diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 2cba59bde0..59b8c45b66 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -177,7 +177,7 @@ KIM package To build with this package, the KIM library with API v2 must be downloaded and built on your system. It must include the KIM models that you want to -use with LAMMPS. If you want to use the :doc:`kim\_query ` +use with LAMMPS. If you want to use the :doc:`kim_query ` command, you also need to have libcurl installed with the matching development headers and the curl-config tool. diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 07d427db49..d626a3e8fd 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -5,11 +5,11 @@ LAMMPS can be built with several optional settings. Each sub-section explain how to do this for building both with CMake and make. | :ref:`C++11 standard compliance test ` when building all of LAMMPS -| :ref:`FFT library ` for use with the :doc:`kspace\_style pppm ` command +| :ref:`FFT library ` for use with the :doc:`kspace_style pppm ` command | :ref:`Size of LAMMPS data types ` | :ref:`Read or write compressed files ` | :ref:`Output of JPG and PNG files ` via the :doc:`dump image ` command -| :ref:`Output of movie files ` via the :doc:`dump\_movie ` command +| :ref:`Output of movie files ` via the :doc:`dump_movie ` command | :ref:`Memory allocation alignment ` | :ref:`Workaround for long long integers ` | :ref:`Error handling exceptions ` when using LAMMPS as a library @@ -66,7 +66,7 @@ FFT library --------------------- When the KSPACE package is included in a LAMMPS build, the -:doc:`kspace\_style pppm ` command performs 3d FFTs which +:doc:`kspace_style pppm ` command performs 3d FFTs which require use of an FFT library to compute 1d FFTs. The KISS FFT library is included with LAMMPS but other libraries can be faster. LAMMPS can use them if they are available on your system. @@ -134,7 +134,7 @@ However, note that long-range Coulombics are only a portion of the per-timestep CPU cost, FFTs are only a portion of long-range Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel communication can be costly). A breakdown of these timings is printed -to the screen at the end of a run using the :doc:`kspace\_style pppm ` command. The :doc:`Run output ` +to the screen at the end of a run using the :doc:`kspace_style pppm ` command. The :doc:`Run output ` doc page gives more details. FFTW is a fast, portable FFT library that should also work on any @@ -235,7 +235,7 @@ support 8-byte integers. It allows for: Atom IDs are not required for atomic systems which do not store bond topology information, though IDs are enabled by default. The -:doc:`atom\_modify id no ` command will turn them off. Atom +:doc:`atom_modify id no ` command will turn them off. Atom IDs are required for molecular systems with bond topology (bonds, angles, dihedrals, etc). Thus if you model a molecular system with more than 2 billion atoms, you need the "bigbig" setting. @@ -341,7 +341,7 @@ Read or write compressed files If this option is enabled, large files can be read or written with gzip compression by several LAMMPS commands, including -:doc:`read\_data `, :doc:`rerun `, and :doc:`dump `. +:doc:`read_data `, :doc:`rerun `, and :doc:`dump `. **CMake variables**\ : diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 5412675ee4..19be6d8cbc 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -131,7 +131,7 @@ OPT. Improper_style potentials ========================= -All LAMMPS :doc:`improper\_style ` commands. Some styles +All LAMMPS :doc:`improper_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. diff --git a/doc/src/Commands_category.rst b/doc/src/Commands_category.rst index b1b0e0cadc..6476c73bbb 100644 --- a/doc/src/Commands_category.rst +++ b/doc/src/Commands_category.rst @@ -18,73 +18,73 @@ Setup simulation box: * :doc:`boundary `, * :doc:`box `, -* :doc:`change\_box `, -* :doc:`create\_box `, +* :doc:`change_box `, +* :doc:`create_box `, * :doc:`dimension `, * :doc:`lattice `, * :doc:`region ` Setup atoms: -* :doc:`atom\_modify `, -* :doc:`atom\_style `, +* :doc:`atom_modify `, +* :doc:`atom_style `, * :doc:`balance `, -* :doc:`create\_atoms `, -* :doc:`create\_bonds `, -* :doc:`delete\_atoms `, -* :doc:`delete\_bonds `, -* :doc:`displace\_atoms `, +* :doc:`create_atoms `, +* :doc:`create_bonds `, +* :doc:`delete_atoms `, +* :doc:`delete_bonds `, +* :doc:`displace_atoms `, * :doc:`group `, * :doc:`mass `, * :doc:`molecule `, -* :doc:`read\_data `, -* :doc:`read\_dump `, -* :doc:`read\_restart `, +* :doc:`read_data `, +* :doc:`read_dump `, +* :doc:`read_restart `, * :doc:`replicate `, * :doc:`set `, * :doc:`velocity ` Force fields: -* :doc:`angle\_coeff `, -* :doc:`angle\_style `, -* :doc:`bond\_coeff `, -* :doc:`bond\_style `, -* :doc:`bond\_write `, +* :doc:`angle_coeff `, +* :doc:`angle_style `, +* :doc:`bond_coeff `, +* :doc:`bond_style `, +* :doc:`bond_write `, * :doc:`dielectric `, -* :doc:`dihedral\_coeff `, -* :doc:`dihedral\_style `, -* :doc:`improper\_coeff `, -* :doc:`improper\_style `, -* :doc:`kspace\_modify `, -* :doc:`kspace\_style `, -* :doc:`pair\_coeff `, -* :doc:`pair\_modify `, -* :doc:`pair\_style `, -* :doc:`pair\_write `, -* :doc:`special\_bonds ` +* :doc:`dihedral_coeff `, +* :doc:`dihedral_style `, +* :doc:`improper_coeff `, +* :doc:`improper_style `, +* :doc:`kspace_modify `, +* :doc:`kspace_style `, +* :doc:`pair_coeff `, +* :doc:`pair_modify `, +* :doc:`pair_style `, +* :doc:`pair_write `, +* :doc:`special_bonds ` Settings: -* :doc:`comm\_modify `, -* :doc:`comm\_style `, +* :doc:`comm_modify `, +* :doc:`comm_style `, * :doc:`info `, -* :doc:`min\_modify `, -* :doc:`min\_style `, -* :doc:`neigh\_modify `, +* :doc:`min_modify `, +* :doc:`min_style `, +* :doc:`neigh_modify `, * :doc:`neighbor `, * :doc:`partition `, -* :doc:`reset\_timestep `, -* :doc:`run\_style `, +* :doc:`reset_timestep `, +* :doc:`run_style `, * :doc:`timer `, * :doc:`timestep ` Operations within timestepping (fixes) and diagnostics (computes): * :doc:`compute `, -* :doc:`compute\_modify `, +* :doc:`compute_modify `, * :doc:`fix `, -* :doc:`fix\_modify `, +* :doc:`fix_modify `, * :doc:`uncompute `, * :doc:`unfix ` @@ -93,22 +93,22 @@ Output: * :doc:`dump image `, * :doc:`dump movie `, * :doc:`dump `, -* :doc:`dump\_modify `, +* :doc:`dump_modify `, * :doc:`restart `, * :doc:`thermo `, -* :doc:`thermo\_modify `, -* :doc:`thermo\_style `, +* :doc:`thermo_modify `, +* :doc:`thermo_style `, * :doc:`undump `, -* :doc:`write\_coeff `, -* :doc:`write\_data `, -* :doc:`write\_dump `, -* :doc:`write\_restart ` +* :doc:`write_coeff `, +* :doc:`write_data `, +* :doc:`write_dump `, +* :doc:`write_restart ` Actions: * :doc:`minimize `, * :doc:`neb `, -* :doc:`neb\_spin `, +* :doc:`neb_spin `, * :doc:`prd `, * :doc:`rerun `, * :doc:`run `, diff --git a/doc/src/Commands_input.rst b/doc/src/Commands_input.rst index c66b530dd0..69d3393d08 100644 --- a/doc/src/Commands_input.rst +++ b/doc/src/Commands_input.rst @@ -45,7 +45,7 @@ belong to the group. (3) Sometimes command B will use values that can be set by command A. This means command A must precede command B in the input script if it is to have the desired effect. For example, the -:doc:`read\_data ` command initializes the system by setting +:doc:`read_data ` command initializes the system by setting up the simulation box and assigning atoms to processors. If default values are not desired, the :doc:`processors ` and :doc:`boundary ` commands need to be used before read\_data to diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst index be953c5277..18fa5b5442 100644 --- a/doc/src/Commands_kspace.rst +++ b/doc/src/Commands_kspace.rst @@ -14,7 +14,7 @@ KSpace solvers ============== -All LAMMPS :doc:`kspace\_style ` solvers. Some styles have +All LAMMPS :doc:`kspace_style ` solvers. Some styles have accelerated versions. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index ee87296863..b7f48a9c36 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -57,8 +57,8 @@ restart2data tool The functionality of the restart2data tool has been folded into the LAMMPS executable directly instead of having a separate tool. A -combination of the commands :doc:`read\_restart ` and -:doc:`write\_data ` can be used to the same effect. For added +combination of the commands :doc:`read_restart ` and +:doc:`write_data ` can be used to the same effect. For added convenience this conversion can also be triggered by :doc:`command line flags ` diff --git a/doc/src/Commands_structure.rst b/doc/src/Commands_structure.rst index b419074212..cd96007bf2 100644 --- a/doc/src/Commands_structure.rst +++ b/doc/src/Commands_structure.rst @@ -26,23 +26,23 @@ read-in from a file. The relevant commands are :doc:`units `, :doc:`dimension `, :doc:`newton `, :doc:`processors `, :doc:`boundary `, -:doc:`atom\_style `, :doc:`atom\_modify `. +:doc:`atom_style `, :doc:`atom_modify `. If force-field parameters appear in the files that will be read, these commands tell LAMMPS what kinds of force fields are being used: -:doc:`pair\_style `, :doc:`bond\_style `, -:doc:`angle\_style `, :doc:`dihedral\_style `, -:doc:`improper\_style `. +:doc:`pair_style `, :doc:`bond_style `, +:doc:`angle_style `, :doc:`dihedral_style `, +:doc:`improper_style `. (2) Atom definition There are 3 ways to define atoms in LAMMPS. Read them in from a data -or restart file via the :doc:`read\_data ` or -:doc:`read\_restart ` commands. These files can contain +or restart file via the :doc:`read_data ` or +:doc:`read_restart ` commands. These files can contain molecular topology information. Or create atoms on a lattice (with no molecular topology), using these commands: :doc:`lattice `, -:doc:`region `, :doc:`create\_box `, -:doc:`create\_atoms `. The entire set of atoms can be +:doc:`region `, :doc:`create_box `, +:doc:`create_atoms `. The entire set of atoms can be duplicated to make a larger simulation using the :doc:`replicate ` command. @@ -53,25 +53,25 @@ can be specified: force field coefficients, simulation parameters, output options, etc. Force field coefficients are set by these commands (they can also be -set in the read-in files): :doc:`pair\_coeff `, -:doc:`bond\_coeff `, :doc:`angle\_coeff `, -:doc:`dihedral\_coeff `, -:doc:`improper\_coeff `, -:doc:`kspace\_style `, :doc:`dielectric `, -:doc:`special\_bonds `. +set in the read-in files): :doc:`pair_coeff `, +:doc:`bond_coeff `, :doc:`angle_coeff `, +:doc:`dihedral_coeff `, +:doc:`improper_coeff `, +:doc:`kspace_style `, :doc:`dielectric `, +:doc:`special_bonds `. Various simulation parameters are set by these commands: -:doc:`neighbor `, :doc:`neigh\_modify `, +:doc:`neighbor `, :doc:`neigh_modify `, :doc:`group `, :doc:`timestep `, -:doc:`reset\_timestep `, :doc:`run\_style `, -:doc:`min\_style `, :doc:`min\_modify `. +:doc:`reset_timestep `, :doc:`run_style `, +:doc:`min_style `, :doc:`min_modify `. Fixes impose a variety of boundary conditions, time integration, and diagnostic options. The :doc:`fix ` command comes in many flavors. Various computations can be specified for execution during a simulation using the :doc:`compute `, -:doc:`compute\_modify `, and :doc:`variable ` +:doc:`compute_modify `, and :doc:`variable ` commands. Output options are set by the :doc:`thermo `, :doc:`dump `, diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index 8137c64e96..2da3e623dc 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -18,7 +18,7 @@ the two simulations will rapidly diverge. See the discussion of the *loop* option in the :doc:`velocity ` command for details and options that avoid this issue. -Similarly, the :doc:`create\_atoms ` command generates a +Similarly, the :doc:`create_atoms ` command generates a lattice of atoms. For the same physical system, the ordering and numbering of atoms by atom ID may be different depending on the number of processors. diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 22a4facdd0..8c457bba83 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -6194,7 +6194,7 @@ keyword to allow for additional bonds to be formed rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the - :doc:`neigh\_modify ` command. The safest settings are + :doc:`neigh_modify ` command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly @@ -6209,7 +6209,7 @@ keyword to allow for additional bonds to be formed rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the - :doc:`neigh\_modify ` command. The safest settings are + :doc:`neigh_modify ` command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly @@ -6224,7 +6224,7 @@ keyword to allow for additional bonds to be formed rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the - :doc:`neigh\_modify ` command. The safest settings are + :doc:`neigh_modify ` command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index 2b2f88204b..7b8f85dc9a 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -118,10 +118,10 @@ Doc page with :doc:`ERROR messages ` *Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost* The communication cutoff defaults to the maximum of what is inferred from pair and bond styles (will be zero, if none are defined) and what is specified - via :doc:`comm\_modify cutoff ` (defaults to 0.0). If this results + via :doc:`comm_modify cutoff ` (defaults to 0.0). If this results to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use incorrect periodic images of atoms in interaction lists. To avoid, either use - :doc:`pair style zero ` with a suitable cutoff or use :doc:`comm\_modify cutoff `. + :doc:`pair style zero ` with a suitable cutoff or use :doc:`comm_modify cutoff `. *Communication cutoff is too small for SNAP micro load balancing, increased to %lf* Self-explanatory. diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index ee978f3521..d4fce71230 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -33,7 +33,7 @@ are for 2d models. .. note:: Some models in LAMMPS treat particles as finite-size spheres, as - opposed to point particles. See the :doc:`atom\_style sphere ` and :doc:`fix nve/sphere ` + opposed to point particles. See the :doc:`atom_style sphere ` and :doc:`fix nve/sphere ` commands for details. By default, for 2d simulations, such particles will still be modeled as 3d spheres, not 2d discs (circles), meaning their moment of inertia will be that of a sphere. If you wish to diff --git a/doc/src/Howto_barostat.rst b/doc/src/Howto_barostat.rst index 0c46c696c7..7f016e0c14 100644 --- a/doc/src/Howto_barostat.rst +++ b/doc/src/Howto_barostat.rst @@ -38,7 +38,7 @@ the kinetic component of the pressure. The barostatting fixes can also use temperature computes that remove bias for the purpose of computing the kinetic component which contributes to the current pressure. See the doc pages for the individual fixes and for the -:doc:`fix\_modify ` command for instructions on how to assign +:doc:`fix_modify ` command for instructions on how to assign a temperature or pressure compute to a barostatting fix. .. note:: @@ -49,16 +49,16 @@ a temperature or pressure compute to a barostatting fix. fixes. Thermodynamic output, which can be setup via the -:doc:`thermo\_style ` command, often includes pressure +:doc:`thermo_style ` command, often includes pressure values. As explained on the doc page for the -:doc:`thermo\_style ` command, the default pressure is +:doc:`thermo_style ` command, the default pressure is setup by the thermo command itself. It is NOT the pressure associated with any barostatting fix you have defined or with any compute you have defined that calculates a pressure. The doc pages for the barostatting fixes explain the ID of the pressure compute they create. Thus if you want to view these pressures, you need to specify them -explicitly via the :doc:`thermo\_style custom ` command. -Or you can use the :doc:`thermo\_modify ` command to +explicitly via the :doc:`thermo_style custom ` command. +Or you can use the :doc:`thermo_modify ` command to re-define what pressure compute is used for default thermodynamic output. diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index 0ec0c16be8..fe8f6482aa 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -6,9 +6,9 @@ coefficients used for a particular system. Here we only discuss formulas implemented in LAMMPS that correspond to formulas commonly used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting coefficients is done either from special sections in an input data file -via the :doc:`read\_data ` command or in the input script with -commands like :doc:`pair\_coeff ` or -:doc:`bond\_coeff ` and so on. See the :doc:`Tools ` doc +via the :doc:`read_data ` command or in the input script with +commands like :doc:`pair_coeff ` or +:doc:`bond_coeff ` and so on. See the :doc:`Tools ` doc page for additional tools that can use CHARMM, AMBER, or Materials Studio generated files to assign force field coefficients and convert their output into LAMMPS input. @@ -30,18 +30,18 @@ The interaction styles listed below compute force field formulas that are consistent with common options in CHARMM or AMBER. See each command's documentation for the formula it computes. -* :doc:`bond\_style ` harmonic -* :doc:`angle\_style ` charmm -* :doc:`dihedral\_style ` charmmfsh -* :doc:`dihedral\_style ` charmm -* :doc:`pair\_style ` lj/charmmfsw/coul/charmmfsh -* :doc:`pair\_style ` lj/charmmfsw/coul/long -* :doc:`pair\_style ` lj/charmm/coul/charmm -* :doc:`pair\_style ` lj/charmm/coul/charmm/implicit -* :doc:`pair\_style ` lj/charmm/coul/long +* :doc:`bond_style ` harmonic +* :doc:`angle_style ` charmm +* :doc:`dihedral_style ` charmmfsh +* :doc:`dihedral_style ` charmm +* :doc:`pair_style ` lj/charmmfsw/coul/charmmfsh +* :doc:`pair_style ` lj/charmmfsw/coul/long +* :doc:`pair_style ` lj/charmm/coul/charmm +* :doc:`pair_style ` lj/charmm/coul/charmm/implicit +* :doc:`pair_style ` lj/charmm/coul/long -* :doc:`special\_bonds ` charmm -* :doc:`special\_bonds ` amber +* :doc:`special_bonds ` charmm +* :doc:`special_bonds ` amber .. note:: @@ -66,16 +66,16 @@ These interaction styles listed below compute force field formulas that are consistent with the COMPASS force field. See each command's documentation for the formula it computes. -* :doc:`bond\_style ` class2 -* :doc:`angle\_style ` class2 -* :doc:`dihedral\_style ` class2 -* :doc:`improper\_style ` class2 +* :doc:`bond_style ` class2 +* :doc:`angle_style ` class2 +* :doc:`dihedral_style ` class2 +* :doc:`improper_style ` class2 -* :doc:`pair\_style ` lj/class2 -* :doc:`pair\_style ` lj/class2/coul/cut -* :doc:`pair\_style ` lj/class2/coul/long +* :doc:`pair_style ` lj/class2 +* :doc:`pair_style ` lj/class2/coul/cut +* :doc:`pair_style ` lj/class2/coul/long -* :doc:`special\_bonds ` lj/coul 0 0 1 +* :doc:`special_bonds ` lj/coul 0 0 1 DREIDING is a generic force field developed by the `Goddard group `_ at Caltech and is useful for predicting structures and dynamics of organic, biological and main-group @@ -92,27 +92,27 @@ The interaction styles listed below compute force field formulas that are consistent with the DREIDING force field. See each command's documentation for the formula it computes. -* :doc:`bond\_style ` harmonic -* :doc:`bond\_style ` morse +* :doc:`bond_style ` harmonic +* :doc:`bond_style ` morse -* :doc:`angle\_style ` harmonic -* :doc:`angle\_style ` cosine -* :doc:`angle\_style ` cosine/periodic +* :doc:`angle_style ` harmonic +* :doc:`angle_style ` cosine +* :doc:`angle_style ` cosine/periodic -* :doc:`dihedral\_style ` charmm -* :doc:`improper\_style ` umbrella +* :doc:`dihedral_style ` charmm +* :doc:`improper_style ` umbrella -* :doc:`pair\_style ` buck -* :doc:`pair\_style ` buck/coul/cut -* :doc:`pair\_style ` buck/coul/long -* :doc:`pair\_style ` lj/cut -* :doc:`pair\_style ` lj/cut/coul/cut -* :doc:`pair\_style ` lj/cut/coul/long +* :doc:`pair_style ` buck +* :doc:`pair_style ` buck/coul/cut +* :doc:`pair_style ` buck/coul/long +* :doc:`pair_style ` lj/cut +* :doc:`pair_style ` lj/cut/coul/cut +* :doc:`pair_style ` lj/cut/coul/long -* :doc:`pair\_style ` hbond/dreiding/lj -* :doc:`pair\_style ` hbond/dreiding/morse +* :doc:`pair_style ` hbond/dreiding/lj +* :doc:`pair_style ` hbond/dreiding/morse -* :doc:`special\_bonds ` dreiding +* :doc:`special_bonds ` dreiding ---------- diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 4819ea97df..f929b9f439 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -12,10 +12,10 @@ as spheres, ellipsoids, line segments, and triangles, but they are simpler entities that body particles. See the :doc:`Howto spherical ` doc page for a general overview of all these particle types. -Body particles are used via the :doc:`atom\_style body ` +Body particles are used via the :doc:`atom_style body ` command. It takes a body style as an argument. The current body styles supported by LAMMPS are as follows. The name in the first -column is used as the *bstyle* argument for the :doc:`atom\_style body ` command. +column is used as the *bstyle* argument for the :doc:`atom_style body ` command. +----------------------+---------------------------------------------------+ | *nparticle* | rigid body with N sub-particles | @@ -129,7 +129,7 @@ arguments: The Nmin and Nmax arguments are used to bound the size of data structures used internally by each particle. -When the :doc:`read\_data ` command reads a data file for this +When the :doc:`read_data ` command reads a data file for this body style, the following information must be provided for each entry in the *Bodies* section of the data file: @@ -149,7 +149,7 @@ particle. The integer line has a single value N. The floating point line(s) list 6 moments of inertia followed by the coordinates of the N sub-particles (x1 to zN) as 3N values. These values can be listed on -as many lines as you wish; see the :doc:`read\_data ` command +as many lines as you wish; see the :doc:`read_data ` command for more details. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the @@ -163,7 +163,7 @@ center-of-mass position of the particle is specified by the x,y,z values in the *Atoms* section of the data file, as is the total mass of the body particle. -The :doc:`pair\_style body/nparticle ` command can be used +The :doc:`pair_style body/nparticle ` command can be used with this body style to compute body/body and body/non-body interactions. For output purposes via the :doc:`compute body/local ` and :doc:`dump local ` @@ -217,7 +217,7 @@ this body style takes two additional arguments: The Nmin and Nmax arguments are used to bound the size of data structures used internally by each particle. -When the :doc:`read\_data ` command reads a data file for this +When the :doc:`read_data ` command reads a data file for this body style, the following information must be provided for each entry in the *Bodies* section of the data file: @@ -243,7 +243,7 @@ vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by followed by a single diameter value = the rounded diameter of the circle that surrounds each vertex. The diameter value can be different for each body particle. These floating-point values can be listed on -as many lines as you wish; see the :doc:`read\_data ` command +as many lines as you wish; see the :doc:`read_data ` command for more details. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the @@ -302,7 +302,7 @@ A disk, whose diameter is 3.0, mass 1.0, is specified as follows: 0 0 0 3.0 -The :doc:`pair\_style body/rounded/polygon ` +The :doc:`pair_style body/rounded/polygon ` command can be used with this body style to compute body/body interactions. The :doc:`fix wall/body/polygon ` command can be used with this body style to compute the interaction of @@ -340,7 +340,7 @@ for this body style takes two additional arguments: The Nmin and Nmax arguments are used to bound the size of data structures used internally by each particle. -When the :doc:`read\_data ` command reads a data file for this +When the :doc:`read_data ` command reads a data file for this body style, the following information must be provided for each entry in the *Bodies* section of the data file: @@ -375,7 +375,7 @@ faces. The last value is the diameter value = the rounded diameter of the sphere that surrounds each vertex. The diameter value can be different for each body particle. These floating-point values can be listed on as many lines as you wish; see the -:doc:`read\_data ` command for more details. Because the +:doc:`read_data ` command for more details. Because the maximum number of vertices per face is hard-coded to be 4 (i.e. quadrilaterals), faces with more than 4 vertices need to be split into triangles or quadrilaterals. For triangular faces, the @@ -459,7 +459,7 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows: 0 0 0 3.0 -The :doc:`pair\_style body/rounded/polhedron ` command can +The :doc:`pair_style body/rounded/polhedron ` command can be used with this body style to compute body/body interactions. The :doc:`fix wall/body/polyhedron ` command can be used with this body style to compute the interaction of body particles @@ -489,7 +489,7 @@ For images created by the :doc:`dump image ` command, if the *body* keyword is set, then each body particle is drawn as a polygon consisting of N line segments. Note that the line segments are drawn between the N vertices, which does not correspond exactly to the -physical extent of the body (because the :doc:`pair\_style rounded/polygon ` defines finite-size +physical extent of the body (because the :doc:`pair_style rounded/polygon ` defines finite-size spheres at those point and the line segments between the spheres are tangent to the spheres). The drawn diameter of each line segment is determined by the *bflag1* parameter for the *body* keyword. The diff --git a/doc/src/Howto_coreshell.rst b/doc/src/Howto_coreshell.rst index c39f87fac2..8b2ba38306 100644 --- a/doc/src/Howto_coreshell.rst +++ b/doc/src/Howto_coreshell.rst @@ -17,7 +17,7 @@ alpha = q(shell)\^2 / k. In a similar fashion the mass of the ion is distributed on the core and the shell with the core having the larger mass. -To run this model in LAMMPS, :doc:`atom\_style ` *full* can +To run this model in LAMMPS, :doc:`atom_style ` *full* can be used since atom charge and bonds are needed. Each kind of core/shell pair requires two atom types and a bond type. The core and shell of a core/shell pair should be bonded to each other with a @@ -63,12 +63,12 @@ defined between the shells. Coulombic interactions are defined between all cores and shells. If desired, additional bonds can be specified between cores. -The :doc:`special\_bonds ` command should be used to +The :doc:`special_bonds ` command should be used to turn-off the Coulombic interaction within core/shell pairs, since that interaction is set by the bond spring. This is done using the -:doc:`special\_bonds ` command with a 1-2 weight = 0.0, +:doc:`special_bonds ` command with a 1-2 weight = 0.0, which is the default value. It needs to be considered whether one has -to adjust the :doc:`special\_bonds ` weighting according +to adjust the :doc:`special_bonds ` weighting according to the molecular topology since the interactions of the shells are bypassed over an extra bond. @@ -81,7 +81,7 @@ core and shell, a pair style with a "cs" suffix needs to be used to implement a valid long-range Coulombic correction. Several such pair styles are provided in the CORESHELL package. See :doc:`this doc page ` for details. All of the core/shell enabled pair styles require the use of a long-range Coulombic solver, as specified -by the :doc:`kspace\_style ` command. Either the PPPM or +by the :doc:`kspace_style ` command. Either the PPPM or Ewald solvers can be used. For the NaCL example problem, these pair style and bond style settings @@ -126,7 +126,7 @@ groups can be defined using the :doc:`group *type*\ ` command. Note that to perform thermostatting using this definition of temperature, the :doc:`fix modify temp ` command should be used to assign the compute to the thermostat fix. Likewise the -:doc:`thermo\_modify temp ` command can be used to make +:doc:`thermo_modify temp ` command can be used to make this temperature be output for the overall system. For the NaCl example, this can be done as follows: @@ -148,7 +148,7 @@ as well as for the application of a barostat, it is necessary to use an additional :doc:`pressure ` compute based on the default :doc:`temperature ` and specifying it as a second argument in :doc:`fix modify ` and -:doc:`thermo\_modify ` resulting in: +:doc:`thermo_modify ` resulting in: .. parsed-literal:: @@ -204,7 +204,7 @@ the molecule ID can be used to define the chunks. If cores are bonded to each other to form larger molecules, the chunks can be identified by the :doc:`fix property/atom ` via assigning a core/shell ID to each atom using a special field in the data file read -by the :doc:`read\_data ` command. This field can then be +by the :doc:`read_data ` command. This field can then be accessed by the :doc:`compute