diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index ce29d39ba6..32b72c544a 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -136,6 +136,7 @@ src directory. .. _cmake_presets: CMake presets for installing many packages +"""""""""""""""""""""""""""""""""""""""""" Instead of specifying all the CMake options via the command-line, CMake allows initializing its settings cache using script files. @@ -168,7 +169,8 @@ one of them as a starting point and customize it to your needs. in a single cmake run, or change settings incrementally by running cmake with new flags. -**Example:** +Example +""""""" .. code-block:: bash diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index c7bded1345..0d0551c008 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -12,7 +12,8 @@ When offloading to a co-processor from a CPU, the same routine is run twice, once on the CPU and once with an offload flag. This allows LAMMPS to run on the CPU cores and co-processor cores simultaneously. -**Currently Available USER-INTEL Styles:** +Currently Available USER-INTEL Styles +""""""""""""""""""""""""""""""""""""" * Angle Styles: charmm, harmonic * Bond Styles: fene, fourier, harmonic @@ -31,9 +32,10 @@ LAMMPS to run on the CPU cores and co-processor cores simultaneously. support computing per-atom stress. If any compute or fix in your input requires it, LAMMPS will abort with an error message. -**Speed-ups to expect:** +Speed-up to expect +""""""""""""""""""" -The speedups will depend on your simulation, the hardware, which +The speedup will depend on your simulation, the hardware, which styles are used, the number of atoms, and the floating-point precision mode. Performance improvements are shown compared to LAMMPS *without using other acceleration packages* as these are @@ -59,7 +61,8 @@ instructions to reproduce. ---------- -**Accuracy and order of operations:** +Accuracy and order of operations +"""""""""""""""""""""""""""""""" In most molecular dynamics software, parallelization parameters (# of MPI, OpenMP, and vectorization) can change the results due @@ -96,7 +99,8 @@ mode should not be used without appropriate validation. ---------- -**Quick Start for Experienced Users:** +Quick Start for Experienced Users +""""""""""""""""""""""""""""""""" LAMMPS should be built with the USER-INTEL package installed. Simulations should be run with 1 MPI task per physical *core*\ , @@ -136,7 +140,8 @@ For Intel Xeon Phi co-processors (Offload): ---------- -**Required hardware/software:** +Required hardware/software +"""""""""""""""""""""""""" When using Intel compilers version 16.0 or later is required. @@ -159,7 +164,8 @@ For best performance, we recommend that the MCDRAM is configured in "Cache" mode can also be used, although the performance might be slightly lower. -**Notes about Simultaneous Multithreading:** +Notes about Simultaneous Multithreading +""""""""""""""""""""""""""""""""""""""" Modern CPUs often support Simultaneous Multithreading (SMT). On Intel processors, this is called Hyper-Threading (HT) technology. @@ -196,7 +202,8 @@ this information can normally be obtained with: cat /proc/cpuinfo -**Building LAMMPS with the USER-INTEL package:** +Building LAMMPS with the USER-INTEL package +""""""""""""""""""""""""""""""""""""""""""" See the :ref:`Build extras ` doc page for instructions. Some additional details are covered here. @@ -263,7 +270,8 @@ recommended CCFLAG options for best performance are "-O2 -fno-alias in most of the example Makefiles is to use "-xHost", however this should not be used when cross-compiling. -**Running LAMMPS with the USER-INTEL package:** +Running LAMMPS with the USER-INTEL package +"""""""""""""""""""""""""""""""""""""""""" Running LAMMPS with the USER-INTEL package is similar to normal use with the exceptions that one should 1) specify that LAMMPS should use @@ -304,7 +312,8 @@ almost all cases. recommended, especially when running on a machine with Intel Hyper-Threading technology disabled. -**Run with the USER-INTEL package from the command line:** +Run with the USER-INTEL package from the command line +""""""""""""""""""""""""""""""""""""""""""""""""""""" To enable USER-INTEL optimizations for all available styles used in the input script, the "-sf intel" :doc:`command-line switch ` can be used without any requirement for @@ -339,7 +348,8 @@ launching MPI applications): mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision -**Or run with the USER-INTEL package by editing an input script:** +Or run with the USER-INTEL package by editing an input script +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" As an alternative to adding command-line arguments, the input script can be edited to enable the USER-INTEL package. This requires adding @@ -361,7 +371,8 @@ Alternatively, the :doc:`suffix intel ` command can be added to the input script to enable USER-INTEL styles for the commands that follow in the input script. -**Tuning for Performance:** +Tuning for Performance +"""""""""""""""""""""" .. note:: @@ -431,7 +442,8 @@ series processors will always perform better using MCDRAM. Please consult your system documentation for the best approach to specify that MPI runs are performed in MCDRAM. -**Tuning for Offload Performance:** +Tuning for Offload Performance +"""""""""""""""""""""""""""""" The default settings for offload should give good performance. @@ -521,7 +533,8 @@ the pair styles in the USER-INTEL package currently support the :doc:`run_style respa ` command; only the "pair" option is supported. -**References:** +References +"""""""""" * 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). diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index 04e4366758..3d3cb4daf1 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -8,18 +8,21 @@ improper), several Kspace styles, and a few fix styles. It uses the OpenMP interface for multi-threading, but can also be compiled without OpenMP support, providing optimized serial styles in that case. -**Required hardware/software:** +Required hardware/software +"""""""""""""""""""""""""" To enable multi-threading, your compiler must support the OpenMP interface. You should have one or more multi-core CPUs, as multiple threads can only be launched by each MPI task on the local node (using shared memory). -**Building LAMMPS with the USER-OMP package:** +Building LAMMPS with the USER-OMP package +""""""""""""""""""""""""""""""""""""""""" See the :ref:`Build extras ` doc page for instructions. -**Run with the USER-OMP package from the command line:** +Run with the USER-OMP package from the command line +""""""""""""""""""""""""""""""""""""""""""""""""""" These examples assume one or more 16-core nodes. @@ -52,7 +55,8 @@ details, including the default values used if it is not specified. It also gives more details on how to set the number of threads via the OMP_NUM_THREADS environment variable. -**Or run with the USER-OMP package by editing an input script:** +Or run with the USER-OMP package by editing an input script +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The discussion above for the mpirun/mpiexec command, MPI tasks/node, and threads/MPI task is the same. @@ -70,7 +74,8 @@ per MPI task to use. The command doc page explains other options and how to set the number of threads via the OMP_NUM_THREADS environment variable. -**Speed-ups to expect:** +Speed-up to expect +"""""""""""""""""" Depending on which styles are accelerated, you should look for a reduction in the "Pair time", "Bond time", "KSpace time", and "Loop @@ -92,7 +97,8 @@ sub-section. A description of the multi-threading strategy used in the USER-OMP package and some performance examples are `presented here `_ -**Guidelines for best performance:** +Guidelines for best performance +""""""""""""""""""""""""""""""" For many problems on current generation CPUs, running the USER-OMP package with a single thread/task is faster than running with multiple diff --git a/doc/src/Speed_opt.rst b/doc/src/Speed_opt.rst index 297177f8d4..338c4f2030 100644 --- a/doc/src/Speed_opt.rst +++ b/doc/src/Speed_opt.rst @@ -7,15 +7,18 @@ Technologies). It contains a handful of pair styles whose compute() methods were rewritten in C++ templated form to reduce the overhead due to if tests and other conditional code. -**Required hardware/software:** +Required hardware/software +"""""""""""""""""""""""""" -None. +Any hardware. Any compiler. -**Building LAMMPS with the OPT package:** +Building LAMMPS with the OPT package +"""""""""""""""""""""""""""""""""""" See the :ref:`Build extras ` doc page for instructions. -**Run with the OPT package from the command line:** +Run with the OPT package from the command line +"""""""""""""""""""""""""""""""""""""""""""""" .. code-block:: bash @@ -25,7 +28,8 @@ See the :ref:`Build extras ` doc page for instructions. Use the "-sf opt" :doc:`command-line switch `, which will automatically append "opt" to styles that support it. -**Or run with the OPT package by editing an input script:** +Or run with the OPT package by editing an input script +"""""""""""""""""""""""""""""""""""""""""""""""""""""" Use the :doc:`suffix opt ` command, or you can explicitly add an "opt" suffix to individual styles in your input script, e.g. @@ -34,13 +38,15 @@ Use the :doc:`suffix opt ` command, or you can explicitly add an pair_style lj/cut/opt 2.5 -**Speed-ups to expect:** +Speed-up to expect +"""""""""""""""""" You should see a reduction in the "Pair time" value printed at the end of a run. On most machines for reasonable problem sizes, it will be a 5 to 20% savings. -**Guidelines for best performance:** +Guidelines for best performance +""""""""""""""""""""""""""""""" Just try out an OPT pair style to see how it performs. diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index f0e9200fa0..8410f0f8c0 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -92,7 +92,10 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index 9c89271f12..7d2fdd5d66 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -135,7 +135,10 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/angle_coeff.rst b/doc/src/angle_coeff.rst index 565d094d4d..07048c1432 100644 --- a/doc/src/angle_coeff.rst +++ b/doc/src/angle_coeff.rst @@ -92,4 +92,7 @@ Related commands :doc:`angle_style ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_cosine.rst b/doc/src/angle_cosine.rst index 84ddabe61d..e39e68b2e1 100644 --- a/doc/src/angle_cosine.rst +++ b/doc/src/angle_cosine.rst @@ -60,4 +60,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_cosine_buck6d.rst b/doc/src/angle_cosine_buck6d.rst index 228b96abc8..4b8497d743 100644 --- a/doc/src/angle_cosine_buck6d.rst +++ b/doc/src/angle_cosine_buck6d.rst @@ -68,4 +68,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index f71d73459c..017b64f8b0 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -62,4 +62,7 @@ Related commands :doc:`angle_coeff `, :doc:`angle_style cosine/squared ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index db22bf2bce..aff4ba2322 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -70,7 +70,10 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst index 9aec7e4caf..26603e48be 100644 --- a/doc/src/angle_cosine_shift.rst +++ b/doc/src/angle_cosine_shift.rst @@ -61,4 +61,7 @@ Related commands :doc:`angle_coeff `, :doc:`angle_style cosine/shift/exp ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index 48e82cfed8..fbdb76aa45 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -74,4 +74,7 @@ Related commands :doc:`angle_style cosine/shift `, :doc:`dihedral_style cosine/shift/exp ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index 0ea824f24f..49ddf59741 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -62,4 +62,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 75fba2632b..5769e756c3 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -62,4 +62,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index 9aba8e6a45..3b4e4f5304 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -113,7 +113,10 @@ Related commands :doc:`angle_coeff `, :doc:`angle_hybrid ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index 6fb1fe25f7..cbe6544271 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -58,4 +58,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index a1494997ec..b36f69cbec 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -57,4 +57,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst index 4c957e1f75..c6ad93c3ec 100644 --- a/doc/src/angle_harmonic.rst +++ b/doc/src/angle_harmonic.rst @@ -69,4 +69,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_hybrid.rst b/doc/src/angle_hybrid.rst index c84b351132..1a562b0118 100644 --- a/doc/src/angle_hybrid.rst +++ b/doc/src/angle_hybrid.rst @@ -95,4 +95,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_mm3.rst b/doc/src/angle_mm3.rst index 988deb8ddc..0905ff6e4c 100644 --- a/doc/src/angle_mm3.rst +++ b/doc/src/angle_mm3.rst @@ -57,4 +57,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_none.rst b/doc/src/angle_none.rst index eea4f2f951..28c194a26a 100644 --- a/doc/src/angle_none.rst +++ b/doc/src/angle_none.rst @@ -37,4 +37,7 @@ Related commands :doc:`angle_style zero ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index 04758d7b7a..71297e60a0 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -65,4 +65,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 567b5a9a08..f5583d5013 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -73,4 +73,7 @@ Related commands :doc:`angle_coeff `, :doc:`angle_style harmonic `, :doc:`pair_style lj/sdk `, :doc:`pair_style lj/sdk/coul/long ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index b89ed53fd8..d8d9476620 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -130,7 +130,8 @@ one that matches the specified keyword. ---------- -**Restart info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This angle style writes the settings for the "angle_style table" command to :doc:`binary restart files `, so a angle_style @@ -152,4 +153,7 @@ Related commands :doc:`angle_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/angle_zero.rst b/doc/src/angle_zero.rst index 22b2e95c04..a0d5a02e1e 100644 --- a/doc/src/angle_zero.rst +++ b/doc/src/angle_zero.rst @@ -51,4 +51,7 @@ Related commands :doc:`angle_style none ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index c94ca65c1c..a4e4ec1500 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -160,7 +160,11 @@ The *first* and *sort* options cannot be used together. Since sorting is on by default, it will be turned off if the *first* keyword is used with a group-ID that is not "all". -**Related commands:** none +Related commands +"""""""""""""""" + +none + Default """"""" diff --git a/doc/src/balance.rst b/doc/src/balance.rst index fbf8c8fb5f..e023b6f2f0 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -548,4 +548,7 @@ Related commands .. _pizza: https://pizza.sandia.gov -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index ec4f5bfe0e..41eb2b4e50 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -65,7 +65,10 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/bond_coeff.rst b/doc/src/bond_coeff.rst index 39d1bbcd17..84a949a018 100644 --- a/doc/src/bond_coeff.rst +++ b/doc/src/bond_coeff.rst @@ -87,4 +87,7 @@ Related commands :doc:`bond_style ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index 2f8be4eb28..8ec117bf24 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -74,7 +74,10 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index 9826aeaf18..5bcb409238 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -72,7 +72,10 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index ce66307853..f09e5761fe 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -59,4 +59,7 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index dcbe24649b..eaa1ee7986 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -65,4 +65,7 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index 933f119a9b..c124bacf0f 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -65,4 +65,7 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds `, :doc:`bond_harmonic ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index 10f961f761..e1b7e990d4 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -64,4 +64,7 @@ Related commands :doc:`bond_harmonic `, :doc:`bond_style harmonic/shift ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_hybrid.rst b/doc/src/bond_hybrid.rst index 74bd39988b..0da93ccade 100644 --- a/doc/src/bond_hybrid.rst +++ b/doc/src/bond_hybrid.rst @@ -76,4 +76,7 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst index 8ea79d9139..2a255e7590 100644 --- a/doc/src/bond_mm3.rst +++ b/doc/src/bond_mm3.rst @@ -55,7 +55,10 @@ Related commands :doc:`bond_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index 5cd61adf3c..64fc61298a 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -60,4 +60,7 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_none.rst b/doc/src/bond_none.rst index 63ca5c1985..b418f5c503 100644 --- a/doc/src/bond_none.rst +++ b/doc/src/bond_none.rst @@ -31,8 +31,15 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" + +none + :doc:`bond_style zero ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index a965c63ea9..75ab4ad347 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -60,7 +60,10 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 71e5105436..ada2f0e1ed 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -108,7 +108,9 @@ Related commands :doc:`pair_style oxdna/excv `, :doc:`pair_style oxdna2/excv `, :doc:`pair_style oxrna2/excv `, :doc:`bond_coeff `, :doc:`fix nve/dotc/langevin ` -**Default:** +Default +""""""" + none diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index 831d8c18ef..d54c19bbd4 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -108,4 +108,7 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_special.rst b/doc/src/bond_special.rst index 5f2cebbb5a..bd93bb644c 100644 --- a/doc/src/bond_special.rst +++ b/doc/src/bond_special.rst @@ -103,4 +103,7 @@ Related commands :doc:`bond_coeff `, :doc:`special_bonds ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index ec22eda83b..9f8ebacef0 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -128,7 +128,8 @@ one that matches the specified keyword. ---------- -**Restart info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This bond style writes the settings for the "bond_style table" command to :doc:`binary restart files `, so a bond_style @@ -150,4 +151,7 @@ Related commands :doc:`bond_coeff `, :doc:`delete_bonds ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_write.rst b/doc/src/bond_write.rst index a062d0a82b..4170029239 100644 --- a/doc/src/bond_write.rst +++ b/doc/src/bond_write.rst @@ -70,4 +70,7 @@ Related commands :doc:`bond_style table `, :doc:`bond_style `, :doc:`bond_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/bond_zero.rst b/doc/src/bond_zero.rst index 42df0472a1..bcbbe8a014 100644 --- a/doc/src/bond_zero.rst +++ b/doc/src/bond_zero.rst @@ -50,4 +50,7 @@ Related commands :doc:`bond_style none ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/box.rst b/doc/src/box.rst index f677b8bb5f..c5937df75c 100644 --- a/doc/src/box.rst +++ b/doc/src/box.rst @@ -58,7 +58,11 @@ This command cannot be used after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command or :doc:`read_restart ` command. -**Related commands:** none +Related commands +"""""""""""""""" + +none + Default """"""" diff --git a/doc/src/clear.rst b/doc/src/clear.rst index 6c4ef9a22c..e9664a6112 100644 --- a/doc/src/clear.rst +++ b/doc/src/clear.rst @@ -37,6 +37,13 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/compute.rst b/doc/src/compute.rst index e31f4fde96..4da3e4ebe6 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -323,4 +323,7 @@ Related commands :doc:`uncompute `, :doc:`compute_modify `, :doc:`fix ave/atom `, :doc:`fix ave/time `, :doc:`fix ave/histo ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_ackland_atom.rst b/doc/src/compute_ackland_atom.rst index 33e0b6cf15..74922ba17b 100644 --- a/doc/src/compute_ackland_atom.rst +++ b/doc/src/compute_ackland_atom.rst @@ -58,7 +58,8 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of which computes this quantity.