygon.rst +++ b/doc/src/pair_body_rounded_polygon.rst @@ -140,5 +140,3 @@ Related commands **(Fraige)** F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, Particuology, 6, 455 (2008). - - diff --git a/doc/src/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst index 3ffdc566b4..23623a640e 100644 --- a/doc/src/pair_body_rounded_polyhedron.rst +++ b/doc/src/pair_body_rounded_polyhedron.rst @@ -135,5 +135,3 @@ Related commands **(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011). - - diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index 25e2d945c2..f4b4ed903d 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -473,5 +473,3 @@ Zimmerman, Phys. Rev. B, 85,115206 (2012). **(Zhou)** X.W. Zhou, D.K. Ward, M. Foster (TBP). - - diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index c879755dfc..1a7d3bae5e 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -231,5 +231,3 @@ Related commands Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964), Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964). - - diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index 6c84dfa179..3f66365fb2 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -154,5 +154,3 @@ Default The default settings for the optional args are flagHI = 1 and flagVF = 1. - - diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 6ab0ad4dd5..b988593b20 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -235,5 +235,3 @@ Related commands **(Khrapak)** Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011). - - diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index c9ebcf97db..90d82253e3 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -157,5 +157,3 @@ Related commands **(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006). - - diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index a7df0880c5..1a90bbc71f 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -192,5 +192,3 @@ Related commands **(Ismail)** Ismail, Tsige, In 't Veld, Grest, Molecular Physics (accepted) (2007). - - diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index beb21f1b80..5a180ed271 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -329,5 +329,3 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). **(Steinbach)** Steinbach, Brooks, J Comput Chem, 15, 667 (1994). - - diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index bcb4c2faad..9579a1f408 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -216,5 +216,3 @@ Related commands **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). - - diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index c920013597..dec45a5f11 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -158,5 +158,3 @@ Related commands :doc:`pair_write ` **Default:** none - - diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index 5be906b1fe..2e4feabfbf 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -223,5 +223,3 @@ Related commands **(Everaers)** Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003). - - diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index 2eef8a6e5c..7cbb1b4029 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -220,5 +220,3 @@ Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, **(Rick)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 (1994). - - diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index 1ddd060b9b..e2d79f03d6 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -127,5 +127,3 @@ Related commands **(Weeks)** "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)" - - diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index fe4d1346e6..08778aab59 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -427,5 +427,3 @@ Phys, 110, 8254 (1999). **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). - - diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index c5a8d64198..3c6090d3f7 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -132,5 +132,3 @@ Related commands **(Jusufi)** Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, 13783 (2008). - - diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index 7184b9a9ea..e0b010a1f8 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -112,5 +112,3 @@ Related commands **(Maaravi)** T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017). - - diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index 7113fe90a2..c71d88a38c 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -211,5 +211,3 @@ Related commands **(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993). - - diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 486f6b298a..0550bc1604 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -314,5 +314,3 @@ Clarendon Press, Oxford, 1987. **(Price)** Price, Stone and Alderton, Mol Phys, 52, 987 (1984). - - diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 43e5967b3b..fde0463f14 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -241,5 +241,3 @@ Comm, 184, 1119-1128 (2013). **(Phillips)** C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput Phys Comm, 230, 7191-7201 (2011). - - diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index 