property/atom ` command, to use as input to the :doc:`compute chunk/atom ` command to define the core/shell pairs as chunks. diff --git a/doc/src/Howto_drude.rst b/doc/src/Howto_drude.rst index d786c66ef8..78eb7ba49f 100644 --- a/doc/src/Howto_drude.rst +++ b/doc/src/Howto_drude.rst @@ -39,19 +39,19 @@ specified via the :doc:`fix drude ` command. The special list of neighbors is automatically refactored to account for the equivalence of core and Drude particles as regards special 1-2 to 1-4 screening. It may be necessary to use the *extra/special/per/atom* -keyword of the :doc:`read\_data ` command. If using :doc:`fix shake `, make sure no Drude particle is in this fix +keyword of the :doc:`read_data ` command. If using :doc:`fix shake `, make sure no Drude particle is in this fix group. There are two ways to thermostat the Drude particles at a low temperature: use either :doc:`fix langevin/drude ` for a Langevin thermostat, or :doc:`fix drude/transform/\* ` for a Nose-Hoover -thermostat. The former requires use of the command :doc:`comm\_modify vel yes `. The latter requires two separate integration +thermostat. The former requires use of the command :doc:`comm_modify vel yes `. The latter requires two separate integration fixes like *nvt* or *npt*\ . The correct temperatures of the reduced degrees of freedom can be calculated using the :doc:`compute temp/drude `. This requires also to use the command *comm\_modify vel yes*. Short-range damping of the induced dipole interactions can be achieved -using Thole functions through the :doc:`pair style thole ` in :doc:`pair\_style hybrid/overlay ` +using Thole functions through the :doc:`pair style thole ` in :doc:`pair_style hybrid/overlay ` with a Coulomb pair style. It may be useful to use *coul/long/cs* or similar from the CORESHELL package if the core and Drude particle come too close, which can cause numerical issues. diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index baf9a38f08..e1572df6c6 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -159,7 +159,7 @@ DC-DP pairs and will treat DP as equivalent to their DC in the *special bonds* relations. It may be necessary to extend the space for storing such special relations. In this case extra space should be reserved by using the *extra/special/per/atom* keyword of either -the :doc:`read\_data ` or :doc:`create\_box ` +the :doc:`read_data ` or :doc:`create_box ` command. With our phenol, there is 1 more special neighbor for which space is required. Otherwise LAMMPS crashes and gives the required value. diff --git a/doc/src/Howto_elastic.rst b/doc/src/Howto_elastic.rst index f249ea2df7..389c8e19de 100644 --- a/doc/src/Howto_elastic.rst +++ b/doc/src/Howto_elastic.rst @@ -16,7 +16,7 @@ most 7\*6/2 = 21 distinct elements. At zero temperature, it is easy to estimate these derivatives by deforming the simulation box in one of the six directions using the -:doc:`change\_box ` command and measuring the change in the +:doc:`change_box ` command and measuring the change in the stress tensor. A general-purpose script that does this is given in the examples/elastic directory described on the :doc:`Examples ` doc page. diff --git a/doc/src/Howto_granular.rst b/doc/src/Howto_granular.rst index d6c983efe1..0bd4fa0349 100644 --- a/doc/src/Howto_granular.rst +++ b/doc/src/Howto_granular.rst @@ -8,7 +8,7 @@ velocity and torque can be imparted to them to cause them to rotate. To run a simulation of a granular model, you will want to use the following commands: -* :doc:`atom\_style sphere ` +* :doc:`atom_style sphere ` * :doc:`fix nve/sphere ` * :doc:`fix gravity ` @@ -21,9 +21,9 @@ calculates rotational kinetic energy which can be :doc:`output with thermodynami Use one of these 3 pair potentials, which compute forces and torques between interacting pairs of particles: -* :doc:`pair\_style ` gran/history -* :doc:`pair\_style ` gran/no\_history -* :doc:`pair\_style ` gran/hertzian +* :doc:`pair_style ` gran/history +* :doc:`pair_style ` gran/no\_history +* :doc:`pair_style ` gran/hertzian These commands implement fix options specific to granular systems: @@ -39,7 +39,7 @@ atoms, and should be used for granular system instead of the fix style For computational efficiency, you can eliminate needless pairwise computations between frozen atoms by using this command: -* :doc:`neigh\_modify ` exclude +* :doc:`neigh_modify ` exclude .. note:: diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index 6a5788cab3..0670bf1e9f 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -88,21 +88,21 @@ Thermodynamic output --------------------------------- The frequency and format of thermodynamic output is set by the -:doc:`thermo `, :doc:`thermo\_style `, and -:doc:`thermo\_modify ` commands. The -:doc:`thermo\_style ` command also specifies what values +:doc:`thermo `, :doc:`thermo_style `, and +:doc:`thermo_modify ` commands. The +:doc:`thermo_style ` command also specifies what values are calculated and written out. Pre-defined keywords can be specified (e.g. press, etotal, etc). Three additional kinds of keywords can also be specified (c\_ID, f\_ID, v\_name), where a :doc:`compute ` or :doc:`fix ` or :doc:`variable ` provides the value to be output. In each case, the compute, fix, or variable must generate -global values for input to the :doc:`thermo\_style custom ` +global values for input to the :doc:`thermo_style custom ` command. Note that thermodynamic output values can be "extensive" or "intensive". The former scale with the number of atoms in the system (e.g. total energy), the latter do not (e.g. temperature). The -setting for :doc:`thermo\_modify norm ` determines whether +setting for :doc:`thermo_modify norm ` determines whether extensive quantities are normalized or not. Computes and fixes produce either extensive or intensive values; see their individual doc pages for details. :doc:`Equal-style variables ` produce only @@ -116,7 +116,7 @@ Dump file output --------------------------- Dump file output is specified by the :doc:`dump ` and -:doc:`dump\_modify ` commands. There are several +:doc:`dump_modify ` commands. There are several pre-defined formats (dump atom, dump xtc, etc). There is also a :doc:`dump custom ` format where the user @@ -151,7 +151,7 @@ specifies one or more quantities as input. These can be global :doc:`compute ` values, global :doc:`fix ` values, or :doc:`variables ` of any style except the atom style which produces per-atom values. Since a variable can refer to keywords used -by the :doc:`thermo\_style custom ` command (like temp or +by the :doc:`thermo_style custom ` command (like temp or press) and individual per-atom values, a wide variety of quantities can be time averaged and/or output in this way. If the inputs are one or more scalar values, then the fix generate a global scalar or vector @@ -304,7 +304,7 @@ vector input could be a column of an array. +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ | Command | Input | Output | +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`thermo\_style custom ` | global scalars | screen, log file | +| :doc:`thermo_style custom ` | global scalars | screen, log file | +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ | :doc:`dump custom ` | per-atom vectors | dump file | +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ diff --git a/doc/src/Howto_replica.rst b/doc/src/Howto_replica.rst index 49150ae985..885cdf050e 100644 --- a/doc/src/Howto_replica.rst +++ b/doc/src/Howto_replica.rst @@ -9,7 +9,7 @@ periodically. These are the relevant commands: * :doc:`neb ` for nudged elastic band calculations -* :doc:`neb\_spin ` for magnetic nudged elastic band calculations +* :doc:`neb_spin ` for magnetic nudged elastic band calculations * :doc:`prd ` for parallel replica dynamics * :doc:`tad ` for temperature accelerated dynamics * :doc:`temper ` for parallel tempering diff --git a/doc/src/Howto_restart.rst b/doc/src/Howto_restart.rst index 608246ccbc..c6dc818816 100644 --- a/doc/src/Howto_restart.rst +++ b/doc/src/Howto_restart.rst @@ -6,16 +6,16 @@ There are 3 ways to continue a long LAMMPS simulation. Multiple run will continue from where the previous run left off. Or binary restart files can be saved to disk using the :doc:`restart ` command. At a later time, these binary files can be read via a -:doc:`read\_restart ` command in a new script. Or they can -be converted to text data files using the :doc:`-r command-line switch ` and read by a :doc:`read\_data ` +:doc:`read_restart ` command in a new script. Or they can +be converted to text data files using the :doc:`-r command-line switch ` and read by a :doc:`read_data ` command in a new script. Here we give examples of 2 scripts that read either a binary restart file or a converted data file and then issue a new run command to continue where the previous run left off. They illustrate what settings must be made in the new script. Details are discussed in the -documentation for the :doc:`read\_restart ` and -:doc:`read\_data ` commands. +documentation for the :doc:`read_restart ` and +:doc:`read_data ` commands. Look at the *in.chain* input script provided in the *bench* directory of the LAMMPS distribution to see the original script that these 2 @@ -95,7 +95,7 @@ Then, this script could be used to re-run the last 50 steps: Note that nearly all the settings specified in the original *in.chain* script must be repeated, except the *pair\_coeff* and *bond\_coeff* commands since the new data file lists the force field coefficients. -Also, the :doc:`reset\_timestep ` command is used to tell +Also, the :doc:`reset_timestep ` command is used to tell LAMMPS the current timestep. This value is stored in restart files, but not in data files. diff --git a/doc/src/Howto_spherical.rst b/doc/src/Howto_spherical.rst index 23ea6435f8..ec199c859b 100644 --- a/doc/src/Howto_spherical.rst +++ b/doc/src/Howto_spherical.rst @@ -45,7 +45,7 @@ like This is because when dipoles interact with each other, they induce torques, and a particle must be finite-size (i.e. have a moment of -inertia) in order to respond and rotate. See the :doc:`atom\_style dipole ` command for details. The "set" command can be +inertia) in order to respond and rotate. See the :doc:`atom_style dipole ` command for details. The "set" command can be used to modify the orientation and length of the dipole moment of individual particles, after then are created. @@ -71,7 +71,7 @@ particles with a triangulated surface. The peri style is used with :doc:`Peridynamic models ` and defines particles as having a volume, that is used internally in the -:doc:`pair\_style peri ` potentials. +:doc:`pair_style peri ` potentials. The body style allows for definition of particles which can represent complex entities, such as surface meshes of discrete points, @@ -80,7 +80,7 @@ is discussed in more detail on the :doc:`Howto body ` doc page. Note that if one of these atom styles is used (or multiple styles via -the :doc:`atom\_style hybrid ` command), not all particles in +the :doc:`atom_style hybrid ` command), not all particles in the system are required to be finite-size or aspherical. For example, in the ellipsoid style, if the 3 shape parameters are set @@ -94,7 +94,7 @@ Some of the pair styles used to compute pairwise interactions between finite-size particles also compute the correct interaction with point particles as well, e.g. the interaction between a point particle and a finite-size particle or between two point particles. If necessary, -:doc:`pair\_style hybrid ` can be used to insure the correct +:doc:`pair_style hybrid ` can be used to insure the correct interactions are computed for the appropriate style of interactions. Likewise, using groups to partition particles (ellipsoids versus spheres versus point particles) will allow you to use the appropriate @@ -114,17 +114,17 @@ When a system with finite-size particles is defined, the particles will only rotate and experience torque if the force field computes such interactions. These are the various :doc:`pair styles ` that generate torque: -* :doc:`pair\_style gran/history ` -* :doc:`pair\_style gran/hertzian ` -* :doc:`pair\_style gran/no\_history ` -* :doc:`pair\_style dipole/cut ` -* :doc:`pair\_style gayberne ` -* :doc:`pair\_style resquared ` -* :doc:`pair\_style brownian ` -* :doc:`pair\_style lubricate ` -* :doc:`pair\_style line/lj ` -* :doc:`pair\_style tri/lj ` -* :doc:`pair\_style body/nparticle ` +* :doc:`pair_style gran/history ` +* :doc:`pair_style gran/hertzian ` +* :doc:`pair_style gran/no\_history ` +* :doc:`pair_style dipole/cut ` +* :doc:`pair_style gayberne ` +* :doc:`pair_style resquared ` +* :doc:`pair_style brownian ` +* :doc:`pair_style lubricate ` +* :doc:`pair_style line/lj ` +* :doc:`pair_style tri/lj ` +* :doc:`pair_style body/nparticle ` The granular pair styles are used with spherical particles. The dipole pair style is used with the dipole atom style, which could be @@ -187,10 +187,10 @@ These include rotational degrees of freedom in their computation. If you wish the thermodynamic output of temperature or pressure to use one of these computes (e.g. for a system entirely composed of finite-size particles), then the compute can be defined and the -:doc:`thermo\_modify ` command used. Note that by default +:doc:`thermo_modify ` command used. Note that by default thermodynamic quantities will be calculated with a temperature that only includes translational degrees of freedom. See the -:doc:`thermo\_style ` command for details. +:doc:`thermo_style ` command for details. These commands can be used to output various attributes of finite-size particles: @@ -235,7 +235,7 @@ Also note that body particles cannot be modeled with the :doc:`fix rigid `. Interactions between pairs of body -particles are computed via a command like :doc:`pair\_style body/nparticle `. +particles are computed via a command like :doc:`pair_style body/nparticle `. .. _lws: http://lammps.sandia.gov diff --git a/doc/src/Howto_thermostat.rst b/doc/src/Howto_thermostat.rst index 89d0c7b693..273876c9fd 100644 --- a/doc/src/Howto_thermostat.rst +++ b/doc/src/Howto_thermostat.rst @@ -23,7 +23,7 @@ can be invoked via the *dpd/tstat* pair style: * :doc:`fix temp/csvr ` * :doc:`fix langevin ` * :doc:`fix temp/rescale ` -* :doc:`pair\_style dpd/tstat ` +* :doc:`pair_style dpd/tstat ` :doc:`Fix nvt ` only thermostats the translational velocity of particles. :doc:`Fix nvt/sllod ` also does this, except @@ -49,7 +49,7 @@ bias removed. Second, the thermostat adjusts only the thermal temperature component of the particle's velocities, which are the velocities with the bias removed. The removed bias is then added back to the adjusted velocities. See the doc pages for the individual -fixes and for the :doc:`fix\_modify ` command for +fixes and for the :doc:`fix_modify ` command for instructions on how to assign a temperature compute to a thermostatting fix. For example, you can apply a thermostat to only the x and z components of velocity by using it in conjunction with @@ -70,16 +70,16 @@ particles without affecting the streaming velocity, by using :doc:`compute temp/ * :doc:`fix nve/asphere ` Thermodynamic output, which can be setup via the -:doc:`thermo\_style ` command, often includes temperature +:doc:`thermo_style ` command, often includes temperature values. As explained on the doc page for the -:doc:`thermo\_style ` command, the default temperature is +:doc:`thermo_style ` command, the default temperature is setup by the thermo command itself. It is NOT the temperature associated with any thermostatting fix you have defined or with any compute you have defined that calculates a temperature. The doc pages for the thermostatting fixes explain the ID of the temperature compute they create. Thus if you want to view these temperatures, you need to -specify them explicitly via the :doc:`thermo\_style custom ` command. Or you can use the -:doc:`thermo\_modify ` command to re-define what +specify them explicitly via the :doc:`thermo_style custom ` command. Or you can use the +:doc:`thermo_modify ` command to re-define what temperature compute is used for default thermodynamic output. diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 449aa8e9f7..c55e22ba60 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -11,12 +11,12 @@ angle style of *harmonic* or *charmm* should also be used. A TIP4P model is run with LAMMPS using either this command for a cutoff model: -:doc:`pair\_style lj/cut/tip4p/cut ` +:doc:`pair_style lj/cut/tip4p/cut ` or these two commands for a long-range model: -* :doc:`pair\_style lj/cut/tip4p/long ` -* :doc:`kspace\_style pppm/tip4p ` +* :doc:`pair_style lj/cut/tip4p/long ` +* :doc:`kspace_style pppm/tip4p ` For both models, the bond lengths and bond angles should be held fixed using the :doc:`fix shake ` command. @@ -24,7 +24,7 @@ using the :doc:`fix shake ` command. These are the additional parameters (in real units) to set for O and H atoms and the water molecule to run a rigid TIP4P model with a cutoff :ref:`(Jorgensen) `. Note that the OM distance is specified in -the :doc:`pair\_style ` command, not as part of the pair +the :doc:`pair_style ` command, not as part of the pair coefficients. | O mass = 15.9994 @@ -95,7 +95,7 @@ typically best in an efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM distance), to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. The OM distance and the LJ -and Coulombic cutoffs are set in the :doc:`pair\_style lj/cut/tip4p/long ` command. +and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long ` command. Wikipedia also has a nice article on `water models `_. diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 6e341907a8..6667e9cf66 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -22,11 +22,11 @@ box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting from the origin given by **a** = (xhi-xlo,0,0); **b** = (0,yhi-ylo,0); **c** = (0,0,zhi-zlo). The 6 parameters (xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box -is created, e.g. by the :doc:`create\_box ` or -:doc:`read\_data ` or :doc:`read\_restart ` +is created, e.g. by the :doc:`create_box ` or +:doc:`read_data ` or :doc:`read_restart ` commands. Additionally, LAMMPS defines box size parameters lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 -parameters, as well as lx,ly,lz, can be output via the :doc:`thermo\_style custom ` command. +parameters, as well as lx,ly,lz, can be output via the :doc:`thermo_style custom ` command. LAMMPS also allows simulations to be performed in triclinic (non-orthogonal) simulation boxes shaped as a parallelepiped with @@ -90,14 +90,14 @@ for details. The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the time the simulation box is created. This happens in one of 3 ways. -If the :doc:`create\_box ` command is used with a region of +If the :doc:`create_box ` command is used with a region of style *prism*\ , then a triclinic box is setup. See the :doc:`region ` command for details. If the -:doc:`read\_data ` command is used to define the simulation +:doc:`read_data ` command is used to define the simulation box, and the header of the data file contains a line with the "xy xz yz" keyword, then a triclinic box is setup. See the -:doc:`read\_data ` command for details. Finally, if the -:doc:`read\_restart ` command reads a restart file which +:doc:`read_data ` command for details. Finally, if the +:doc:`read_restart ` command reads a restart file which was written from a simulation using a triclinic box, then a triclinic box will be setup for the restarted simulation. @@ -105,20 +105,20 @@ Note that you can define a triclinic box with all 3 tilt factors = 0.0, so that it is initially orthogonal. This is necessary if the box will become non-orthogonal, e.g. due to the :doc:`fix npt ` or :doc:`fix deform ` commands. Alternatively, you can use the -:doc:`change\_box ` command to convert a simulation box from +:doc:`change_box ` command to convert a simulation box from orthogonal to triclinic and vice versa. As with orthogonal boxes, LAMMPS defines triclinic box size parameters lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. The 9 parameters, as well as lx,ly,lz, can be output via the -:doc:`thermo\_style custom ` command. +:doc:`thermo_style custom ` command. To avoid extremely tilted boxes (which would be computationally inefficient), LAMMPS normally requires that no tilt factor can skew the box more than half the distance of the parallel box length, which is the 1st dimension in the tilt factor (x for xz). This is required both when the simulation box is created, e.g. via the -:doc:`create\_box ` or :doc:`read\_data ` commands, +:doc:`create_box ` or :doc:`read_data ` commands, as well as when the box shape changes dynamically during a simulation, e.g. via the :doc:`fix deform ` or :doc:`fix npt ` commands. @@ -173,7 +173,7 @@ The inverse relationship can be written as follows: The values of *a*\ , *b*\ , *c* , *alpha*\ , *beta* , and *gamma* can be printed out or accessed by computes using the -:doc:`thermo\_style custom ` keywords +:doc:`thermo_style custom ` keywords *cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , *cellbeta*\ , *cellgamma*\ , respectively. @@ -213,7 +213,7 @@ One use of triclinic simulation boxes is to model solid-state crystals with triclinic symmetry. The :doc:`lattice ` command can be used with non-orthogonal basis vectors to define a lattice that will tile a triclinic simulation box via the -:doc:`create\_atoms ` command. +:doc:`create_atoms ` command. A second use is to run Parrinello-Rahman dynamics via the :doc:`fix npt ` command, which will adjust the xy, xz, yz tilt factors to compensate for off-diagonal components of the pressure diff --git a/doc/src/Howto_walls.rst b/doc/src/Howto_walls.rst index f04b7f1057..eed28f2ed1 100644 --- a/doc/src/Howto_walls.rst +++ b/doc/src/Howto_walls.rst @@ -11,8 +11,8 @@ tangential direction. Rough walls, built of particles, can be created in various ways. The particles themselves can be generated like any other particle, via the -:doc:`lattice ` and :doc:`create\_atoms ` commands, -or read in via the :doc:`read\_data ` command. +:doc:`lattice ` and :doc:`create_atoms ` commands, +or read in via the :doc:`read_data ` command. Their motion can be constrained by many different commands, so that they do not move at all, move together as a group at constant velocity @@ -34,7 +34,7 @@ the motion of individual particles can be specified with particle position. For rough walls, it may be useful to turn off pairwise interactions -between wall particles via the :doc:`neigh\_modify exclude ` command. +between wall particles via the :doc:`neigh_modify exclude ` command. Rough walls can also be created by specifying frozen particles that do not move and do not interact with mobile particles, and then tethering @@ -47,11 +47,11 @@ granular particles; all the other commands create smooth walls. * :doc:`fix wall/reflect ` - reflective flat walls * :doc:`fix wall/lj93 ` - flat walls, with Lennard-Jones 9/3 potential * :doc:`fix wall/lj126 ` - flat walls, with Lennard-Jones 12/6 potential -* :doc:`fix wall/colloid ` - flat walls, with :doc:`pair\_style colloid ` potential +* :doc:`fix wall/colloid ` - flat walls, with :doc:`pair_style colloid ` potential * :doc:`fix wall/harmonic ` - flat walls, with repulsive harmonic spring potential * :doc:`fix wall/morse ` - flat walls, with Morse potential * :doc:`fix wall/region ` - use region surface as wall -* :doc:`fix wall/gran ` - flat or curved walls with :doc:`pair\_style granular ` potential +* :doc:`fix wall/gran ` - flat or curved walls with :doc:`pair_style granular ` potential The *lj93*\ , *lj126*\ , *colloid*\ , *harmonic*\ , and *morse* styles all allow the flat walls to move with a constant velocity, or oscillate in diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index 67d37b917a..d8dd0a0531 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -96,9 +96,9 @@ commands) Atom creation -------------------------- -(:doc:`read\_data `, :doc:`lattice `, -:doc:`create\_atoms `, :doc:`delete\_atoms `, -:doc:`displace\_atoms `, :doc:`replicate ` commands) +(:doc:`read_data `, :doc:`lattice `, +:doc:`create_atoms `, :doc:`delete_atoms `, +:doc:`displace_atoms `, :doc:`replicate ` commands) * read in atom coords from files * create atoms on one or more lattices (e.g. grain boundaries) @@ -133,7 +133,7 @@ Ensembles, constraints, and boundary conditions Integrators --------------------------- -(:doc:`run `, :doc:`run\_style `, :doc:`minimize ` commands) +(:doc:`run `, :doc:`run_style `, :doc:`minimize ` commands) * velocity-Verlet integrator * Brownian dynamics diff --git a/doc/src/Modify_fix.rst b/doc/src/Modify_fix.rst index cafde08af6..d4c4fa046f 100644 --- a/doc/src/Modify_fix.rst +++ b/doc/src/Modify_fix.rst @@ -146,7 +146,7 @@ implementing the grow\_arrays, copy\_arrays, pack\_exchange, and unpack\_exchange methods. Similarly, the pack\_restart and unpack\_restart methods can be implemented to store information about the fix in restart files. If you wish an integrator or force -constraint fix to work with rRESPA (see the :doc:`run\_style ` +constraint fix to work with rRESPA (see the :doc:`run_style ` command), the initial\_integrate, post\_force\_integrate, and final\_integrate\_respa methods can be implemented. The thermo method enables a fix to contribute values to thermodynamic output, as printed diff --git a/doc/src/Modify_thermo.rst b/doc/src/Modify_thermo.rst index f3a3f00e2f..d95b98ab40 100644 --- a/doc/src/Modify_thermo.rst +++ b/doc/src/Modify_thermo.rst @@ -7,7 +7,7 @@ to the screen and log file; see the file thermo.cpp. There are two styles defined in thermo.cpp: "one" and "multi". There is also a flexible "custom" style which allows the user to explicitly list keywords for quantities to print when thermodynamic info is -output. See the :doc:`thermo\_style ` command for a list +output. See the :doc:`thermo_style ` command for a list of defined quantities. The thermo styles (one, multi, etc) are simply lists of keywords. @@ -20,7 +20,7 @@ for output. Search for the word "customize" with references to "keyword" in thermo.cpp to see the several locations where code will need to be added. -Note that the :doc:`thermo\_style custom ` command already allows +Note that the :doc:`thermo_style custom ` command already allows for thermo output of quantities calculated by :doc:`fixes `, :doc:`computes `, and :doc:`variables `. Thus, it may be simpler to compute what you wish via one of those constructs, than diff --git a/doc/src/Modify_variable.rst b/doc/src/Modify_variable.rst index bd3f70588b..40e2e9e6a3 100644 --- a/doc/src/Modify_variable.rst +++ b/doc/src/Modify_variable.rst @@ -5,7 +5,7 @@ There is one class that computes and stores :doc:`variable ` information in LAMMPS; see the file variable.cpp. The value associated with a variable can be periodically printed to the screen via the :doc:`print `, :doc:`fix print `, or -:doc:`thermo\_style custom ` commands. Variables of style +:doc:`thermo_style custom ` commands. Variables of style "equal" can compute complex equations that involve the following types of arguments: @@ -19,7 +19,7 @@ of arguments: atom values = x[123], y[3], vx[34], ... compute values = c_mytemp[0], c_thermo_press[3], ... -Adding keywords for the :doc:`thermo\_style custom ` +Adding keywords for the :doc:`thermo_style custom ` command (which can then be accessed by variables) is discussed on the :doc:`Modify thermo ` doc page. diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 376bc0acda..efdd222cf1 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -72,8 +72,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles. * src/ASPHERE: filenames -> commands * :doc:`Howto spherical ` -* :doc:`pair\_style gayberne ` -* :doc:`pair\_style resquared ` +* :doc:`pair_style gayberne ` +* :doc:`pair_style resquared ` * `doc/PDF/pair\_gayberne\_extra.pdf `_ * `doc/PDF/pair\_resquared\_extra.pdf `_ * examples/ASPHERE @@ -101,9 +101,9 @@ overview. * src/BODY filenames -> commands * :doc:`Howto\_body ` -* :doc:`atom\_style body ` +* :doc:`atom_style body ` * :doc:`fix nve/body ` -* :doc:`pair\_style body/nparticle ` +* :doc:`pair_style body/nparticle ` * examples/body @@ -123,11 +123,11 @@ CLASS2 molecular force field. **Supporting info:** * src/CLASS2: filenames -> commands -* :doc:`bond\_style class2 ` -* :doc:`angle\_style class2 ` -* :doc:`dihedral\_style class2 ` -* :doc:`improper\_style class2 ` -* :doc:`pair\_style lj/class2 ` +* :doc:`bond_style class2 ` +* :doc:`angle_style class2 ` +* :doc:`dihedral_style class2 ` +* :doc:`improper_style class2 ` +* :doc:`pair_style lj/class2 ` ---------- @@ -153,11 +153,11 @@ Higdon's group at UIUC. * src/COLLOID: filenames -> commands * :doc:`fix wall/colloid ` -* :doc:`pair\_style colloid ` -* :doc:`pair\_style yukawa/colloid ` -* :doc:`pair\_style brownian ` -* :doc:`pair\_style lubricate ` -* :doc:`pair\_style lubricateU ` +* :doc:`pair_style colloid ` +* :doc:`pair_style yukawa/colloid ` +* :doc:`pair_style brownian ` +* :doc:`pair_style lubricate ` +* :doc:`pair_style lubricateU ` * examples/colloid * examples/srd @@ -219,9 +219,9 @@ this package. * :doc:`Howto coreshell ` * :doc:`Howto polarizable ` * :doc:`compute temp/cs ` -* :doc:`pair\_style born/coul/long/cs ` -* :doc:`pair\_style buck/coul/long/cs ` -* :doc:`pair\_style lj/cut/coul/long/cs ` +* :doc:`pair_style born/coul/long/cs ` +* :doc:`pair_style buck/coul/long/cs ` +* :doc:`pair_style lj/cut/coul/long/cs ` * examples/coreshell @@ -241,10 +241,10 @@ short-range or long-range interactions. **Supporting info:** * src/DIPOLE: filenames -> commands -* :doc:`atom\_style dipole ` -* :doc:`pair\_style lj/cut/dipole/cut ` -* :doc:`pair\_style lj/cut/dipole/long ` -* :doc:`pair\_style lj/long/dipole/long ` +* :doc:`atom_style dipole ` +* :doc:`pair_style lj/cut/dipole/cut ` +* :doc:`pair_style lj/cut/dipole/long ` +* :doc:`pair_style lj/long/dipole/long ` * examples/dipole @@ -309,8 +309,8 @@ potentials. * :doc:`Howto granular ` * :doc:`fix pour ` * :doc:`fix wall/gran ` -* :doc:`pair\_style gran/hooke ` -* :doc:`pair\_style gran/hertz/history ` +* :doc:`pair_style gran/hooke ` +* :doc:`pair_style gran/hertz/history ` * examples/granregion * examples/pour * bench/in.chute @@ -335,13 +335,13 @@ This package contains a set of commands that serve as a wrapper on the `Open Knowledgebase of Interatomic Models (OpenKIM) `_ repository of interatomic models (IMs) enabling compatible ones to be used in LAMMPS simulations. -This includes :doc:`kim\_init and kim\_interactions ` +This includes :doc:`kim_init and kim\_interactions ` commands to select, initialize and instantiate the IM, and a -:doc:`kim\_query ` command to perform web queries +:doc:`kim_query ` command to perform web queries for material property predictions of OpenKIM IMs. Support for KIM IMs that conform to the `KIM Application Programming Interface (API) `_ -is provided by the :doc:`pair\_style kim ` command. +is provided by the :doc:`pair_style kim ` command. .. note:: @@ -361,7 +361,7 @@ and is funded by the `National Science Foundation `_. **Authors:** Ryan Elliott (U Minnesota) is the main developer for the KIM API and the *pair\_style kim* command. Axel Kohlmeyer (Temple U) and -Ellad Tadmor (U Minnesota) contributed to the :doc:`kim\_commands ` +Ellad Tadmor (U Minnesota) contributed to the :doc:`kim_commands ` interface in close collaboration with Ryan Elliott. **Install:** @@ -370,8 +370,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu **Supporting info:** -* :doc:`kim\_commands ` -* :doc:`pair\_style kim ` +* :doc:`kim_commands ` +* :doc:`pair_style kim ` * src/KIM: filenames -> commands * src/KIM/README * lib/kim/README @@ -458,12 +458,12 @@ different FFT options for your LAMPMS build. **Supporting info:** * src/KSPACE: filenames -> commands -* :doc:`kspace\_style ` +* :doc:`kspace_style ` * `doc/PDF/kspace.pdf `_ * :doc:`Howto tip3p ` * :doc:`Howto tip4p ` * :doc:`Howto spc ` -* :doc:`pair\_style coul ` +* :doc:`pair_style coul ` * :doc:`Commands pair ` page for styles with "long" or "msm" in name * examples/peptide * bench/in.rhodo @@ -558,7 +558,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC * :doc:`fix bond/create ` * :doc:`fix bond/swap ` * :doc:`fix gcmc ` -* :doc:`pair\_style dsmc ` +* :doc:`pair_style dsmc ` * http://lammps.sandia.gov/movies.html#gcmc @@ -642,13 +642,13 @@ force fields, and a TIP4P water model. **Supporting info:** * src/MOLECULE: filenames -> commands -* :doc:`atom\_style ` -* :doc:`bond\_style ` -* :doc:`angle\_style ` -* :doc:`dihedral\_style ` -* :doc:`improper\_style ` -* :doc:`pair\_style hbond/dreiding/lj ` -* :doc:`pair\_style lj/charmm/coul/charmm ` +* :doc:`atom_style ` +* :doc:`bond_style ` +* :doc:`angle_style ` +* :doc:`dihedral_style ` +* :doc:`improper_style ` +* :doc:`pair_style hbond/dreiding/lj ` +* :doc:`pair_style lj/charmm/coul/charmm ` * :doc:`Howto bioFF ` * examples/cmap * examples/dreiding @@ -678,8 +678,8 @@ written and read in parallel. * src/MPIIO: filenames -> commands * :doc:`dump ` * :doc:`restart ` -* :doc:`write\_restart ` -* :doc:`read\_restart ` +* :doc:`write_restart ` +* :doc:`read_restart ` ---------- @@ -779,8 +779,8 @@ Foster (UTSA). * `doc/PDF/PDLammps\_overview.pdf `_ * `doc/PDF/PDLammps\_EPS.pdf `_ * `doc/PDF/PDLammps\_VES.pdf `_ -* :doc:`atom\_style peri ` -* :doc:`pair\_style peri/\* ` +* :doc:`atom_style peri ` +* :doc:`pair_style peri/\* ` * :doc:`compute damage/atom ` * :doc:`compute plasticity/atom ` * examples/peri @@ -902,7 +902,7 @@ another set. * :doc:`prd ` * :doc:`tad ` * :doc:`temper `, -* :doc:`run\_style verlet/split ` +* :doc:`run_style verlet/split ` * examples/neb * examples/prd * examples/tad @@ -981,7 +981,7 @@ computes which analyze attributes of the potential. **Supporting info:** * src/SNAP: filenames -> commands -* :doc:`pair\_style snap ` +* :doc:`pair_style snap ` * :doc:`compute sna/atom ` * :doc:`compute snad/atom ` * :doc:`compute snav/atom ` @@ -1007,12 +1007,12 @@ the usual manner via MD. Various pair, fix, and compute styles. * src/SPIN: filenames -> commands * :doc:`Howto spins ` -* :doc:`pair\_style spin/dipole/cut ` -* :doc:`pair\_style spin/dipole/long ` -* :doc:`pair\_style spin/dmi ` -* :doc:`pair\_style spin/exchange ` -* :doc:`pair\_style spin/magelec ` -* :doc:`pair\_style spin/neel ` +* :doc:`pair_style spin/dipole/cut ` +* :doc:`pair_style spin/dipole/long ` +* :doc:`pair_style spin/dmi ` +* :doc:`pair_style spin/exchange ` +* :doc:`pair_style spin/magelec ` +* :doc:`pair_style spin/neel ` * :doc:`fix nve/spin ` * :doc:`fix precession/spin ` * :doc:`compute spin ` @@ -1172,7 +1172,7 @@ This package has :ref:`specific installation instructions ` on the : * src/USER-AWPMD: filenames -> commands * src/USER-AWPMD/README -* :doc:`pair\_style awpmd/cut ` +* :doc:`pair_style awpmd/cut ` * examples/USER/awpmd @@ -1233,10 +1233,10 @@ stability. * src/USER-CGDNA: filenames -> commands * /src/USER-CGDNA/README -* :doc:`pair\_style oxdna/\* ` -* :doc:`pair\_style oxdna2/\* ` -* :doc:`bond\_style oxdna/\* ` -* :doc:`bond\_style oxdna2/\* ` +* :doc:`pair_style oxdna/\* ` +* :doc:`pair_style oxdna2/\* ` +* :doc:`bond_style oxdna/\* ` +* :doc:`bond_style oxdna2/\* ` * :doc:`fix nve/dotc/langevin ` @@ -1261,8 +1261,8 @@ acids. * src/USER-CGSDK: filenames -> commands * src/USER-CGSDK/README -* :doc:`pair\_style lj/sdk/\* ` -* :doc:`angle\_style sdk ` +* :doc:`pair_style lj/sdk/\* ` +* :doc:`angle_style sdk ` * examples/USER/cgsdk * http://lammps.sandia.gov/pictures.html#cg @@ -1397,12 +1397,12 @@ Brennan (ARL). * :doc:`fix eos/table/rx ` * :doc:`fix shardlow ` * :doc:`fix rx ` -* :doc:`pair\_style table/rx ` -* :doc:`pair\_style dpd/fdt ` -* :doc:`pair\_style dpd/fdt/energy ` -* :doc:`pair\_style exp6/rx ` -* :doc:`pair\_style multi/lucy ` -* :doc:`pair\_style multi/lucy/rx ` +* :doc:`pair_style table/rx ` +* :doc:`pair_style dpd/fdt ` +* :doc:`pair_style dpd/fdt/energy ` +* :doc:`pair_style exp6/rx ` +* :doc:`pair_style multi/lucy ` +* :doc:`pair_style multi/lucy/rx ` * examples/USER/dpd @@ -1434,8 +1434,8 @@ Devemy (CNRS), and Agilio Padua (U Blaise Pascal). * :doc:`fix drude ` * :doc:`fix drude/transform/\* ` * :doc:`compute temp/drude ` -* :doc:`pair\_style thole ` -* :doc:`pair\_style lj/cut/thole/long ` +* :doc:`pair_style thole ` +* :doc:`pair_style lj/cut/thole/long ` * examples/USER/drude * tools/drude @@ -1464,14 +1464,14 @@ tools/eff; see its README file. * src/USER-EFF: filenames -> commands * src/USER-EFF/README -* :doc:`atom\_style electron ` +* :doc:`atom_style electron ` * :doc:`fix nve/eff ` * :doc:`fix nvt/eff ` * :doc:`fix npt/eff ` * :doc:`fix langevin/eff ` * :doc:`compute temp/eff ` -* :doc:`pair\_style eff/cut ` -* :doc:`pair\_style eff/inline ` +* :doc:`pair_style eff/cut ` +* :doc:`pair_style eff/inline ` * examples/USER/eff * tools/eff/README * tools/eff @@ -1501,7 +1501,7 @@ for using this package in tools/fep; see its README file. * src/USER-FEP/README * :doc:`fix adapt/fep ` * :doc:`compute fep ` -* :doc:`pair\_style \*/soft ` +* :doc:`pair_style \*/soft ` * examples/USER/fep * tools/fep/README * tools/fep @@ -1644,7 +1644,7 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. * src/USER-MGPT: filenames -> commands * src/USER-MGPT/README -* :doc:`pair\_style mgpt ` +* :doc:`pair_style mgpt ` * examples/USER/mgpt @@ -1729,7 +1729,7 @@ Sandia. * src/USER-MEAMC: filenames -> commands * src/USER-MEAMC/README -* :doc:`pair\_style meam/c ` +* :doc:`pair_style meam/c ` * examples/meamc @@ -1757,10 +1757,10 @@ algorithm. * src/USER-MESO: filenames -> commands * src/USER-MESO/README -* :doc:`atom\_style edpd ` -* :doc:`pair\_style edpd ` -* :doc:`pair\_style mdpd ` -* :doc:`pair\_style tdpd ` +* :doc:`atom_style edpd ` +* :doc:`pair_style edpd ` +* :doc:`pair_style mdpd ` +* :doc:`pair_style tdpd ` * :doc:`fix mvv/dpd ` * examples/USER/meso * http://lammps.sandia.gov/movies.html#mesodpd @@ -1796,10 +1796,10 @@ Rochus Schmid (Ruhr-University Bochum). * src/USER-MOFFF: filenames -> commands * src/USER-MOFFF/README -* :doc:`pair\_style buck6d/coul/gauss ` -* :doc:`angle\_style class2 ` -* :doc:`angle\_style cosine/buck6d ` -* :doc:`improper\_style inversion/harmonic ` +* :doc:`pair_style buck6d/coul/gauss ` +* :doc:`angle_style class2 ` +* :doc:`angle_style cosine/buck6d ` +* :doc:`improper_style inversion/harmonic ` * examples/USER/mofff @@ -1965,8 +1965,8 @@ USER-PHONON package A :doc:`fix phonon ` command that calculates dynamical matrices, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations. -And a :doc:`dynamical\_matrix ` as well as a -:doc:`third\_order ` command to compute the dynamical matrix +And a :doc:`dynamical_matrix ` as well as a +:doc:`third_order ` command to compute the dynamical matrix and third order tensor from finite differences. **Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" @@ -1977,8 +1977,8 @@ and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order" * src/USER-PHONON: filenames -> commands * src/USER-PHONON/README * :doc:`fix phonon ` -* :doc:`dynamical\_matrix ` -* :doc:`third\_order ` +* :doc:`dynamical_matrix ` +* :doc:`third_order ` * examples/USER/phonon @@ -2088,7 +2088,7 @@ USER-QUIP package **Contents:** -A :doc:`pair\_style quip ` command which wraps the `QUIP libAtoms library `_, which includes a variety of interatomic +A :doc:`pair_style quip ` command which wraps the `QUIP libAtoms library `_, which includes a variety of interatomic potentials, including Gaussian Approximation Potential (GAP) models developed by the Cambridge University group. @@ -2109,7 +2109,7 @@ This package has :ref:`specific installation instructions ` on the :d * src/USER-QUIP: filenames -> commands * src/USER-QUIP/README -* :doc:`pair\_style quip ` +* :doc:`pair_style quip ` * examples/USER/quip @@ -2134,7 +2134,7 @@ for monitoring molecules as bonds are created and destroyed. * src/USER-REAXC: filenames -> commands * src/USER-REAXC/README -* :doc:`pair\_style reax/c ` +* :doc:`pair_style reax/c ` * :doc:`fix reax/c/bonds ` * :doc:`fix reax/c/species ` * examples/reax @@ -2172,8 +2172,8 @@ This package has :ref:`specific installation instructions ` on th * src/USER-SCAFACOS: filenames -> commands * src/USER-SCAFACOS/README -* :doc:`kspace\_style scafacos ` -* :doc:`kspace\_modify ` +* :doc:`kspace_style scafacos ` +* :doc:`kspace_modify ` * examples/USER/scafacos @@ -2201,7 +2201,7 @@ Sciences, Iran). * src/USER-SDPD: filenames -> commands * src/USER-SDPD/README -* :doc:`pair\_style sdpd/taitwater/isothermal ` +* :doc:`pair_style sdpd/taitwater/isothermal ` * :doc:`fix meso/move ` * :doc:`fix rigid/meso ` * examples/USER/sdpd @@ -2268,7 +2268,7 @@ Tetot (LAAS-CNRS, France). * src/USER-SMTBQ: filenames -> commands * src/USER-SMTBQ/README -* :doc:`pair\_style smtbq ` +* :doc:`pair_style smtbq ` * examples/USER/smtbq @@ -2438,13 +2438,13 @@ which discuss the `QuickFF `_ methodology. **Supporting info:** * src/USER-YAFF/README -* :doc:`angle\_style cross ` -* :doc:`angle\_style mm3 ` -* :doc:`bond\_style mm3 ` -* :doc:`improper\_style distharm ` -* :doc:`improper\_style sqdistharm ` -* :doc:`pair\_style mm3/switch3/coulgauss/long ` -* :doc:`pair\_style lj/switch3/coulgauss/long ` +* :doc:`angle_style cross ` +* :doc:`angle_style mm3 ` +* :doc:`bond_style mm3 ` +* :doc:`improper_style distharm ` +* :doc:`improper_style sqdistharm ` +* :doc:`pair_style mm3/switch3/coulgauss/long ` +* :doc:`pair_style lj/switch3/coulgauss/long ` * examples/USER/yaff diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst index c234f8198d..f7a768d066 100644 --- a/doc/src/Packages_standard.rst +++ b/doc/src/Packages_standard.rst @@ -29,29 +29,29 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`BODY ` | body-style particles | :doc:`Howto body ` | body | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`CLASS2 ` | class 2 force fields | :doc:`pair\_style lj/class2 ` | n/a | no | +| :ref:`CLASS2 ` | class 2 force fields | :doc:`pair_style lj/class2 ` | n/a | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`COLLOID ` | colloidal particles | :doc:`atom\_style colloid ` | colloid | no | +| :ref:`COLLOID ` | colloidal particles | :doc:`atom_style colloid ` | colloid | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`COMPRESS ` | I/O compression | :doc:`dump \*/gz ` | n/a | sys | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`CORESHELL ` | adiabatic core/shell model | :doc:`Howto coreshell ` | coreshell | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`DIPOLE ` | point dipole particles | :doc:`pair\_style dipole/cut ` | dipole | no | +| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style dipole/cut ` | dipole | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`GRANULAR ` | granular systems | :doc:`Howto granular ` | pour | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`KIM ` | OpenKIM wrapper | :doc:`pair\_style kim ` | kim | ext | +| :ref:`KIM ` | OpenKIM wrapper | :doc:`pair_style kim ` | kim | ext | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`KOKKOS ` | Kokkos-enabled styles | :doc:`Speed kokkos ` | `Benchmarks `_ | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`KSPACE ` | long-range Coulombic solvers | :doc:`kspace\_style ` | peptide | no | +| :ref:`KSPACE ` | long-range Coulombic solvers | :doc:`kspace_style ` | peptide | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`LATTE ` | quantum DFTB forces via LATTE | :doc:`fix latte ` | latte | ext | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`MANYBODY ` | many-body potentials | :doc:`pair\_style tersoff ` | shear | no | +| :ref:`MANYBODY ` | many-body potentials | :doc:`pair_style tersoff ` | shear | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`MC ` | Monte Carlo options | :doc:`fix gcmc ` | n/a | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ @@ -67,7 +67,7 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`OPT ` | optimized pair styles | :doc:`Speed opt ` | `Benchmarks `_ | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`PERI ` | Peridynamics models | :doc:`pair\_style peri ` | peri | no | +| :ref:`PERI ` | Peridynamics models | :doc:`pair_style peri ` | peri | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`POEMS ` | coupled rigid body motion | :doc:`fix poems ` | rigid | int | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ @@ -81,7 +81,7 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`SHOCK ` | shock loading methods | :doc:`fix msst ` | n/a | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`SNAP ` | quantum-fitted potential | :doc:`pair\_style snap ` | snap | no | +| :ref:`SNAP ` | quantum-fitted potential | :doc:`pair_style snap ` | snap | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`SPIN ` | magnetic atomic spin dynamics | :doc:`Howto spins ` | SPIN | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 702d014c57..2059e00c85 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -35,13 +35,13 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-ATC ` | Atom-to-Continuum coupling | :doc:`fix atc ` | USER/atc | int | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair\_style awpmd/cut ` | USER/awpmd | int | +| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair_style awpmd/cut ` | USER/awpmd | int | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-BOCS ` | BOCS bottom up coarse graining | :doc:`fix bocs ` | USER/bocs | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair\_style lj/sdk ` | USER/cgsdk | no | +| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ @@ -51,7 +51,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-EFF ` | electron force field | :doc:`pair\_style eff/cut ` | USER/eff | no | +| :ref:`USER-EFF ` | electron force field | :doc:`pair_style eff/cut ` | USER/eff | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-FEP ` | free energy perturbation | :doc:`compute fep ` | USER/fep | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ @@ -63,15 +63,15 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair\_style meam/c ` | meamc | no | +| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MESO ` | mesoscale DPD models | :doc:`pair\_style edpd ` | USER/meso | no | +| :ref:`USER-MESO ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/meso | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair\_style mgpt ` | USER/mgpt | no | +| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MISC ` | single-file contributions | USER-MISC/README | USER/misc | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair\_style buck6d/coul/gauss ` | USER/mofff | no | +| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair_style buck6d/coul/gauss ` | USER/mofff | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MOLFILE ` | `VMD `_ molfile plug-ins | :doc:`dump molfile ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ @@ -89,17 +89,17 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair\_style quip ` | USER/quip | ext | +| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair\_style reaxc ` | reax | no | +| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace\_style scafacos ` | USER/scafacos | ext | +| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair\_style sdpd/taitwater/isothermal ` | USER/sdpd | no | +| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal ` | USER/sdpd | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-SMD ` | smoothed Mach dynamics | `SMD User Guide `_ | USER/smd | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair\_style smtbq ` | USER/smtbq | no | +| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair_style smtbq ` | USER/smtbq | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-SPH ` | smoothed particle hydrodynamics | `SPH User Guide `_ | USER/sph | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ @@ -109,7 +109,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-VTK ` | dump output via VTK | :doc:`compute vtk ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle\_style cross ` | USER/yaff | no | +| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle_style cross ` | USER/yaff | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ .. _MOFplus: https://www.mofplus.org/content/show/MOF-FF diff --git a/doc/src/Python_call.rst b/doc/src/Python_call.rst index 6b53b263c3..2ce0b88cb5 100644 --- a/doc/src/Python_call.rst +++ b/doc/src/Python_call.rst @@ -7,7 +7,7 @@ code directly from an input script: * :doc:`python ` * :doc:`variable python ` * :doc:`fix python/invoke ` -* :doc:`pair\_style python ` +* :doc:`pair_style python ` The :doc:`python ` command which can be used to define and execute a Python function that you write the code for. The Python @@ -51,7 +51,7 @@ and callbacks to LAMMPS. The :doc:`fix python/invoke ` command can execute Python code at selected timesteps during a simulation run. -The :doc:`pair\_style python ` command allows you to define +The :doc:`pair_style python ` command allows you to define pairwise potentials as python code which encodes a single pairwise interaction. This is useful for rapid development and debugging of a new potential. diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 1e0091f057..e45a4d3053 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -354,14 +354,14 @@ all P processors from 0 to P-1. The mapping of these ranks to physical processors is done by MPI before LAMMPS begins. It may be useful in some cases to alter the rank order. E.g. to insure that cores within each node are ranked in a desired order. Or when using -the :doc:`run\_style verlet/split ` command with 2 partitions +the :doc:`run_style verlet/split ` command with 2 partitions to insure that a specific Kspace processor (in the 2nd partition) is matched up with a specific set of processors in the 1st partition. See the :doc:`Speed tips ` doc page for more details. If the keyword *nth* is used with a setting *N*\ , then it means every Nth processor will be moved to the end of the ranking. This is useful -when using the :doc:`run\_style verlet/split ` command with 2 +when using the :doc:`run_style verlet/split ` command with 2 partitions via the -partition command-line switch. The first set of processors will be in the first partition, the 2nd set in the 2nd partition. The -reorder command-line switch can alter this so that @@ -446,7 +446,7 @@ run: The specified restartfile and/or datafile name may contain the wild-card character "\*". The restartfile name may also contain the wild-card character "%". The meaning of these characters is explained on the -:doc:`read\_restart ` and :doc:`write\_data ` doc +:doc:`read_restart ` and :doc:`write_data ` doc pages. The use of "%" means that a parallel restart file can be read. Note that a filename such as file.\* may need to be enclosed in quotes or the "\*" character prefixed with a backslash ("\") to avoid shell @@ -454,7 +454,7 @@ expansion of the "\*" character. Following restartfile argument, the optional word "remap" may be used. This has the same effect like adding it to a -:doc:`read\_restart ` command, and operates as explained on +:doc:`read_restart ` command, and operates as explained on its doc page. This is useful if reading the restart file triggers an error that atoms have been lost. In that case, use of the remap flag should allow the data file to still be produced. @@ -466,7 +466,7 @@ The syntax following restartfile (or remap), namely datafile keyword value ... -is identical to the arguments of the :doc:`write\_data ` +is identical to the arguments of the :doc:`write_data ` command. See its doc page for details. This includes its optional keyword/value settings. @@ -490,7 +490,7 @@ run: Note that the specified restartfile and dumpfile names may contain wild-card characters ("\*","%") as explained on the -:doc:`read\_restart ` and :doc:`write\_dump ` doc +:doc:`read_restart ` and :doc:`write_dump ` doc pages. The use of "%" means that a parallel restart file and/or parallel dump file can be read and/or written. Note that a filename such as file.\* may need to be enclosed in quotes or the "\*" character @@ -499,7 +499,7 @@ character. Note that following the restartfile argument, the optional word "remap" can be used. This has the effect as adding it to the -:doc:`read\_restart ` command, as explained on its doc page. +:doc:`read_restart ` command, as explained on its doc page. This is useful if reading the restart file triggers an error that atoms have been lost. In that case, use of the remap flag should allow the dump file to still be produced. @@ -511,12 +511,12 @@ The syntax following restartfile (or remap), namely group-ID dumpstyle dumpfile arg1 arg2 ... -is identical to the arguments of the :doc:`write\_dump ` +is identical to the arguments of the :doc:`write_dump ` command. See its doc page for details. This includes what per-atom fields are written to the dump file and optional dump\_modify settings, including ones that affect how parallel dump files are written, e.g. the *nfile* and *fileper* keywords. See the -:doc:`dump\_modify ` doc page for details. +:doc:`dump_modify ` doc page for details. ---------- @@ -566,7 +566,7 @@ Along with the "-package" command-line switch, this is a convenient mechanism for invoking accelerator packages and their options without having to edit an input script. -As an example, all of the packages provide a :doc:`pair\_style lj/cut ` variant, with style names lj/cut/gpu, +As an example, all of the packages provide a :doc:`pair_style lj/cut ` variant, with style names lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style can be specified explicitly in your input script, e.g. pair\_style lj/cut/gpu. If the -suffix switch is used the specified suffix diff --git a/doc/src/Run_output.rst b/doc/src/Run_output.rst index 41a6dcd4f3..b8cdf6cc29 100644 --- a/doc/src/Run_output.rst +++ b/doc/src/Run_output.rst @@ -125,10 +125,10 @@ number of histogram counts is equal to the number of processors. The last section gives aggregate statistics (across all processors) for pair-wise neighbors and special neighbors that LAMMPS keeps track -of (see the :doc:`special\_bonds ` command). The number +of (see the :doc:`special_bonds ` command). The number of times neighbor lists were rebuilt is tallied, as is the number of potentially *dangerous* rebuilds. If atom movement triggered neighbor -list rebuilding (see the :doc:`neigh\_modify ` command), +list rebuilding (see the :doc:`neigh_modify ` command), then dangerous reneighborings are those that were triggered on the first timestep atom movement was checked for. If this count is non-zero you may wish to reduce the delay factor to insure no force @@ -171,7 +171,7 @@ perform a 1d line minimization in the search direction. See the ---------- -If a :doc:`kspace\_style ` long-range Coulombics solver +If a :doc:`kspace_style ` long-range Coulombics solver that performs FFTs was used during the run (PPPM, Ewald), then additional information is printed, e.g. diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index dca32f1bb1..f9ade13401 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -4,7 +4,7 @@ GPU package The GPU package was developed by Mike Brown while at SNL and ORNL and his collaborators, particularly Trung Nguyen (now at Northwestern). It provides GPU versions of many pair styles and for parts of the -:doc:`kspace\_style pppm ` for long-range Coulombics. +:doc:`kspace_style pppm ` for long-range Coulombics. It has the following general features: * It is designed to exploit common GPU hardware configurations where one diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index f70852701b..95a7ef9e6b 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -385,7 +385,7 @@ follow in the input script. The USER-INTEL package will perform better with modifications to the input script when :doc:`PPPM ` is used: - :doc:`kspace\_modify diff ad ` should be added to the + :doc:`kspace_modify diff ad ` should be added to the input script. Long-Range Thread (LRT) mode is an option to the :doc:`package intel ` command that can improve performance when using @@ -537,7 +537,7 @@ supported with offload, however, the same effect can often be accomplished by setting cutoffs for excluded atom types to 0. None of the pair styles in the USER-INTEL package currently support the "inner", "middle", "outer" options for rRESPA integration via the -:doc:`run\_style respa ` command; only the "pair" option is +:doc:`run_style respa ` command; only the "pair" option is supported. **References:** diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index fab7f671d7..1b9a1caaf5 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -129,14 +129,14 @@ circumstances: where MPI parallelism is maxed out. For example, this can happen when using the :doc:`PPPM solver ` for long-range electrostatics on large numbers of nodes. The scaling of the KSpace - calculation (see the :doc:`kspace\_style ` command) becomes + calculation (see the :doc:`kspace_style ` command) becomes the performance-limiting factor. Using multi-threading allows less MPI tasks to be invoked and can speed-up the long-range solver, while increasing overall performance by parallelizing the pairwise and bonded calculations via OpenMP. Likewise additional speedup can be sometimes be achieved by increasing the length of the Coulombic cutoff and thus reducing the work done by the long-range solver. Using the - :doc:`run\_style verlet/split ` command, which is compatible + :doc:`run_style verlet/split ` command, which is compatible with the USER-OMP package, is an alternative way to reduce the number of MPI tasks assigned to the KSpace calculation. diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index 3ec76d4de2..6c62d40706 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -1,7 +1,7 @@ Accelerator packages ==================== -Accelerated versions of various :doc:`pair\_style `, +Accelerated versions of various :doc:`pair_style `, :doc:`fixes `, :doc:`computes `, and other commands have been added to LAMMPS, which will typically run faster than the standard non-accelerated versions. Some require appropriate hardware @@ -62,13 +62,13 @@ the same, and the numerical results it produces should also be the same, except for precision and round-off effects. For example, all of these styles are accelerated variants of the -Lennard-Jones :doc:`pair\_style lj/cut `: +Lennard-Jones :doc:`pair_style lj/cut `: -* :doc:`pair\_style lj/cut/gpu ` -* :doc:`pair\_style lj/cut/intel ` -* :doc:`pair\_style lj/cut/kk ` -* :doc:`pair\_style lj/cut/omp ` -* :doc:`pair\_style lj/cut/opt ` +* :doc:`pair_style lj/cut/gpu ` +* :doc:`pair_style lj/cut/intel ` +* :doc:`pair_style lj/cut/kk ` +* :doc:`pair_style lj/cut/omp ` +* :doc:`pair_style lj/cut/opt ` To see what accelerate styles are currently available for a particular style, find the style name in the `Commands\_all `_ diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index baee955201..21146cd908 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -60,7 +60,7 @@ Post-processing tools +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`amber2lmp ` | :ref:`binary2txt ` | :ref:`ch2lmp ` | :ref:`colvars ` | :ref:`eff ` | :ref:`fep ` | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ -| :ref:`lmp2arc ` | :ref:`lmp2cfg ` | :ref:`matlab ` | :ref:`phonon ` | :ref:`pymol\_asphere ` | :ref:`python ` | +| :ref:`lmp2arc ` | :ref:`lmp2cfg ` | :ref:`matlab ` | :ref:`phonon ` | :ref:`pymol_asphere ` | :ref:`python ` | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`reax ` | :ref:`replica ` | :ref:`smd ` | :ref:`spin ` | :ref:`xmgrace ` | | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ @@ -268,7 +268,7 @@ eam database tool The tools/eam\_database directory contains a Fortran program that will generate EAM alloy setfl potential files for any combination of 16 elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, -Zr. The files can then be used with the :doc:`pair\_style eam/alloy ` command. +Zr. The files can then be used with the :doc:`pair_style eam/alloy ` command. The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, and is based on his paper: @@ -288,7 +288,7 @@ eam generate tool The tools/eam\_generate directory contains several one-file C programs that convert an analytic formula into a tabulated :doc:`embedded atom method (EAM) ` setfl potential file. The potentials they produce are in the potentials directory, and can be used with the -:doc:`pair\_style eam/alloy ` command. +:doc:`pair_style eam/alloy ` command. The source files and potentials were provided by Gerolf Ziegenhain (gerolf at ziegenhain.com). diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index 92ab8b5ea3..34843fe855 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -48,9 +48,9 @@ See :ref:`(MacKerell) ` for a description of the CHARMM force field. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/radian\^2) * :math:`\theta_0` (degrees) @@ -97,7 +97,7 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index 9d1ff8e8e7..ae5330d964 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -51,9 +51,9 @@ the equilibrium bond lengths. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for -each angle type via the :doc:`angle\_coeff ` command as in +each angle type via the :doc:`angle_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. These are the 4 coefficients for the :math:`E_a` formula: @@ -66,7 +66,7 @@ These are the 4 coefficients for the :math:`E_a` formula: :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of the various :math:`K` are in per-radian. -For the :math:`E_{bb}` formula, each line in a :doc:`angle\_coeff ` +For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff ` command in the input script lists 4 coefficients, the first of which is "bb" to indicate they are BondBond coefficients. In a data file, these coefficients should be listed under a "BondBond Coeffs" heading @@ -78,7 +78,7 @@ the angle type. * :math:`r_1` (distance) * :math:`r_2` (distance) -For the :math:`E_{ba}` formula, each line in a :doc:`angle\_coeff ` +For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff ` command in the input script lists 5 coefficients, the first of which is "ba" to indicate they are BondAngle coefficients. In a data file, these coefficients should be listed under a "BondAngle Coeffs" heading @@ -154,7 +154,7 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cosine.rst b/doc/src/angle_cosine.rst index 68bfdbb82b..583f43bc40 100644 --- a/doc/src/angle_cosine.rst +++ b/doc/src/angle_cosine.rst @@ -39,9 +39,9 @@ The *cosine* angle style uses the potential where :math:`K` is defined for each angle type. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) @@ -82,6 +82,6 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cosine_buck6d.rst b/doc/src/angle_cosine_buck6d.rst index 2d00863b02..bb024c3474 100644 --- a/doc/src/angle_cosine_buck6d.rst +++ b/doc/src/angle_cosine_buck6d.rst @@ -33,9 +33,9 @@ where :math:`K` is the energy constant, :math:`n` is the periodic multiplicity a :math:`\theta_0` is the equilibrium angle. The coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands in the following order: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands in the following order: * :math:`K` (energy) * :math:`n` @@ -49,7 +49,7 @@ the short range (vdW) interaction belonging to the :doc:`pair\_buck6d ` between the end atoms of the angle. For this reason this angle style only works in combination with the :doc:`pair\_buck6d ` styles and needs -the :doc:`special\_bonds ` 1-3 interactions to be weighted +the :doc:`special_bonds ` 1-3 interactions to be weighted 0.0 to prevent double counting. @@ -62,7 +62,7 @@ Restrictions *cosine/buck6d* can only be used in combination with the :doc:`pair\_buck6d ` style and with a -:doc:`special\_bonds ` 0.0 weighting of 1-3 interactions. +:doc:`special_bonds ` 0.0 weighting of 1-3 interactions. This angle style can only be used if LAMMPS was built with the USER-MOFFF package. See the :doc:`Build package ` doc @@ -71,6 +71,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index 9af93cb06a..f83b03b36d 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -37,9 +37,9 @@ where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`\theta_0` (degrees) @@ -84,6 +84,6 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff `, :doc:`angle\_style cosine/squared ` +:doc:`angle_coeff `, :doc:`angle_style cosine/squared ` **Default:** none diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index caaf15007a..c8ede7e03d 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -42,9 +42,9 @@ where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle See :ref:`(Mayo) ` for a description of the DREIDING force field The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`C` (energy) * :math:`B` = 1 or -1 @@ -92,7 +92,7 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst index bd7b6416c7..00b494bc08 100644 --- a/doc/src/angle_cosine_shift.rst +++ b/doc/src/angle_cosine_shift.rst @@ -39,9 +39,9 @@ between :math:`-U_{\text{min}}` and zero. In the neighborhood of the minimum the spring constant is :math:`\frac{U_{\text{min}}}{2}`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`U_{\text{min}}` (energy) * :math:`\theta` (angle) @@ -82,7 +82,7 @@ USER-MISC package. Related commands """""""""""""""" -:doc:`angle\_coeff `, +:doc:`angle_coeff `, :doc:`angle\_cosine\_shift\_exp ` **Default:** none diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index 331ccb9da7..ae810f9f33 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -48,9 +48,9 @@ order in :math:`a` for :math:`a < 0.001`. In this limit the potential reduces to cosineshifted potential. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`U_min` (energy) * :math:`\theta` (angle) @@ -93,7 +93,7 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff `, +:doc:`angle_coeff `, :doc:`angle\_cosine\_shift `, :doc:`dihedral\_cosine\_shift\_exp ` diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index b1a516880d..ee9258dda8 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -37,9 +37,9 @@ where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`\theta_0` (degrees) @@ -84,6 +84,6 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 7dcff0264f..eb5865c060 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -37,9 +37,9 @@ the bond stretch-bond stretch term and :math:`K_{BS0}` and :math:`K_{BS1}` are t of the bond stretch-angle stretch terms. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K_{SS}` (energy/distance\^2) * :math:`K_{BS0}` (energy/distance/rad) @@ -62,6 +62,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index 351572cc22..cfa4313b30 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -79,9 +79,9 @@ where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i` and :math:`j`, respectively. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`\gamma_0` (degrees) @@ -136,7 +136,7 @@ This angle style should not be used with SHAKE. Related commands """""""""""""""" -:doc:`angle\_coeff `, :doc:`angle\_hybrid ` +:doc:`angle_coeff `, :doc:`angle_hybrid ` **Default:** none diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index c814b7224e..d290e2d1f7 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -33,9 +33,9 @@ The *fourier* angle style uses the potential The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`C_0` (real) @@ -79,6 +79,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index 5ad8b386d0..d19dd19753 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -33,9 +33,9 @@ The *fourier/simple* angle style uses the potential The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`c` (real) @@ -78,6 +78,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst index 1066621729..6b9ed776f5 100644 --- a/doc/src/angle_harmonic.rst +++ b/doc/src/angle_harmonic.rst @@ -43,9 +43,9 @@ where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/radian\^2) * :math:`\theta_0` (degrees) @@ -90,6 +90,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_mm3.rst b/doc/src/angle_mm3.rst index 7cf7f9e720..6d6c6d874c 100644 --- a/doc/src/angle_mm3.rst +++ b/doc/src/angle_mm3.rst @@ -36,9 +36,9 @@ prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ... The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/radian\^2) * :math:`\theta_0` (degrees) @@ -57,6 +57,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index 104c0be802..bbf1dd618e 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -37,9 +37,9 @@ where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`\theta_0` (degrees) * :math:`K_2` (energy/radian\^2) @@ -86,6 +86,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 0af22a5372..9f9b1ee532 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -39,12 +39,12 @@ where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a pre with the *repulsive* part of the non-bonded *lj/sdk* pair style between the atoms 1 and 3. This angle potential is intended for coarse grained MD simulations with the CMM parameterization using the -:doc:`pair\_style lj/sdk `. Relative to the pair\_style +:doc:`pair_style lj/sdk `. Relative to the pair\_style *lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden jumps. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above: +:doc:`angle_coeff ` command as in the example above: * :math:`K` (energy/radian\^2) * :math:`\theta_0` (degrees) @@ -91,7 +91,7 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff `, :doc:`angle\_style harmonic `, :doc:`pair\_style lj/sdk `, -:doc:`pair\_style lj/sdk/coul/long ` +:doc:`angle_coeff `, :doc:`angle_style harmonic `, :doc:`pair_style lj/sdk `, +:doc:`pair_style lj/sdk/coul/long ` **Default:** none diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index ac2720d4f2..147727dd66 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -39,14 +39,14 @@ Description """"""""""" Modify certain attributes of atoms defined and stored within LAMMPS, -in addition to what is specified by the :doc:`atom\_style ` +in addition to what is specified by the :doc:`atom_style ` command. The *id* and *map* keywords must be specified before a simulation box is defined; other keywords can be specified any time. The *id* keyword determines whether non-zero atom IDs can be assigned to each atom. If the value is *yes*\ , which is the default, IDs are assigned, whether you use the :doc:`create atoms ` or -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands to initialize atoms. If the value is *no* the IDs for all atoms are assumed to be 0. @@ -77,7 +77,7 @@ efficiently by creating a "map", which is either an *array* or *hash* table, as described below. When the *map* keyword is not specified in your input script, LAMMPS -only creates a map for :doc:`atom\_styles ` for molecular +only creates a map for :doc:`atom_styles ` for molecular systems which have permanent bonds (angles, etc). No map is created for atomic systems, since it is normally not needed. However some LAMMPS commands require a map, even for atomic systems, and will @@ -103,7 +103,7 @@ of owned atoms. This in only useful when the specified group is a small fraction of all the atoms, and there are other operations LAMMPS is performing that will be sped-up significantly by being able to loop over the smaller set of atoms. Otherwise the reordering required by -this option will be a net slow-down. The :doc:`neigh\_modify include ` and :doc:`comm\_modify group ` +this option will be a net slow-down. The :doc:`neigh_modify include ` and :doc:`comm_modify group ` commands are two examples of commands that require this setting to work efficiently. Several :doc:`fixes `, most notably time integration fixes like :doc:`fix nve `, also take advantage of diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index d2ebc220d6..d0707559d7 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -50,8 +50,8 @@ Description Define what style of atoms to use in a simulation. This determines what attributes are associated with the atoms. This command must be -used before a simulation is setup via a :doc:`read\_data `, -:doc:`read\_restart `, or :doc:`create\_box ` +used before a simulation is setup via a :doc:`read_data `, +:doc:`read_restart `, or :doc:`create_box ` command. .. note:: @@ -68,12 +68,12 @@ style more general than needed, though it may be slightly inefficient. The choice of style affects what quantities are stored by each atom, what quantities are communicated between processors to enable forces to be computed, and what quantities are listed in the data file read -by the :doc:`read\_data ` command. +by the :doc:`read_data ` command. These are the additional attributes of each style and the typical kinds of physical systems they are used to model. All styles store coordinates, velocities, atom IDs and types. See the -:doc:`read\_data `, :doc:`create\_atoms `, and +:doc:`read_data `, :doc:`create_atoms `, and :doc:`set ` commands for info on how to set these various quantities. @@ -173,7 +173,7 @@ per-particle mass and volume. The *dpd* style is for dissipative particle dynamics (DPD) particles. Note that it is part of the USER-DPD package, and is not for use with -the :doc:`pair\_style dpd or dpd/stat ` commands, which can +the :doc:`pair_style dpd or dpd/stat ` commands, which can simply use atom\_style atomic. Atom\_style dpd extends DPD particle properties with internal temperature (dpdTheta), internal conductive energy (uCond), internal mechanical energy (uMech), and internal @@ -240,7 +240,7 @@ can be advantageous for large-scale coarse-grained systems. another CO2, then you probably do not want each molecule file to define 2 atom types and a single bond type, because they will conflict with each other when a mixture system of H2O and CO2 molecules is - defined, e.g. by the :doc:`read\_data ` command. Rather the + defined, e.g. by the :doc:`read_data ` command. Rather the H2O molecule should define atom types 1 and 2, and bond type 1. And the CO2 molecule should define atom types 3 and 4 (or atom types 3 and 2 if a single oxygen type is desired), and bond type 2. @@ -317,7 +317,7 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. Many of the styles listed above are only enabled if LAMMPS was built with a specific package, as listed below. See the :doc:`Build package ` doc page for more info. @@ -354,7 +354,7 @@ The *wavepacket* style is part of the USER-AWPMD package for the Related commands """""""""""""""" -:doc:`read\_data `, :doc:`pair\_style ` +:doc:`read_data `, :doc:`pair_style ` Default """"""" diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 67146b2ba9..9da86342ec 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -132,8 +132,8 @@ forced even if the current balance is perfect (1.0) be specifying a exceed the *thresh* parameter if a "grid" style is specified when the current partitioning is "tiled". The meaning of "grid" vs "tiled" is explained below. This is to allow forcing of the partitioning to - "grid" so that the :doc:`comm\_style brick ` command can then - be used to replace a current :doc:`comm\_style tiled ` + "grid" so that the :doc:`comm_style brick ` command can then + be used to replace a current :doc:`comm_style tiled ` setting. When the balance command completes, it prints statistics about the @@ -151,7 +151,7 @@ fractions of the box length) are also printed. create a logical 3d grid cannot achieve perfect balance for many irregular distributions of particles. Likewise, if a portion of the system is a perfect lattice, e.g. the initial system is generated by - the :doc:`create\_atoms ` command, then "grid" methods may + the :doc:`create_atoms ` command, then "grid" methods may be unable to achieve exact balance. This is because entire lattice planes will be owned or not owned by a single processor. @@ -165,7 +165,7 @@ fractions of the box length) are also printed. proportional to particle count, and changing the relative size and shape of processor sub-domains may lead to additional computational and communication overheads, e.g. in the PPPM solver used via the - :doc:`kspace\_style ` command. Thus you should benchmark + :doc:`kspace_style ` command. Thus you should benchmark the run times of a simulation before and after balancing. @@ -201,9 +201,9 @@ fashion so as to have equal numbers of particles (or weight) in each sub-box, as in the rightmost diagram above. The "grid" methods can be used with either of the -:doc:`comm\_style ` command options, *brick* or *tiled*\ . The -"tiling" methods can only be used with :doc:`comm\_style tiled `. Note that it can be useful to use a "grid" -method with :doc:`comm\_style tiled ` to return the domain +:doc:`comm_style ` command options, *brick* or *tiled*\ . The +"tiling" methods can only be used with :doc:`comm_style tiled `. Note that it can be useful to use a "grid" +method with :doc:`comm_style tiled ` to return the domain partitioning to a logical 3d grid of processors so that "comm\_style brick" can afterwords be specified for subsequent :doc:`run ` commands. @@ -384,7 +384,7 @@ multiple groups, its weight is the product of the weight factors. This weight style is useful in combination with pair style :doc:`hybrid `, e.g. when combining a more costly many-body potential with a fast pair-wise potential. It is also useful when -using :doc:`run\_style respa ` where some portions of the +using :doc:`run_style respa ` where some portions of the system have many bonded interactions and others none. It assumes that the computational cost for each group remains constant over time. This is a purely empirical weighting, so a series test runs to tune @@ -555,13 +555,13 @@ For 2d simulations, the *z* style cannot be used. Nor can a "z" appear in *dimstr* for the *shift* style. Balancing through recursive bisectioning (\ *rcb* style) requires -:doc:`comm\_style tiled ` +:doc:`comm_style tiled ` Related commands """""""""""""""" :doc:`group `, :doc:`processors `, -:doc:`fix balance `, :doc:`comm\_style ` +:doc:`fix balance `, :doc:`comm_style ` .. _pizza: http://pizza.sandia.gov diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index e3098ef6dc..7b07c8a69a 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -41,9 +41,9 @@ where :math:`r_0` is the equilibrium bond distance. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`r_0` (distance) * :math:`K_2` (energy/distance\^2) @@ -87,7 +87,7 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_coeff.rst b/doc/src/bond_coeff.rst index 281dfc7095..157403a301 100644 --- a/doc/src/bond_coeff.rst +++ b/doc/src/bond_coeff.rst @@ -31,7 +31,7 @@ Description Specify the bond force field coefficients for one or more bond types. The number and meaning of the coefficients depends on the bond style. Bond coefficients can also be set in the data file read by the -:doc:`read\_data ` command or in a restart file. +:doc:`read_data ` command or in a restart file. N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be @@ -69,7 +69,7 @@ corresponds to the 1st example above would be listed as The list of all bond styles defined in LAMMPS is given on the -:doc:`bond\_style ` doc page. They are also listed in more +:doc:`bond_style ` doc page. They are also listed in more compact form on the :doc:`Commands bond ` doc page. On either of those pages, click on the style to display the formula it @@ -85,8 +85,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. A bond style must be defined before any bond coefficients are set, either in the input script or in a data file. @@ -94,6 +94,6 @@ either in the input script or in a data file. Related commands """""""""""""""" -:doc:`bond\_style ` +:doc:`bond_style ` **Default:** none diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index d952321c20..a36db3a170 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -46,9 +46,9 @@ first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^2) * :math:`R_0` (distance) @@ -89,14 +89,14 @@ This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. -You typically should specify :doc:`special\_bonds fene ` -or :doc:`special\_bonds lj/coul 0 1 1 ` to use this bond +You typically should specify :doc:`special_bonds fene ` +or :doc:`special_bonds lj/coul 0 1 1 ` to use this bond style. LAMMPS will issue a warning it that's not the case. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index 5b5b858330..8a05e141d7 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -43,9 +43,9 @@ effectively change the bead size of the bonded atoms. The first term now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^2) * :math:`R_0` (distance) @@ -87,14 +87,14 @@ This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. -You typically should specify :doc:`special\_bonds fene ` -or :doc:`special\_bonds lj/coul 0 1 1 ` to use this bond +You typically should specify :doc:`special_bonds fene ` +or :doc:`special_bonds lj/coul 0 1 1 ` to use this bond style. LAMMPS will issue a warning it that's not the case. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index 5d0a4ab1c6..3b935568bb 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -37,9 +37,9 @@ where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/4 factor is included in :math:`K`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^4) * :math:`r_0` (distance) @@ -81,6 +81,6 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index d65f0337f0..06af4037f6 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -43,9 +43,9 @@ where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^2) * :math:`r_0` (distance) @@ -87,6 +87,6 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index cc39bda7a7..26373790a2 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -39,9 +39,9 @@ The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`U_{\text{min}}` (energy) @@ -86,7 +86,7 @@ page for more info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds `, -:doc:`bond\_harmonic ` +:doc:`bond_coeff `, :doc:`delete_bonds `, +:doc:`bond_harmonic ` **Default:** none diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index 459acfdbfb..6b7e7d4fbb 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -39,9 +39,9 @@ The bond potential is zero for distances :math:`r > r_c`. The potential is :math at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`U_{\text{min}}` (energy) * :math:`r_0` (distance) @@ -84,8 +84,8 @@ page for more info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds `, -:doc:`bond\_harmonic `, +:doc:`bond_coeff `, :doc:`delete_bonds `, +:doc:`bond_harmonic `, :doc:`bond\_harmonic\_shift ` **Default:** none diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst index 5794592ce4..e7baa78ea0 100644 --- a/doc/src/bond_mm3.rst +++ b/doc/src/bond_mm3.rst @@ -39,9 +39,9 @@ Note that the MM3 papers contains an error in Eq (1): (7/12)2.55 should be replaced with (7/12)2.55\^2 The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^2) * :math:`r_0` (distance) @@ -57,7 +57,7 @@ page for more info. Related commands """""""""""""""" -:doc:`bond\_coeff ` +:doc:`bond_coeff ` **Default:** none diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index 26471424c5..13f24855f3 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -37,9 +37,9 @@ where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffnes parameter, and :math:`D` determines the depth of the potential well. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`D` (energy) * :math:`\alpha` (inverse distance) @@ -82,6 +82,6 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index 0003257e0b..4f8a0c881e 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -37,9 +37,9 @@ to define an anharmonic spring :ref:`(Rector) ` of equilibrium length :math:`r_0` and maximum extension lamda. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`\epsilon` (energy) * :math:`r_0` (distance) @@ -82,7 +82,7 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 03863eb5cf..2b7ba54708 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -52,9 +52,9 @@ phosphate backbone in the oxDNA/oxRNA force field for coarse-grained modelling of DNA/RNA. The following coefficients must be defined for the bond type via the -:doc:`bond\_coeff ` command as given in the above example, or +:doc:`bond_coeff ` command as given in the above example, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * :math:`\epsilon` (energy) @@ -68,7 +68,7 @@ commands: *oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and coaxial stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding interaction *oxdna/hbond* (see also documentation of - :doc:`pair\_style oxdna/excv `). For the oxDNA2 + :doc:`pair_style oxdna/excv `). For the oxDNA2 :ref:`(Snodin) ` bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/hbond* and an additional Debye-Hueckel pair style @@ -111,8 +111,8 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the 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 ` +:doc:`pair_style oxdna/excv `, :doc:`pair_style oxdna2/excv `, :doc:`pair_style oxrna2/excv `, +:doc:`bond_coeff `, :doc:`fix nve/dotc/langevin ` **Default:** diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index 898aa9315a..89b1a0a131 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -37,9 +37,9 @@ due to a polymer being stretched). The :math:`\sigma` and :math:`\epsilon` used LJ portion of the formula are both set equal to 1.0 by LAMMPS. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^4) * :math:`B_1` (distance) @@ -75,12 +75,12 @@ LAMMPS does the second task via a computational sleight-of-hand. It subtracts the pairwise interaction as part of the bond computation. When the bond breaks, the subtraction stops. For this to work, the pairwise interaction must always be computed by the -:doc:`pair\_style ` command, whether the bond is broken or -not. This means that :doc:`special\_bonds ` must be set +:doc:`pair_style ` command, whether the bond is broken or +not. This means that :doc:`special_bonds ` must be set to 1,1,1, as indicated as a restriction below. Note that when bonds are dumped to a file via the :doc:`dump local ` command, bonds with type 0 are not included. The -:doc:`delete\_bonds ` command can also be used to query the +:doc:`delete_bonds ` command can also be used to query the status of broken bonds or permanently delete them, e.g.: @@ -123,13 +123,13 @@ This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. -The *quartic* style requires that :doc:`special\_bonds ` +The *quartic* style requires that :doc:`special_bonds ` parameters be set to 1,1,1. Three- and four-body interactions (angle, dihedral, etc) cannot be used with *quartic* bonds. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index dd3acb6833..a0908606e4 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -32,12 +32,12 @@ Description Set the formula(s) LAMMPS uses to compute bond interactions between pairs of atoms. In LAMMPS, a bond differs from a pairwise -interaction, which are set via the :doc:`pair\_style ` +interaction, which are set via the :doc:`pair_style ` command. Bonds are defined between specified pairs of atoms and remain in force for the duration of the simulation (unless the bond breaks which is possible in some bond potentials). The list of bonded -atoms is read in by a :doc:`read\_data ` or -:doc:`read\_restart ` command from a data or restart file. +atoms is read in by a :doc:`read_data ` or +:doc:`read_restart ` command from a data or restart file. By contrast, pair potentials are typically defined between all pairs of atoms within a cutoff distance and the set of active interactions changes over time. @@ -46,12 +46,12 @@ Hybrid models where bonds are computed using different bond potentials can be setup using the *hybrid* bond style. The coefficients associated with a bond style can be specified in a -data or restart file or via the :doc:`bond\_coeff ` command. +data or restart file or via the :doc:`bond_coeff ` command. All bond potentials store their coefficient data in binary restart -files which means bond\_style and :doc:`bond\_coeff ` commands +files which means bond\_style and :doc:`bond_coeff ` commands do not need to be re-specified in an input script that restarts a -simulation. See the :doc:`read\_restart ` command for +simulation. See the :doc:`read_restart ` command for details on how to do this. The one exception is that bond\_style *hybrid* only stores the list of sub-styles in the restart file; bond coefficients need to be re-specified. @@ -59,7 +59,7 @@ coefficients need to be re-specified. .. note:: When both a bond and pair style is defined, the - :doc:`special\_bonds ` command often needs to be used to + :doc:`special_bonds ` command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise exist between 2 bonded atoms. @@ -122,7 +122,7 @@ individual bond potentials tell if it is part of a package. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` Default """"""" diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index 5378df3cff..79ad429222 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -90,7 +90,7 @@ keyword followed by one or more numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`bond\_style table ` command. Let +specified in the :doc:`bond_style table ` command. Let Ntable = *N* in the bond_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It diff --git a/doc/src/bond_zero.rst b/doc/src/bond_zero.rst index 43a0af33e2..329cd9d13a 100644 --- a/doc/src/bond_zero.rst +++ b/doc/src/bond_zero.rst @@ -31,14 +31,14 @@ commands. As an example, the :doc:`compute bond/local ` command can be used to compute distances for the list of pairs of bond -atoms listed in the data file read by the :doc:`read\_data ` +atoms listed in the data file read by the :doc:`read_data ` command. If no bond style is defined, this command cannot be used. The optional *nocoeff* flag allows to read data files with a BondCoeff section for any bond style. Similarly, any bond\_coeff commands will only be checked for the bond type number and the rest ignored. -Note that the :doc:`bond\_coeff ` command must be used for +Note that the :doc:`bond_coeff ` command must be used for all bond types. If specified, there can be only one value, which is going to be used to assign an equilibrium distance, e.g. for use with :doc:`fix shake `. @@ -50,6 +50,6 @@ Restrictions Related commands """""""""""""""" -:doc:`bond\_style none ` +:doc:`bond_style none ` **Default:** none diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index 909ee3b446..2a9896c2c8 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -39,8 +39,8 @@ Set the style of boundaries for the global simulation box in each dimension. A single letter assigns the same style to both the lower and upper face of the box. Two letters assigns the first style to the lower face and the second style to the upper face. The initial size -of the simulation box is set by the :doc:`read\_data `, -:doc:`read\_restart `, or :doc:`create\_box ` +of the simulation box is set by the :doc:`read_data `, +:doc:`read_restart `, or :doc:`create_box ` commands. The style *p* means the box is periodic, so that particles interact @@ -56,7 +56,7 @@ side of the box to the other. For style *f*\ , the position of the face is fixed. If an atom moves outside the face it will be deleted on the next timestep that reneighboring occurs. This will typically generate an error unless -you have set the :doc:`thermo\_modify lost ` option to +you have set the :doc:`thermo_modify lost ` option to allow for lost atoms. For style *s*\ , the position of the face is set so as to encompass the @@ -73,7 +73,7 @@ shrink-wrapped dimensions more closely, by using *m* style boundaries For style *m*\ , shrink-wrapping occurs, but is bounded by the value specified in the data or restart file or set by the -:doc:`create\_box ` command. For example, if the upper z +:doc:`create_box ` command. For example, if the upper z face has a value of 50.0 in the data file, the face will always be positioned at 50.0 or above, even if the maximum z-extent of all the atoms becomes less than 50.0. This can be useful if you start a @@ -99,9 +99,9 @@ Restrictions 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. See the -:doc:`change\_box ` command for how to change the simulation +:doc:`read_data ` or :doc:`create_box ` command or +:doc:`read_restart ` command. See the +:doc:`change_box ` command for how to change the simulation box boundaries after it has been defined. For 2d simulations, the z dimension must be periodic. @@ -109,7 +109,7 @@ For 2d simulations, the z dimension must be periodic. Related commands """""""""""""""" -See the :doc:`thermo\_modify ` command for a discussion +See the :doc:`thermo_modify ` command for a discussion of lost atoms. Default diff --git a/doc/src/box.rst b/doc/src/box.rst index 3338e138fb..9ef8316dae 100644 --- a/doc/src/box.rst +++ b/doc/src/box.rst @@ -36,8 +36,8 @@ Set attributes of the simulation box. For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword allows simulation domains to be created with arbitrary tilt factors, -e.g. via the :doc:`create\_box ` or -:doc:`read\_data ` commands. Tilt factors determine how +e.g. via the :doc:`create_box ` or +:doc:`read_data ` commands. Tilt factors determine how skewed the triclinic box is; see the :doc:`Howto triclinic ` doc page for a discussion of triclinic boxes in LAMMPS. @@ -60,8 +60,8 @@ Restrictions 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. +:doc:`read_data ` or :doc:`create_box ` command or +:doc:`read_restart ` command. **Related commands:** none diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst index bc34db9262..3430d25c72 100644 --- a/doc/src/change_box.rst +++ b/doc/src/change_box.rst @@ -77,12 +77,12 @@ conditions for the simulation box, similar to the :doc:`boundary ` command. The size and shape of the initial simulation box are specified by the -:doc:`create\_box ` or :doc:`read\_data ` or -:doc:`read\_restart ` command used to setup the simulation. +:doc:`create_box ` or :doc:`read_data ` or +:doc:`read_restart ` command used to setup the simulation. The size and shape may be altered by subsequent runs, e.g. by use of the :doc:`fix npt ` or :doc:`fix deform ` commands. -The :doc:`create\_box `, :doc:`read data `, and -:doc:`read\_restart ` commands also determine whether the +The :doc:`create_box `, :doc:`read data `, and +:doc:`read_restart ` commands also determine whether the simulation box is orthogonal or triclinic and their doc pages explain the meaning of the xy,xz,yz tilt factors. @@ -108,7 +108,7 @@ new owning processors. This means that you cannot use the change\_box command to enlarge a shrink-wrapped box, e.g. to make room to insert more atoms via the - :doc:`create\_atoms ` command, because the simulation box + :doc:`create_atoms ` command, because the simulation box will be re-shrink-wrapped before the change\_box command completes. Instead you could do something like this, assuming the simulation box is non-periodic and atoms extend from 0 to 20 in all dimensions: @@ -289,11 +289,11 @@ smaller. See the :doc:`boundary ` command for more explanation of these style options. Note that the "boundary" command itself can only be used before the -simulation box is defined via a :doc:`read\_data ` or -:doc:`create\_box ` or :doc:`read\_restart ` +simulation box is defined via a :doc:`read_data ` or +:doc:`create_box ` or :doc:`read_restart ` command. This command allows the boundary conditions to be changed later in your input script. Also note that the -:doc:`read\_restart ` will change boundary conditions to +:doc:`read_restart ` will change boundary conditions to match what is stored in the restart file. So if you wish to change them, you should use the change\_box command after the read\_restart command. @@ -306,8 +306,8 @@ The *ortho* and *triclinic* keywords convert the simulation box to be orthogonal or triclinic (non-orthogonal). The simulation box is defined as either orthogonal or triclinic when -it is created via the :doc:`create\_box `, -:doc:`read\_data `, or :doc:`read\_restart ` +it is created via the :doc:`create_box `, +:doc:`read_data `, or :doc:`read_restart ` commands. These keywords allow you to toggle the existing simulation box from diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 9375bd60c9..5526646261 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -50,8 +50,8 @@ processors and stored as properties of ghost atoms. .. note:: These options apply to the currently defined comm style. When - you specify a :doc:`comm\_style ` or - :doc:`read\_restart ` command, all communication settings + you specify a :doc:`comm_style ` or + :doc:`read_restart ` command, all communication settings are restored to their default or stored values, including those previously reset by a comm\_modify command. Thus if your input script specifies a comm\_style or read\_restart command, you should use the @@ -138,17 +138,17 @@ find the needed atoms. side of the simulation box, across a periodic boundary. This will typically lead to bad dynamics (i.e. the bond length is now the simulation box length). To detect if this is happening, see the - :doc:`neigh\_modify cluster ` command. + :doc:`neigh_modify cluster ` command. The *group* keyword will limit communication to atoms in the specified group. This can be useful for models where no ghost atoms are needed for some kinds of particles. All atoms (not just those in the specified group) will still migrate to new processors as they move. The group specified with this option must also be specified via the -:doc:`atom\_modify first ` command. +:doc:`atom_modify first ` command. The *vel* keyword enables velocity information to be communicated with -ghost particles. Depending on the :doc:`atom\_style `, +ghost particles. Depending on the :doc:`atom_style `, velocity info includes the translational velocity, angular velocity, and angular momentum of a particle. If the *vel* option is set to *yes*\ , then ghost atoms store these quantities; if *no* then they do @@ -167,12 +167,12 @@ Restrictions Communication mode *multi* is currently only available for -:doc:`comm\_style ` *brick*\ . +:doc:`comm_style ` *brick*\ . Related commands """""""""""""""" -:doc:`comm\_style `, :doc:`neighbor ` +:doc:`comm_style `, :doc:`neighbor ` Default """"""" diff --git a/doc/src/comm_style.rst b/doc/src/comm_style.rst index 1d733b7c40..528f05ecf1 100644 --- a/doc/src/comm_style.rst +++ b/doc/src/comm_style.rst @@ -46,11 +46,11 @@ Note that this command does not actually define a partitioning of the simulation box (a domain decomposition), rather it determines what kinds of decompositions are allowed and the pattern of communication used to enable the decomposition. A decomposition is created when the -simulation box is first created, via the :doc:`create\_box ` -or :doc:`read\_data ` or :doc:`read\_restart ` +simulation box is first created, via the :doc:`create_box ` +or :doc:`read_data ` or :doc:`read_restart ` commands. For both the *brick* and *tiled* styles, the initial decomposition will be the same, as described by -:doc:`create\_box ` and :doc:`processors ` +:doc:`create_box ` and :doc:`processors ` commands. The decomposition can be changed via the :doc:`balance ` or :doc:`fix balance ` commands. @@ -64,7 +64,7 @@ cells. Related commands """""""""""""""" -:doc:`comm\_modify `, :doc:`processors `, +:doc:`comm_modify `, :doc:`processors `, :doc:`balance `, :doc:`fix balance ` Default diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 9c66c58bd9..56de4f4225 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -106,7 +106,7 @@ ways: * The results of computes that calculate a global temperature or pressure can be used by fixes that do thermostatting or barostatting or when atom velocities are created. -* Global values can be output via the :doc:`thermo\_style custom ` or :doc:`fix ave/time ` command. +* Global values can be output via the :doc:`thermo_style custom ` or :doc:`fix ave/time ` command. Or the values can be referenced in a :doc:`variable equal ` or :doc:`variable atom ` command. * Per-atom values can be output via the :doc:`dump custom ` command. @@ -147,7 +147,7 @@ in the input script: Additional computes for other quantities are created if the thermo style requires it. See the documentation for the -:doc:`thermo\_style ` command. +:doc:`thermo_style ` command. Fixes that calculate temperature or pressure, i.e. for thermostatting or barostatting, may also create computes. These are discussed in the @@ -155,10 +155,10 @@ documentation for specific :doc:`fix ` commands. In all these cases, the default computes LAMMPS creates can be replaced by computes defined by the user in the input script, as -described by the :doc:`thermo\_modify ` and :doc:`fix modify ` commands. +described by the :doc:`thermo_modify ` and :doc:`fix modify ` commands. Properties of either a default or user-defined compute can be modified -via the :doc:`compute\_modify ` command. +via the :doc:`compute_modify ` command. Computes can be deleted with the :doc:`uncompute ` command. @@ -329,7 +329,7 @@ Restrictions Related commands """""""""""""""" -:doc:`uncompute `, :doc:`compute\_modify `, :doc:`fix ave/atom `, :doc:`fix ave/time `, :doc:`fix ave/histo ` +:doc:`uncompute `, :doc:`compute_modify `, :doc:`fix ave/atom `, :doc:`fix ave/time `, :doc:`fix ave/histo ` **Default:** none diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index 3c8af03b10..363091a033 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -60,9 +60,9 @@ neighbor atom in each requested ADF. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses a neighbor list, it also means those pairs will not be included in the ADF. This does not apply when @@ -72,7 +72,7 @@ neighbor atom in each requested ADF. zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the ADF for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. .. note:: @@ -81,7 +81,7 @@ neighbor atom in each requested ADF. pair style is defined, e.g. the :doc:`rerun ` command is being used to post-process a dump file of snapshots you must insure ghost atom information out to the largest value of *Router* + *skin* is communicated, via the - :doc:`comm\_modify cutoff ` command, else the ADF computation + :doc:`comm_modify cutoff ` command, else the ADF computation cannot be performed, and LAMMPS will give an error message. The *skin* value is what is specified with the :doc:`neighbor ` command. @@ -221,7 +221,7 @@ your model. Related commands """""""""""""""" -:doc:`compute rdf `, :doc:`fix ave/time `, :doc:`compute\_modify ` +:doc:`compute rdf `, :doc:`fix ave/time `, :doc:`compute_modify ` Default """"""" diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst index 2b025ea217..49b9849f05 100644 --- a/doc/src/compute_angle.rst +++ b/doc/src/compute_angle.rst @@ -31,13 +31,13 @@ hybrid" angle\_hybrid.html command. These values are made accessible for output or further processing by other commands. The group 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 +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:** 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 +number of sub\_styles defined by the :doc:`angle_style hybrid ` command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index 15b484a3bc..e6efe50b42 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -90,7 +90,7 @@ and output the statistics in various ways: The :doc:`dump local ` command will output the energy, angle, cosine(angle), cosine\^2(angle) for every angle in the system. The -:doc:`thermo\_style ` command will print the average of +:doc:`thermo_style ` command will print the average of those quantities via the :doc:`compute reduce ` command with thermo output. And the :doc:`fix ave/histo ` command will histogram the cosine(angle) values and write them to a @@ -104,8 +104,8 @@ The local data stored by this command is generated by looping over all the atoms owned on a processor and their angles. An angle will only be included if all 3 atoms in the angle are in the specified compute group. Any angles that have been broken (see the -:doc:`angle\_style ` command) by setting their angle type to -0 are not included. Angles that have been turned off (see the :doc:`fix shake ` or :doc:`delete\_bonds ` commands) by +:doc:`angle_style ` command) by setting their angle type to +0 are not included. Angles that have been turned off (see the :doc:`fix shake ` or :doc:`delete_bonds ` commands) by setting their angle type negative are written into the file, but their energy will be 0.0. diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index 5da4adecac..2637e4774a 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -56,7 +56,7 @@ non-zero chunk IDs. momentum in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index eb431aafc2..5d6a492c66 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -64,7 +64,7 @@ group. For a body particle, the *integer* keywords refer to fields calculated by the body style for each sub-particle. The body style, as specified -by the :doc:`atom\_style body `, determines how many fields +by the :doc:`atom_style body `, determines how many fields exist and what they are. See the :doc:`Howto\_body ` doc page for details of the different styles. diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst index 74c1ccb262..43e9a64cbb 100644 --- a/doc/src/compute_bond.rst +++ b/doc/src/compute_bond.rst @@ -26,18 +26,18 @@ Description """"""""""" Define a computation that extracts the bond energy calculated by each -of the bond sub-styles used in the :doc:`bond\_style hybrid ` command. These values are made accessible +of the bond sub-styles used in the :doc:`bond_style hybrid ` command. These values are made accessible for output or further processing by other commands. The group specified for this command is ignored. -This compute is useful when using :doc:`bond\_style hybrid ` +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:** 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. +number of sub\_styles defined by the :doc:`bond_style hybrid ` command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index 23d052c734..9559dd0f35 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -143,7 +143,7 @@ output the statistics in various ways: The :doc:`dump local ` command will output the energy, distance, distance\^2 for every bond in the system. The -:doc:`thermo\_style ` command will print the average of +:doc:`thermo_style ` command will print the average of those quantities via the :doc:`compute reduce ` command with thermo output. And the :doc:`fix ave/histo ` command will histogram the distance\^2 values and write them to a file. @@ -155,10 +155,10 @@ command will histogram the distance\^2 values and write them to a file. The local data stored by this command is generated by looping over all the atoms owned on a processor and their bonds. A bond will only be included if both atoms in the bond are in the specified compute group. -Any bonds that have been broken (see the :doc:`bond\_style ` +Any bonds that have been broken (see the :doc:`bond_style ` command) by setting their bond type to 0 are not included. Bonds that have been turned off (see the :doc:`fix shake ` or -:doc:`delete\_bonds ` commands) by setting their bond type +:doc:`delete_bonds ` commands) by setting their bond type negative are written into the file, but their energy will be 0.0. Note that as atoms migrate from processor to processor, there will be diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index 4cead81df8..a88d5fa61b 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -247,7 +247,7 @@ assigned to the atom. The *type* style uses the atom type as the chunk ID. *Nchunk* is set to the number of atom types defined for the simulation, e.g. via the -:doc:`create\_box ` or :doc:`read\_data ` commands. +:doc:`create_box ` or :doc:`read_data ` commands. ---------- diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index df1614858c..cab2e60ecc 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -47,7 +47,7 @@ cluster. A fragment is similarly defined as a set of atoms, each of which has an explicit bond (i.e. defined via a :doc:`data file `, -the :doc:`create\_bonds ` command, or through fixes like +the :doc:`create_bonds ` command, or through fixes like :doc:`fix bond/create `, :doc:`fix bond/swap `, or :doc:`fix bond/break `). The cluster ID or fragment ID of every atom in the cluster will be set to the smallest atom ID of any atom @@ -76,9 +76,9 @@ multiple compute/dump commands, each of a *cluster/atom* or .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included when computing the clusters. This @@ -88,7 +88,7 @@ multiple compute/dump commands, each of a *cluster/atom* or zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the clusters for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. **Output info:** diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst index 8a9381e37e..ac20b3cb73 100644 --- a/doc/src/compute_com.rst +++ b/doc/src/compute_com.rst @@ -38,7 +38,7 @@ are the x,y,z coordinates of the center of mass. "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst index d143f911f6..15cf528517 100644 --- a/doc/src/compute_com_chunk.rst +++ b/doc/src/compute_com_chunk.rst @@ -54,7 +54,7 @@ non-zero chunk IDs. center-of-mass in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of - the :doc:`read\_data ` command for a discussion of image flags + the :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst index 0d8563d2ce..c6c58a5ea4 100644 --- a/doc/src/compute_contact_atom.rst +++ b/doc/src/compute_contact_atom.rst @@ -51,7 +51,7 @@ Restrictions This compute requires that atoms store a radius as defined by the -:doc:`atom\_style sphere ` command. +:doc:`atom_style sphere ` command. Related commands """""""""""""""" diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index 2e55d3a673..db87284cc2 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -101,16 +101,16 @@ too frequently. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the coordination count. One way to get around this, is to write a dump file, and use the :doc:`rerun ` command to compute the coordination for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. **Output info:** diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst index 087b25c393..695031e05e 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -26,17 +26,17 @@ Description """"""""""" Define a computation that extracts the dihedral energy calculated by -each of the dihedral sub-styles used in the :doc:`dihedral\_style hybrid ` command. These values are made +each of the dihedral sub-styles used in the :doc:`dihedral_style hybrid ` command. These values are made accessible for output or further processing by other commands. The 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 +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:** 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 +number of sub\_styles defined by the :doc:`dihedral_style hybrid ` command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 18c268a70f..ce7a9ede84 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -51,7 +51,7 @@ processors, equals the number of dihedral angles in the system, modified by the group parameter as explained below. The value *phi* is the dihedral angle, as defined in the diagram on -the :doc:`dihedral\_style ` doc page. +the :doc:`dihedral_style ` doc page. The value *v\_name* can be used together with the *set* keyword to compute a user-specified function of the dihedral angle phi. The @@ -88,7 +88,7 @@ the system and output the statistics in various ways: The :doc:`dump local ` command will output the angle, cosine(angle), cosine\^2(angle) for every dihedral in the system. The -:doc:`thermo\_style ` command will print the average of +:doc:`thermo_style ` command will print the average of those quantities via the :doc:`compute reduce ` command with thermo output. And the :doc:`fix ave/histo ` command will histogram the cosine(angle) values and write them to a diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index 5c80b62faa..8d70f1ef13 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -59,7 +59,7 @@ non-zero chunk IDs. dipole in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of - the :doc:`read\_data ` command for a discussion of image flags + the :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index 57e2037305..797e132480 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -51,7 +51,7 @@ the compute command was issued. The value of the displacement will be Initial coordinates are stored in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. - See the Atoms section of the :doc:`read\_data ` command for a + See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and 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. @@ -100,7 +100,7 @@ something like the following commands: dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} & refresh c_dsp delay 100 -The :doc:`dump\_modify thresh ` command will only output +The :doc:`dump_modify thresh ` command will only output atoms that have displaced more than 0.6 Angstroms on each snapshot (assuming metal units). The dump\_modify *refresh* option triggers a call to this compute at the end of every dump. @@ -121,7 +121,7 @@ atoms is 0.0. If an initial dump snapshot is desired, containing the initial reference positions of all atoms, one way to do this is illustrated above. An initial write\_dump command can be used before the first run. It will contain the positions of all the atoms, -Options in the :doc:`dump\_modify ` command above will +Options in the :doc:`dump_modify ` command above will append new output to that same file and delay the output until a later timestep. The *delay* setting avoids a second time = 0 snapshot which would be empty. @@ -140,7 +140,7 @@ for an overview of LAMMPS output options. The per-atom array values will be in distance :doc:`units `. This compute supports the *refresh* option as explained above, for use -in conjunction with :doc:`dump\_modify refresh ` to generate +in conjunction with :doc:`dump_modify refresh ` to generate incremental dump files. Restrictions diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index f85c0259f8..39b07865c2 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -60,14 +60,14 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. Related commands """""""""""""""" :doc:`compute dpd/atom `, -:doc:`thermo\_style ` +:doc:`thermo_style ` **Default:** none diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst index 2970141a19..a517f572be 100644 --- a/doc/src/compute_dpd_atom.rst +++ b/doc/src/compute_dpd_atom.rst @@ -50,7 +50,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. Related commands diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index 03dd4e9af5..ce9a4e26b2 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -52,7 +52,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_style edpd ` +:doc:`pair_style edpd ` **Default:** none diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index c50d21df99..be17f8bedc 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -28,7 +28,7 @@ Description Define a computation that calculates the rotational kinetic energy of a group of aspherical particles. The aspherical particles can be ellipsoids, or line segments, or triangles. See the -:doc:`atom\_style ` and :doc:`read\_data ` commands +:doc:`atom_style ` and :doc:`read_data ` commands for descriptions of these options. For all 3 types of particles, the rotational kinetic energy is @@ -58,14 +58,14 @@ Restrictions This compute requires that ellipsoidal particles atoms store a shape and quaternion orientation and angular momentum as defined by the -:doc:`atom\_style ellipsoid ` command. +:doc:`atom_style ellipsoid ` command. This compute requires that line segment particles atoms store a length -and orientation and angular velocity as defined by the :doc:`atom\_style line ` command. +and orientation and angular velocity as defined by the :doc:`atom_style line ` command. This compute requires that triangular particles atoms store a size and shape and quaternion orientation and angular momentum as defined by -the :doc:`atom\_style tri ` command. +the :doc:`atom_style tri ` command. All particles in the group must be finite-size. They cannot be point particles. diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index fa1396681c..d1df476435 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -52,7 +52,7 @@ Restrictions This compute requires that atoms store a radius and angular velocity -(omega) as defined by the :doc:`atom\_style sphere ` command. +(omega) as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres or point particles. They cannot be aspherical. Point particles will not diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index c54d0ee8fa..0f2fdc18c1 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -140,7 +140,7 @@ lengths or other internal coordinates :ref:`(Boresch, Karplus) ` The *pair* attribute enables various parameters of potentials defined -by the :doc:`pair\_style ` and :doc:`pair\_coeff ` +by the :doc:`pair_style ` and :doc:`pair_coeff ` commands to be changed, if the pair style supports it. The *pstyle* argument is the name of the pair style. For example, @@ -212,7 +212,7 @@ Note that it is easy to add new potentials and their parameters to this list. All it typically takes is adding an extract() method to the pair\_\*.cpp file associated with the potential. -Similar to the :doc:`pair\_coeff ` command, I and J can be +Similar to the :doc:`pair_coeff ` command, I and J can be specified in one of two ways. Explicit numeric values can be used for each, as in the 1st example above. I <= J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same @@ -226,10 +226,10 @@ means all types from 1 to N. A leading asterisk means all types from (inclusive). Note that only type pairs with I <= J are considered; if asterisks imply type pairs where J < I, they are ignored. -If :doc:`pair\_style hybrid or hybrid/overlay ` is being +If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will be a sub-style name. You must specify I,J arguments that correspond to type pair values defined (via the -:doc:`pair\_coeff ` command) for that sub-style. +:doc:`pair_coeff ` command) for that sub-style. The *v\_name* argument for keyword *pair* is the name of an :doc:`equal-style variable ` which will be evaluated each time @@ -257,7 +257,7 @@ is the variable name. The *tail* keyword controls the calculation of the tail correction to "van der Waals" pair energies beyond the cutoff, if this has been -activated via the :doc:`pair\_modify ` command. If the +activated via the :doc:`pair_modify ` command. If the perturbation is small, the tail contribution to the energy difference between the reference and perturbed systems should be negligible. diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index 7345bd1031..390f4f7c6a 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -55,7 +55,7 @@ interactions with atoms in the specified group2. The energies computed by the *pair* keyword do not include tail corrections, even if they are enabled via the - :doc:`pair\_modify ` command. + :doc:`pair_modify ` command. If the *molecule* keyword is set to *inter* or *intra* than an additional check is made based on the molecule IDs of the two atoms in @@ -65,7 +65,7 @@ molecules. For the *intra* setting, the two atoms must be in the same molecule. If the *kspace* keyword is set to *yes*\ , which is not the default, and -if a :doc:`kspace\_style ` is defined, then the interaction +if a :doc:`kspace_style ` is defined, then the interaction energy will include a Kspace component which is the long-range Coulombic energy between all the atoms in the first group and all the atoms in the 2nd group. Likewise, the interaction force calculated by @@ -107,9 +107,9 @@ frequently. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this compute uses a neighbor list, it also means those pairs will not be included in the group/group interaction. @@ -119,7 +119,7 @@ frequently. numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the group/group interactions for snapshots in the dump file. - The rerun script can use a :doc:`special\_bonds ` command + The rerun script can use a :doc:`special_bonds ` command that includes all pairs in the neighbor list. If you desire a breakdown of the interactions into a pairwise and diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index 15636a9275..89d11799e0 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -51,7 +51,7 @@ and taking a sqrt() would be invalid. The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. - See the Atoms section of the :doc:`read\_data ` command for a + See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index 4726a14d0e..7ed70e0968 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -78,7 +78,7 @@ ordered xx, yy, zz, xy, xz, yz. The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. - See the Atoms section of the :doc:`read\_data ` command for a + See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index 5461825923..bfabd48132 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -57,7 +57,7 @@ is bounded between zero (if all points are spherically symmetric) and one The coordinates of an atom contribute to the gyration tensor in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" - coordinates. See the Atoms section of the :doc:`read\_data ` + coordinates. See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index fa839aea35..5b88cbd4dc 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -58,7 +58,7 @@ The tensor keyword must be specified in the compute gyration/chunk command. The coordinates of an atom contribute to the gyration tensor in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" - coordinates. See the Atoms section of the :doc:`read\_data ` + coordinates. See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index 3b7058d3d3..cb36d30da4 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -111,7 +111,7 @@ to the thermal conductivity :math:`\kappa`: The heat flux can be output every so many timesteps (e.g. via the -:doc:`thermo\_style custom ` command). Then as a +:doc:`thermo_style custom ` command). Then as a post-processing operation, an auto-correlation can be performed, its integral estimated, and the Green-Kubo formula above evaluated. diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index 0807f2ff7f..16ecaf5b41 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -87,16 +87,16 @@ too frequently. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the order parameter. This difficulty can be circumvented by writing a dump file, and using the :doc:`rerun ` command to compute the order parameter for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. **Output info:** diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index d8e7a6b31a..61e598948e 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -58,8 +58,8 @@ restricted to simulations in the NVT ensemble. While this compute may be used with any potential in LAMMPS, it will provide inaccurate results for potentials that do not go to 0 at the truncation distance; :doc:`pair\_lj\_smooth\_linear ` and Ewald summation should -work fine, while :doc:`pair\_lj ` will perform poorly unless -the potential is shifted (via :doc:`pair\_modify ` shift) or the cutoff is large. Furthermore, computation of the heat capacity with +work fine, while :doc:`pair_lj ` will perform poorly unless +the potential is shifted (via :doc:`pair_modify ` shift) or the cutoff is large. Furthermore, computation of the heat capacity with this compute is restricted to those that implement the single\_hessian method in Pair. Implementing single\_hessian in additional pair styles is simple. Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at @@ -127,7 +127,7 @@ The *anharmonic* keyword will instruct the compute to return anharmonic properties rather than the full properties, which include lattice, harmonic and anharmonic contributions. When using this keyword, the compute must be first active (it must be included -via a :doc:`thermo\_style custom ` command) while the atoms are +via a :doc:`thermo_style custom ` command) while the atoms are still at their lattice sites (before equilibration). The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover (:doc:`fix nvt `) or @@ -156,7 +156,7 @@ The following example illustrates the placement of this command in the input scr .. note:: - The :doc:`fix\_modify energy yes ` command must also be specified if a fix is to contribute potential energy to this command. + The :doc:`fix_modify energy yes ` command must also be specified if a fix is to contribute potential energy to this command. An example input script that uses this compute is included in examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index 27cd5f5902..aec2bfbbf5 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -26,17 +26,17 @@ Description """"""""""" Define a computation that extracts the improper energy calculated by -each of the improper sub-styles used in the :doc:`improper\_style hybrid ` command. These values are made +each of the improper sub-styles used in the :doc:`improper_style hybrid ` command. These values are made accessible for output or further processing by other commands. The 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 +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:** 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 +number of sub\_styles defined by the :doc:`improper_style hybrid ` command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index 6daad705b5..fc651d324a 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -40,7 +40,7 @@ the group parameter as explained below. The value *chi* is the improper angle, as defined in the doc pages for the individual improper styles listed on -:doc:`improper\_style ` doc page. +:doc:`improper_style ` doc page. The local data stored by this command is generated by looping over all the atoms owned on a processor and their impropers. An improper will diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index 029245d883..a60c98b3c3 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -55,7 +55,7 @@ non-zero chunk IDs. tensor in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst index 8d7fd3e5f4..baccf848b5 100644 --- a/doc/src/compute_ke.rst +++ b/doc/src/compute_ke.rst @@ -34,7 +34,7 @@ and v are the mass and velocity of the particle. There is a subtle difference between the quantity calculated by this compute and the kinetic energy calculated by the *ke* or *etotal* keyword used in thermodynamic output, as specified by the -:doc:`thermo\_style ` command. For this compute, kinetic +:doc:`thermo_style ` command. For this compute, kinetic energy is "translational" kinetic energy, calculated by the simple formula above. For thermodynamic output, the *ke* keyword infers kinetic energy from the temperature of the system with 1/2 Kb T of diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst index db08516b61..bbe7aa1013 100644 --- a/doc/src/compute_ke_atom_eff.rst +++ b/doc/src/compute_ke_atom_eff.rst @@ -39,7 +39,7 @@ electron, and s to its radial velocity, respectively. There is a subtle difference between the quantity calculated by this compute and the kinetic energy calculated by the *ke* or *etotal* keyword used in thermodynamic output, as specified by the -:doc:`thermo\_style ` command. For this compute, kinetic +:doc:`thermo_style ` command. For this compute, kinetic energy is "translational" plus electronic "radial" kinetic energy, calculated by the simple formula above. For thermodynamic output, the *ke* keyword infers kinetic energy from the temperature of the system @@ -49,7 +49,7 @@ eFF. .. note:: The temperature in eFF should be monitored via the :doc:`compute temp/eff ` command, which can be printed with - thermodynamic output by using the :doc:`thermo\_modify ` + thermodynamic output by using the :doc:`thermo_modify ` command, as shown in the following example: diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst index c635b9fecc..981e238bbe 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -38,7 +38,7 @@ radial velocity of the electron, respectively. There is a subtle difference between the quantity calculated by this compute and the kinetic energy calculated by the *ke* or *etotal* keyword used in thermodynamic output, as specified by the -:doc:`thermo\_style ` command. For this compute, kinetic +:doc:`thermo_style ` command. For this compute, kinetic energy is "translational" and "radial" (only for electrons) kinetic energy, calculated by the simple formula above. For thermodynamic output, the *ke* keyword infers kinetic energy from the temperature of @@ -51,7 +51,7 @@ degrees of freedom. IMPRORTANT NOTE: The temperature in eFF models should be monitored via the :doc:`compute temp/eff ` command, which can be printed with thermodynamic output by using the -:doc:`thermo\_modify ` command, as shown in the following +:doc:`thermo_modify ` command, as shown in the following example: diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst index 4d47d58cd0..4b472566e7 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -80,7 +80,7 @@ solids undergoing thermal motion. Initial coordinates are stored in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. - See the Atoms section of the :doc:`read\_data ` command for a + See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index 18d1ae4440..f8a2ee1dc1 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -84,7 +84,7 @@ compute command was first invoked. "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index bd0b8f91de..dd8a3be806 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -56,7 +56,7 @@ non-zero chunk IDs. velocity in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index b7a1442a62..70b96a9fc5 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -115,16 +115,16 @@ too frequently. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the order parameter. This difficulty can be circumvented by writing a dump file, and using the :doc:`rerun ` command to compute the order parameter for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. **Output info:** diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst index 924ddc7cca..03da8acddb 100644 --- a/doc/src/compute_pair.rst +++ b/doc/src/compute_pair.rst @@ -41,7 +41,7 @@ by other commands. The group specified for this command is **ignored**\ . The specified *pstyle* must be a pair style used in your simulation -either by itself or as a sub-style in a :doc:`pair\_style hybrid or hybrid/overlay ` command. If the sub-style is +either by itself or as a sub-style in a :doc:`pair_style hybrid or hybrid/overlay ` command. If the sub-style is used more than once, an additional number *nsub* has to be specified in order to choose which instance of the sub-style will be used by the compute. Not specifying the number in this case will cause the @@ -55,7 +55,7 @@ be tallied in *ecoul*\ . Everything else (whether it is a Lennard-Jones style van der Waals interaction or not) is tallied in *evdwl*\ . If *evalue* is blank or specified as *epair*\ , then *epair* is stored as a global scalar by this compute. This is useful when using -:doc:`pair\_style hybrid ` if you want to know the portion +:doc:`pair_style hybrid ` if you want to know the portion of the total energy contributed by one sub-style. If *evalue* is specified as *evdwl* or *ecoul*\ , then just that portion of the energy is stored as a global scalar. @@ -64,10 +64,10 @@ is stored as a global scalar. The energy returned by the *evdwl* keyword does not include tail corrections, even if they are enabled via the - :doc:`pair\_modify ` command. + :doc:`pair_modify ` command. Some pair styles tally additional quantities, e.g. a breakdown of -potential energy into 14 components is tallied by the :doc:`pair\_style reax/c ` command. These values (1 or more) +potential energy into 14 components is tallied by the :doc:`pair_style reax/c ` command. These values (1 or more) are stored as a global vector by this compute. See the doc page for :doc:`individual pair styles ` for info on these values. diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index 4e61852f2c..39abd67f6c 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -56,7 +56,7 @@ pairwise neighbor list. Info about an individual pairwise interaction will only be included if both atoms in the pair are in the specified compute group, and if the current pairwise distance is less than the force cutoff distance for that interaction, as defined by the -:doc:`pair\_style ` and :doc:`pair\_coeff ` +:doc:`pair_style ` and :doc:`pair_coeff ` commands. The value *dist* is the distance between the pair of atoms. @@ -100,7 +100,7 @@ will be in whatever units the pair style defines. The optional *cutoff* keyword determines how the force cutoff distance for an interaction is determined. For the default setting of *type*\ , -the pairwise cutoff defined by the :doc:`pair\_style ` +the pairwise cutoff defined by the :doc:`pair_style ` command for the types of the two atoms is used. For the *radius* setting, the sum of the radii of the two particles is used as a cutoff. For example, this is appropriate for granular particles which @@ -135,9 +135,9 @@ Here is an example of how to do this: specifically, this will be true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set - by the :doc:`special\_bonds ` command. An exception is if + by the :doc:`special_bonds ` command. An exception is if long-range Coulombics are being computed via the - :doc:`kspace\_style ` command, then atom pairs with + :doc:`kspace_style ` command, then atom pairs with weighting factors of zero are still included in the neighbor list, so that a portion of the long-range interaction contribution can be computed in the pair style. Hence in that case, those atom pairs will diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index 88f6b5f7f6..d3d23e590c 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -42,7 +42,7 @@ keywords were listed. If any extra keywords are listed, then only those components are summed to compute the potential energy. The Kspace contribution requires 1 extra FFT each timestep the energy -is calculated, if using the PPPM solver via the :doc:`kspace\_style pppm ` command. Thus it can increase the cost of the +is calculated, if using the PPPM solver via the :doc:`kspace_style pppm ` command. Thus it can increase the cost of the PPPM calculation if it is needed on a large fraction of the simulation timesteps. @@ -53,7 +53,7 @@ potential energy. .. note:: - The :doc:`fix\_modify energy yes ` command must also be + The :doc:`fix_modify energy yes ` command must also be specified if a fix is to contribute potential energy to this command. A compute of this style with the ID of "thermo\_pe" is created when diff --git a/doc/src/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst index bedc508d71..bd4dcd2d57 100644 --- a/doc/src/compute_pe_atom.rst +++ b/doc/src/compute_pe_atom.rst @@ -48,13 +48,13 @@ atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that energy is assigned in equal portions to each atom in the set. E.g. 1/4 of the dihedral energy to each of the 4 atoms. -The :doc:`dihedral\_style charmm ` style calculates +The :doc:`dihedral_style charmm ` style calculates pairwise interactions between 1-4 atoms. The energy contribution of these terms is included in the pair energy, not the dihedral energy. The KSpace contribution is calculated using the method in :ref:`(Heyes) ` for the Ewald method and a related method for PPPM, -as specified by the :doc:`kspace\_style pppm ` command. +as specified by the :doc:`kspace_style pppm ` command. For PPPM, the calculation requires 1 extra FFT each timestep that per-atom energy is calculated. This `document `_ describes how the long-range per-atom energy calculation is performed. @@ -66,7 +66,7 @@ per-atom potential energy. .. note:: - The :doc:`fix\_modify energy yes ` command must also be + The :doc:`fix_modify energy yes ` command must also be specified if a fix is to contribute per-atom potential energy to this command. @@ -84,7 +84,7 @@ in the last 2 columns of thermo output: .. note:: The per-atom energy does not include any Lennard-Jones tail - corrections to the energy added by the :doc:`pair\_modify tail yes ` command, since those are contributions to the + corrections to the energy added by the :doc:`pair_modify tail yes ` command, since those are contributions to the global system energy. **Output info:** diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index d708b88ab0..3ee7f86fbd 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -156,7 +156,7 @@ Related commands """""""""""""""" :doc:`compute temp `, :doc:`compute stress/atom `, -:doc:`thermo\_style `, +:doc:`thermo_style `, **Default:** none diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst index d2ffb275ca..8d5cbb7b25 100644 --- a/doc/src/compute_pressure_cylinder.rst +++ b/doc/src/compute_pressure_cylinder.rst @@ -76,7 +76,7 @@ Related commands """""""""""""""" :doc:`compute temp `, :doc:`compute stress/atom `, -:doc:`thermo\_style `, +:doc:`thermo_style `, **Default:** none diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst index f5a3d47945..59f7608f44 100644 --- a/doc/src/compute_pressure_uef.rst +++ b/doc/src/compute_pressure_uef.rst @@ -38,7 +38,7 @@ value of the pressure. A :doc:`compute pressure ` may be used for that purpose. The keywords and output information are documented in -:doc:`compute\_pressure `. +:doc:`compute_pressure `. Restrictions """""""""""" diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index d388b4fc09..ff4388f989 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -82,13 +82,13 @@ atom pairs in the neighbor list are considered (out to the neighbor cutoff = force cutoff + :doc:`neighbor skin `). For *patom1* and *patom2*\ , the distance between the atoms must be less than the force cutoff distance for that pair to be included, as defined by the -:doc:`pair\_style ` and :doc:`pair\_coeff ` +:doc:`pair_style ` and :doc:`pair_coeff ` commands. The optional *cutoff* keyword determines how the force cutoff distance for an interaction is determined for the *patom1* and *patom2* attributes. For the default setting of *type*\ , the pairwise cutoff -defined by the :doc:`pair\_style ` command for the types of +defined by the :doc:`pair_style ` command for the types of the two atoms is used. For the *radius* setting, the sum of the radii of the two particles is used as a cutoff. For example, this is appropriate for granular particles which only interact when they are @@ -106,7 +106,7 @@ specified compute group. Likewise for angles, dihedrals, etc. For bonds and angles, a bonds/angles that have been broken by setting their bond/angle type to 0 will not be included. Bonds/angles that have been turned off (see the :doc:`fix shake ` or -:doc:`delete\_bonds ` commands) by setting their bond/angle +:doc:`delete_bonds ` commands) by setting their bond/angle type negative are written into the file. This is consistent with the :doc:`compute bond/local ` and :doc:`compute angle/local ` commands @@ -120,7 +120,7 @@ atom indices from this command and output by the :doc:`dump local ` comman The *natom1* and *natom2*\ , or *patom1* and *patom2* attributes refer to the atom IDs of the 2 atoms in each pairwise interaction computed -by the :doc:`pair\_style ` command. The *ntype1* and +by the :doc:`pair_style ` command. The *ntype1* and *ntype2*\ , or *ptype1* and *ptype2* attributes refer to the atom types of the 2 atoms in each pairwise interaction. @@ -133,13 +133,13 @@ of the 2 atoms in each pairwise interaction. specifically, this may be true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set - by the :doc:`special\_bonds ` command. + by the :doc:`special_bonds ` command. The *batom1* and *batom2* attributes refer to the atom IDs of the 2 atoms in each :doc:`bond `. The *btype* attribute refers to the type of the bond, from 1 to Nbtypes = # of bond types. The number of bond types is defined in the data file read by the -:doc:`read\_data ` command. +:doc:`read_data ` command. The attributes that start with "a", "d", "i", refer to similar values for :doc:`angles `, :doc:`dihedrals `, and diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index 19ab21475a..a11e1a1c97 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -45,7 +45,7 @@ Define a computation that calculates the radial distribution function (RDF), also called g(r), and the coordination number for a group of particles. Both are calculated in histogram form by binning pairwise distances into *Nbin* bins from 0.0 to the maximum force cutoff -defined by the :doc:`pair\_style ` command or the cutoff +defined by the :doc:`pair_style ` command or the cutoff distance *Rcut* specified via the *cutoff* keyword. The bins are of uniform size in radial distance. Thus a single bin encompasses a thin shell of distances in 3d and a thin ring of distances in 2d. @@ -53,9 +53,9 @@ shell of distances in 3d and a thin ring of distances in 2d. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses a neighbor list, it also means those pairs will not be included in the RDF. This does not apply when @@ -65,11 +65,11 @@ shell of distances in 3d and a thin ring of distances in 2d. zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the RDF for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. By default the RDF is computed out to the maximum force cutoff defined -by the :doc:`pair\_style ` command. If the *cutoff* keyword +by the :doc:`pair_style ` command. If the *cutoff* keyword is used, then the RDF is computed accurately out to the *Rcut* > 0.0 distance specified. @@ -87,7 +87,7 @@ distance specified. timestep, whichever is less frequent), which is inefficient. LAMMPS will warn you if this is the case. If you specify a *Rcut* > force cutoff, you must insure ghost atom information out to *Rcut* + *skin* - is communicated, via the :doc:`comm\_modify cutoff ` + is communicated, via the :doc:`comm_modify cutoff ` command, else the RDF computation cannot be performed, and LAMMPS will give an error message. The *skin* value is what is specified with the :doc:`neighbor ` command. In this case, you are forcing a @@ -120,7 +120,7 @@ by *itypeN* are the central atom, and atoms of any of the range of types represented by *jtypeN* are the distribution atom. Pairwise distances are generated by looping over a pairwise neighbor -list, just as they would be in a :doc:`pair\_style ` +list, just as they would be in a :doc:`pair_style ` computation. The distance between two atoms I and J is included in a specific histogram if the following criteria are met: @@ -205,12 +205,12 @@ change from zero to one at the location of the spike in g(r). parallel efficiency and scaling. For systems, where only the type of atoms changes (e.g. when using :doc:`fix atom/swap `), you need to explicitly request the dynamic normalization updates - via :doc:`compute\_modify dynamic yes ` + via :doc:`compute_modify dynamic yes ` Related commands """""""""""""""" -:doc:`fix ave/time `, :doc:`compute\_modify `, +:doc:`fix ave/time `, :doc:`compute_modify `, :doc:`compute adf ` Default diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index ff67fa9651..283c5da95d 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -203,7 +203,7 @@ inputs specified. As discussed below, for the *sum* and *sumsq* modes, the value(s) produced by this compute are all "extensive", meaning their value scales linearly with the number of atoms involved. If normalized -values are desired, this compute can be accessed by the :doc:`thermo\_style custom ` command with :doc:`thermo\_modify norm yes ` set as an option. Or it can be accessed by a +values are desired, this compute can be accessed by the :doc:`thermo_style custom ` command with :doc:`thermo_modify norm yes ` set as an option. Or it can be accessed by a :doc:`variable ` that divides by the appropriate atom count. diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 8556b3971b..2bcd983237 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -222,15 +222,15 @@ ordered in which they are listed. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the calculation. One way to get around this, is to write a dump file, and use the :doc:`rerun ` command to compute the bispectrum components for snapshots in the dump - file. The rerun script can use a :doc:`special\_bonds ` + file. The rerun script can use a :doc:`special_bonds ` command that includes all pairs in the neighbor list. ;line @@ -320,7 +320,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_style snap ` +:doc:`pair_style snap ` Default """"""" diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index c37a8cc52d..45d6027871 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -152,14 +152,14 @@ i.e. computed values for contributions from bonds and two-body pair styles, such as :doc:`Lennard-Jones `, will be the same, while contributions from angles, dihedrals and impropers will be different. -The :doc:`dihedral\_style charmm ` style calculates +The :doc:`dihedral_style charmm ` style calculates pairwise interactions between 1-4 atoms. The virial contribution of these terms is included in the pair virial, not the dihedral virial. The KSpace contribution is calculated using the method in :ref:`(Heyes) ` for the Ewald method and by the methodology described in :ref:`(Sirk) ` for PPPM. The choice of KSpace solver is specified -by the :doc:`kspace\_style pppm ` command. Note that for +by the :doc:`kspace_style pppm ` command. Note that for PPPM, the calculation requires 6 extra FFTs each timestep that per-atom stress is calculated. Thus it can significantly increase the cost of the PPPM calculation if it is needed on a large fraction of @@ -210,7 +210,7 @@ result. I.e. the last 2 columns of thermo output will be the same: .. note:: The per-atom 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 + corrections to the pressure added by the :doc:`pair_modify tail yes ` command, since those are contributions to the global system pressure. **Output info:** diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index aadc78050c..892924575d 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -67,7 +67,7 @@ configurational stress (conf), and/or total stress (total). NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. 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. +corrections to the pressure added by the :doc:`pair_modify tail yes ` command, since those are contributions to the global system pressure. **Output info:** diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index ed7af54d2a..b6e5497f2d 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -54,7 +54,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_style tdpd ` +:doc:`pair_style tdpd ` **Default:** none diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index 052da705ac..b9b00c7469 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -31,7 +31,7 @@ Description Define a computation that calculates the temperature of a group of atoms. A compute of this style can be used by any command that -computes a temperature, e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +computes a temperature, e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2), @@ -47,14 +47,14 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. A compute of this style with the ID of "thermo\_temp" is created when LAMMPS starts up, as if this command were in the input script: diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index 46743c780e..499065ca5c 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -59,7 +59,7 @@ rotational). use a combination of interaction potentials and fixes that induce no torque or otherwise constrain some of all of your particles so that this is not the case. Then there are less dof and you should use the - :doc:`compute\_modify extra ` command to adjust the dof + :doc:`compute_modify extra ` command to adjust the dof accordingly. For example, an aspherical particle with all three of its shape @@ -94,14 +94,14 @@ vector are ordered xx, yy, zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform @@ -153,7 +153,7 @@ This compute is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute requires that atoms store angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index e17227fe3e..3464a584b1 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -57,7 +57,7 @@ rotational). rotational dof. It is possible to use a combination of interaction potentials and fixes that induce no torque or otherwise constrain some of all of your particles so that this is not the case. Then there are - less dof and you should use the :doc:`compute\_modify extra ` command to adjust the dof accordingly. + less dof and you should use the :doc:`compute_modify extra ` command to adjust the dof accordingly. The translational kinetic energy is computed the same as is described by the :doc:`compute temp ` command. The rotational @@ -74,14 +74,14 @@ vector are ordered xx, yy, zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform @@ -133,7 +133,7 @@ This compute is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute requires that atoms store angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. Related commands diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index cc9e70a0c5..37b6a05264 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -89,7 +89,7 @@ Note that the number of atoms contributing to the temperature is calculated each time the temperature is evaluated since it is assumed the atoms may be dynamically assigned to chunks. Thus there is no need to use the *dynamic* option of the -:doc:`compute\_modify ` command for this compute style. +:doc:`compute_modify ` command for this compute style. If any optional values are specified, then per-chunk quantities are also calculated and stored in a global array, as described below. diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index 083e9f652c..d81ede2e43 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -31,7 +31,7 @@ atoms, after subtracting out the center-of-mass velocity of the group. This is useful if the group is expected to have a non-zero net velocity for some reason. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. After the center-of-mass velocity has been subtracted from each atom, the temperature is calculated by the formula KE = dim/2 N k T, where @@ -48,7 +48,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the center-of-mass velocity by this fix is essentially computing the temperature after a "bias" has been removed from the @@ -63,7 +63,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 7d5843e1db..e735a79b6f 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -38,7 +38,7 @@ enables correct temperature calculation and thermostatting of core/shell pairs where it is desirable for the internal degrees of freedom of the core/shell pairs to not be influenced by a thermostat. A compute of this style can be used by any command that computes a -temperature via :doc:`fix\_modify ` e.g. :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +temperature via :doc:`fix_modify ` e.g. :doc:`fix temp/rescale `, :doc:`fix npt `, etc. Note that this compute does not require all ions to be polarized, hence defined as core/shell pairs. One can mix core/shell pairs and diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index 88dbc62422..779ce2de71 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -33,7 +33,7 @@ induced by use of the :doc:`fix deform ` command. A compute of this style is created by the :doc:`fix nvt/sllod ` command to compute the thermal temperature of atoms for thermostatting purposes. A compute of this style can also be used by any command -that computes a temperature, e.g. :doc:`thermo\_modify `, +that computes a temperature, e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The deformation fix changes the box size and/or shape over time, so @@ -74,7 +74,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the box deformation velocity component by this fix is essentially computing the temperature after a "bias" has been removed @@ -104,7 +104,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index 98b28aa76a..fab6275f0a 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -34,7 +34,7 @@ induced by use of the :doc:`fix deform ` command. A compute of this style is created by the :doc:`fix nvt/sllod/eff ` command to compute the thermal temperature of atoms for thermostatting purposes. A compute of this style can also be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix npt/eff `, +e.g. :doc:`thermo_modify `, :doc:`fix npt/eff `, etc. The calculation performed by this compute is exactly like that diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index fbebf02ea9..fc45a5ba2b 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -77,7 +77,7 @@ assumed to be constant for the duration of the run unless the Related commands """""""""""""""" -:doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`pair\_style thole `, :doc:`compute temp ` +:doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`pair_style thole `, :doc:`compute temp ` **Default:** none diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index b83a9cbec9..e15832a25b 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -29,14 +29,14 @@ Description Define a computation that calculates the temperature of a group of nuclei and electrons in the :doc:`electron force field ` model. A compute of this style can be used by commands that compute a -temperature, e.g. :doc:`thermo\_modify `, :doc:`fix npt/eff `, etc. +temperature, e.g. :doc:`thermo_modify `, :doc:`fix npt/eff `, etc. The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2 for nuclei and sum of 1/2 (m v\^2 + 3/4 m s\^2) for electrons, where s includes the radial electron velocity contributions), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms (only total -number of nuclei in the eFF (see the :doc:`pair\_eff ` +number of nuclei in the eFF (see the :doc:`pair_eff ` command) in the group, k = Boltzmann constant, and T = temperature. This expression is summed over all nuclear and electronic degrees of freedom, essentially by setting the kinetic contribution to the heat @@ -50,7 +50,7 @@ densities two to five times the density of liquid H2 ranges from For eFF models, in order to override the default temperature reported by LAMMPS in the thermodynamic quantities reported via the :doc:`thermo ` command, the user should apply a - :doc:`thermo\_modify ` command, as shown in the following + :doc:`thermo_modify ` command, as shown in the following example: @@ -68,14 +68,14 @@ again, the radial electronic velocities are also considered. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index 51e92dc4c4..ce493802d6 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -29,7 +29,7 @@ Description Define a computation that calculates the temperature of a group of atoms, after excluding one or more velocity components. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2), @@ -48,7 +48,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of velocity components by this fix is essentially computing the temperature after a "bias" has been removed from the @@ -63,7 +63,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 67dcf3fd49..d7bbc74aea 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -55,7 +55,7 @@ velocity field, before computing the kinetic energy. This can be useful for thermostatting a collection of atoms undergoing a complex flow, e.g. via a profile-unbiased thermostat (PUT) as described in :ref:`(Evans) `. A compute of this style can be used by any command -that computes a temperature, e.g. :doc:`thermo\_modify `, +that computes a temperature, e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The *xflag*\ , *yflag*\ , *zflag* settings determine which components of @@ -107,7 +107,7 @@ bin. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the spatially-averaged velocity field by this fix is essentially computing the temperature after a "bias" has been removed @@ -122,7 +122,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. .. note:: diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index a4fc86d541..b2161c53d7 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -40,7 +40,7 @@ Define a computation that calculates the temperature of a group of atoms, after subtracting out an ramped velocity profile before computing the kinetic energy. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The meaning of the arguments for this command which define the velocity ramp are the same as for the :doc:`velocity ramp ` @@ -70,7 +70,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the ramped velocity component by this fix is essentially computing the temperature after a "bias" has been removed @@ -85,7 +85,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index 284b38d3b1..38432a18ca 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -31,7 +31,7 @@ atoms in a geometric region. This can be useful for thermostatting one portion of the simulation box. E.g. a McDLT simulation where one side is cooled, and the other side is heated. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, etc. Note that a *region*\ -style temperature can be used to thermostat with :doc:`fix temp/rescale ` or :doc:`fix langevin `, but should probably not be used with @@ -54,7 +54,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is calculated each time the temperature is evaluated since it is assumed atoms can enter/leave the region. Thus there is no need to use the *dynamic* -option of the :doc:`compute\_modify ` command for this +option of the :doc:`compute_modify ` command for this compute style. The removal of atoms outside the region by this fix is essentially @@ -77,7 +77,7 @@ motion, such as :doc:`fix shake ` and :doc:`fix rigid `. the region boundary, and hence the concept is somewhat ill-defined. If needed the number of subtracted degrees-of-freedom can be set explicitly using the *extra* option of the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index b09752a4e2..37d690848e 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -30,7 +30,7 @@ Define a computation that calculates the temperature of a group of nuclei and electrons in the :doc:`electron force field ` model, within a geometric region using the electron force field. A compute of this style can be used by commands that compute a -temperature, e.g. :doc:`thermo\_modify `. +temperature, e.g. :doc:`thermo_modify `. The operation of this compute is exactly like that described by the :doc:`compute temp/region ` command, except that diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index 75912482d8..47a94b3923 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -30,7 +30,7 @@ atoms, after subtracting out the center-of-mass velocity and angular velocity of This is useful if the group is expected to have a non-zero net velocity and/or global rotation motion for some reason. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. After the center-of-mass velocity and angular velocity has been subtracted from each atom, the temperature is calculated by the formula KE = dim/2 N k T, where @@ -47,7 +47,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the center-of-mass velocity and angular velocity by this fix is essentially computing the temperature after a "bias" has been removed from the @@ -62,7 +62,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index 6008874ce4..285a232d56 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -59,7 +59,7 @@ each has 3 degrees of freedom (2 translational, 1 rotational). combination of interaction potentials and fixes that induce no torque or otherwise constrain some of all of your particles so that this is not the case. Then there are less dof and you should use the - :doc:`compute\_modify extra ` command to adjust the dof + :doc:`compute_modify extra ` command to adjust the dof accordingly. The translational kinetic energy is computed the same as is described @@ -81,14 +81,14 @@ the vector are ordered xx, yy, zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform @@ -137,7 +137,7 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres, or point diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index e21e6caf6d..6c0b04e3bb 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -54,7 +54,7 @@ described in :ref:`Eike `. Typically this compute will be used in conjunction with the :doc:`fix adapt ` command which can perform alchemical transformations by adjusting the strength of an interaction potential as a simulation runs, as defined by one or more -:doc:`pair\_style ` or :doc:`kspace\_style ` +:doc:`pair_style ` or :doc:`kspace_style ` commands. This scaling is done via a prefactor on the energy, forces, virial calculated by the pair or K-Space style. The prefactor is often a function of a *lambda* parameter which may be adjusted from 0 @@ -100,7 +100,7 @@ lambda. Note that the *name1* variable is also typically given as an argument to the :doc:`fix adapt ` command. An alchemical simulation may use several pair potentials together, -invoked via the :doc:`pair\_style hybrid or hybrid/overlay ` +invoked via the :doc:`pair_style hybrid or hybrid/overlay ` command. The total dUs/dlambda for the overall system is calculated as the sum of each contributing term as listed by the keywords in the compute ti command. Individual pair potentials can be listed, which diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst index d673aee13e..b9b5fd82bf 100644 --- a/doc/src/compute_torque_chunk.rst +++ b/doc/src/compute_torque_chunk.rst @@ -55,7 +55,7 @@ non-zero chunk IDs. "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and 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. diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 7474fe1a25..2f25339c21 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -178,8 +178,8 @@ Voro++ software in the src/VORONOI/README file. systems, but may lead to underestimation of Voronoi volumes in low density systems. By default, the set of ghost atoms stored by each processor is determined by the cutoff used for - :doc:`pair\_style ` interactions. The cutoff can be set - explicitly via the :doc:`comm\_modify cutoff ` command. The + :doc:`pair_style ` interactions. The cutoff can be set + explicitly via the :doc:`comm_modify cutoff ` command. The Voronoi cells for atoms adjacent to empty regions will extend into those regions up to the communication cutoff in x, y, or z. In that situation, an exterior face is created at the cutoff distance normal @@ -198,7 +198,7 @@ Voro++ software in the src/VORONOI/README file. Voronoi cell can be obtained by dividing its volume by the z extent of the simulation box. Note that you define the z extent of the simulation box for 2d simulations when using the - :doc:`create\_box ` or :doc:`read\_data ` commands. + :doc:`create_box ` or :doc:`read_data ` commands. **Output info:** diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 595095e213..ea49d99ab1 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -75,9 +75,9 @@ Description This command creates atoms (or molecules) on a lattice, or a single atom (or molecule), or a random collection of atoms (or molecules), as an alternative to reading in their coordinates explicitly via a -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` command. A simulation box must already exist, which is typically -created via the :doc:`create\_box ` command. Before using +created via the :doc:`create_box ` command. Before using this command, a lattice must also be defined using the :doc:`lattice ` command, unless you specify the *single* style with units = box or the *random* style. For the remainder of this doc @@ -145,13 +145,13 @@ used multiple times, to add multiple sets of particles to the simulation. For example, grain boundaries can be created, by interleaving create\_atoms with :doc:`lattice ` commands specifying different orientations. By using the create\_atoms command -in conjunction with the :doc:`delete\_atoms ` command, +in conjunction with the :doc:`delete_atoms ` command, reasonably complex geometries can be created, or a protein can be solvated with a surrounding box of water molecules. In all these cases, care should be taken to insure that new atoms do not overlap existing atoms inappropriately, especially if molecules -are being added. The :doc:`delete\_atoms ` command can be +are being added. The :doc:`delete_atoms ` command can be used to remove overlapping atoms or molecules. .. note:: @@ -160,10 +160,10 @@ used to remove overlapping atoms or molecules. that are outside the simulation box; they will just be ignored by LAMMPS. This is true even if you are using shrink-wrapped box boundaries, as specified by the :doc:`boundary ` command. - However, you can first use the :doc:`change\_box ` command to + However, you can first use the :doc:`change_box ` command to temporarily expand the box, then add atoms via create\_atoms, then finally use change\_box command again if needed to re-shrink-wrap the - new atoms. See the :doc:`change\_box ` doc page for an + new atoms. See the :doc:`change_box ` doc page for an example of how to do this, using the create\_atoms *single* style to insert a new atom outside the current simulation box. @@ -200,12 +200,12 @@ not overlap, regardless of their relative orientations. .. note:: - If the :doc:`create\_box ` command is used to create + If the :doc:`create_box ` command is used to create the simulation box, followed by the create\_atoms command with its *mol* option for adding molecules, then you typically need to use the - optional keywords allowed by the :doc:`create\_box ` command + optional keywords allowed by the :doc:`create_box ` command for extra bonds (angles,etc) or extra special neighbors. This is - because by default, the :doc:`create\_box ` command sets up a + because by default, the :doc:`create_box ` command sets up a non-molecular system which doesn't allow molecules to be added. @@ -264,7 +264,7 @@ create a sinusoidal surface. Note that the surface is "rough" due to individual lattice points being "above" or "below" the mathematical expression for the sinusoidal curve. If a finer lattice were used, the sinusoid would appear to be "smoother". Also note the use of the -"xlat" and "ylat" :doc:`thermo\_style ` keywords which +"xlat" and "ylat" :doc:`thermo_style ` keywords which converts lattice spacings to distance. Click on the image for a larger version. @@ -366,7 +366,7 @@ Restrictions """""""""""" -An :doc:`atom\_style ` must be previously defined to use this +An :doc:`atom_style ` must be previously defined to use this command. A rotation vector specified for a single molecule must be in @@ -375,8 +375,8 @@ the z-direction for a 2d model. Related commands """""""""""""""" -:doc:`lattice `, :doc:`region `, :doc:`create\_box `, -:doc:`read\_data `, :doc:`read\_restart ` +:doc:`lattice `, :doc:`region `, :doc:`create_box `, +:doc:`read_data `, :doc:`read_restart ` Default """"""" diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index 185c1ebfd7..9b9c814c9a 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -66,15 +66,15 @@ or 4 specified atoms. The new bond (angle, dihedral, improper) interactions will then be computed during a simulation by the bond (angle, dihedral, improper) potential defined by -the :doc:`bond\_style `, :doc:`bond\_coeff `, -:doc:`angle\_style `, :doc:`angle\_coeff `, -:doc:`dihedral\_style `, -:doc:`dihedral\_coeff `, :doc:`improper\_style `, -:doc:`improper\_coeff ` commands. +the :doc:`bond_style `, :doc:`bond_coeff `, +:doc:`angle_style `, :doc:`angle_coeff `, +:doc:`dihedral_style `, +:doc:`dihedral_coeff `, :doc:`improper_style `, +:doc:`improper_coeff ` commands. The *many* style is useful for adding bonds to a system, e.g. between nearest neighbors in a lattice of atoms, without having to enumerate -all the bonds in the data file read by the :doc:`read\_data ` +all the bonds in the data file read by the :doc:`read_data ` command. The *single* styles are useful for adding bonds, angles, dihedrals, impropers @@ -97,10 +97,10 @@ data file for a complex system of molecules. bonds per atom are set to large enough values. And similarly for angles, dihedrals and impropers. Otherwise an error may occur when too many bonds (angles, dihedrals, impropers) are added to an atom. If the - :doc:`read\_data ` command is used to define the system, these + :doc:`read_data ` command is used to define the system, these parameters can be set via the "bond types" and "extra bond per atom" fields in the header section of the data file. If the - :doc:`create\_box ` command is used to define the system, + :doc:`create_box ` command is used to define the system, these 2 parameters can be set via its optional "bond/types" and "extra/bond/per/atom" arguments. And similarly for angles, dihedrals and impropers. See the doc pages for these 2 commands for details. @@ -122,9 +122,9 @@ The following settings must have been made in an input script before this style is used: * special\_bonds weight for 1-2 interactions must be 0.0 -* a :doc:`pair\_style ` must be defined -* no :doc:`kspace\_style ` defined -* minimum :doc:`pair\_style ` cutoff + :doc:`neighbor ` skin >= *rmax* +* a :doc:`pair_style ` must be defined +* no :doc:`kspace_style ` defined +* minimum :doc:`pair_style ` cutoff + :doc:`neighbor ` skin >= *rmax* These settings are required so that a neighbor list can be created to search for nearby atoms. Pairs of atoms that are already bonded @@ -134,8 +134,8 @@ a distance that encompasses the *rmax* for new bonds to create. An additional requirement for this style is that your system must be ready to perform a simulation. This means, for example, that all -:doc:`pair\_style ` coefficients be set via the -:doc:`pair\_coeff ` command. A :doc:`bond\_style ` +:doc:`pair_style ` coefficients be set via the +:doc:`pair_coeff ` command. A :doc:`bond_style ` command and all bond coefficients must also be set, even if no bonds exist before this command is invoked. This is because the building of neighbor list requires initialization and setup of a simulation, @@ -143,7 +143,7 @@ similar to what a :doc:`run ` command would require. Note that you can change any of these settings after this command executes, e.g. if you wish to use long-range Coulombic interactions -via the :doc:`kspace\_style ` command for your subsequent +via the :doc:`kspace_style ` command for your subsequent simulation. @@ -157,7 +157,7 @@ between 1 and the number of bond types defined. The *single/angle* style creates a single angle of type *atype* between three atoms with IDs *aatom1*\ , *aatom2*\ , and *aatom3*\ . The ordering of the atoms is the same as in the *Angles* section of a data -file read by the :doc:`read\_data ` command. I.e. the 3 atoms are +file read by the :doc:`read_data ` command. I.e. the 3 atoms are ordered linearly within the angle; the central atom is *aatom2*\ . *Atype* must be a value between 1 and the number of angle types defined. @@ -165,14 +165,14 @@ defined. The *single/dihedral* style creates a single dihedral of type *dtype* between four atoms with IDs *datom1*\ , *datom2*\ , *datom3*\ , and *datom4*\ . The ordering of the atoms is the same as in the *Dihedrals* section of a data file -read by the :doc:`read\_data ` command. I.e. the 4 atoms are ordered +read by the :doc:`read_data ` command. I.e. the 4 atoms are ordered linearly within the dihedral. *dtype* must be a value between 1 and the number of dihedral types defined. The *single/improper* style creates a single improper of type *itype* between four atoms with IDs *iatom1*\ , *iatom2*\ , *iatom3*\ , and *iatom4*\ . The ordering of the atoms is the same as in the *Impropers* section of a data file -read by the :doc:`read\_data ` command. I.e. the 4 atoms are ordered +read by the :doc:`read_data ` command. I.e. the 4 atoms are ordered linearly within the improper. *itype* must be a value between 1 and the number of improper types defined. @@ -190,7 +190,7 @@ with the *many* style. This is an expensive operation since the bond topology for the system must be walked to find all 1-2, 1-3, 1-4 interactions to store in an internal list, which is used when pairwise interactions are weighted; -see the :doc:`special\_bonds ` command for details. +see the :doc:`special_bonds ` command for details. Thus if you are adding a few bonds or a large list of angles all at the same time, by using this command repeatedly, it is more efficient @@ -221,12 +221,12 @@ Restrictions This command cannot be used with molecular systems defined using molecule template files via the :doc:`molecule ` and -:doc:`atom\_style template ` commands. +:doc:`atom_style template ` commands. Related commands """""""""""""""" -:doc:`create\_atoms `, :doc:`delete\_bonds ` +:doc:`create_atoms `, :doc:`delete_bonds ` Default """"""" diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 1bffab90b5..4e19def87d 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -108,7 +108,7 @@ using the :doc:`change box ` command with its *ortho* and not make the lo/hi box dimensions (as defined in your :doc:`region ` command) radically smaller/larger than the extent of the atoms you eventually plan to create, e.g. via the - :doc:`create\_atoms ` command. For example, if your atoms + :doc:`create_atoms ` command. For example, if your atoms extend from 0 to 50, you should not specify the box bounds as -10000 and 10000. This is because as described above, LAMMPS uses the specified box size to layout the 3d grid of processors. A huge @@ -128,13 +128,13 @@ bond (angle, dihedral, improper) interactions, or for molecules with special 