- -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index 08e7dcfd35..6ec5c5bc10 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -173,7 +173,8 @@ example: compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5 fix 1 all ave/time 100 1 100 c_myADF[*] file tmp.adf mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array with the number of rows = *Nbins*\ , and the number of columns = 1 + 2\*Ntriples, where Ntriples is the diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst index 60f929197c..d028cdec99 100644 --- a/doc/src/compute_angle.rst +++ b/doc/src/compute_angle.rst @@ -32,7 +32,8 @@ specified for this command is ignored. This compute is useful when using :doc:`angle_style hybrid ` if you want to know the portion of the total energy contributed by one or more of the hybrid sub-styles. -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length N where N is the number of sub_styles defined by the :doc:`angle_style hybrid ` command, which can be accessed by indices @@ -52,4 +53,7 @@ Related commands :doc:`compute pe `, :doc:`compute pair ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index fe0af199e2..169ef4f238 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -119,7 +119,8 @@ Here is an example of how to do this: compute 2 all angle/local theta eng dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_2[1] c_2[2] -**Output info:** +Output info +""""""""""" This compute calculates a local vector or local array depending on the number of values. The length of the vector or number of rows in the @@ -142,4 +143,7 @@ Related commands :doc:`dump local `, :doc:`compute property/local ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index eb5e8fd013..da27cb3d19 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -68,7 +68,8 @@ command, for example: compute myChunk all angmom/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = @@ -89,4 +90,7 @@ Related commands :doc:`variable angmom() function ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_basal_atom.rst b/doc/src/compute_basal_atom.rst index ac628d2b6d..a5558e6232 100644 --- a/doc/src/compute_basal_atom.rst +++ b/doc/src/compute_basal_atom.rst @@ -44,7 +44,8 @@ which computes this quantity. An example input script that uses this compute is provided in examples/USER/misc/basal. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom array with 3 columns, which can be accessed by indices 1-3 by any command that uses per-atom values from @@ -69,7 +70,10 @@ Related commands :doc:`compute centro/atom `, :doc:`compute ackland/atom ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index 395a8ebf91..e0369049cb 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -74,7 +74,8 @@ command. compute 1 all body/local type 1 2 3 dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] -**Output info:** +Output info +""""""""""" This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the @@ -97,4 +98,7 @@ Related commands :doc:`dump local ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst index 59ac05630a..00b99d1f9f 100644 --- a/doc/src/compute_bond.rst +++ b/doc/src/compute_bond.rst @@ -32,7 +32,8 @@ This compute is useful when using :doc:`bond_style hybrid ` if you want to know the portion of the total energy contributed by one or more of the hybrid sub-styles. -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length N where N is the number of sub_styles defined by the :doc:`bond_style hybrid ` command, which can be accessed by indices 1-N. @@ -52,4 +53,7 @@ Related commands :doc:`compute pe `, :doc:`compute pair ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index 32d756d52a..5264a86634 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -169,7 +169,8 @@ Here is an example of how to do this: compute 2 all bond/local dist engpot dump 1 all local 1000 tmp.dump index c_1[*] c_2[*] -**Output info:** +Output info +""""""""""" This compute calculates a local vector or local array depending on the number of values. The length of the vector or number of rows in the @@ -196,4 +197,7 @@ Related commands :doc:`dump local `, :doc:`compute property/local ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_centro_atom.rst b/doc/src/compute_centro_atom.rst index 312582eb90..489b7845ce 100644 --- a/doc/src/compute_centro_atom.rst +++ b/doc/src/compute_centro_atom.rst @@ -101,7 +101,8 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each with a *centro/atom* style. -**Output info:** +Output info +""""""""""" By default, this compute calculates the centrosymmetry value for each atom as a per-atom vector, which can be accessed by any command that diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index a3d915b8a4..a650c8fb0a 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -620,7 +620,8 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector (the chunk ID), which can be accessed by any command that uses per-atom values from a compute diff --git a/doc/src/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst index d486da4e3e..9e6489f828 100644 --- a/doc/src/compute_chunk_spread_atom.rst +++ b/doc/src/compute_chunk_spread_atom.rst @@ -188,7 +188,8 @@ it is in. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector or array, which can be accessed by any command that uses per-atom values from a compute as @@ -212,4 +213,7 @@ Related commands :doc:`compute chunk/atom `, :doc:`fix ave/chunk `, :doc:`compute reduce/chunk ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index 3772b0dd0b..77149306dc 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -104,7 +104,8 @@ style computes. because it does not perform a full update of the bond topology data structures within LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -122,7 +123,9 @@ Related commands :doc:`compute coord/atom ` -**Default:** +Default +""""""" + The default for fragment/atom is single no. diff --git a/doc/src/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst index 27bff636a2..41d7113b60 100644 --- a/doc/src/compute_cna_atom.rst +++ b/doc/src/compute_cna_atom.rst @@ -79,7 +79,8 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each with a *cna/atom* style. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -98,7 +99,10 @@ Related commands :doc:`compute centro/atom ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_cnp_atom.rst b/doc/src/compute_cnp_atom.rst index c87082dc07..1a1b509162 100644 --- a/doc/src/compute_cnp_atom.rst +++ b/doc/src/compute_cnp_atom.rst @@ -86,7 +86,8 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each with a *cnp/atom* style. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -118,7 +119,10 @@ Related commands :doc:`compute cna/atom ` :doc:`compute centro/atom ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst index af36b34b2b..203eaaf687 100644 --- a/doc/src/compute_com.rst +++ b/doc/src/compute_com.rst @@ -40,7 +40,8 @@ are the x,y,z coordinates of the center of mass. how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length 3, which can be accessed by indices 1-3 by any command that uses global vector values @@ -59,4 +60,7 @@ Related commands :doc:`compute com/chunk ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst index dd27702652..3165acfbcc 100644 --- a/doc/src/compute_com_chunk.rst +++ b/doc/src/compute_com_chunk.rst @@ -66,7 +66,8 @@ command, for example: compute myChunk all com/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = @@ -87,4 +88,7 @@ Related commands :doc:`compute com ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst index b8b3c695d6..f22a78c63c 100644 --- a/doc/src/compute_contact_atom.rst +++ b/doc/src/compute_contact_atom.rst @@ -34,7 +34,8 @@ sum of the radii of the two particles. The value of the contact number will be 0.0 for atoms not in the specified compute group. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, whose values can be accessed by any command that uses per-atom values from a compute as @@ -55,4 +56,7 @@ Related commands :doc:`compute coord/atom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index becbf95b6b..cbf879b8bd 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -120,7 +120,8 @@ too frequently. ---------- -**Output info:** +Output info +""""""""""" For *cstyle* cutoff, this compute can calculate a per-atom vector or array. If single *type1* keyword is specified (or if none are diff --git a/doc/src/compute_damage_atom.rst b/doc/src/compute_damage_atom.rst index ab17584ccd..2439bd5a1b 100644 --- a/doc/src/compute_damage_atom.rst +++ b/doc/src/compute_damage_atom.rst @@ -40,7 +40,8 @@ This command can be used with all the Peridynamic pair styles. The damage value will be 0.0 for atoms not in the specified compute group. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -61,4 +62,7 @@ Related commands :doc:`compute dilatation/atom `, :doc:`compute plasticity/atom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst index ed87b727ec..0bbcb370b5 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -31,7 +31,8 @@ group specified for this command is ignored. This compute is useful when using :doc:`dihedral_style hybrid ` if you want to know the portion of the total energy contributed by one or more of the hybrid sub-styles. -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length N where N is the number of sub_styles defined by the :doc:`dihedral_style hybrid ` command. which can be accessed by indices @@ -51,4 +52,7 @@ Related commands :doc:`compute pe `, :doc:`compute pair ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 6fd1401292..75c0e69790 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -113,7 +113,8 @@ Here is an example of how to do this: compute 2 all dihedral/local phi dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1] -**Output info:** +Output info +""""""""""" This compute calculates a local vector or local array depending on the number of values. The length of the vector or number of rows in the @@ -135,4 +136,7 @@ Related commands :doc:`dump local `, :doc:`compute property/local ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_dilatation_atom.rst b/doc/src/compute_dilatation_atom.rst index 46ebef8220..85b5770c64 100644 --- a/doc/src/compute_dilatation_atom.rst +++ b/doc/src/compute_dilatation_atom.rst @@ -43,7 +43,8 @@ This command can only be used with a subset of the Peridynamic :doc:`pair styles The dilatation value will be 0.0 for atoms not in the specified compute group. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -64,4 +65,7 @@ Related commands :doc:`compute damage/atom `, :doc:`compute plasticity/atom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index f08b1d67d9..d1bc5de4c9 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -71,7 +71,8 @@ command, for example: compute myChunk all dipole/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = @@ -92,4 +93,7 @@ Related commands :doc:`compute com/chunk ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index cb44d153ac..9079538fd8 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -121,7 +121,8 @@ would be empty. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a per-atom array with 4 columns, which can be accessed by indices 1-4 by any command that uses per-atom values from @@ -143,4 +144,7 @@ Related commands :doc:`compute msd `, :doc:`dump custom `, :doc:`fix store/state ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index c106522b57..a3b68451db 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -46,7 +46,8 @@ where :math:`N` is the number of particles in the system ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length 5 (:math:`U^{cond}`, :math:`U^{mech}`, :math:`U^{chem}`, :math:`\theta_{avg}`, :math:`N`), @@ -71,7 +72,10 @@ Related commands :doc:`compute dpd/atom `, :doc:`thermo_style ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst index d1a683db87..85dc977c52 100644 --- a/doc/src/compute_dpd_atom.rst +++ b/doc/src/compute_dpd_atom.rst @@ -33,7 +33,8 @@ total chemical energy and average internal temperature of the entire system or group of dpd particles. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle array with 4 columns (:math:`u^{cond}`, :math:`u^{mech}`, :math:`u^{chem}`, :math:`\theta`), which can be accessed @@ -60,7 +61,10 @@ Related commands :doc:`dump custom `, :doc:`compute dpd ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index 8670e70b48..e31974f98a 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -31,7 +31,8 @@ of each eDPD particle based on the local equilibrium hypothesis. For more details please see :ref:`(Espanol1997) ` and :ref:`(Li2014) `. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See the @@ -51,7 +52,10 @@ Related commands :doc:`pair_style edpd ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst index 85a180df74..59b0059376 100644 --- a/doc/src/compute_entropy_atom.rst +++ b/doc/src/compute_entropy_atom.rst @@ -109,7 +109,8 @@ and for bcc sodium (lattice constant 4.23 Angstroms), compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 -**Output info:** +Output info +""""""""""" By default, this compute calculates the pair entropy value for each atom as a per-atom vector, which can be accessed by any command that diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index ab0c1fe59b..0210279560 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -40,7 +40,8 @@ from its angular momentum if needed. treated as ellipsoids, not ellipses, meaning their moments of inertia will be the same as in 3d. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as @@ -67,8 +68,15 @@ the :doc:`atom_style tri ` command. All particles in the group must be finite-size. They cannot be point particles. -**Related commands:** none +Related commands +"""""""""""""""" + +none + :doc:`compute erotate/sphere ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst index f07751eff5..b5b594f781 100644 --- a/doc/src/compute_erotate_rigid.rst +++ b/doc/src/compute_erotate_rigid.rst @@ -38,7 +38,8 @@ compute command is ignored. The rotational energy of all the rigid bodies defined by the fix rigid command in included in the calculation. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the summed rotational energy of all the rigid bodies). This value can be used by any command that @@ -59,4 +60,7 @@ Related commands :doc:`compute ke/rigid ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index 17656ef0be..c10d13c318 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -35,7 +35,8 @@ of inertia for a sphere and w is the particle's angular velocity. spheres, not disks, meaning their moment of inertia will be the same as in 3d. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as @@ -60,4 +61,7 @@ Related commands :doc:`compute erotate/asphere ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst index f7450be9c2..b12669ed0c 100644 --- a/doc/src/compute_erotate_sphere_atom.rst +++ b/doc/src/compute_erotate_sphere_atom.rst @@ -39,7 +39,8 @@ The value of the rotational kinetic energy will be 0.0 for atoms not in the specified compute group or for point particles with a radius = 0.0. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -57,4 +58,7 @@ Related commands :doc:`dump custom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst index 679e455465..a147ca0d7d 100644 --- a/doc/src/compute_event_displace.rst +++ b/doc/src/compute_event_displace.rst @@ -43,7 +43,8 @@ further than the threshold distance. then this compute will not be able to distinguish that motion from local atom displacements and may generate "false positives." -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the flag). This value can be used by any command that uses a global scalar value from a compute as @@ -65,4 +66,7 @@ Related commands :doc:`prd `, :doc:`tad ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index 50ad50561b..0832d6191a 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -279,7 +279,8 @@ trajectories during which the volume fluctuates or changes :ref:`(Allen and Tild ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length 3 which contains the energy difference ( :math:`U_1-U_0` ) as c_ID[1], the diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index e9adb0317b..1c8ff6c85e 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -205,7 +205,8 @@ assignment of global values to atoms. ---------- -**Output info:** +Output info +""""""""""" If a single input is specified this compute produces a per-atom vector. If multiple inputs are specified, this compute produces a @@ -228,4 +229,7 @@ Related commands :doc:`compute `, :doc:`fix `, :doc:`variable `, :doc:`compute chunk/atom `, :doc:`compute reduce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index 03ae693b56..b22689d4b3 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -128,7 +128,8 @@ group-group calculations are performed. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. @@ -154,7 +155,11 @@ system and not valid if particles have been moved since. Not all :doc:`Kspace styles ` support the calculation of group/group interactions. The regular *ewald* and *pppm* styles do. -**Related commands:** none +Related commands +"""""""""""""""" + +none + Default """"""" diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index 42ca1e53e5..da0b14abe8 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -56,7 +56,8 @@ and taking a sqrt() would be invalid. reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (:math:`R_g`) and a global vector of length 6 (:math:`{R_g}^2` tensor), which can be accessed by indices 1-6. These @@ -78,4 +79,7 @@ Related commands :doc:`compute gyration/chunk `, :doc:`compute gyration/shape ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index 2ba632ded1..eaa048c111 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -92,7 +92,8 @@ command, for example: compute myChunk all gyration/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global vector if the *tensor* keyword is not specified and a global array if it is. The length of the vector or @@ -112,8 +113,15 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" + +none + :doc:`compute gyration ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index 81fc628a21..fced528015 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -63,7 +63,8 @@ is bounded between zero (if all points are spherically symmetric) and one atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length 6, which can be accessed by indices 1-6. The first three values are the @@ -87,7 +88,10 @@ Related commands :doc:`compute gyration ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index 94904f757d..375dc85134 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -64,7 +64,8 @@ The tensor keyword must be specified in the compute gyration/chunk command. atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. -**Output info:** +Output info +""""""""""" This compute calculates a global array with six columns, which can be accessed by indices 1-6. The first three columns are the @@ -89,7 +90,10 @@ Related commands :doc:`compute gyration/chunk ` :doc:`compute gyration/shape ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index 1b28c08ae5..3e8469617f 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -119,7 +119,8 @@ result should be: average conductivity ~0.29 in W/mK. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length 6. The first 3 components are the :math:`x`, :math:`y`, :math:`z` @@ -157,7 +158,10 @@ Related commands :doc:`fix ave/correlate `, :doc:`variable ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index 31f7dbe662..a8e70245df 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -97,7 +97,8 @@ too frequently. :doc:`special_bonds ` command that includes all pairs in the neighbor list. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom array with 2 columns, giving the real and imaginary parts :math:`q_n`, a complex number restricted to the diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index e00fdde841..5efb133bea 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -155,7 +155,8 @@ An example input script that uses this compute is included in examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA properties fluctuate less than the corresponding conventional properties. -**Output info:** +Output info +""""""""""" This compute calculates a global vector that includes the n properties requested as arguments to the command (the potential energy, pressure and/or heat @@ -182,7 +183,10 @@ Related commands formulation of the hessian provided by Pair's single_hessian, which is used by this compute. -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index 0a264a74e7..3eb008c3b2 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -31,7 +31,8 @@ group specified for this command is ignored. This compute is useful when using :doc:`improper_style hybrid ` if you want to know the portion of the total energy contributed by one or more of the hybrid sub-styles. -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length N where N is the number of sub_styles defined by the :doc:`improper_style hybrid ` command. which can be accessed by indices @@ -51,4 +52,7 @@ Related commands :doc:`compute pe `, :doc:`compute pair ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index 7a14daf161..4c4af36149 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -60,7 +60,8 @@ Here is an example of how to do this: compute 2 all improper/local chi dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1] -**Output info:** +Output info +""""""""""" This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the @@ -82,4 +83,7 @@ Related commands :doc:`dump local `, :doc:`compute property/local ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index f667929807..638a0baec8 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -67,7 +67,8 @@ command, for example: compute myChunk all inertia/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = @@ -88,4 +89,7 @@ Related commands :doc:`variable inertia() function ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst index d98d39247c..786f17b1d8 100644 --- a/doc/src/compute_ke.rst +++ b/doc/src/compute_ke.rst @@ -43,7 +43,8 @@ that calculate temperature can subtract out different non-thermal components of velocity and/or include different degrees of freedom (translational, rotational, etc). -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the summed KE). This value can be used by any command that uses a global scalar value from a @@ -62,4 +63,7 @@ Related commands :doc:`compute erotate/sphere ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_ke_atom.rst b/doc/src/compute_ke_atom.rst index 42294dbca1..8828ee4e3f 100644 --- a/doc/src/compute_ke_atom.rst +++ b/doc/src/compute_ke_atom.rst @@ -32,7 +32,8 @@ the velocity of each atom. The value of the kinetic energy will be 0.0 for atoms not in the specified compute group. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -50,4 +51,7 @@ Related commands :doc:`dump custom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst index 7aa89d0dfc..3ff9ce0c1f 100644 --- a/doc/src/compute_ke_atom_eff.rst +++ b/doc/src/compute_ke_atom_eff.rst @@ -60,7 +60,8 @@ of freedom in eFF. The value of the kinetic energy will be 0.0 for atoms (nuclei or electrons) not in the specified compute group. -**Output info:** +Output info +""""""""""" This compute calculates a scalar quantity for each atom, which can be accessed by any command that uses per-atom computes as input. See the @@ -80,4 +81,7 @@ Related commands :doc:`dump custom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst index f1cffebc56..874ae8d629 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -64,7 +64,8 @@ freedom. See :doc:`compute temp/eff `. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as @@ -80,6 +81,13 @@ Restrictions This compute is part of the USER-EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/compute_ke_rigid.rst b/doc/src/compute_ke_rigid.rst index fd4706de19..c8bd663da7 100644 --- a/doc/src/compute_ke_rigid.rst +++ b/doc/src/compute_ke_rigid.rst @@ -37,7 +37,8 @@ compute command is ignored. The kinetic energy of all the rigid bodies defined by the fix rigid command in included in the calculation. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the summed KE of all the rigid bodies). This value can be used by any command that uses a @@ -58,4 +59,7 @@ Related commands :doc:`compute erotate/rigid ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_mesont.rst b/doc/src/compute_mesont.rst index 654b06c4a3..bf0ade16c1 100644 --- a/doc/src/compute_mesont.rst +++ b/doc/src/compute_mesont.rst @@ -31,7 +31,8 @@ These computes define computations for the stretching (estretch), bending evaluated value is selected by a parameter passed to the compute: estretch, ebend, etube. -**Output info:** +Output info +""""""""""" These computes calculate per-node (per-atom) vectors, which can be accessed by any command that uses per-atom values from a compute as input, and global @@ -52,5 +53,8 @@ Related commands :doc:`dump custom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_mliap.rst b/doc/src/compute_mliap.rst index 4ef41f1e47..fcc336e682 100644 --- a/doc/src/compute_mliap.rst +++ b/doc/src/compute_mliap.rst @@ -138,7 +138,8 @@ too frequently. ---------- -**Output info:** +Output info +""""""""""" Compute *mliap* evaluates a global array. The columns are arranged into diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst index af968efb59..bcc5f3d421 100644 --- a/doc/src/compute_momentum.rst +++ b/doc/src/compute_momentum.rst @@ -29,7 +29,8 @@ of a group of particles. The momentum of each particles is computed as m v, where m and v are the mass and velocity of the particle. -**Output info:** +Output info +""""""""""" This compute calculates a global vector (the summed momentum) of length 3. This value can be used by any command that uses a global @@ -48,4 +49,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst index f88e960802..02b5550093 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -95,7 +95,8 @@ solids undergoing thermal motion. with subsequent positions as if they were from a single sample, instead of many, which will change the values of msd somewhat. -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length 4, which can be accessed by indices 1-4 by any command that uses global vector values diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index d9cd83c3e0..ee2c4612d7 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -105,7 +105,8 @@ command, for example: compute myChunk all msd/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = @@ -126,4 +127,7 @@ Related commands :doc:`compute msd ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst index 267269ec4b..63d8deb2cd 100644 --- a/doc/src/compute_msd_nongauss.rst +++ b/doc/src/compute_msd_nongauss.rst @@ -59,7 +59,8 @@ displacement of each atom is calculated. See the :doc:`compute msd ` doc page for further important NOTEs, which also apply to this compute. -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length 3, which can be accessed by indices 1-3 by any command that uses global vector values diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index 73895b585c..d0af88b1a4 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -68,7 +68,8 @@ command, for example: compute myChunk all omega/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = @@ -89,4 +90,7 @@ Related commands :doc:`variable omega() function ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index f176fdd30c..c8ab4d7b9b 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -151,7 +151,8 @@ too frequently. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a per-atom array with *nlvalues* columns, giving the :math:`Q_l` values for each atom, which are real numbers on the diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst index 40c758ebf0..1b074203aa 100644 --- a/doc/src/compute_pair.rst +++ b/doc/src/compute_pair.rst @@ -68,7 +68,8 @@ potential energy into 14 components is tallied by the :doc:`pair_style reax/c

` for info on these values. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar which is *epair* or *evdwl* or *ecoul*\ . If the pair style supports it, it also calculates a global diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index 31030cd97e..e269aaadfe 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -138,7 +138,8 @@ Here is an example of how to do this: computed in the pair style. Hence in that case, those atom pairs will be part of the local data created by this command. -**Output info:** +Output info +""""""""""" This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index 813b577490..4597ea7533 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -65,7 +65,8 @@ See the "thermo_style" command for more details. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the potential energy). This value can be used by any command that uses a global scalar value from @@ -84,4 +85,7 @@ Related commands :doc:`compute pe/atom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst index b616cecd89..91aaaf867c 100644 --- a/doc/src/compute_pe_atom.rst +++ b/doc/src/compute_pe_atom.rst @@ -84,7 +84,8 @@ in the last 2 columns of thermo output: corrections to the energy added by the :doc:`pair_modify tail yes ` command, since those are contributions to the global system energy. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -101,7 +102,10 @@ Related commands :doc:`compute pe `, :doc:`compute stress/atom ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst index 939017f5e9..b78f706afd 100644 --- a/doc/src/compute_plasticity_atom.rst +++ b/doc/src/compute_plasticity_atom.rst @@ -38,7 +38,8 @@ This command can be invoked for one of the Peridynamic :doc:`pair styles `, :doc:`compute dilatation/atom ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 57e5bc26ef..b89d17bc5a 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -116,7 +116,8 @@ where "thermo_temp" is the ID of a similarly defined compute of style ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices @@ -138,7 +139,10 @@ Related commands :doc:`compute temp `, :doc:`compute stress/atom `, :doc:`thermo_style `, -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst index 104e68d533..d1102cd9bc 100644 --- a/doc/src/compute_pressure_cylinder.rst +++ b/doc/src/compute_pressure_cylinder.rst @@ -41,7 +41,8 @@ number density, P_rhorho, P_phiphi, and P_zz. The number of rows is governed by the values of Rmax and bin_width. Pressure tensor values are output in pressure units. -**Output info:** +Output info +""""""""""" This compute calculates a global array with 5 columns and Rmax/bin_width rows. The output columns are: R (distance units), number density (inverse @@ -75,7 +76,10 @@ Related commands :doc:`compute temp `, :doc:`compute stress/atom `, :doc:`thermo_style `, -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst index 07302ba46d..bdd212cf5c 100644 --- a/doc/src/compute_pressure_uef.rst +++ b/doc/src/compute_pressure_uef.rst @@ -59,4 +59,7 @@ Related commands :doc:`fix nvt/uef `, :doc:`compute temp/uef ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index 021518713d..ec9322bb7b 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -160,7 +160,8 @@ floating-point properties that have been added to each atom via the command is used specific names are given to each attribute which are what is specified as the "name" portion of *i_name* or *d_name*. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector or per-atom array depending on the number of input values. If a single input is specified, a @@ -189,4 +190,7 @@ Related commands :doc::doc:`fix ave/atom `, :doc:`fix ave/chunk :doc:`, `fix property/atom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index e567c96a80..246ab09120 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -88,7 +88,8 @@ command, for example: compute myChunk2 all com/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global vector or global array depending on the number of input values. The length of the vector or number of @@ -116,4 +117,7 @@ Related commands :doc:`fix ave/chunk ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index 4e29bb7fc0..dd92334266 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -140,7 +140,8 @@ The attributes that start with "a", "d", "i", refer to similar values for :doc:`angles `, :doc:`dihedrals `, and :doc:`impropers `. -**Output info:** +Output info +""""""""""" This compute calculates a local vector or local array depending on the number of input values. The length of the vector or number of rows in diff --git a/doc/src/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst index 112ed1ea6a..fb590f6e4c 100644 --- a/doc/src/compute_ptm_atom.rst +++ b/doc/src/compute_ptm_atom.rst @@ -84,7 +84,8 @@ too frequently or to have multiple compute/dump commands, each with a unless the optional *group2-ID* argument is given, then only members of that group are considered as neighbors. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom array, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -120,7 +121,10 @@ Related commands :doc:`compute centro/atom ` :doc:`compute cna/atom ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index 9f292accd1..a9e6674816 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -152,7 +152,8 @@ example: compute myRDF all rdf 50 fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp.rdf mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array with the number of rows = *Nbins*\ , and the number of columns = 1 + 2\*Npairs, where Npairs is the diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index 7599343d2e..bf7d0dc28c 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -196,7 +196,8 @@ values are desired, this compute can be accessed by the :doc:`thermo_style custo ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar if a single input value is specified or a global vector of length N where N is the number of @@ -222,4 +223,7 @@ Related commands :doc:`compute `, :doc:`fix `, :doc:`variable ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index 34619efd06..07edda4569 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -160,7 +160,8 @@ handful of large micelles. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global vector if a single input value is specified, otherwise a global array is output. The number of columns @@ -184,4 +185,7 @@ Related commands :doc:`compute chunk/atom `, :doc:`compute reduce `, :doc:`compute chunk/spread/atom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst index 4fc0f3c2dd..f7bb6d6166 100644 --- a/doc/src/compute_rigid_local.rst +++ b/doc/src/compute_rigid_local.rst @@ -150,7 +150,8 @@ LAMMPS. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the @@ -187,4 +188,7 @@ Related commands :doc:`dump local `, :doc:`compute reduce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index 6e2f6a35cf..1057208900 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -228,7 +228,8 @@ type. Valid chemical symbols for compute saed are: If the *echo* keyword is specified, compute saed will provide extra reporting information to the screen. -**Output info:** +Output info +""""""""""" This compute calculates a global vector. The length of the vector is the number of reciprocal lattice nodes that are explored by the mesh. diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index c8211269bc..2d558b871f 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -89,7 +89,8 @@ of columns equal to the number of inputs specified. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global vector if a single input value is specified or a global array with N columns where N is the number of @@ -123,4 +124,7 @@ Related commands :doc:`compute `, :doc:`fix `, :doc:`compute reduce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst index 01c543af38..71630b827d 100644 --- a/doc/src/compute_smd_contact_radius.rst +++ b/doc/src/compute_smd_contact_radius.rst @@ -35,7 +35,8 @@ Mach Dynamics in LAMMPS. The value of the contact radius will be 0.0 for particles not in the specified compute group. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. @@ -55,4 +56,7 @@ Related commands :doc:`dump custom ` smd/hertz smd/tri_surface -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst index 3f02ac5c74..ee3671e20c 100644 --- a/doc/src/compute_smd_damage.rst +++ b/doc/src/compute_smd_damage.rst @@ -48,4 +48,7 @@ Related commands :doc:`smd/plastic_strain `, :doc:`smd/tlsph_stress ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst index 56b8a81c01..980d31454e 100644 --- a/doc/src/compute_smd_hourglass_error.rst +++ b/doc/src/compute_smd_hourglass_error.rst @@ -56,7 +56,8 @@ LAMMPS was built with that package. See the :doc:`Build package This quantity will be computed only for particles which interact with tlsph pair style. -**Related Commands:** +Related commands +"""""""""""""""" :doc:`smd/tlsph_defgrad ` diff --git a/doc/src/compute_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst index 7613d5bb3e..c4df459d5f 100644 --- a/doc/src/compute_smd_internal_energy.rst +++ b/doc/src/compute_smd_internal_energy.rst @@ -29,7 +29,8 @@ the sum of potential energy and heat. See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. -**Output Info:** +Output Info +""""""""""" This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. @@ -46,7 +47,10 @@ LAMMPS was built with that package. See the :doc:`Build package only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. -**Related Commands:** +Related commands +"""""""""""""""" + +none Default """"""" diff --git a/doc/src/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst index 772169310f..81bacdc4bb 100644 --- a/doc/src/compute_smd_plastic_strain.rst +++ b/doc/src/compute_smd_plastic_strain.rst @@ -54,4 +54,7 @@ Related commands :doc:`smd/tlsph/strain/rate `, :doc:`smd/tlsph/strain ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst index 7b0480a211..cdcd377b41 100644 --- a/doc/src/compute_smd_plastic_strain_rate.rst +++ b/doc/src/compute_smd_plastic_strain_rate.rst @@ -54,4 +54,7 @@ Related commands :doc:`smd/tlsph/strain/rate `, :doc:`smd/tlsph/strain ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst index 50c74b8c26..e7cdb8a9d3 100644 --- a/doc/src/compute_smd_rho.rst +++ b/doc/src/compute_smd_rho.rst @@ -31,7 +31,8 @@ due to mechanical deformation. See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. @@ -51,4 +52,7 @@ Related commands :doc:`compute smd/vol ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst index c599b82709..d74b684c5d 100644 --- a/doc/src/compute_smd_tlsph_defgrad.rst +++ b/doc/src/compute_smd_tlsph_defgrad.rst @@ -30,7 +30,8 @@ Total-Lagrangian SPH pair style. See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute outputs a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values @@ -56,4 +57,7 @@ Related commands :doc:`smd/hourglass/error ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst index 7835f0642d..888140c534 100644 --- a/doc/src/compute_smd_tlsph_dt.rst +++ b/doc/src/compute_smd_tlsph_dt.rst @@ -35,7 +35,8 @@ stable time increment accessible for output purposes. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. @@ -58,4 +59,7 @@ Related commands :doc:`smd/adjust/dt ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst index 202f1640d6..5d34f1acef 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.rst +++ b/doc/src/compute_smd_tlsph_num_neighs.rst @@ -30,7 +30,8 @@ Total-Lagrangian SPH pair style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. @@ -53,4 +54,7 @@ Related commands :doc:`smd/ulsph/num/neighs ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst index f4ed10a232..d9ce1e3d9a 100644 --- a/doc/src/compute_smd_tlsph_shape.rst +++ b/doc/src/compute_smd_tlsph_shape.rst @@ -31,7 +31,8 @@ Total-Lagrangian SPH pair style. See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector of vectors, which can be accessed by any command that uses per-particle values from a compute @@ -60,4 +61,7 @@ Related commands :doc:`smd/contact/radius ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst index 24c5937462..b89311eb4b 100644 --- a/doc/src/compute_smd_tlsph_strain.rst +++ b/doc/src/compute_smd_tlsph_strain.rst @@ -29,7 +29,8 @@ for particles interacting via the Total-Lagrangian SPH pair style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values @@ -57,4 +58,7 @@ Related commands :doc:`smd/tlsph/strain/rate `, :doc:`smd/tlsph/stress ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst index 0eb68432c1..d1fc399b42 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.rst +++ b/doc/src/compute_smd_tlsph_strain_rate.rst @@ -29,7 +29,8 @@ particles interacting via the Total-Lagrangian SPH pair style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values @@ -55,4 +56,7 @@ Related commands :doc:`compute smd/tlsph/strain `, :doc:`compute smd/tlsph/stress ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst index 10d01ea9c0..d3711954c5 100644 --- a/doc/src/compute_smd_tlsph_stress.rst +++ b/doc/src/compute_smd_tlsph_stress.rst @@ -29,7 +29,8 @@ particles interacting via the Total-Lagrangian SPH pair style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values @@ -57,4 +58,7 @@ Related commands :doc:`compute smd/tlsph/strain `, :doc:`cmopute smd/tlsph/strain/rate ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst index ad33df3ef8..d797891618 100644 --- a/doc/src/compute_smd_triangle_vertices.rst +++ b/doc/src/compute_smd_triangle_vertices.rst @@ -29,7 +29,8 @@ corresponding to the triangle-elements of a mesh created by the :doc:`fix smd/wa See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute returns a per-particle vector of vectors, which can be accessed by any command that uses per-particle values from a compute @@ -61,4 +62,7 @@ Related commands :doc:`fix smd/move/tri/surf `, :doc:`fix smd/wall_surface ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_ulsph_effm.rst b/doc/src/compute_smd_ulsph_effm.rst index 94b1a6b6fe..e6d6b772a0 100644 --- a/doc/src/compute_smd_ulsph_effm.rst +++ b/doc/src/compute_smd_ulsph_effm.rst @@ -29,7 +29,8 @@ particles interacting via the updated Lagrangian SPH pair style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. @@ -53,4 +54,7 @@ Related commands :doc:`pair smd/ulsph ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_ulsph_num_neighs.rst b/doc/src/compute_smd_ulsph_num_neighs.rst index 70824fc517..3579a88079 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.rst +++ b/doc/src/compute_smd_ulsph_num_neighs.rst @@ -30,7 +30,8 @@ the updated Lagrangian SPH pair style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute returns a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. @@ -52,4 +53,7 @@ Related commands :doc:`compute smd/tlsph/num/neighs ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_ulsph_strain.rst b/doc/src/compute_smd_ulsph_strain.rst index dbf6751bf7..09f06b084b 100644 --- a/doc/src/compute_smd_ulsph_strain.rst +++ b/doc/src/compute_smd_ulsph_strain.rst @@ -29,7 +29,8 @@ particles interacting via the updated Lagrangian SPH pair style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle tensor, which can be accessed by any command that uses per-particle values from a compute as input. @@ -55,4 +56,7 @@ Related commands :doc:`compute smd/tlsph/strain ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_ulsph_strain_rate.rst b/doc/src/compute_smd_ulsph_strain_rate.rst index 7f911e9332..391367321a 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.rst +++ b/doc/src/compute_smd_ulsph_strain_rate.rst @@ -30,7 +30,8 @@ style. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values @@ -56,4 +57,7 @@ Related commands :doc:`compute smd/tlsph/strain/rate ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_ulsph_stress.rst b/doc/src/compute_smd_ulsph_stress.rst index c74b37508a..e1db7640a6 100644 --- a/doc/src/compute_smd_ulsph_stress.rst +++ b/doc/src/compute_smd_ulsph_stress.rst @@ -28,7 +28,8 @@ Define a computation that outputs the Cauchy stress tensor. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values @@ -55,4 +56,7 @@ Related commands :doc:`compute smd/ulsph/strain `, :doc:`compute smd/ulsph/strain/rate ` :doc:`compute smd/tlsph/stress ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst index abcc6fca22..4f9314ac32 100644 --- a/doc/src/compute_smd_vol.rst +++ b/doc/src/compute_smd_vol.rst @@ -29,7 +29,8 @@ of the per-particle volumes of the group for which the fix is defined. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Output info:** +Output info +""""""""""" This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. @@ -53,4 +54,7 @@ Related commands :doc:`compute smd/rho ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 4c8c7e1383..7e74a1bd61 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -310,7 +310,8 @@ are not both set or not both unset. ---------- -**Output info:** +Output info +""""""""""" Compute *sna/atom* calculates a per-atom array, each column corresponding to a particular bispectrum component. The total number diff --git a/doc/src/compute_sph_e_atom.rst b/doc/src/compute_sph_e_atom.rst index f35976ed10..08378c7c99 100644 --- a/doc/src/compute_sph_e_atom.rst +++ b/doc/src/compute_sph_e_atom.rst @@ -36,7 +36,8 @@ LAMMPS. The value of the internal energy will be 0.0 for atoms not in the specified compute group. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -56,4 +57,7 @@ Related commands :doc:`dump custom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_sph_rho_atom.rst b/doc/src/compute_sph_rho_atom.rst index 4237bf0bf5..975ebf996d 100644 --- a/doc/src/compute_sph_rho_atom.rst +++ b/doc/src/compute_sph_rho_atom.rst @@ -35,7 +35,8 @@ LAMMPS. The value of the SPH density will be 0.0 for atoms not in the specified compute group. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -55,4 +56,7 @@ Related commands :doc:`dump custom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_sph_t_atom.rst b/doc/src/compute_sph_t_atom.rst index 1766e1d712..2f8ad12f45 100644 --- a/doc/src/compute_sph_t_atom.rst +++ b/doc/src/compute_sph_t_atom.rst @@ -40,7 +40,8 @@ LAMMPS. The value of the internal energy will be 0.0 for atoms not in the specified compute group. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See @@ -60,4 +61,7 @@ Related commands :doc:`dump custom ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_spin.rst b/doc/src/compute_spin.rst index 49243e9650..aaf9d8cc74 100644 --- a/doc/src/compute_spin.rst +++ b/doc/src/compute_spin.rst @@ -55,7 +55,8 @@ the total magnetization, and the magnetic temperature. Three variables are assigned to those quantities. The thermo and thermo_style commands print them every 10 timesteps. -**Output info:** +Output info +""""""""""" The array values are "intensive". The array values will be in metal units (:doc:`units `). @@ -71,7 +72,9 @@ has to be "spin" for this compute to be valid. none -**Default:** +Default +""""""" + none diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index b8b3cb0ea1..2bdab03bda 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -209,7 +209,8 @@ result. I.e. the last 2 columns of thermo output will be the same: corrections to the pressure added by the :doc:`pair_modify tail yes ` command, since those are contributions to the global system pressure. -**Output info:** +Output info +""""""""""" This compute *stress/atom* calculates a per-atom array with 6 columns, which can be accessed by indices 1-6 by any command that uses per-atom values from @@ -238,7 +239,10 @@ Related commands :doc:`compute pe `, :doc:`compute pressure ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index 83a8374702..4d0d21cb87 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -67,7 +67,8 @@ NOTE 1: The configurational stress is computed considering all pairs of atoms wh NOTE 2: The local stress does not include any Lennard-Jones tail corrections to the pressure added by the :doc:`pair_modify tail yes ` command, since those are contributions to the global system pressure. -**Output info:** +Output info +""""""""""" Compute *stress/mop* calculates a global vector (indices starting at 1), with 3 values for each declared keyword (in the order the keywords have been @@ -105,7 +106,10 @@ Related commands :doc:`compute stress/atom ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index f49c872306..281425763a 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -63,7 +63,8 @@ pairwise property computations. ---------- -**Output info:** +Output info +""""""""""" Compute *pe/tally* calculates a global scalar (the energy) and a per atom scalar (the contributions of the single atom to the global @@ -105,4 +106,7 @@ Related commands *compute group/group*\ _compute_group_group.html, *compute heat/flux*\ _compute_heat_flux.html -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index 00eee60f62..dc18145e72 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -32,7 +32,8 @@ The chemical concentration of each species is defined as the number of molecules carried by a tDPD particle for dilute solution. For more details see :ref:`(Li2015) `. -**Output info:** +Output info +""""""""""" This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See the @@ -53,7 +54,10 @@ Related commands :doc:`pair_style tdpd ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index 81186c8cbc..ac11aa155c 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -73,7 +73,8 @@ thermostatting. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -96,4 +97,7 @@ Related commands :doc:`compute temp/partial `, :doc:`compute temp/region `, :doc:`compute pressure ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index 46fadc2ff5..ef04cad327 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -123,7 +123,8 @@ rotational degrees of freedom. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -156,4 +157,7 @@ Related commands :doc:`compute temp ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index 75477eff36..f334c1e11b 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -103,7 +103,8 @@ rotational degrees of freedom. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -132,4 +133,7 @@ Related commands :doc:`compute temp ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index 89bef3a327..77e2568fce 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -201,7 +201,8 @@ molecule. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index b21db2ac27..07ae9ad648 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -67,7 +67,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -90,4 +91,7 @@ Related commands :doc:`compute temp ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index edd1d0b139..6b9f0a7e83 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -84,7 +84,8 @@ The internal energy of core/shell pairs can be calculated by the defined as core/shell pairs. See the :doc:`Howto coreshell ` doc page doc page for more discussion on how to do this. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -109,7 +110,10 @@ Related commands :doc:`compute temp `, :doc:`compute temp/chunk ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index d73670485b..026064000c 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -108,7 +108,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -132,4 +133,7 @@ Related commands :doc:`compute temp/ramp `, :doc:`compute temp/profile `, :doc:`fix deform `, :doc:`fix nvt/sllod ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index b5d6659573..03be4a89fd 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -43,7 +43,8 @@ translational degrees of freedom for each nuclei or electron are affected by the streaming velocity adjustment. The radial velocity component of the electrons is not affected. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -69,4 +70,7 @@ Related commands :doc:`compute temp/ramp `, :doc:`fix deform `, :doc:`fix nvt/sllod/eff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index 8cb9849a24..418f2e1e5d 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -43,7 +43,8 @@ velocities of the Drude particles with respect to their cores. Non-polarizable atoms are considered as cores. Their velocities contribute to the temperature of the cores. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6, which can be accessed by indices 1-6, whose components @@ -76,4 +77,7 @@ Related commands :doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`pair_style thole `, :doc:`compute temp ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index 84a2028920..6bbad345e2 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -78,7 +78,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. -**Output info:** +Output info +""""""""""" The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector @@ -96,4 +97,7 @@ Related commands :doc:`compute temp/partial `, :doc:`compute temp/region `, :doc:`compute pressure ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index bcc7a92f84..fc3bfc5c88 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -73,7 +73,8 @@ thermostatting. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -96,4 +97,7 @@ Related commands :doc:`compute temp `, :doc:`compute temp/region `, :doc:`compute pressure ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 53870fa300..0fa8ce5807 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -134,7 +134,8 @@ thermostatting. Using this compute in conjunction with a thermostatting fix, as explained there, will effectively implement a profile-unbiased thermostat (PUT), as described in :ref:`(Evans) `. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature). Depending on the setting of the *out* keyword, it also calculates a global diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 4ac22bdfef..078ac66002 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -88,7 +88,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index e207d75d9f..5bf80c8f09 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -81,7 +81,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -104,4 +105,7 @@ Related commands :doc:`compute temp `, :doc:`compute pressure ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index a05cc5597c..622b3eb203 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -35,7 +35,8 @@ The operation of this compute is exactly like that described by the the formula for the temperature itself includes the radial electron velocity contributions, as discussed by the :doc:`compute temp/eff ` command. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -60,4 +61,7 @@ Related commands :doc:`compute temp/region `, :doc:`compute temp/eff `, :doc:`compute pressure ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index 7d3ed4d63d..e489136d2b 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -66,7 +66,8 @@ See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform thermostatting. -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. @@ -91,4 +92,7 @@ Related commands :doc:`compute temp ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index f0cd4c3ba0..b39bad80c0 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -110,7 +110,8 @@ rotational degrees of freedom. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. diff --git a/doc/src/compute_temp_uef.rst b/doc/src/compute_temp_uef.rst index 2ce288a66f..11bfca48e9 100644 --- a/doc/src/compute_temp_uef.rst +++ b/doc/src/compute_temp_uef.rst @@ -51,4 +51,7 @@ Related commands :doc:`fix nvt/uef `, :doc:`compute pressure/uef ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index 30ea9f7057..4a2f9cca21 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -113,7 +113,8 @@ du/dl can be found in the paper by :ref:`Eike `. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar, namely dUs/dlambda. This value can be used by any command that uses a global scalar value from @@ -135,7 +136,10 @@ Related commands :doc:`fix adapt ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst index 258ce03aa0..61ecdf0e6e 100644 --- a/doc/src/compute_torque_chunk.rst +++ b/doc/src/compute_torque_chunk.rst @@ -67,7 +67,8 @@ command, for example: compute myChunk all torque/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = @@ -88,4 +89,7 @@ Related commands :doc:`variable torque() function ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_vacf.rst b/doc/src/compute_vacf.rst index 1ca69e104a..7b5ea78a3a 100644 --- a/doc/src/compute_vacf.rst +++ b/doc/src/compute_vacf.rst @@ -57,7 +57,8 @@ following manner, using the :doc:`variable trap() ` function: quantities will also have the same ID, and thus be initialized correctly with time=0 atom velocities from the restart file. -**Output info:** +Output info +""""""""""" This compute calculates a global vector of length 4, which can be accessed by indices 1-4 by any command that uses global vector values @@ -76,4 +77,7 @@ Related commands :doc:`compute msd ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst index 415038d7c2..fd874998ab 100644 --- a/doc/src/compute_vcm_chunk.rst +++ b/doc/src/compute_vcm_chunk.rst @@ -57,7 +57,8 @@ command, for example: compute myChunk all vcm/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector -**Output info:** +Output info +""""""""""" This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = @@ -73,6 +74,13 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index 6f783b481e..862f65a482 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -114,7 +114,8 @@ thermostatting. ---------- -**Output info:** +Output info +""""""""""" This compute calculates a global scalar (the temperature) and a global vector of length 7, which can be accessed by indices 1-7. diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index a5d99d5de9..8998115841 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -188,7 +188,8 @@ Voro++ software in the src/VORONOI/README file. simulation box for 2d simulations when using the :doc:`create_box ` or :doc:`read_data ` commands. -**Output info:** +Output info +""""""""""" By default, this compute calculates a per-atom array with 2 columns. In regular dynamic tessellation mode the first column is the @@ -235,4 +236,8 @@ Related commands :doc:`dump custom `, :doc:`dump local ` -**Default:** *neighbors* no, *peratom* yes +Default +""""""" + +*neighbors* no, *peratom* yes + diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index 29bb2d2d3b..d927b6599f 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -203,7 +203,8 @@ type. Valid chemical symbols for compute xrd are: If the *echo* keyword is specified, compute xrd will provide extra reporting information to the screen. -**Output info:** +Output info +""""""""""" This compute calculates a global array. The number of rows in the array is the number of reciprocal lattice nodes that are explored diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 917a4b3b0a..d179e3f673 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -153,4 +153,7 @@ Related commands :doc:`read_data `, :doc:`create_atoms `, :doc:`region ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index 9c42b5a2a0..ffb06e55b2 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -155,4 +155,7 @@ Related commands :doc:`neigh_modify ` exclude, :doc:`special_bonds `, :doc:`fix shake ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index feee4a6b95..bbaaaf2dd4 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -149,7 +149,10 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst index 2b8cfa21b3..907102a4f6 100644 --- a/doc/src/dihedral_class2.rst +++ b/doc/src/dihedral_class2.rst @@ -170,7 +170,10 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst index 71bd931c5f..b60c3c3d6c 100644 --- a/doc/src/dihedral_coeff.rst +++ b/doc/src/dihedral_coeff.rst @@ -102,4 +102,7 @@ Related commands :doc:`dihedral_style ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index 1ad0b07f72..9648bc5387 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -73,4 +73,7 @@ Related commands :doc:`dihedral_coeff `, :doc:`angle_style cosine/shift/exp ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index 1e3a77212f..d795488107 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -65,4 +65,7 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst index a0769062e4..f6e9794d3e 100644 --- a/doc/src/dihedral_harmonic.rst +++ b/doc/src/dihedral_harmonic.rst @@ -76,4 +76,7 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 737006626e..58738dd7a7 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -67,7 +67,10 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst index 9fe4478f67..c0a803755d 100644 --- a/doc/src/dihedral_hybrid.rst +++ b/doc/src/dihedral_hybrid.rst @@ -96,4 +96,7 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index ba1b0279da..c13d45863f 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -59,4 +59,7 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index c2b8a54ac3..e2223382e2 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -59,4 +59,7 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_none.rst b/doc/src/dihedral_none.rst index eda8d1c39e..9aba2fac13 100644 --- a/doc/src/dihedral_none.rst +++ b/doc/src/dihedral_none.rst @@ -36,4 +36,7 @@ Related commands :doc:`dihedral_style zero ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst index c95ef2d9eb..a2be0b5b2d 100644 --- a/doc/src/dihedral_opls.rst +++ b/doc/src/dihedral_opls.rst @@ -72,7 +72,10 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index 7d309a1b13..9c4a707562 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -64,4 +64,7 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst index 67919aa77f..be672a3699 100644 --- a/doc/src/dihedral_spherical.rst +++ b/doc/src/dihedral_spherical.rst @@ -97,4 +97,7 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index 089ee1109f..9ed7249572 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -179,7 +179,8 @@ that matches the specified keyword. .. include:: accel_styles.rst -**Restart info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This dihedral style writes the settings for the "dihedral_style table" command to :doc:`binary restart files `, so a dihedral_style @@ -201,4 +202,7 @@ Related commands :doc:`dihedral_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst index 34e604088b..a29844da19 100644 --- a/doc/src/dihedral_table_cut.rst +++ b/doc/src/dihedral_table_cut.rst @@ -196,7 +196,8 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. -**Restart info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This dihedral style writes the settings for the "dihedral_style table/cut" command to :doc:`binary restart files `, so a dihedral_style @@ -218,7 +219,10 @@ Related commands :doc:`dihedral_coeff `, :doc:`dihedral_style table ` -**Default:** none +Default +""""""" + +none .. _dihedralcut-Salerno: diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 7d8dcd496a..3df68edfd5 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -44,8 +44,15 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" + +none + :doc:`dihedral_style none ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst index fdefad62ff..8c6a4937d7 100644 --- a/doc/src/dump_cfg_uef.rst +++ b/doc/src/dump_cfg_uef.rst @@ -54,4 +54,7 @@ Related commands :doc:`dump `, :doc:`fix nvt/uef ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/echo.rst b/doc/src/echo.rst index 6fc00aa1e6..94951e5e79 100644 --- a/doc/src/echo.rst +++ b/doc/src/echo.rst @@ -35,7 +35,11 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" + +none + Default """"""" diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 3528645317..95ec059b6c 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -402,4 +402,7 @@ Related commands :doc:`unfix `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_accelerate_cos.rst b/doc/src/fix_accelerate_cos.rst index b8d1cca59c..7fad6be913 100644 --- a/doc/src/fix_accelerate_cos.rst +++ b/doc/src/fix_accelerate_cos.rst @@ -74,7 +74,8 @@ In order to get meaningful result, the group ID of this fix should be all. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 4a9bc99e9b..638895ecc9 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -401,7 +401,8 @@ restored when the restarted run finally completes. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" If the *atom* keyword is used and the *scale* or *reset* keyword is set to *yes*, then this fix writes information to a restart file so diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index d587690473..0666d3965d 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -289,7 +289,8 @@ parameters on the outermost rRESPA level. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 32867a3252..f2f7a69f6c 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -115,7 +115,8 @@ converge properly. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst index 2b5a7ce8ce..b716f94dc8 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -50,7 +50,8 @@ time. Thus it is easy to specify a time-dependent torque. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -93,4 +94,7 @@ Related commands :doc:`fix addforce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst index 6246787075..754183b55b 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -86,7 +86,8 @@ define the lattice spacings. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index 81a16b907a..8e9ab0ceb2 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -118,7 +118,8 @@ Note coupling and post-processing can be combined in the same simulations using ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. The :doc:`fix_modify ` options relevant to this diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index 2ad289e91e..a2d365dbe2 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -141,7 +141,8 @@ you MUST enable the :doc:`fix_modify ` *energy* option for that fix. The doc pages for individual :doc:`fix ` commands specify if this should be done. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the fix to :doc:`binary restart files `. This includes information about the random number generator seed, the next timestep for MC exchanges, the number diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 93ff48ce0f..e506b62cfa 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -149,7 +149,8 @@ per-atom quantities to time average. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global scalar or vector quantities are @@ -175,4 +176,7 @@ Related commands :doc:`compute `, :doc:`fix ave/histo `, :doc:`fix ave/chunk `, :doc:`fix ave/time `, :doc:`variable `, -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index 91331502c3..d2dbaa320a 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -456,7 +456,8 @@ dimensions. Those values are always in distance :doc:`units `. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index d6a74e8a32..386b16ff9a 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -310,7 +310,8 @@ included in the variable formula or via the *prefactor* keyword. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -361,7 +362,10 @@ Related commands :doc:`compute `, :doc:`fix ave/time `, :doc:`fix ave/atom `, :doc:`fix ave/chunk `, :doc:`fix ave/histo `, :doc:`variable ` -**Default:** none +Default +""""""" + +none 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 24ba504f1b..c740099aae 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -110,7 +110,8 @@ corresponds to about 10 KB. For the meaning of the additional optional keywords, see the :doc:`fix ave/correlate ` doc page. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Contrary to :doc:`fix ave/correlate ` this fix does **not** provide access to its internal data to various output @@ -134,7 +135,10 @@ Related commands :doc:`fix ave/correlate ` -**Default:** none +Default +""""""" + +none The option defaults for keywords that are also keywords for the :doc:`fix ave/correlate ` command are as follows: type = auto, start = 0, no file output, title 1,2 = strings as described on diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 353077d667..7c4ef88fd6 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -329,7 +329,8 @@ the histogram. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -369,7 +370,10 @@ Related commands :doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/chunk `, :doc:`fix ave/time `, :doc:`variable `, :doc:`fix ave/correlate `, -**Default:** none +Default +""""""" + +none The option defaults are mode = scalar, kind = figured out from input arguments, ave = one, start = 0, no file output, beyond = ignore, and diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index efa8095d69..ad1aca233c 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -304,7 +304,8 @@ appropriate fields from the fix ave/time command. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index 69be0ba9df..36e1e28ea6 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -75,7 +75,8 @@ to it. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -107,4 +108,7 @@ Related commands :doc:`fix setforce `, :doc:`fix addforce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 0753794aa7..1875ab744f 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -361,7 +361,8 @@ each processor, instead of 4, and "SQUARES" replaced by "CUBES". ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -404,4 +405,7 @@ Related commands .. _pizza: https://pizza.sandia.gov -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_bocs.rst b/doc/src/fix_bocs.rst index 5315aa81a1..b5a00b2687 100644 --- a/doc/src/fix_bocs.rst +++ b/doc/src/fix_bocs.rst @@ -94,7 +94,8 @@ example, the ID of the fix bocs command is 1 ). This fix is part of the USER-BOCS package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -**Related:** +Further information +""""""""""""""""""" For more details about the pressure correction and the entire BOCS software package, visit the `BOCS package on GitHub `_ and read the release diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index 3994b58b12..4f2e2840ab 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -115,7 +115,8 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index c69cf773ce..d0c7fb985c 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -232,7 +232,8 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index d5f917bfdb..b6f3be773f 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -510,7 +510,8 @@ local command. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Cumulative reaction counts for each reaction are written to :doc:`binary restart files `. These values are associated with the reaction name (react-ID). diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst index 9427b0e780..248c4cc8e9 100644 --- a/doc/src/fix_bond_swap.rst +++ b/doc/src/fix_bond_swap.rst @@ -139,7 +139,8 @@ effect on this fix. ---------- -**Restart, fix_modify, thermo output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not saved in restart files, this means you cannot do "exact" @@ -189,7 +190,10 @@ Related commands :doc:`fix atom/swap ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst index 71708165dd..7a9abdfe26 100644 --- a/doc/src/fix_box_relax.rst +++ b/doc/src/fix_box_relax.rst @@ -308,7 +308,8 @@ It also means that changing attributes of *thermo_temp* or ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst index 2e0cf84cc5..0200966a34 100644 --- a/doc/src/fix_client_md.rst +++ b/doc/src/fix_client_md.rst @@ -66,7 +66,8 @@ LAMMPS and another code in tandem to perform a coupled simulation. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -102,4 +103,7 @@ Related commands :doc:`message `, :doc:`server ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index a968eb910e..14e83f49e6 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -90,7 +90,8 @@ the note below about how to include the CMAP energy when performing an ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the list of CMAP cross-terms to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a @@ -140,7 +141,10 @@ Related commands :doc:`fix_modify `, :doc:`read_data ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index 20315624d6..fbc39f3f2f 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -90,7 +90,8 @@ fix that thermostats all atoms in the fix colvars group. This will be used to provide the colvars module with the current thermostat target temperature. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the current status of the colvars module into :doc:`binary restart files `. This is in addition to the text diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 2fd5f17c95..0b7332cdd7 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -190,7 +190,8 @@ equal-style versus internal-style variable interchangeably. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Currently, no information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -221,4 +222,7 @@ Related commands :doc:`fix adapt ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 2c3824231c..70b15f0d79 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -565,7 +565,8 @@ command if you want to include lattice spacings in a variable formula. .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix will restore the initial box settings from :doc:`binary restart files `, which allows the fix to be properly continue deformation, when using the start/stop options of the :doc:`run ` diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 31df74ce9b..42975eb0b2 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -271,7 +271,8 @@ units of distance or velocity. the :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the deposition to :doc:`binary restart files `. This includes information about how many particles have been deposited, the random number generator seed, the diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index cb30c286d2..6d510f1825 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -74,7 +74,10 @@ Related commands :doc:`fix nve ` :doc:`fix eos/cv ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 5ea1c85fb4..4373645c84 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -64,7 +64,8 @@ cuboid domain to apply the source flux to. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -87,7 +88,10 @@ Related commands :doc:`pair_style edpd `, :doc:`pair_style tdpd `, :doc:`compute edpd/temp/atom `, :doc:`compute tdpd/cc/atom ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst index 792d4725cc..6bf9b909c6 100644 --- a/doc/src/fix_drag.rst +++ b/doc/src/fix_drag.rst @@ -38,7 +38,8 @@ application. This command can be used to steer one or more atoms to a new location in the simulation. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -64,4 +65,7 @@ Related commands :doc:`fix spring `, :doc:`fix spring/self `, :doc:`fix spring/rg `, :doc:`fix smd ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst index db13d8d052..b3b04832d2 100644 --- a/doc/src/fix_drude.rst +++ b/doc/src/fix_drude.rst @@ -48,4 +48,7 @@ Related commands :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair_style thole ` -**Default:** None +Default +""""""" + +none diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 607c161572..bda2d25b1f 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -182,7 +182,8 @@ to add a *fix momentum* command: ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -198,7 +199,10 @@ Related commands :doc:`compute temp/drude `, :doc:`pair_style thole ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index 861134f745..a413f8f60d 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -80,7 +80,8 @@ Note that the cumulative simulation time (in time units), which accounts for changes in the timestep size as a simulation proceeds, can be accessed by the :doc:`thermo_style time ` keyword. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index 0410803c13..227e048c8c 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -114,7 +114,8 @@ minimization will not converge properly. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -169,4 +170,7 @@ Related commands :doc:`fix addforce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst index 10622c8b3e..2065ec5033 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -163,7 +163,8 @@ constraints will be satisfied. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -182,7 +183,10 @@ Related commands :doc:`fix heat `, :doc:`fix thermal/conductivity `, :doc:`compute temp `, :doc:`compute temp/region ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index cead9f7a12..76455e88df 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -129,7 +129,8 @@ scientific publications, experimental databases or by using of the impact parameter of the ion; these results can be used to derive the stopping power. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index b0c890af3a..e92011cb11 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -36,7 +36,8 @@ not move from their initial z coordinate. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -51,6 +52,13 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst index 50281b6e71..5cbe0053ff 100644 --- a/doc/src/fix_eos_cv.rst +++ b/doc/src/fix_eos_cv.rst @@ -54,7 +54,10 @@ Related commands :doc:`fix shardlow `, :doc:`pair dpd/fdt ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst index 57cacc0da5..ad734c391a 100644 --- a/doc/src/fix_eos_table.rst +++ b/doc/src/fix_eos_table.rst @@ -118,4 +118,7 @@ Related commands :doc:`fix shardlow `, :doc:`pair dpd/fdt ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index 1335f8f845..bd13398e0a 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -194,4 +194,7 @@ Related commands :doc:`fix rx `, :doc:`pair dpd/fdt ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst index d6b9c6ae34..5eae16b196 100644 --- a/doc/src/fix_evaporate.rst +++ b/doc/src/fix_evaporate.rst @@ -72,7 +72,8 @@ incur overhead due to the cost of building neighbor lists. :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index 58f40406da..fb71888025 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -147,7 +147,8 @@ of properties that the caller code may want to communicate to LAMMPS ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -184,6 +185,13 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst index ac23175875..3888c439c5 100644 --- a/doc/src/fix_ffl.rst +++ b/doc/src/fix_ffl.rst @@ -72,7 +72,8 @@ step and it flips the momenta of the atoms. If no_flip is chosen, no flip will be executed and the integration will be the same as a standard Langevin thermostat :ref:`(Bussi) `. The other flipping types are : rescale - hard - soft. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The instantaneous values of the extended variables are written to :doc:`binary restart files `. Because the state of the random diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst index 1731ef94a2..ee608e5361 100644 --- a/doc/src/fix_filter_corotate.rst +++ b/doc/src/fix_filter_corotate.rst @@ -60,7 +60,8 @@ If the clusters are chosen suitably, the :doc:`run_style respa ` is s ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about these fixes is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to these fixes. No global or per-atom quantities are @@ -79,7 +80,10 @@ Currently, it does not support :doc:`molecule templates `. Related commands """""""""""""""" -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index 7b9e001bd3..b40fefff0e 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -116,7 +116,8 @@ flow/gauss fixes, one that specifies *fix_modify respa 3* and one with ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index cca0b6eb7d..f81954ff5d 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -40,7 +40,8 @@ using :doc:`fix setforce `. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -70,4 +71,7 @@ Related commands :doc:`atom_style sphere `, :doc:`fix setforce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index 9a51bea97c..8ea84303bc 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -395,7 +395,8 @@ The *group* keyword adds all inserted atoms to the adds all inserted atoms of the specified type to the :doc:`group ` of the group-ID value. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the fix to :doc:`binary restart files `. This includes information about the random number generator seed, the next timestep for MC exchanges, the number diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index cb93804b1a..c47e30a880 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -123,7 +123,8 @@ momentum will not drift over time. ---------- -**Restart, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The instantaneous values of the extended variables are written to :doc:`binary restart files `. Because the state of the random diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index fb6006d514..1f14c7245d 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -99,7 +99,8 @@ input matrix for :doc:`fix gle `. While the GLE scheme is more general, the form used by :doc:`fix gld ` can be more directly related to the representation of an implicit solvent environment. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The instantaneous values of the extended variables are written to :doc:`binary restart files `. Because the state of the random diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index 3f9a2d5ae7..5f06f6d22a 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -100,7 +100,8 @@ field. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -131,4 +132,7 @@ Related commands :doc:`atom_style sphere `, :doc:`fix addforce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index eef39c1ffc..e57f1889e1 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -83,7 +83,8 @@ to large temperature changes. Replicas are easily added where needed. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -102,7 +103,10 @@ Related commands :doc:`temper/grem `, :doc:`fix nvt `, :doc:`fix npt `, :doc:`thermo_modify ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 0bc3154cdb..964132518d 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -150,7 +150,8 @@ is printed; the run simply exits. The latter may be desirable for post-processing tools that extract thermodynamic information from log files. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst index 03596febd8..19bc3d84ca 100644 --- a/doc/src/fix_heat.rst +++ b/doc/src/fix_heat.rst @@ -108,7 +108,8 @@ their velocities. Thus you must still use an integration fix not normally be used on atoms that have their temperature controlled by another fix - e.g. :doc:`fix nvt ` or :doc:`fix langevin ` fix. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -132,4 +133,7 @@ Related commands :doc:`fix ehex `, :doc:`compute temp `, :doc:`compute temp/region ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index c24d405b55..52f542f647 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -197,7 +197,8 @@ algorithm. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -266,7 +267,10 @@ Related commands :doc:`hyper `, :doc:`fix hyper/local ` -**Default:** None +Default +""""""" + +none ---------- diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index a8e7483dac..da197cad20 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -365,7 +365,8 @@ enabled by these keywords. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index fe54e5bf50..3b84ec6f72 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -137,7 +137,8 @@ screen output is active. .. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global scalar or vector or per-atom @@ -160,6 +161,13 @@ be assigned 0-based consecutive index numbers. When using multiple active IMD connections at the same time, each needs to use a different port number. -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index ef62506591..2a77e27268 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -176,7 +176,8 @@ contains *xlat*\ , *ylat*\ , *zlat* keywords of the variable k equal 100.0/xlat/xlat fix 1 all indent $k sphere ... -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -212,7 +213,11 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" + +none + Default """"""" diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index d60b25248d..1d1ed795cd 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -69,7 +69,8 @@ If the cell varies too wildly, it may be advisable to re-initialize these interactions at each call. This behavior can be requested by setting the *reset* switch. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" There is no restart information associated with this fix, since all the dynamical parameters are dealt with by i-PI. diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index 4445dc240a..80f4964242 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -272,7 +272,8 @@ target temperature. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not saved in restart files, this means you cannot do "exact" diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index 249c297c98..ad5a876712 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -256,7 +256,8 @@ Comments: ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not saved in restart files, this means you cannot do "exact" diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index 36768d25b2..29df472d83 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -65,7 +65,8 @@ The operation of this fix is exactly like that described by the thermostatting is also applied to the radial electron velocity for electron particles. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not diff --git a/doc/src/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst index 9a70cc1cd1..c73968df48 100644 --- a/doc/src/fix_langevin_spin.rst +++ b/doc/src/fix_langevin_spin.rst @@ -70,7 +70,8 @@ different numbers of processors. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not saved in restart files, this means you cannot do "exact" @@ -97,7 +98,10 @@ Related commands :doc:`fix nve/spin `, :doc:`fix precession/spin ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index f1469153a7..0d6488af26 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -104,7 +104,8 @@ larger system sizes and longer time scales ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -159,9 +160,16 @@ doing 99% or more of the work to compute quantum-accurate forces. be run on a single MPI task. For details, see the :doc:`neb ` command doc page and the :doc:`-partition command-line switch ` -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none ---------- diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index f450fdb8f0..b2b85b8f5f 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -324,7 +324,8 @@ published research. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Due to the large size of the fluid data, this fix writes it's own binary restart files, if requested, independent of the main LAMMPS diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index a595ba2ce5..479f480e50 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -50,7 +50,8 @@ be changed by specifying the keyword *linear*\ , along with a set of three flags set to 0/1 in order to exclude/ include the corresponding dimension. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst index 874ff21893..c6f5048126 100644 --- a/doc/src/fix_lb_pc.rst +++ b/doc/src/fix_lb_pc.rst @@ -29,7 +29,8 @@ forces, using the integration algorithm described in :ref:`Mackay et al. ` has been set; do not use this integration algorithm if the force coupling constant has been set by default. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -52,7 +53,10 @@ Related commands :doc:`fix lb/fluid ` :doc:`fix lb/rigid/pc/sphere ` -**Default:** None. +Default +""""""" + +none. ---------- diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst index 42fb21ca69..66b5f5f8d5 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.rst +++ b/doc/src/fix_lb_rigid_pc_sphere.rst @@ -82,7 +82,8 @@ the rigid fix (although it includes fewer optional arguments, and assumes the constituent atoms are point particles); see :doc:`fix rigid ` for a complete documentation. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about the *rigid* and *rigid/nve* fixes are written to :doc:`binary restart files `. diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst index 6d7431c780..da8922c92f 100644 --- a/doc/src/fix_lb_viscous.rst +++ b/doc/src/fix_lb_viscous.rst @@ -51,7 +51,8 @@ research. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" As described in the :doc:`fix viscous ` documentation: @@ -86,7 +87,10 @@ Related commands :doc:`fix lb/fluid `, :doc:`fix lb/pc `, :doc:`fix lb/rigid/pc/sphere ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_lineforce.rst b/doc/src/fix_lineforce.rst index b02acfa9f4..e82f6ed556 100644 --- a/doc/src/fix_lineforce.rst +++ b/doc/src/fix_lineforce.rst @@ -32,7 +32,8 @@ plane perpendicular to the line. If the initial velocity of the atom is 0.0 (or along the line), then it should continue to move along the line thereafter. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -52,4 +53,7 @@ Related commands :doc:`fix planeforce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst index 8cb9723277..6d13fab7b8 100644 --- a/doc/src/fix_manifoldforce.rst +++ b/doc/src/fix_manifoldforce.rst @@ -34,7 +34,8 @@ adequately though. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst index b1ea27e872..06b0d16686 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -206,7 +206,8 @@ spacings can be different in x,y,z. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the original coordinates of moving particles to :doc:`binary restart files `, as well as the initial timestep, so that the motion can be continuous in a restarted simulation. See the diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index dbf599f29c..ca6e19005e 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -82,7 +82,8 @@ initial velocities with zero aggregate linear and/or angular momentum. .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are @@ -105,4 +106,7 @@ Related commands :doc:`fix recenter `, :doc:`velocity ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index 84f7dbe965..7ede1f3050 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -203,7 +203,8 @@ spacings can be different in x,y,z. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the original coordinates of moving atoms to :doc:`binary restart files `, as well as the initial timestep, so that the motion can be continuous in a restarted simulation. See the @@ -241,6 +242,9 @@ Related commands :doc:`fix nve `, :doc:`displace_atoms ` -**Default:** none +Default +""""""" + +none The option default is units = lattice. diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst index 81a59ad7ee..fe32acdbd5 100644 --- a/doc/src/fix_mscg.rst +++ b/doc/src/fix_mscg.rst @@ -118,7 +118,11 @@ Currently, the MS-CG library is not setup to run in parallel with MPI, so this fix can only be used in a serial LAMMPS build and run on a single processor. -**Related commands:** none +Related commands +"""""""""""""""" + +none + Default """"""" diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst index b76af36bb8..14158227d0 100644 --- a/doc/src/fix_msst.rst +++ b/doc/src/fix_msst.rst @@ -122,7 +122,8 @@ timestepping. DFTB+ will communicate its info to LAMMPS via that fix. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of all internal variables to :doc:`binary restart files `. See the :doc:`read_restart ` diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index 77ca08e0c5..c7e9b64c96 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -76,7 +76,8 @@ addition to position and velocity, and must be used with the ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 3612192d5b..848369d3ea 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -203,7 +203,8 @@ Finally, note that the last replica may never reach the target energy if it is stuck in a local minima which has a larger energy than the target energy. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst index 93729ac96f..16baba44c0 100644 --- a/doc/src/fix_neb_spin.rst +++ b/doc/src/fix_neb_spin.rst @@ -47,7 +47,8 @@ The nudging forces are calculated as explained in :ref:`(BessarabB) `). See this reference for more explanation about their expression. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 3668523ad9..64a3c3b061 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -572,7 +572,8 @@ the various ways to do this. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" These fixes writes the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index b5fecf279f..4d4d536ac2 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -105,7 +105,8 @@ to the temperature or kinetic energy from the electron radial velocity. the user must allow for these degrees of freedom to equilibrate (i.e. equi-partitioning of energy) through time integration. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" See the doc page for the :doc:`fix nvt, npt, and nph ` commands for details. diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 27851d89a1..272f84d520 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -171,7 +171,8 @@ See the :doc:`compute temp/uef ` and :doc:`compute pressure/ue that the IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID + underscore + "press". -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The fix writes the state of all the thermostat and barostat variables, as well as the cumulative strain applied, to :doc:`binary restart files `. See the :doc:`read_restart ` command diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index 4c6f94b865..2e5dd16c8f 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -84,7 +84,8 @@ It also means that changing attributes of *thermo_temp* or .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -132,4 +133,7 @@ Related commands :doc:`fix nph `, :doc:`fix nve_asphere `, :doc:`fix nvt_asphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nph_body.rst b/doc/src/fix_nph_body.rst index 8ded05b04e..fd517b5243 100644 --- a/doc/src/fix_nph_body.rst +++ b/doc/src/fix_nph_body.rst @@ -81,7 +81,8 @@ It also means that changing attributes of *thermo_temp* or .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -125,4 +126,7 @@ Related commands :doc:`fix nph `, :doc:`fix nve_body `, :doc:`fix nvt_body `, :doc:`fix npt_body `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index 3e5e382048..efa6ca38b5 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -97,7 +97,8 @@ It also means that changing attributes of *thermo_temp* or .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -145,4 +146,7 @@ Related commands :doc:`fix nph `, :doc:`fix nve_sphere `, :doc:`fix nvt_sphere `, :doc:`fix npt_sphere `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index 4fa9287e08..c46e98fe3e 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -149,7 +149,8 @@ It also means that changing attributes of *thermo_temp* or ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the values of :math:`E_0`, :math:`V_0`, and :math:`P_0`, as well as the state of all the thermostat and barostat variables to diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index edf82261af..5537365359 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -106,7 +106,8 @@ thermal degrees of freedom, and the bias is added back in. .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the @@ -157,4 +158,7 @@ Related commands :doc:`fix npt `, :doc:`fix nve_asphere `, :doc:`fix nvt_asphere `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_npt_body.rst b/doc/src/fix_npt_body.rst index 9c3e99890e..412d522a45 100644 --- a/doc/src/fix_npt_body.rst +++ b/doc/src/fix_npt_body.rst @@ -103,7 +103,8 @@ thermal degrees of freedom, and the bias is added back in. .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the @@ -150,4 +151,7 @@ Related commands :doc:`fix npt `, :doc:`fix nve_body `, :doc:`fix nvt_body `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index 672c1c6723..034a2c9c8d 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -466,7 +466,8 @@ of the underlying non-Hamiltonian equations of motion. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index ad6af88446..4e8188ac0c 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -119,7 +119,8 @@ thermal degrees of freedom, and the bias is added back in. .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the @@ -169,4 +170,7 @@ Related commands :doc:`fix npt `, :doc:`fix nve_sphere `, :doc:`fix nvt_sphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_numdiff.rst b/doc/src/fix_numdiff.rst index 974826d1f2..0c4f731ea0 100644 --- a/doc/src/fix_numdiff.rst +++ b/doc/src/fix_numdiff.rst @@ -81,7 +81,8 @@ atom will undergo. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are @@ -107,4 +108,7 @@ Related commands :doc:`dynamical_matrix `, -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index 6679ab1ea7..0026d38e8c 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -43,7 +43,8 @@ ensemble. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -60,4 +61,7 @@ Related commands :doc:`fix nvt `, :doc:`fix npt ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index 3161fd1fb5..f1441fdd3c 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -34,7 +34,8 @@ trajectory consistent with the microcanonical ensemble. This fix differs from the :doc:`fix nve ` command, which assumes point particles and only updates their position and velocity. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -67,4 +68,7 @@ Related commands :doc:`fix nve `, :doc:`fix nve/sphere ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst index b518781d6c..6bc4b98c7f 100644 --- a/doc/src/fix_nve_asphere_noforce.rst +++ b/doc/src/fix_nve_asphere_noforce.rst @@ -35,7 +35,8 @@ Dynamics, since the velocity and angular momentum are updated by the ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -62,4 +63,7 @@ Related commands :doc:`fix nve/noforce `, :doc:`fix nve/asphere ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst index 45bb002617..b112aacd60 100644 --- a/doc/src/fix_nve_awpmd.rst +++ b/doc/src/fix_nve_awpmd.rst @@ -33,7 +33,8 @@ the electron wave functions are also updated. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -52,4 +53,7 @@ Related commands :doc:`fix nve ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve_body.rst b/doc/src/fix_nve_body.rst index ad68abb0d4..7a763e7d42 100644 --- a/doc/src/fix_nve_body.rst +++ b/doc/src/fix_nve_body.rst @@ -32,7 +32,8 @@ particles. This fix differs from the :doc:`fix nve ` command, which assumes point particles and only updates their position and velocity. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -58,4 +59,7 @@ Related commands :doc:`fix nve `, :doc:`fix nve/sphere `, :doc:`fix nve/asphere ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst index a7018a337e..ac60b40f47 100644 --- a/doc/src/fix_nve_dot.rst +++ b/doc/src/fix_nve_dot.rst @@ -54,7 +54,10 @@ Related commands :doc:`fix nve/dotc/langevin `, :doc:`fix nve ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index 5322d5bbb3..4ffead3f25 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -138,7 +138,10 @@ Related commands :doc:`fix nve `, :doc:`fix langevin `, :doc:`fix nve/dot `, :doc:`bond_style oxdna/fene `, :doc:`bond_style oxdna2/fene `, :doc:`pair_style oxdna/excv `, :doc:`pair_style oxdna2/excv ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst index 78e6352b6e..2c14bb07a9 100644 --- a/doc/src/fix_nve_eff.rst +++ b/doc/src/fix_nve_eff.rst @@ -30,7 +30,8 @@ system trajectory consistent with the microcanonical ensemble. The operation of this fix is exactly like that described by the :doc:`fix nve ` command, except that the radius and radial velocity of electrons are also updated. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -49,4 +50,7 @@ Related commands :doc:`fix nve `, :doc:`fix nvt/eff `, :doc:`fix npt/eff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve_limit.rst b/doc/src/fix_nve_limit.rst index 98d691d6b9..0c572c6c6a 100644 --- a/doc/src/fix_nve_limit.rst +++ b/doc/src/fix_nve_limit.rst @@ -60,7 +60,8 @@ very large for overlapped configurations. that need this fix, then turn fix shake on when doing normal dynamics with a fixed-size timestep. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -88,4 +89,7 @@ Related commands :doc:`fix nve `, :doc:`fix nve/noforce `, :doc:`pair_style soft ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst index d47bf34f61..b65c543529 100644 --- a/doc/src/fix_nve_line.rst +++ b/doc/src/fix_nve_line.rst @@ -32,7 +32,8 @@ segment particles. This fix differs from the :doc:`fix nve ` command, which assumes point particles and only updates their position and velocity. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -54,4 +55,7 @@ Related commands :doc:`fix nve `, :doc:`fix nve/asphere ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index 1caedf88e1..b24277a8c7 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -69,7 +69,8 @@ conserved. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -92,7 +93,11 @@ Related commands :doc:`fix nvt/manifold/rattle `, :doc:`fix manifoldforce ` -**Default:** every = 0, tchain = 3 +Default +""""""" + +every = 0, tchain = 3 + ---------- diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst index d45648694a..167da24475 100644 --- a/doc/src/fix_nve_noforce.rst +++ b/doc/src/fix_nve_noforce.rst @@ -37,7 +37,8 @@ unchanged, and can thus be printed by the :doc:`dump ` command or queried with an equal-style :doc:`variable ` that uses the fcm() group function to compute the total force on the group of atoms. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -54,4 +55,7 @@ Related commands :doc:`fix nve ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index 70bafc95a8..59d951782a 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -74,7 +74,8 @@ moment of inertia, as used in the time integration. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -102,7 +103,10 @@ Related commands :doc:`fix nve `, :doc:`fix nve/asphere ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst index f5fdb7cc7d..ad4376e8ec 100644 --- a/doc/src/fix_nve_tri.rst +++ b/doc/src/fix_nve_tri.rst @@ -33,7 +33,8 @@ using triangular particles. This fix differs from the :doc:`fix nve ` command, which assumes point particles and only updates their position and velocity. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -55,4 +56,7 @@ Related commands :doc:`fix nve `, :doc:`fix nve/asphere ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nvk.rst b/doc/src/fix_nvk.rst index 415e3256b4..6226635010 100644 --- a/doc/src/fix_nvk.rst +++ b/doc/src/fix_nvk.rst @@ -39,7 +39,8 @@ energy prior to this fix. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -58,9 +59,16 @@ This fix has not yet been implemented to work with the RESPA integrator. This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none ---------- diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index 02640222f1..a08dae765c 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -89,7 +89,8 @@ thermal degrees of freedom, and the bias is added back in. .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -133,4 +134,7 @@ Related commands :doc:`fix nvt `, :doc:`fix nve_asphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst index 28dccdfff5..b608c93f27 100644 --- a/doc/src/fix_nvt_body.rst +++ b/doc/src/fix_nvt_body.rst @@ -86,7 +86,8 @@ thermal degrees of freedom, and the bias is added back in. .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -126,4 +127,7 @@ Related commands :doc:`fix nvt `, :doc:`fix nve_body `, :doc:`fix npt_body `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index 198208ca0d..f822df5b8d 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -49,7 +49,8 @@ parameters, see the :doc:`Howto manifold ` doc page. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst index 624111813a..b5051b8692 100644 --- a/doc/src/fix_nvt_sllod.rst +++ b/doc/src/fix_nvt_sllod.rst @@ -121,7 +121,8 @@ thermal degrees of freedom, and the bias is added back in. .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst index 49ad9f608c..09fc1ecff6 100644 --- a/doc/src/fix_nvt_sllod_eff.rst +++ b/doc/src/fix_nvt_sllod_eff.rst @@ -38,7 +38,8 @@ page), is performed with a :doc:`compute temp/deform/eff `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index 8adb8160db..dd4cf9cb3f 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -103,7 +103,8 @@ thermal degrees of freedom, and the bias is added back in. .. include:: accel_styles.rst -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that @@ -146,4 +147,7 @@ Related commands :doc:`fix nvt `, :doc:`fix nve_sphere `, :doc:`fix nvt_asphere `, :doc:`fix npt_sphere `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst index 04186404e6..180a394ba0 100644 --- a/doc/src/fix_oneway.rst +++ b/doc/src/fix_oneway.rst @@ -39,7 +39,8 @@ membrane, or as an implementation of Maxwell's demon. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -56,4 +57,7 @@ Related commands :doc:`fix wall/reflect ` command -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index ca5ba83108..51edbd48ad 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -140,7 +140,8 @@ equal-and-opposite neighbors. A pair of orientation files for a Sigma=5 tilt boundary are shown below. A tutorial that can help for writing the orientation files is given in :ref:`(Wicaksono2) ` -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -179,7 +180,10 @@ Related commands :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_orient_eco.rst b/doc/src/fix_orient_eco.rst index ac324adf78..bdfab21c9d 100644 --- a/doc/src/fix_orient_eco.rst +++ b/doc/src/fix_orient_eco.rst @@ -90,7 +90,8 @@ simulation. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc: `binary restart files `. @@ -122,7 +123,10 @@ Related commands :doc:`fix_orient ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index 4eed4efc5b..65106c34d5 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -150,7 +150,8 @@ The calculated dynamical matrix elements are written out in points in the log file is in the units of the basis vectors of the corresponding reciprocal lattice. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_planeforce.rst b/doc/src/fix_planeforce.rst index c90a3b6bbe..d0f1b8102e 100644 --- a/doc/src/fix_planeforce.rst +++ b/doc/src/fix_planeforce.rst @@ -32,7 +32,8 @@ force perpendicular to the plane. If the initial velocity of the atom is 0.0 (or in the plane), then it should continue to move in the plane thereafter. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -52,4 +53,7 @@ Related commands :doc:`fix lineforce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index aeef6cff50..e2eadfe6bd 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -75,7 +75,8 @@ correctly read and parsed. The names of the files in which the results are stored from the various analysis options performed by PLUMED will be specified by the user in the PLUMED input file. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" When performing a restart of a calculation that involves PLUMED you must include a RESTART command in the PLUMED input file as detailed in the diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index 5e84188154..0f173fcc4e 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -104,7 +104,8 @@ body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -131,7 +132,10 @@ Related commands :doc:`fix rigid `, :doc:`delete_bonds `, :doc:`neigh_modify ` exclude -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index 26f1cd0eae..7757191482 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -225,7 +225,8 @@ line or triangle particles with the insertion region. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. This means you must be careful when restarting a pouring simulation, when the restart file was written in the middle of diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 99dffc61dd..92819684cc 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -131,7 +131,8 @@ Those styles can be combined within one single command line. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" By default, the energy associated to this fix is not added to the potential energy of the system. @@ -165,7 +166,9 @@ Related commands :doc:`atom_style spin ` -**Default:** +Default +""""""" + none diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst index f1366e0449..eb7adafc57 100644 --- a/doc/src/fix_press_berendsen.rst +++ b/doc/src/fix_press_berendsen.rst @@ -190,7 +190,8 @@ or pressure during thermodynamic output via the :doc:`thermo_style custom `. diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst index 82b26d4ef3..c59cc4161d 100644 --- a/doc/src/fix_print.rst +++ b/doc/src/fix_print.rst @@ -89,7 +89,8 @@ keyword was used. By default, the title line is as follows: where ID is replaced with the fix-ID. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index b6b5a6051f..3a1bfb3166 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -57,7 +57,8 @@ on through the *types* keyword. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -93,4 +94,8 @@ Eur. Phys. J. B 15, 105-113, 2000. **(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012. -**Default:** types +Default +""""""" + +types + diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 2a1a863f42..eaf246c1a3 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -268,7 +268,8 @@ example to heavy water: ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart ` diff --git a/doc/src/fix_python_move.rst b/doc/src/fix_python_move.rst index 07f61c2b85..15014ef4fe 100644 --- a/doc/src/fix_python_move.rst +++ b/doc/src/fix_python_move.rst @@ -82,7 +82,8 @@ Examples for how to do this are in the *examples/python* folder. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -101,4 +102,7 @@ Related commands :doc:`fix nve `, :doc:`fix python/invoke ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index 112c5f1842..8444312681 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -144,7 +144,8 @@ supported by LAMMPS, but are not implemented for QBMSST. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Because the state of the random number generator is not written to :doc:`binary restart files `, this fix cannot be restarted diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index ea53fc2b2e..f656049e73 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -193,7 +193,8 @@ better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . arbitrary choices of these parameters. We do not develop these QEq parameters. See the examples/qeq directory for some examples. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about these fixes is written to :doc:`binary restart files `. No global scalar or vector or per-atom quantities are stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used @@ -212,7 +213,10 @@ Related commands :doc:`fix qeq/reax `, :doc:`fix qeq/comb ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index 20e2139de1..f70ecb1dd5 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -69,7 +69,8 @@ equilibration calculation is written to the specified file. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst index f729779267..0fd5e78578 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -71,7 +71,8 @@ The optional *dual* keyword allows to perform the optimization of the S and T matrices in parallel. This is only supported for the *qeq/reax/omp* style. Otherwise they are processed separately. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. No global scalar or vector or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used @@ -100,7 +101,10 @@ Related commands :doc:`pair_style reax/c ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index 4eb45e490f..81bb315e23 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -42,7 +42,8 @@ to be adapted if necessary before being finalized. Details about how to use this fix are currently documented in the description of the QM/MM interface code itself in lib/qmmm/README. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global scalar or vector or per-atom @@ -61,6 +62,13 @@ The fix is only functional when LAMMPS is built as a library and linked with a compatible QM program and a QM/MM front end into a QM/MM executable. See the lib/qmmm/README file for details. -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst index 6dfabcbaa7..594b8b78a7 100644 --- a/doc/src/fix_qtb.rst +++ b/doc/src/fix_qtb.rst @@ -145,7 +145,8 @@ Mbytes. ---------- -**Restart, fix_modify, output, run start/stop, minimizie info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator is not diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index 820a925eb8..52f0581929 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -58,7 +58,8 @@ version, but will also take longer to write. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -88,4 +89,7 @@ Related commands :doc:`pair_style reax/c `, :doc:`fix reax/c/species ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index cd0266b2f2..275086b52b 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -112,7 +112,8 @@ average bond-order for the species analysis output on timestep 100. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst index a1c215e9a7..583b4d46c5 100644 --- a/doc/src/fix_recenter.rst +++ b/doc/src/fix_recenter.rst @@ -93,7 +93,8 @@ velocities with zero aggregate linear and/or angular momentum. simulation scenario is to use the :doc:`fix spring ` command to tether the molecule in place. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index fdc5be06bc..5d902182ab 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -216,7 +216,8 @@ current dihedral angle :math:`\phi` is equal to :math:`\phi_0`. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -254,6 +255,13 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst index be4780c7d8..38bde220ef 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -56,7 +56,10 @@ Related commands :doc:`thermo_style ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 318975d91b..a143817303 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -740,7 +740,8 @@ rigid/nvt. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about the 4 NVE rigid styles is written to :doc:`binary restart files `. The exception is if the *infile* or *mol* keyword is used, in which case an auxiliary file is written out diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index ec05fd170a..2acd81a268 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -288,7 +288,8 @@ cross periodic boundaries during the simulation. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information is written to :doc:`binary restart files `. If the *infile* keyword is used, an auxiliary file is written out diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index 82c8f66374..7a3a95f069 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -222,4 +222,7 @@ Related commands :doc:`fix shardlow `, :doc:`pair dpd/fdt/energy ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst index 145a10c93a..9dd8fb8641 100644 --- a/doc/src/fix_saed_vtk.rst +++ b/doc/src/fix_saed_vtk.rst @@ -165,7 +165,8 @@ The *overwrite* keyword will continuously overwrite the output file with the latest output, so that it only contains one timestep worth of output. This option can only be used with the *ave running* setting. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index 59de49fbe0..b417b369e5 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -111,7 +111,8 @@ instructions on how to use the accelerated styles effectively. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -148,4 +149,7 @@ Related commands :doc:`fix addforce `, :doc:`fix aveforce ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 9983d30519..5f720d86ea 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -184,7 +184,8 @@ LAMMPS closely follows (:ref:`Andersen (1983) `). ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to keeping the constraints to the @@ -217,9 +218,16 @@ degrees (e.g. linear CO2 molecule). This causes numeric difficulties. You can use :doc:`fix rigid or fix rigid/small ` instead to make a linear molecule rigid. -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none ---------- diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index 0e1c36516e..3c046dae74 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -79,7 +79,10 @@ Related commands :doc:`pair_style dpd/fdt `, :doc:`fix eos/cv ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index 1a24154b49..8cbae29adf 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -99,7 +99,8 @@ can then later be used to compute the potential of mean force (PMF) by averaging over multiple independent trajectories along the same pulling path. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" The fix stores the direction of the spring, current pulling target distance and the running PMF to :doc:`binary restart files `. @@ -146,7 +147,10 @@ Related commands :doc:`fix spring/rg `, :doc:`fix colvars `, :doc:`fix plumed ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst index d91ad1392d..fb19c07b15 100644 --- a/doc/src/fix_smd_adjust_dt.rst +++ b/doc/src/fix_smd_adjust_dt.rst @@ -46,7 +46,8 @@ additional safety factor *s_fact* is applied to the time increment. See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Currently, no part of USER-SMD supports restarting nor minimization. @@ -61,4 +62,7 @@ Related commands :doc:`smd/tlsph_dt ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst index ef91414788..867141bd6f 100644 --- a/doc/src/fix_smd_integrate_tlsph.rst +++ b/doc/src/fix_smd_integrate_tlsph.rst @@ -41,7 +41,8 @@ The *limit_velocity* keyword will control the velocity, scaling the norm of the velocity vector to max_vel in case it exceeds this velocity limit. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. @@ -57,4 +58,7 @@ Related commands :doc:`smd/integrate_ulsph ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index c355abf17b..f7ba223965 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -49,7 +49,8 @@ of adjustment per timestep. Typical values are *adjust_radius_factor* The *limit_velocity* keyword will control the velocity, scaling the norm of the velocity vector to max_vel in case it exceeds this velocity limit. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. @@ -60,6 +61,13 @@ Restrictions This fix is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst index 3aa40a75c2..293f5401a2 100644 --- a/doc/src/fix_smd_move_triangulated_surface.rst +++ b/doc/src/fix_smd_move_triangulated_surface.rst @@ -63,7 +63,8 @@ rotation axis to the particle. See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. @@ -80,4 +81,7 @@ Related commands :doc:`smd/triangle_mesh_vertices `, :doc:`smd/wall_surface ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index eb92f435e1..53aa5f649c 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -63,7 +63,8 @@ specified geometric :doc:`region ` in order to have its velocity set by ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Currently, no part of USER-SMD supports restarting nor minimization None of the :doc:`fix_modify ` options @@ -83,6 +84,13 @@ Restrictions This fix is part of the USER-SMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none diff --git a/doc/src/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst index 6bebcdf6c2..38efee0977 100644 --- a/doc/src/fix_smd_wall_surface.rst +++ b/doc/src/fix_smd_wall_surface.rst @@ -50,7 +50,8 @@ directory. See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. @@ -75,4 +76,7 @@ Related commands :doc:`smd/move_tri_surf `, :doc:`smd/tri_surface ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_sph.rst b/doc/src/fix_sph.rst index 7e9159cac4..1b482e0252 100644 --- a/doc/src/fix_sph.rst +++ b/doc/src/fix_sph.rst @@ -32,7 +32,8 @@ Hydrodynamics. See `this PDF guide `_ to using SPH in LAMMPS. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -51,4 +52,7 @@ Related commands :doc:`fix sph/stationary ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_sph_stationary.rst b/doc/src/fix_sph_stationary.rst index cd0d3e4d73..5fa3f1d04d 100644 --- a/doc/src/fix_sph_stationary.rst +++ b/doc/src/fix_sph_stationary.rst @@ -32,7 +32,8 @@ space. SPH stands for Smoothed Particle Hydrodynamics. See `this PDF guide `_ to using SPH in LAMMPS. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -51,4 +52,7 @@ Related commands :doc:`fix sph ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst index 527e6325f4..06b9279c4d 100644 --- a/doc/src/fix_spring.rst +++ b/doc/src/fix_spring.rst @@ -97,7 +97,8 @@ last example holds the ion a distance 5 away from the pore axis spring connecting two groups or a group and the tether point can cross a periodic boundary and its length be calculated correctly. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -149,4 +150,7 @@ Related commands :doc:`fix drag `, :doc:`fix spring/self `, :doc:`fix spring/rg `, :doc:`fix smd ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst index db90cb505c..a2d9945a0b 100644 --- a/doc/src/fix_spring_chunk.rst +++ b/doc/src/fix_spring_chunk.rst @@ -48,7 +48,8 @@ chunk. Note that *K* thus represents the spring constant for the total force on each chunk of atoms, not for a spring applied to each atom. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the locations of the initial per-chunk center of mass coordinates to :doc:`binary restart files `. See the @@ -98,4 +99,7 @@ Related commands :doc:`fix spring `, :doc:`fix spring/self `, :doc:`fix spring/rg ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst index 2329bb6e4a..21035f9def 100644 --- a/doc/src/fix_spring_rg.rst +++ b/doc/src/fix_spring_rg.rst @@ -57,7 +57,8 @@ for the aggregate force on the group of atoms, not a per-atom force. If :math:`R_{G0}` is specified as NULL, then the RG of the group is computed at the time the fix is specified, and that value is used as the target. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the currently used reference RG (:math:`R_{G0}`) to :doc:`binary restart files `. See the :doc:`read_restart @@ -90,4 +91,7 @@ Related commands :doc:`fix spring `, :doc:`fix spring/self ` :doc:`fix drag `, :doc:`fix smd ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_spring_self.rst b/doc/src/fix_spring_self.rst index 38da0013b1..8c5442943f 100644 --- a/doc/src/fix_spring_self.rst +++ b/doc/src/fix_spring_self.rst @@ -41,7 +41,8 @@ directions, but it can be limited to the xy-, xz-, yz-plane and the x-, y-, or z-direction, thus restraining the atoms to a line or a plane, respectively. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the original coordinates of tethered atoms to :doc:`binary restart files `, so that the spring effect will be the same in a restarted simulation. See the @@ -86,4 +87,7 @@ Related commands :doc:`fix drag `, :doc:`fix spring `, :doc:`fix smd `, :doc:`fix spring/rg ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 70f07cc0bf..f3a10df321 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -340,7 +340,8 @@ particles. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst index d9ccd162fd..f6bed4d4af 100644 --- a/doc/src/fix_store_force.rst +++ b/doc/src/fix_store_force.rst @@ -49,7 +49,8 @@ potentially modify the force on each atom. Examples of such fixes are to include certain constraints (e.g. fix shake) in the stored force, then it could be specified after some fixes and before others. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -71,4 +72,7 @@ Related commands :doc:`fix store_state ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index b8fee6b5ea..5f42e3ef5d 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -102,7 +102,8 @@ The requested values are stored in a per-atom vector or array as discussed below. Zeroes are stored for atoms not in the specified group. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart ` diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index e837a21847..ae9f8a933a 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/doc/src/fix_temp_berendsen.rst @@ -117,7 +117,8 @@ thermal degrees of freedom, and the bias is added back in. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the cumulative global energy change to :doc:`binary restart files `. See the @@ -164,7 +165,10 @@ Related commands :doc:`fix_modify `, :doc:`compute temp `, :doc:`fix press/berendsen ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 9c3a722be1..10c92dc2f2 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -125,7 +125,8 @@ thermal degrees of freedom, and the bias is added back in. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" These fixes write the cumulative global energy change and the random number generator states to :doc:`binary restart files `. @@ -174,7 +175,10 @@ Related commands :doc:`fix_modify `, :doc:`compute temp `, :doc:`fix temp/berendsen ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index 7e6f212d04..b00d8e446a 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -124,7 +124,8 @@ thermal degrees of freedom, and the bias is added back in. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the cumulative global energy change to :doc:`binary restart files `. See the :doc:`read_restart ` @@ -164,4 +165,7 @@ Related commands :doc:`fix langevin `, :doc:`fix nvt `, :doc:`fix_modify ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst index 5173e6addc..4ad175b62f 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/doc/src/fix_temp_rescale_eff.rst @@ -35,7 +35,8 @@ The operation of this fix is exactly like that described by the :doc:`fix temp/r is also applied to the radial electron velocity for electron particles. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -72,4 +73,7 @@ Related commands :doc:`fix langevin/eff `, :doc:`fix nvt/eff `, :doc:`fix_modify `, :doc:`fix temp rescale `, -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst index fe290dfc0c..ae8420089a 100644 --- a/doc/src/fix_tfmc.rst +++ b/doc/src/fix_tfmc.rst @@ -116,7 +116,8 @@ rotational component of the tfMC displacements after every iteration. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index 6b8b670694..96dbc43540 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/doc/src/fix_thermal_conductivity.rst @@ -108,7 +108,8 @@ fluid, in appropriate units. See the :ref:`Muller-Plathe paper accurately infer a thermal conductivity and should try increasing the Nevery parameter. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst index 258e380842..08bd6ff2a8 100644 --- a/doc/src/fix_ti_spring.rst +++ b/doc/src/fix_ti_spring.rst @@ -23,7 +23,8 @@ Syntax *function* value = function-ID function-ID = ID of the switching function (1 or 2) -**Example:** +Example +""""""" .. code-block:: LAMMPS @@ -116,7 +117,8 @@ increase in computational resources cost. option will *NOT* solve this problem). The Langevin thermostat (:doc:`fix langevin `) correctly thermostats the system and we advise its usage with ti/spring command. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the original coordinates of tethered atoms to :doc:`binary restart files `, so that the spring effect will be the same in a restarted simulation. See the :doc:`read restart ` command for info on how to re-specify a fix diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst index 521da5ecb2..9c9d77820d 100644 --- a/doc/src/fix_tmd.rst +++ b/doc/src/fix_tmd.rst @@ -89,7 +89,8 @@ to prevent it being overwritten. For more information about TMD, see :ref:`(Schlitter1) ` and :ref:`(Schlitter2) `. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored @@ -117,9 +118,16 @@ To read gzipped target files, you must compile LAMMPS with the -DLAMMPS_GZIP option. See the :doc:`Build settings ` doc page for details. -**Related commands:** none +Related commands +"""""""""""""""" -**Default:** none +none + + +Default +""""""" + +none ---------- diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index ae759c1b13..97cb0cd05b 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -281,7 +281,8 @@ ignored. The lines with the even numbers are treated as follows: ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" These fixes write the state of the electronic subsystem and the energy exchange between the subsystems to :doc:`binary restart files `. See the :doc:`read_restart ` command @@ -334,7 +335,10 @@ Related commands :doc:`fix langevin `, :doc:`fix dt/reset ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 81922dea8a..b2c05b1af7 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -123,7 +123,8 @@ quantities to be stored by fix vector. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -164,4 +165,7 @@ Related commands :doc:`compute `, :doc:`variable ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index e31cbf2e45..d238c099b5 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -113,7 +113,8 @@ system using a :doc:`PPPM solver ` since PPPM does not currently support non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; thus it does not suffer from this limitation. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst index 88d619e56c..ab2f867f33 100644 --- a/doc/src/fix_viscous.rst +++ b/doc/src/fix_viscous.rst @@ -84,7 +84,8 @@ more easily be used as a thermostat. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are @@ -112,4 +113,7 @@ Related commands :doc:`fix langevin ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 1a922227f2..d4120ca625 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -323,7 +323,8 @@ perturbation on the particles: ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index a93d71369f..6430317d43 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -87,7 +87,8 @@ the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for @@ -108,4 +109,7 @@ Related commands :doc:`atom_style body `, :doc:`pair_style body/rounded/polygon ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index 35be8e9259..ad6540de1d 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -83,7 +83,8 @@ the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for @@ -104,4 +105,7 @@ Related commands :doc:`atom_style body `, :doc:`pair_style body/rounded/polyhedron ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index fb986fb73e..4ebbf35ba1 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -176,7 +176,8 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for the wall at whatever *radius* has been defined. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the shear friction state of atoms interacting with the wall to :doc:`binary restart files `, so that a simulation can @@ -234,4 +235,7 @@ Related commands :doc:`pair_style gran/\* ` :doc:`pair_style granular ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 5d40bdd639..7d62d71a1d 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -199,7 +199,8 @@ values for the 6 wall/particle coefficients than for particle/particle interactions. E.g. if you wish to model the wall as a different material. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Similar to :doc:`fix wall/gran ` command, this fix writes the shear friction state of atoms interacting with the wall to :doc:`binary restart files `, so that a simulation can continue @@ -274,4 +275,7 @@ Related commands :doc:`pair_style granular `, :doc:`region ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index 626634ec83..00cad094eb 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -90,7 +90,8 @@ define the lattice spacings. ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index ffdb32422a..44cde8f3d5 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -143,7 +143,8 @@ perturbation on the particles: ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are @@ -170,7 +171,9 @@ Related commands :doc:`fix wall/lj93 `, :doc:`fix oneway ` -**Default:** +Default +""""""" + The default for the units keyword is lattice. diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index b3f4733c56..2359e27255 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -189,7 +189,8 @@ interaction energy is 0.0 at the cutoff distance. For a full description of these wall styles, see fix_style :doc:`wall ` -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. @@ -239,4 +240,7 @@ Related commands :doc:`fix wall/harmonic `, :doc:`fix wall/gran ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index 5df7345a4d..72e7c771b7 100644 --- a/doc/src/fix_wall_srd.rst +++ b/doc/src/fix_wall_srd.rst @@ -177,7 +177,8 @@ perturbation on the particles: ---------- -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. @@ -205,4 +206,7 @@ Related commands :doc:`fix srd ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/fix_widom.rst b/doc/src/fix_widom.rst index 0d191740af..7b9380edcf 100644 --- a/doc/src/fix_widom.rst +++ b/doc/src/fix_widom.rst @@ -156,7 +156,8 @@ with non-neutral systems. See the :doc:`compute group/group ` documentation for more details about simulating non-neutral systems with kspace on. -**Restart, fix_modify, output, run start/stop, minimize info:** +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the state of the fix to :doc:`binary restart files `. This includes information about the random number generator diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst index 84e7b6df32..8c265db197 100644 --- a/doc/src/group2ndx.rst +++ b/doc/src/group2ndx.rst @@ -65,4 +65,7 @@ Related commands :doc:`group `, :doc:`dump `, :doc:`fix colvars ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/if.rst b/doc/src/if.rst index 96a0eca42e..3f39edceb3 100644 --- a/doc/src/if.rst +++ b/doc/src/if.rst @@ -204,4 +204,7 @@ Related commands :doc:`variable `, :doc:`print ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst index 4c49da2aeb..eb6b8eab2c 100644 --- a/doc/src/improper_class2.rst +++ b/doc/src/improper_class2.rst @@ -118,7 +118,10 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/improper_coeff.rst b/doc/src/improper_coeff.rst index 8fd8269fd5..c7a79571a4 100644 --- a/doc/src/improper_coeff.rst +++ b/doc/src/improper_coeff.rst @@ -93,4 +93,7 @@ Related commands :doc:`improper_style ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index e5073dd600..70885acc28 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -72,4 +72,7 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index 4bee3c2acf..bde510c3f7 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -75,4 +75,7 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst index d5f07f9971..1486550c9f 100644 --- a/doc/src/improper_distance.rst +++ b/doc/src/improper_distance.rst @@ -62,4 +62,7 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst index 113941bee4..e29ae95ac5 100644 --- a/doc/src/improper_distharm.rst +++ b/doc/src/improper_distharm.rst @@ -56,4 +56,7 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 4a721854f1..04ce9ba994 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -68,4 +68,7 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index 204d7e95c4..e1b78d21db 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -102,4 +102,7 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst index a36d05e719..cc26e14ce5 100644 --- a/doc/src/improper_hybrid.rst +++ b/doc/src/improper_hybrid.rst @@ -71,4 +71,7 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst index 4a4ad9e863..1c57b5daf1 100644 --- a/doc/src/improper_inversion_harmonic.rst +++ b/doc/src/improper_inversion_harmonic.rst @@ -66,4 +66,7 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_none.rst b/doc/src/improper_none.rst index c1c194041a..bb50eaa121 100644 --- a/doc/src/improper_none.rst +++ b/doc/src/improper_none.rst @@ -36,4 +36,7 @@ Related commands :doc:`improper_style zero ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst index 2f8723a68c..09a661700f 100644 --- a/doc/src/improper_sqdistharm.rst +++ b/doc/src/improper_sqdistharm.rst @@ -57,4 +57,7 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst index 7ed7fe4dd0..10981248d9 100644 --- a/doc/src/improper_umbrella.rst +++ b/doc/src/improper_umbrella.rst @@ -72,7 +72,10 @@ Related commands :doc:`improper_coeff ` -**Default:** none +Default +""""""" + +none ---------- diff --git a/doc/src/improper_zero.rst b/doc/src/improper_zero.rst index 354c0d486e..193c527b2a 100644 --- a/doc/src/improper_zero.rst +++ b/doc/src/improper_zero.rst @@ -44,8 +44,15 @@ Restrictions """""""""""" none -**Related commands:** none +Related commands +"""""""""""""""" + +none + :doc:`improper_style none ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/include.rst b/doc/src/include.rst index e98ffa05e4..6d146061db 100644 --- a/doc/src/include.rst +++ b/doc/src/include.rst @@ -42,4 +42,7 @@ Related commands :doc:`variable `, :doc:`jump ` -**Default:** none +Default +""""""" + +none diff --git a/doc/src/jump.rst b/doc/src/jump.rst index bad13630ab..27ecb53c79 100644 --- a/doc/src/jump.rst +++ b/doc/src/jump.rst @@ -145,4 +145,7 @@ Related commands :doc:`variable `, :doc:`include `, :doc:`label