793904d906..c893f68a1c 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -200,5 +200,3 @@ Related commands particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", J. Chem. Phys., 135, 204105 (2011). - - diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst index eee7e95da3..ca04efcece 100644 --- a/doc/src/pair_drip.rst +++ b/doc/src/pair_drip.rst @@ -160,5 +160,3 @@ Related commands **(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) - - diff --git a/doc/src/pair_dsmc.rst b/doc/src/pair_dsmc.rst index ee9dda0760..7848486eac 100644 --- a/doc/src/pair_dsmc.rst +++ b/doc/src/pair_dsmc.rst @@ -171,5 +171,3 @@ Related commands **(Bird)** G. A. Bird, "Molecular Gas Dynamics and the Direct Simulation of Gas Flows" (1994). - - diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index 9ade81aaea..eecb594ef8 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -169,5 +169,3 @@ The option default for the *neigh* keyword is 10. **(Tainter 2015)** Tainter, Shi, and Skinner, 11, 2268 (2015) - - diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index 53975e862f..d3356007cd 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -548,5 +548,3 @@ Materials Science & Engineering, 7, 075005 (2009). **(Caro)** A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005) - - diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index f1b8314527..6cc388b3cc 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -187,5 +187,3 @@ Related commands **(EDIP)** J F Justo et al, Phys Rev B 58, 2539 (1998). - - diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index bb709558cf..fc4c5f0964 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -351,5 +351,3 @@ Dense Matter, Phys Rev Lett, 99:185003 (2007). Long-term Non-adiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments, J Comp Chem, 32, 497-512 (2011). - - diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index 05c0184dde..133a81c0dc 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -197,5 +197,3 @@ Related commands **(Zhou)** Zhou, submitted for publication (2010). Please contact Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov. - - diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index caa51e26df..c44c87ae17 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -207,5 +207,3 @@ Related commands :doc:`pair_coeff ` **Default:** fractional weighting - - diff --git a/doc/src/pair_extep.rst b/doc/src/pair_extep.rst index 563514e4f2..4564bde074 100644 --- a/doc/src/pair_extep.rst +++ b/doc/src/pair_extep.rst @@ -52,5 +52,3 @@ Related commands **(Los2017)** J. H. Los et al. "Extended Tersoff potential for boron nitride: Energetics and elastic properties of pristine and defective h-BN", Phys. Rev. B 96 (184108), 2017. - - diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index 0a9b2ad68a..20bd84a567 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -426,5 +426,3 @@ Related commands **(Beutler)** Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem Phys Lett, 222, 529 (1994). - - diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index 0074607ea6..b4270eac30 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -210,5 +210,3 @@ Related commands **(Jusufi)** Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, 13783 (2008). - - diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 37103cd002..f735c5a021 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -257,5 +257,3 @@ Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008). **(Allen)** Allen and Germano, Mol Phys 104, 3225-3235 (2006). - - diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index fed7df07ae..7cc3ada389 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -308,5 +308,3 @@ E, 64, p 051302 (2001). **(Zhang)** Zhang and Makse, Phys Rev E, 72, p 011301 (2005). - - diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index d26863dc79..c94061e396 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -871,5 +871,3 @@ Technology, 233, 30-46. **(Otis R. Walton)** Walton, O.R., Personal Communication - - diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index 84c56deead..f49401553b 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -186,5 +186,3 @@ Related commands **(Marrink)** Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004). - - diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index b09a43496f..08d689cf27 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -138,5 +138,3 @@ Related commands **(Gao)** Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504. - - diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index cfd9904215..c1370a8b1c 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -279,5 +279,3 @@ Related commands **(Liu)** Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8) 2798 (2009) - - diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index d58d5b98ac..747a865049 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -437,5 +437,3 @@ Related commands :doc:`pair_coeff ` **Default:** none - - diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index 31d96e6a08..8299a02d62 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -196,5 +196,3 @@ Related commands **(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020). - - diff --git a/doc/src/pair_kim.rst b/doc/src/pair_kim.rst index b7aa5f172f..88a47f900a 100644 --- a/doc/src/pair_kim.rst +++ b/doc/src/pair_kim.rst @@ -128,5 +128,3 @@ Related commands :doc:`pair_coeff `, :doc:`kim_commands ` **Default:** none - - diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index 313a6e9e59..9d5d03da09 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -165,5 +165,3 @@ Related commands **(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020). - - diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index 847e696a4f..4ba7bf0f9f 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -89,5 +89,3 @@ Related commands **(vanWijk)** M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014) - - diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst index eb53eb3b5b..5430b2dd23 100644 --- a/doc/src/pair_lcbop.rst +++ b/doc/src/pair_lcbop.rst @@ -109,5 +109,3 @@ Related commands **(Los and Fasolino)** J. H. Los and A. Fasolino, Phys. Rev. B 68, 024107 (2003). - - diff --git a/doc/src/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst index 15213cda6b..1389bf66aa 100644 --- a/doc/src/pair_lebedeva_z.rst +++ b/doc/src/pair_lebedeva_z.rst @@ -76,5 +76,3 @@ Related commands **(Lebedeva et al.)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011) - - diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst index e4c311feba..4c52e82b42 100644 --- a/doc/src/pair_line_lj.rst +++ b/doc/src/pair_line_lj.rst @@ -152,5 +152,3 @@ Related commands :doc:`pair_coeff `, :doc:`pair_style tri/lj ` **Default:** none - - diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 7ecc418670..4f41ce3a54 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -444,5 +444,3 @@ Phys, 79, 926 (1983). **(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006). - - diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 61c8ba6af3..45f4cd783a 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -119,5 +119,3 @@ Related commands :doc:`pair_coeff ` **Default:** none - - diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index 70a13cc166..aa30adc6ed 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -149,5 +149,3 @@ Related commands **(Ravelo)** Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). - - diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 81c569a191..e2d2d644a1 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -143,5 +143,3 @@ Related commands :doc:`pair_coeff ` **Default:** none - - diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index abdf3699a3..82f3782dae 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -271,5 +271,3 @@ Related commands **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). - - diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index 4256254f6e..f5e0bd53a3 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -133,5 +133,3 @@ Related commands :doc:`pair_coeff `, :doc:`pair lj/smooth/linear ` **Default:** none - - diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index f46c83452e..5eb09d972f 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -126,5 +126,3 @@ Related commands **(Toxvaerd)** Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011). - - diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index 5c899febef..cc7263b36e 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -97,5 +97,3 @@ Related commands :doc:`pair_coeff ` **Default:** none - - diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst index fc006863ed..ddcbf0c820 100644 --- a/doc/src/pair_local_density.rst +++ b/doc/src/pair_local_density.rst @@ -246,5 +246,3 @@ Related commands **(Rosenberger)** Rosenberger, Sanyal, Shell and van der Vegt, Journal of Chemical Physics, 2019, 151 (4), 044111. - - diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index 00212e375b..67e7c33879 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -251,5 +251,3 @@ his thesis for more details: A. Kumar, "Microscale Dynamics in Suspensions of Non-spherical Particles", Thesis, University of Illinois Urbana-Champaign, (2010). (`https://www.ideals.illinois.edu/handle/2142/16032 `_) - - diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index 0a9fcd982e..1c9cb7225d 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -235,5 +235,3 @@ The default settings for the optional args are flagHI = 1 and flagVF = **(Kumar)** Kumar and Higdon, Phys Rev E, 82, 051401 (2010). - - diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 7d0c0b42a0..11725a5f7d 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -189,5 +189,3 @@ Related commands **(Mei)** Mei, Davenport, Fernando, Phys Rev B, 43 4653 (1991) - - diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index 97565e17a2..222a058acf 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -193,5 +193,3 @@ Kress, Modelling Simulation Materials Science Engineering, 8, 825 **(Zhang)** Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016). - - diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index a5dafb5406..c87b1f09e0 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -160,5 +160,3 @@ Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000). The spline-based MEAM+SW format was first devised and used to develop potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger, and Hyoungki Park at The Ohio State University. - - diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index 5a8c70646e..95f46c30cf 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -471,5 +471,3 @@ This report may be accessed on-line via `this link `_. **(ZBL)** J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges of Ions in Matter", Vol 1, 1985, Pergamon Press. - - diff --git a/doc/src/pair_meso.rst b/doc/src/pair_meso.rst index 91f9e55c7e..915461d485 100644 --- a/doc/src/pair_meso.rst +++ b/doc/src/pair_meso.rst @@ -330,5 +330,3 @@ DOI: 10.1063/1.4812366. **(Li2015\_JCP)** Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI: 10.1063/1.4923254. - - diff --git a/doc/src/pair_mesocnt.rst b/doc/src/pair_mesocnt.rst index 94f7d7d554..41c47fc957 100644 --- a/doc/src/pair_mesocnt.rst +++ b/doc/src/pair_mesocnt.rst @@ -154,5 +154,3 @@ Related commands **(Volkov2)** Volkov, Simov and Zhigilei, APS Meeting Abstracts, Q31.013 (2008). - - diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 2460eba2fe..646bbac84a 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -247,5 +247,3 @@ Series, 46, 254 (2006). **(Oppelstrup)** Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published. - - diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index a1d5518480..61eeb1f0f4 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -119,5 +119,3 @@ Related commands **(Avendano)** C. Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011). - - diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index 8113692249..865014e597 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -99,5 +99,3 @@ Related commands :doc:`pair_coeff ` **Default:** none - - diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index 64cec312d7..68ab45457c 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -333,5 +333,3 @@ mixing. See the doc pages for individual pair styles for details. **(Sun)** Sun, J Phys Chem B, 102, 7338-7364 (1998). - - diff --git a/doc/src/pair_momb.rst b/doc/src/pair_momb.rst index fe0ad9e0b0..d923bd7b90 100644 --- a/doc/src/pair_momb.rst +++ b/doc/src/pair_momb.rst @@ -89,5 +89,3 @@ Related commands **(Zhou)** Zhou, Saidi, Fichthorn, J Phys Chem C, 118(6), 3366-3374 (2014). - - diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 8232251163..1eb3d53ed0 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -163,5 +163,3 @@ Related commands :doc:`pair_coeff `, :doc:`pair_style */soft ` **Default:** none - - diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index 663beaa65c..6363dd9b7d 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -227,5 +227,3 @@ Related commands **(Moore)** Moore, J Chem Phys, 144, 104501 (2016). - - diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index a1f2979e71..5a56cfb48e 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -278,5 +278,3 @@ Related commands **(Moore)** Moore, J Chem Phys, 144, 104501 (2016). - - diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index 9425a98952..2f2270a6a5 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -112,5 +112,3 @@ Related commands :doc:`pair_coeff ` **Default:** none - - diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index f9d9444198..f8ae4f7a91 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -194,5 +194,3 @@ Related commands **(Clarke)** Clarke and Smith, J Chem Phys, 84, 2290 (1986). - - diff --git a/doc/src/pair_none.rst b/doc/src/pair_none.rst index 27cd107829..43f56d20bc 100644 --- a/doc/src/pair_none.rst +++ b/doc/src/pair_none.rst @@ -51,5 +51,3 @@ Related commands :doc:`pair_style zero ` **Default:** none - - diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index f77bdf0b38..8faef5decd 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -143,5 +143,3 @@ Related commands .. _Sulc1: **(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). - - diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 7210070da0..8c903f023f 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -153,5 +153,3 @@ Related commands .. _Ouldridge2: **(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). - - diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index 06d920a786..f9f183ea27 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -247,5 +247,3 @@ viscoelasticity model for peridynamics. Sandia National Lab Report, **(Mitchell2011a)** Mitchell. A Nonlocal, Ordinary, State-Based Plasticity Model for Peridynamics. Sandia National Lab Report, 3166:1-34 (2011). - - diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index ce3f73bd53..d623480a85 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -281,5 +281,3 @@ F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015). **(Daw)** M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984). - - diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index 7acaa52db8..3545a83003 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -248,5 +248,3 @@ Related commands :doc:`pair style table ` **Default:** none - - diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index bd74c2e12c..304edced31 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -117,5 +117,3 @@ Review Letters 104, 136403 (2010). **(Bartok\_PhD)** A Bartok-Partay, PhD Thesis, University of Cambridge, (2010). - - diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index a0f6f23b72..9f433fe237 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -394,5 +394,3 @@ Journal of Physical Chemistry A, 112, 1040-1053 (2008). **(Liu)** L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011). - - diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 186ab8f7af..0f287e150e 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -253,5 +253,3 @@ Related commands **(Berardi)** Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006). - - diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index b1c9ec8618..6277c82be9 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -196,5 +196,3 @@ Related commands **(DeVane)** Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008). - - diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst index ca0d2c528c..00608b6610 100644 --- a/doc/src/pair_sdpd_taitwater_isothermal.rst +++ b/doc/src/pair_sdpd_taitwater_isothermal.rst @@ -123,5 +123,3 @@ The default seed is 0 (before mixing). **(Espanol and Revenga)** Espanol, Revenga, Physical Review E, 67, 026705 (2003). - - diff --git a/doc/src/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst index 6738d59394..1488444da5 100644 --- a/doc/src/pair_smd_hertz.rst +++ b/doc/src/pair_smd_hertz.rst @@ -65,6 +65,3 @@ Related commands ---------- - - - diff --git a/doc/src/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst index 272940513f..2c452a76c6 100644 --- a/doc/src/pair_smd_tlsph.rst +++ b/doc/src/pair_smd_tlsph.rst @@ -81,6 +81,3 @@ Related commands ---------- - - - diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 5d856231b0..535481e649 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -66,6 +66,3 @@ Related commands ---------- - - - diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index b3e6d261e3..3a5ec41f0f 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -96,6 +96,3 @@ Related commands ---------- - - - diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index 60bb8ae25c..6296517f66 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -293,5 +293,3 @@ Phys, 110, 8254 (1999). **(Rick)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 (1994). - - diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 3598816165..af2c4accfa 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -245,5 +245,3 @@ Related commands **(Bartok2013)** Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013). - - diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index 01da695704..a5e29ef0ab 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -151,5 +151,3 @@ Related commands :doc:`pair_coeff `, :doc:`fix nve/limit `, :doc:`fix adapt ` **Default:** none - - diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst index f816376c2d..3322a1aa10 100644 --- a/doc/src/pair_sph_heatconduction.rst +++ b/doc/src/pair_sph_heatconduction.rst @@ -67,5 +67,3 @@ Related commands :doc:`pair_coeff `, pair\_sph/rhosum **Default:** none - - diff --git a/doc/src/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst index f82f3fde0b..da38341ded 100644 --- a/doc/src/pair_sph_idealgas.rst +++ b/doc/src/pair_sph_idealgas.rst @@ -86,5 +86,3 @@ Related commands **(Monaghan)** Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983). - - diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst index 5c51eb5844..d69fd1ba0a 100644 --- a/doc/src/pair_sph_lj.rst +++ b/doc/src/pair_sph_lj.rst @@ -91,5 +91,3 @@ Related commands **(Monaghan)** Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983). - - diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst index 8b6f913393..dad7b1852a 100644 --- a/doc/src/pair_sph_rhosum.rst +++ b/doc/src/pair_sph_rhosum.rst @@ -68,5 +68,3 @@ Related commands :doc:`pair_coeff `, pair\_sph/taitwater **Default:** none - - diff --git a/doc/src/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst index e60215cf6d..35bc64e578 100644 --- a/doc/src/pair_sph_taitwater.rst +++ b/doc/src/pair_sph_taitwater.rst @@ -89,5 +89,3 @@ Related commands **(Monaghan)** Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983). - - diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst index d310ab93dc..8a89702341 100644 --- a/doc/src/pair_sph_taitwater_morris.rst +++ b/doc/src/pair_sph_taitwater_morris.rst @@ -87,5 +87,3 @@ Related commands **(Morris)** Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997). - - diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index 1760e5a204..5c7c5306c8 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -89,5 +89,3 @@ Related commands :doc:`fix nve/spin ` **Default:** none - - diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 4f2e995fd0..719c546365 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -106,5 +106,3 @@ Physical Review B, 88(18), 184422. (2013). **(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018). - - diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 5f9364648a..63361ece2b 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -88,5 +88,3 @@ Related commands **(Tranchida)** Tranchida, Plimpton, Thibaudeau, and Thompson, Journal of Computational Physics, 372, 406-425, (2018). - - diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index 0ffa856975..a1138db382 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -183,5 +183,3 @@ The default keyword value is exclude = yes. **(Sirk)** Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012. - - diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 3ef9638851..5fedfcbf30 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -357,5 +357,3 @@ Default .. parsed-literal:: pair_style none - - diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index f396d13cf4..425dcf1f16 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -239,5 +239,3 @@ Related commands **(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985). - - diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index d83c3d852a..042e989209 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -294,5 +294,3 @@ Related commands **(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). - - diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index b28e224d27..38e431ff5c 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -281,5 +281,3 @@ Related commands **(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). - - diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index e7287ded1c..ab9d714499 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -287,5 +287,3 @@ Condens. Matter, 15, 5649(2003). **(Tersoff\_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) - - diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index 3b5152f8cd..dbe0b4d95b 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -245,5 +245,3 @@ Comp. Mat. Science, 39, 457 (2007). **(Schelling)** Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008). - - diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index d093d67f3b..2ad3be9d7d 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -299,5 +299,3 @@ Condens. Matter, 15, 5649(2003). **(Tersoff\_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) - - diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index f783a85d78..538d555b0d 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -213,5 +213,3 @@ Related commands **(Thole)** Chem Phys, 59, 341 (1981). - - diff --git a/doc/src/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst index 32b2f27be0..c5fbd90e1d 100644 --- a/doc/src/pair_tri_lj.rst +++ b/doc/src/pair_tri_lj.rst @@ -121,5 +121,3 @@ Related commands :doc:`pair_coeff `, :doc:`pair_style line/lj ` **Default:** none - - diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index 2912a4ab5c..3bb4e83a0e 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -160,5 +160,3 @@ Related commands **(Freitas)** Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016). - - diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index 24742d4498..de29985f56 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -282,5 +282,3 @@ J. P. Rino. J. Appl. Phys. 101, 103515 (2007). **(Branicio2009)** Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002 - - diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 20b51f9485..7a67bcc5bd 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -84,5 +84,3 @@ Related commands :doc:`pair_style `, :doc:`pair_coeff ` **Default:** none - - diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 019306c584..c3a8e9fc71 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -119,5 +119,3 @@ Related commands :doc:`pair_coeff ` **Default:** none - - diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index 79de73676d..76bf010fb9 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -174,5 +174,3 @@ Related commands **(Safran)** Safran, Statistical Thermodynamics of Surfaces, Interfaces, And Membranes, Westview Press, ISBN: 978-0813340791 (2003). - - diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index c72e580cb1..8e34341172 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -162,5 +162,3 @@ Related commands **(Ziegler)** J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985. - - diff --git a/doc/src/pair_zero.rst b/doc/src/pair_zero.rst index 85d9a17371..d03cd03f76 100644 --- a/doc/src/pair_zero.rst +++ b/doc/src/pair_zero.rst @@ -92,5 +92,3 @@ Related commands :doc:`pair_style none ` **Default:** none - - diff --git a/doc/src/partition.rst b/doc/src/partition.rst index 62506e9f9d..7ad5a4b3ed 100644 --- a/doc/src/partition.rst +++ b/doc/src/partition.rst @@ -75,5 +75,3 @@ Related commands :doc:`run_style verlet/split ` **Default:** none - - diff --git a/doc/src/prd.rst b/doc/src/prd.rst index 83db49cdf6..212439ddce 100644 --- a/doc/src/prd.rst +++ b/doc/src/prd.rst @@ -364,5 +364,3 @@ geom gaussian, and time = steps. **(Voter2002)** Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002). - - diff --git a/doc/src/print.rst b/doc/src/print.rst index 637d417c95..93534ba9b5 100644 --- a/doc/src/print.rst +++ b/doc/src/print.rst @@ -94,5 +94,3 @@ Default """"""" The option defaults are no file output, screen = yes, and universe = no. - - diff --git a/doc/src/processors.rst b/doc/src/processors.rst index 84959962dc..2b30653167 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -378,5 +378,3 @@ Default The option defaults are Px Py Pz = \* \* \*, grid = onelevel, and map = cart. - - diff --git a/doc/src/python.rst b/doc/src/python.rst index 6fc92a2f98..79818dc719 100644 --- a/doc/src/python.rst +++ b/doc/src/python.rst @@ -549,5 +549,3 @@ Related commands :doc:`shell `, :doc:`variable `, :doc:`fix python/invoke ` **Default:** none - - diff --git a/doc/src/quit.rst b/doc/src/quit.rst index cf9ea8dcf3..9741a7477d 100644 --- a/doc/src/quit.rst +++ b/doc/src/quit.rst @@ -51,5 +51,3 @@ Related commands :doc:`if ` **Default:** none - - diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index ece112a57c..ce466108cf 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -1438,5 +1438,3 @@ Default """"""" The default for all the *extra* keywords is 0. - - diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index 322fb49aad..acf08866a9 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -416,7 +416,3 @@ The option defaults are box = yes, replace = yes, purge = no, trim = no, add = no, scaled = no, wrapped = yes, and format = native. .. _vmd: http://www.ks.uiuc.edu/Research/vmd - - - - diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index 0a61425fa1..06f4ddb2e3 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -281,5 +281,3 @@ Related commands :doc:`write_restart `, :doc:`restart ` **Default:** none - - diff --git a/doc/src/region.rst b/doc/src/region.rst index 6d40a55ce7..f1d008cbd3 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -428,5 +428,3 @@ Default The option defaults are side = in, units = lattice, and no move or rotation. - - diff --git a/doc/src/replicate.rst b/doc/src/replicate.rst index 063c3fff0c..94d899a459 100644 --- a/doc/src/replicate.rst +++ b/doc/src/replicate.rst @@ -109,5 +109,3 @@ command before and redefined after the replicate command. **Related commands:** none **Default:** none - - diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index 552d51bb22..aa244e7d72 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -232,5 +232,3 @@ Default The option defaults are first = 0, last = a huge value (effectively infinity), start = same as first, stop = same as last, every = 0, skip = 1; - - diff --git a/doc/src/reset_ids.rst b/doc/src/reset_ids.rst index 2f40fc7fe9..3bcc0a5b61 100644 --- a/doc/src/reset_ids.rst +++ b/doc/src/reset_ids.rst @@ -62,5 +62,3 @@ Related commands :doc:`delete_atoms ` **Default:** none - - diff --git a/doc/src/reset_timestep.rst b/doc/src/reset_timestep.rst index e17260ea94..e287605fbb 100644 --- a/doc/src/reset_timestep.rst +++ b/doc/src/reset_timestep.rst @@ -65,5 +65,3 @@ Related commands :doc:`rerun ` **Default:** none - - diff --git a/doc/src/restart.rst b/doc/src/restart.rst index 38d8a9350d..6ff78d2f97 100644 --- a/doc/src/restart.rst +++ b/doc/src/restart.rst @@ -197,5 +197,3 @@ Default .. parsed-literal:: restart 0 - - diff --git a/doc/src/run.rst b/doc/src/run.rst index d2aace9c99..440d21d959 100644 --- a/doc/src/run.rst +++ b/doc/src/run.rst @@ -234,5 +234,3 @@ Default The option defaults are start = the current timestep, stop = current timestep + N, pre = yes, and post = yes. - - diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index b1f4f08881..663e61b308 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -367,5 +367,3 @@ to rRESPA levels is as follows: **(Tuckerman)** Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990 (1992). - - diff --git a/doc/src/server.rst b/doc/src/server.rst index 93466566bc..c0aeef2565 100644 --- a/doc/src/server.rst +++ b/doc/src/server.rst @@ -74,5 +74,3 @@ Related commands :doc:`message `, :doc:`fix client/md ` **Default:** none - - diff --git a/doc/src/server_mc.rst b/doc/src/server_mc.rst index 835f5e711c..1953cac687 100644 --- a/doc/src/server_mc.rst +++ b/doc/src/server_mc.rst @@ -130,5 +130,3 @@ Related commands :doc:`message ` **Default:** none - - diff --git a/doc/src/server_md.rst b/doc/src/server_md.rst index 38c93b510b..c21753f9e4 100644 --- a/doc/src/server_md.rst +++ b/doc/src/server_md.rst @@ -167,5 +167,3 @@ Related commands :doc:`message `, :doc:`fix client/md ` **Default:** none - - diff --git a/doc/src/set.rst b/doc/src/set.rst index fb026d9535..8214ce8ba9 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -506,5 +506,3 @@ Related commands :doc:`read_data ` **Default:** none - - diff --git a/doc/src/shell.rst b/doc/src/shell.rst index f12faf835e..9cb94dd93f 100644 --- a/doc/src/shell.rst +++ b/doc/src/shell.rst @@ -121,5 +121,3 @@ executing the *cd* command will silently do nothing. **Related commands:** none **Default:** none - - diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index af8f611e07..1306535f0b 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -293,5 +293,3 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990). - - diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst index aa2ea22979..f24bdadfdc 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -110,5 +110,3 @@ Related commands :doc:`-suffix command-line switch ` **Default:** none - - diff --git a/doc/src/tad.rst b/doc/src/tad.rst index 49dfd27581..206c915e3f 100644 --- a/doc/src/tad.rst +++ b/doc/src/tad.rst @@ -332,5 +332,3 @@ the :doc:`timestep ` command, and *neb\_log* = "none". **(Voter2002)** Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002). - - diff --git a/doc/src/temper.rst b/doc/src/temper.rst index 1e374592ff..018d8b9b7a 100644 --- a/doc/src/temper.rst +++ b/doc/src/temper.rst @@ -175,5 +175,3 @@ Related commands :doc:`variable `, :doc:`prd `, :doc:`neb ` **Default:** none - - diff --git a/doc/src/temper_grem.rst b/doc/src/temper_grem.rst index 85872cc8d7..150e2f27db 100644 --- a/doc/src/temper_grem.rst +++ b/doc/src/temper_grem.rst @@ -126,5 +126,3 @@ Related commands **(Kim)** Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010). - - diff --git a/doc/src/temper_npt.rst b/doc/src/temper_npt.rst index 8dc5a967d2..e8db3eca86 100644 --- a/doc/src/temper_npt.rst +++ b/doc/src/temper_npt.rst @@ -81,5 +81,3 @@ Related commands **(Mori)** Y. Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010). - - diff --git a/doc/src/thermo.rst b/doc/src/thermo.rst index 54d2534aca..08e1e4cbbb 100644 --- a/doc/src/thermo.rst +++ b/doc/src/thermo.rst @@ -69,5 +69,3 @@ Default .. parsed-literal:: thermo 0 - - diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index bb383efb19..a1ae2516d8 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -193,5 +193,3 @@ The defaults for the line and format options depend on the thermo style. For styles "one" and "custom", the line and format defaults are "one", "%8d", and "%12.8g". For style "multi", the line and format defaults are "multi", "%8d", and "%14.4f". - - diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 0b592730af..4b2b875e56 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -444,5 +444,3 @@ Default .. parsed-literal:: thermo_style one - - diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index b8358b3cd0..464ce82cf2 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -72,5 +72,3 @@ Default """"""" The default settings are file = "third\_order.dat", binary = no - - diff --git a/doc/src/timer.rst b/doc/src/timer.rst index 535649a7d9..b833542d09 100644 --- a/doc/src/timer.rst +++ b/doc/src/timer.rst @@ -133,5 +133,3 @@ Default timer normal nosync timer timeout off timer every 10 - - diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst index 5bb784eff4..f3faaf25d2 100644 --- a/doc/src/timestep.rst +++ b/doc/src/timestep.rst @@ -67,5 +67,3 @@ Default +--------------------------------+------------+-----------------------+ | nano | nsec | 0.00045 nsec | +--------------------------------+------------+-----------------------+ - - diff --git a/doc/src/uncompute.rst b/doc/src/uncompute.rst index 936dcb0fbc..0950dd6bb2 100644 --- a/doc/src/uncompute.rst +++ b/doc/src/uncompute.rst @@ -39,5 +39,3 @@ Related commands :doc:`compute ` **Default:** none - - diff --git a/doc/src/undump.rst b/doc/src/undump.rst index 516fc8002d..98c18ea8f7 100644 --- a/doc/src/undump.rst +++ b/doc/src/undump.rst @@ -38,5 +38,3 @@ Related commands :doc:`dump ` **Default:** none - - diff --git a/doc/src/unfix.rst b/doc/src/unfix.rst index d61843c768..d85436c275 100644 --- a/doc/src/unfix.rst +++ b/doc/src/unfix.rst @@ -39,5 +39,3 @@ Related commands :doc:`fix ` **Default:** none - - diff --git a/doc/src/units.rst b/doc/src/units.rst index 8b138fd4e1..5527208831 100644 --- a/doc/src/units.rst +++ b/doc/src/units.rst @@ -231,5 +231,3 @@ Default .. parsed-literal:: units lj - - diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 70c7accf5f..9aeb9dc4ba 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -1474,5 +1474,3 @@ Related commands :doc:`temper `, :doc:`fix print `, :doc:`print ` **Default:** none - - diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index e45249dc51..631ef80263 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -281,5 +281,3 @@ Default The keyword defaults are dist = uniform, sum = no, mom = yes, rot = no, bias = no, loop = all, and units = lattice. The temp and rigid keywords are not defined by default. - - diff --git a/doc/src/write_coeff.rst b/doc/src/write_coeff.rst index 5379439133..d7c82cbeb6 100644 --- a/doc/src/write_coeff.rst +++ b/doc/src/write_coeff.rst @@ -51,5 +51,3 @@ Related commands :doc:`read_data `, :doc:`write_restart `, :doc:`write_data ` - - diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index 373a1edf26..3d7b7cf607 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -145,5 +145,3 @@ Default """"""" The option defaults are pair = ii. - - diff --git a/doc/src/write_dump.rst b/doc/src/write_dump.rst index 0509aeea75..ae0975cf11 100644 --- a/doc/src/write_dump.rst +++ b/doc/src/write_dump.rst @@ -98,5 +98,3 @@ Default The defaults are listed on the doc pages for the :doc:`dump ` and :doc:`dump image ` and :doc:`dump_modify ` commands. - -