1-2,1-3,1-4 neighbors to be added later. These optional keywords serve the same purpose as the analogous keywords that can be used in a data file which are recognized by the -:doc:`read\_data ` command when it sets up a system. +:doc:`read_data ` command when it sets up a system. Note that if these keywords are not used, then the create\_box command creates an atomic (non-molecular) simulation that does not allow bonds between pairs of atoms to be defined, or a :doc:`bond potential ` to be specified, or for molecules with special neighbors to be added to the system by commands such as -:doc:`create\_atoms mol `, :doc:`fix deposit ` +:doc:`create_atoms mol `, :doc:`fix deposit ` or :doc:`fix pour `. As an example, see the examples/deposit/in.deposit.molecule script, @@ -153,13 +153,13 @@ Restrictions """""""""""" -An :doc:`atom\_style ` and :doc:`region ` must have +An :doc:`atom_style ` and :doc:`region ` must have been previously defined to use this command. Related commands """""""""""""""" -:doc:`read\_data `, :doc:`create\_atoms `, +:doc:`read_data `, :doc:`create_atoms `, :doc:`region ` **Default:** none diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index f2db9aeb3a..ca684b4a11 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -90,24 +90,24 @@ different numbers of processors. If the *compress* keyword is set to *yes*\ , then after atoms are deleted, then atom IDs are re-assigned so that they run from 1 to the number of atoms in the system. Note that this is not done for -molecular systems (see the :doc:`atom\_style ` command), +molecular systems (see the :doc:`atom_style ` command), regardless of the *compress* setting, since it would foul up the bond connectivity that has already been assigned. However, the -:doc:`reset\_ids ` command can be used after this command to +:doc:`reset_ids ` command can be used after this command to accomplish the same thing. Note that the re-assignment of IDs is not really a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. Instead the IDs for all atoms are erased, and new IDs are assigned so that the atoms owned by individual processors have consecutive IDs, as -the :doc:`create\_atoms ` command explains. +the :doc:`create_atoms ` command explains. A molecular system with fixed bonds, angles, dihedrals, or improper interactions, is one where the topology of the interactions is typically defined in the data file read by the -:doc:`read\_data ` command, and where the interactions -themselves are defined with the :doc:`bond\_style `, -:doc:`angle\_style `, etc commands. If you delete atoms +:doc:`read_data ` command, and where the interactions +themselves are defined with the :doc:`bond_style `, +:doc:`angle_style `, etc commands. If you delete atoms from such a system, you must be careful not to end up with bonded interactions that are stored by remaining atoms but which include deleted atoms. This will cause LAMMPS to generate a "missing atoms" @@ -149,7 +149,7 @@ find overlapping atom pairs, it also means that you must define a between any pair of atoms types (plus the :doc:`neighbor ` skin) >= the specified overlap cutoff. -If the :doc:`special\_bonds ` command is used with a +If the :doc:`special_bonds ` command is used with a setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not appear in the neighbor list, and thus will not be considered for deletion by the *overlap* styles. You probably don't want to be @@ -157,12 +157,12 @@ deleting one atom in a bonded pair anyway. The *bond yes* option cannot be used with molecular systems defined using molecule template files via the :doc:`molecule ` and -:doc:`atom\_style template ` commands. +:doc:`atom_style template ` commands. Related commands """""""""""""""" -:doc:`create\_atoms `, :doc:`reset\_ids ` +:doc:`create_atoms `, :doc:`reset_ids ` Default """"""" diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index f964d059a6..7a12376eee 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -48,7 +48,7 @@ dihedrals, impropers. This command is useful for deleting interactions that have been previously turned off by bond-breaking potentials. It is also useful for turning off topology interactions between frozen or rigid atoms. Pairwise interactions can be turned -off via the :doc:`neigh\_modify exclude ` command. The +off via the :doc:`neigh_modify exclude ` command. The :doc:`fix shake ` command also effectively turns off certain bond and angle interactions. @@ -83,7 +83,7 @@ must also be of the specified type. Styles *angle*\ , *dihedral*\ , and For style *bond*\ , you can set the type to 0 to delete bonds that have been previously broken by a bond-breaking potential (which sets the -bond type to 0 when a bond is broken); e.g. see the :doc:`bond\_style quartic ` command. +bond type to 0 when a bond is broken); e.g. see the :doc:`bond_style quartic ` command. For style *stats* no interactions are turned off (or on); the status of all interactions in the specified group is simply reported. This @@ -96,7 +96,7 @@ permanently remove the interaction. E.g. a bond\_type of 2 is set to -2. The neighbor list creation routines will not include such an interaction in their interaction lists. The default is also to not alter the list of 1-2, 1-3, 1-4 neighbors computed by the -:doc:`special\_bonds ` command and used to weight pairwise +:doc:`special_bonds ` command and used to weight pairwise force and energy calculations. This means that pairwise computations will proceed as if the bond (or angle, etc) were still turned on. @@ -144,7 +144,7 @@ shared by multiple processors. This means that your system must be ready to perform a simulation before using this command (force fields setup, atom masses set, etc). Just as would be needed to run dynamics, the force field you define should define a cutoff -(e.g. through a :doc:`pair\_style ` command) which is long +(e.g. through a :doc:`pair_style ` command) which is long enough for a processor to acquire the ghost atoms its needs to compute bond, angle, etc interactions. @@ -157,8 +157,8 @@ which case you probably should be recomputing the weighting list. Related commands """""""""""""""" -:doc:`neigh\_modify ` exclude, -:doc:`special\_bonds `, :doc:`fix shake ` +:doc:`neigh_modify ` exclude, +:doc:`special_bonds `, :doc:`fix shake ` **Default:** none diff --git a/doc/src/dielectric.rst b/doc/src/dielectric.rst index 96fc861d97..44a8f4176c 100644 --- a/doc/src/dielectric.rst +++ b/doc/src/dielectric.rst @@ -29,7 +29,7 @@ long-range) to this value. The constant is unitless, since it is used to reduce the strength of the interactions. The value is used in the denominator of the formulas for Coulombic interactions - e.g. a value of 4.0 reduces the Coulombic interactions to 25% of their default -strength. See the :doc:`pair\_style ` command for more +strength. See the :doc:`pair_style ` command for more details. Restrictions @@ -39,7 +39,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_style ` +:doc:`pair_style ` Default """"""" diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index 52e636dd75..46da2f9458 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -56,15 +56,15 @@ field. The newer *charmmfsw* style was released in March 2017. We recommend it be used instead of the older *charmm* style when running a simulation with the CHARMM force field, either with long-range - Coulombics or a Coulombic cutoff, via the :doc:`pair\_style lj/charmmfsw/coul/long ` and :doc:`pair\_style lj/charmmfsw/coul/charmmfsh ` commands respectively. + Coulombics or a Coulombic cutoff, via the :doc:`pair_style lj/charmmfsw/coul/long ` and :doc:`pair_style lj/charmmfsw/coul/charmmfsh ` commands respectively. Otherwise the older *charmm* style is fine to use. See the discussion - below and more details on the :doc:`pair\_style charmm ` doc + below and more details on the :doc:`pair_style charmm ` doc page. The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * K (energy) * n (integer >= 0) @@ -78,8 +78,8 @@ With the CHARMM dihedral style, interactions between the 1st and 4th atoms in a dihedral are skipped during the normal non-bonded force computation and instead evaluated as part of the dihedral using special epsilon and sigma values specified with the -:doc:`pair\_coeff ` command of pair styles that contain -"lj/charmm" (e.g. :doc:`pair\_style lj/charmm/coul/long `) +:doc:`pair_coeff ` command of pair styles that contain +"lj/charmm" (e.g. :doc:`pair_style lj/charmm/coul/long `) In 6-membered rings, the same 1-4 interaction would be computed twice (once for the clockwise 1-4 pair in dihedral 1-2-3-4 and once in the counterclockwise dihedral 1-6-5-4) and thus the weighting factor has @@ -107,9 +107,9 @@ distance between the two atoms is within the switching region of the pairwise potential defined by the corresponding CHARMM pair style, i.e. within the outer cutoff specified for the pair style. The *charmmfsw* style should only be used when using the corresponding -:doc:`pair\_style lj/charmmfsw/coul/charmmfsw ` or -:doc:`pair\_style lj/charmmfsw/coul/long ` commands. Use -the *charmm* style with the older :doc:`pair\_style ` +:doc:`pair_style lj/charmmfsw/coul/charmmfsw ` or +:doc:`pair_style lj/charmmfsw/coul/long ` commands. Use +the *charmm* style with the older :doc:`pair_style ` commands that have just "charmm" in their style name. See the discussion on the :doc:`CHARMM pair\_style ` doc page for details. @@ -158,7 +158,7 @@ When using run\_style :doc:`respa `, these dihedral styles must be assigned to the same r-RESPA level as *pair* or *outer*\ . When used in combination with CHARMM pair styles, the 1-4 -:doc:`special\_bonds ` scaling factors must be set to 0.0. +:doc:`special_bonds ` scaling factors must be set to 0.0. Otherwise non-bonded contributions for these 1-4 pairs will be computed multiple times. @@ -169,7 +169,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst index f8f6a01bc4..fd26167f65 100644 --- a/doc/src/dihedral_class2.rst +++ b/doc/src/dihedral_class2.rst @@ -50,9 +50,9 @@ See :ref:`(Sun) ` for a description of the COMPASS class2 force fi Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, +:doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. These are the 6 coefficients for the Ed formula: @@ -65,7 +65,7 @@ These are the 6 coefficients for the Ed formula: * phi3 (degrees) For the Embt formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 5 coefficients, the first of which is "mbt" to indicate they are MiddleBondTorsion coefficients. In a data file, these coefficients should be listed under a "MiddleBondTorsion Coeffs" heading and you @@ -79,7 +79,7 @@ dihedral type. * r2 (distance) For the Eebt formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 9 coefficients, the first of which is "ebt" to indicate they are EndBondTorsion coefficients. In a data file, these coefficients should be listed under a "EndBondTorsion Coeffs" heading and you must @@ -97,7 +97,7 @@ type. * r3 (distance) For the Eat formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 9 coefficients, the first of which is "at" to indicate they are AngleTorsion coefficients. In a data file, these coefficients should be listed under a "AngleTorsion Coeffs" heading and you must leave out @@ -118,7 +118,7 @@ to radians internally; hence the units of D and E are in energy/radian. For the Eaat formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 4 coefficients, the first of which is "aat" to indicate they are AngleAngleTorsion coefficients. In a data file, these coefficients should be listed under a "AngleAngleTorsion Coeffs" heading and you @@ -134,7 +134,7 @@ Theta1 and theta2 are specified in degrees, but LAMMPS converts them to radians internally; hence the units of M are in energy/radian\^2. For the Ebb13 formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 4 coefficients, the first of which is "bb13" to indicate they are BondBond13 coefficients. In a data file, these coefficients should be listed under a "BondBond13 Coeffs" heading and you must leave out the @@ -182,7 +182,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst index a2cddfa6e9..4a3f0cd487 100644 --- a/doc/src/dihedral_coeff.rst +++ b/doc/src/dihedral_coeff.rst @@ -30,7 +30,7 @@ Description Specify the dihedral force field coefficients for one or more dihedral types. The number and meaning of the coefficients depends on the dihedral style. Dihedral coefficients can also be set in the data file read by the -:doc:`read\_data ` command or in a restart file. +:doc:`read_data ` command or in a restart file. N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be @@ -63,7 +63,7 @@ corresponds to the 1st example above would be listed as 1 80.0 1 3 -The :doc:`dihedral\_style class2 ` is an exception to +The :doc:`dihedral_style class2 ` is an exception to this rule, in that an additional argument is used in the input script to allow specification of the cross-term coefficients. See its doc page for details. @@ -84,7 +84,7 @@ page for details. The list of all dihedral styles defined in LAMMPS is given on the -:doc:`dihedral\_style ` doc page. They are also listed +:doc:`dihedral_style ` doc page. They are also listed in more compact form on the :ref:`Commands dihedral ` doc page. On either of those pages, click on the style to display the formula it @@ -100,8 +100,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. A dihedral style must be defined before any dihedral coefficients are set, either in the input script or in a data file. @@ -109,7 +109,7 @@ set, either in the input script or in a data file. Related commands """""""""""""""" -:doc:`dihedral\_style ` +:doc:`dihedral_style ` **Default:** none diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index 7a2f2bf2db..2a9aadc99e 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -45,9 +45,9 @@ behaved in the limit a->0, where it has been implemented to linear order in a for a < 0.001. The following coefficients must be defined for each dihedral type via -the :doc:`dihedral\_coeff ` command as in the example +the :doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * umin (energy) @@ -91,7 +91,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff `, +:doc:`dihedral_coeff `, :doc:`angle\_cosine\_shift\_exp ` **Default:** none diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index 83f2349cd5..0156cdce26 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -35,9 +35,9 @@ The *fourier* dihedral style uses the potential: :align: center The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * m (integer >=1) * K1 (energy) @@ -85,7 +85,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst index bdcfbf38ae..8f711f0f63 100644 --- a/doc/src/dihedral_harmonic.rst +++ b/doc/src/dihedral_harmonic.rst @@ -38,9 +38,9 @@ The *harmonic* dihedral style uses the potential :align: center The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * K (energy) * d (+1 or -1) @@ -97,7 +97,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index d348bf03de..19086e1aeb 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -40,9 +40,9 @@ so as to balance secondary (largely driven by local interactions) and tertiary structure (driven by long-range interactions). The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * A (energy) * B (energy) @@ -85,7 +85,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst index c878cbb9ca..f67b1185fe 100644 --- a/doc/src/dihedral_hybrid.rst +++ b/doc/src/dihedral_hybrid.rst @@ -32,7 +32,7 @@ example, dihedrals in a polymer flow (of dihedral type 1) could be computed with a *harmonic* potential and dihedrals in the wall boundary (of dihedral type 2) could be computed with a *helix* potential. The assignment of dihedral type to style is made via the -:doc:`dihedral\_coeff ` command or in the data file. +:doc:`dihedral_coeff ` command or in the data file. In the dihedral\_coeff commands, the name of a dihedral style must be added after the dihedral type, with the remaining coefficients being @@ -43,7 +43,7 @@ K, d, n. All other dihedral types (2-N) are computed with a *helix* potential with coefficients 10, 10, 10 for A, B, C. If dihedral coefficients are specified in the data file read via the -:doc:`read\_data ` command, then the same rule applies. +:doc:`read_data ` command, then the same rule applies. E.g. "harmonic" or "helix", must be added after the dihedral type, for each line in the "Dihedral Coeffs" section, e.g. @@ -101,7 +101,7 @@ restart file, you need to re-specify dihedral\_coeff commands. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index bd66014bd7..e304685a68 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -32,9 +32,9 @@ The *multi/harmonic* dihedral style uses the potential :align: center The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * A1 (energy) * A2 (energy) @@ -79,7 +79,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index 51ddd6a109..ceb87e4651 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -32,9 +32,9 @@ The *nharmonic* dihedral style uses the potential: :align: center The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * n (integer >=1) * A1 (energy) @@ -79,7 +79,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_none.rst b/doc/src/dihedral_none.rst index ebae5c32d6..8955323bb5 100644 --- a/doc/src/dihedral_none.rst +++ b/doc/src/dihedral_none.rst @@ -24,9 +24,9 @@ Description Using a dihedral style of none means dihedral forces and energies are not computed, even if quadruplets of dihedral atoms were listed in the -data file read by the :doc:`read\_data ` command. +data file read by the :doc:`read_data ` command. -See the :doc:`dihedral\_style zero ` command for a way to +See the :doc:`dihedral_style zero ` command for a way to calculate dihedral statistics, but compute no dihedral interactions. Restrictions @@ -36,7 +36,7 @@ Restrictions Related commands """""""""""""""" -:doc:`dihedral\_style zero ` +:doc:`dihedral_style zero ` **Default:** none diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst index 4cd21423a2..5edbcd870b 100644 --- a/doc/src/dihedral_opls.rst +++ b/doc/src/dihedral_opls.rst @@ -45,9 +45,9 @@ This dihedral potential is used in the OPLS force field and is described in :ref:`(Watkins) `. The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * K1 (energy) * K2 (energy) @@ -91,7 +91,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index d145d596ba..9634e729e9 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -35,9 +35,9 @@ This dihedral potential can be used to keep a dihedral in a predefined value (cis=zero, right-hand convention is used). The following coefficients must be defined for each dihedral type via -the :doc:`dihedral\_coeff ` command as in the example +the :doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy/radian\^2) @@ -80,7 +80,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst index 4c59e7297f..ef5a3801e2 100644 --- a/doc/src/dihedral_spherical.rst +++ b/doc/src/dihedral_spherical.rst @@ -52,9 +52,9 @@ The coefficient 69.3 is the harmonic spring constant for phi after division by sin(74.4)\*sin(48.1) (the minima positions for theta1 and theta2). The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in +:doc:`dihedral_coeff ` command as in the example above, or in the Dihedral Coeffs section of a data file read by the -:doc:`read\_data ` command: +:doc:`read_data ` command: * n (integer >= 1) * C1 (energy) @@ -94,7 +94,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index 553cfbde7c..81d1ddabdd 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -29,21 +29,21 @@ Description Set the formula(s) LAMMPS uses to compute dihedral interactions between quadruplets of atoms, which remain in force for the duration of the simulation. The list of dihedral quadruplets is read in by a -:doc:`read\_data ` or :doc:`read\_restart ` command +:doc:`read_data ` or :doc:`read_restart ` command from a data or restart file. Hybrid models where dihedrals are computed using different dihedral potentials can be setup using the *hybrid* dihedral style. The coefficients associated with a dihedral style can be specified in -a data or restart file or via the :doc:`dihedral\_coeff ` +a data or restart file or via the :doc:`dihedral_coeff ` command. All dihedral potentials store their coefficient data in binary restart files which means dihedral\_style and -:doc:`dihedral\_coeff ` commands do not need to be +:doc:`dihedral_coeff ` commands do not need to be re-specified in an input script that restarts a simulation. See the -:doc:`read\_restart ` command for details on how to do +:doc:`read_restart ` command for details on how to do this. The one exception is that dihedral\_style *hybrid* only stores the list of sub-styles in the restart file; dihedral coefficients need to be re-specified. @@ -51,7 +51,7 @@ to be re-specified. .. note:: When both a dihedral and pair style is defined, the - :doc:`special\_bonds ` command often needs to be used to + :doc:`special_bonds ` command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise exist between 4 bonded atoms. @@ -79,7 +79,7 @@ coefficients you specify. bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed dihedral equation applies to each individual dihedral. Thus you need to define *K* appropriately via the - :doc:`dihedral\_coeff ` command to account for this + :doc:`dihedral_coeff ` command to account for this difference if necessary. @@ -88,11 +88,11 @@ coefficients you specify. Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients -specified by the associated :doc:`dihedral\_coeff ` command. +specified by the associated :doc:`dihedral_coeff ` command. Click on the style to display the formula it computes, any additional arguments specified in the dihedral\_style command, and coefficients -specified by the associated :doc:`dihedral\_coeff ` +specified by the associated :doc:`dihedral_coeff ` command. There are also additional accelerated pair styles included in the @@ -137,7 +137,7 @@ individual dihedral potentials tell if it is part of a package. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` Default """"""" diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index 03c05f7893..fb3e620adc 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -34,7 +34,7 @@ Description The *table* dihedral style creates interpolation tables of length *Ntable* from dihedral potential and derivative values listed in a file(s) as a function of the dihedral angle "phi". The files are read -by the :doc:`dihedral\_coeff ` command. +by the :doc:`dihedral_coeff ` command. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and derivative values at each of @@ -54,7 +54,7 @@ coefficients are chosen from this list, and a cubic polynomial is used to compute the energy and the derivative at this angle. The following coefficients must be defined for each dihedral type via -the :doc:`dihedral\_coeff ` command as in the example +the :doc:`dihedral_coeff ` command as in the example above. * filename @@ -102,7 +102,7 @@ A section begins with a non-blank line whose 1st character is not a between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the initial text must match the argument specified in the -:doc:`dihedral\_coeff ` command. The next line lists (in +:doc:`dihedral_coeff ` command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. @@ -131,7 +131,7 @@ strange numerical behavior can occur in the large remaining gap. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the N -specified in the :doc:`dihedral\_style table ` command. +specified in the :doc:`dihedral_style table ` command. Let *Ntable* is the number of table entries requested dihedral\_style command, and let *Nfile* be the parameter following "N" in the tabulated file ("30" in the sparse example above). What LAMMPS does @@ -223,7 +223,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst index 78b9346e61..809a858f00 100644 --- a/doc/src/dihedral_table_cut.rst +++ b/doc/src/dihedral_table_cut.rst @@ -33,7 +33,7 @@ The *table/cut* dihedral style creates interpolation tables of length file(s) as a function of the dihedral angle "phi". In addition, an analytic cutoff that is quadratic in the bond-angle (theta) is applied in order to regularize the dihedral interaction. The dihedral table -files are read by the :doc:`dihedral\_coeff ` command. +files are read by the :doc:`dihedral_coeff ` command. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and derivative values at each of @@ -53,7 +53,7 @@ coefficients are chosen from this list, and a cubic polynomial is used to compute the energy and the derivative at this angle. The following coefficients must be defined for each dihedral type via -the :doc:`dihedral\_coeff ` command as in the example +the :doc:`dihedral_coeff ` command as in the example above. * style (aat) @@ -121,7 +121,7 @@ A section begins with a non-blank line whose 1st character is not a between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the initial text must match the argument specified in the -:doc:`dihedral\_coeff ` command. The next line lists (in +:doc:`dihedral_coeff ` command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. @@ -150,7 +150,7 @@ strange numerical behavior can occur in the large remaining gap. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the N -specified in the :doc:`dihedral\_style table ` command. +specified in the :doc:`dihedral_style table ` command. Let *Ntable* is the number of table entries requested dihedral\_style command, and let *Nfile* be the parameter following "N" in the tabulated file ("30" in the sparse example above). What LAMMPS does @@ -220,7 +220,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff `, :doc:`dihedral\_style table ` +:doc:`dihedral_coeff `, :doc:`dihedral_style table ` **Default:** none diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 7edf15e213..38715735ce 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -30,7 +30,7 @@ accessible to other commands. As an example, the :doc:`compute dihedral/local ` command can be used to compute the theta values for the list of quadruplets of dihedral atoms -listed in the data file read by the :doc:`read\_data ` +listed in the data file read by the :doc:`read_data ` command. If no dihedral style is defined, this command cannot be used. @@ -38,7 +38,7 @@ The optional *nocoeff* flag allows to read data files with a DihedralCoeff section for any dihedral style. Similarly, any dihedral\_coeff commands will only be checked for the dihedral type number and the rest ignored. -Note that the :doc:`dihedral\_coeff ` command must be +Note that the :doc:`dihedral_coeff ` command must be used for all dihedral types, though no additional values are specified. @@ -48,7 +48,7 @@ Restrictions **Related commands:** none -:doc:`dihedral\_style none ` +:doc:`dihedral_style none ` **Default:** none diff --git a/doc/src/dimension.rst b/doc/src/dimension.rst index c50d92c5f8..1ccb3930d6 100644 --- a/doc/src/dimension.rst +++ b/doc/src/dimension.rst @@ -27,7 +27,7 @@ Description Set the dimensionality of the simulation. By default LAMMPS runs 3d simulations. To run a 2d simulation, this command should be used prior to setting up a simulation box via the -:doc:`create\_box ` or :doc:`read\_data ` commands. +:doc:`create_box ` or :doc:`read_data ` commands. Restart files also store this setting. See the discussion on the :doc:`Howto 2d ` doc page for @@ -45,7 +45,7 @@ Restrictions This command must be used before the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. Related commands """""""""""""""" diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index 2cf5849a10..2764940dde 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -69,7 +69,7 @@ displacement(s). The scale factor implied by the *units* keyword will also be applied to the variable result. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Atom-style variables can specify the same formulas as equal-style variables but can also include per-atom values, such as @@ -100,7 +100,7 @@ rotation axis is consistent with the right-hand rule: if your right-hand thumb points along *R*\ , then your fingers wrap around the axis in the direction of positive theta. -If the defined :doc:`atom\_style ` assigns an orientation to +If the defined :doc:`atom_style ` assigns an orientation to each atom (:doc:`atom styles ` ellipsoid, line, tri, body), then that property is also updated appropriately to correspond to the atom's rotation. @@ -125,7 +125,7 @@ define the lattice spacing. :doc:`boundary ` command) are enforced which may change the box size. Other than this effect, this command does not change the size or shape of the simulation box. See the - :doc:`change\_box ` command if that effect is desired. + :doc:`change_box ` command if that effect is desired. .. note:: @@ -153,7 +153,7 @@ the z-axis are allowed. Related commands """""""""""""""" -:doc:`lattice `, :doc:`change\_box `, +:doc:`lattice `, :doc:`change_box `, :doc:`fix move ` Default diff --git a/doc/src/dump.rst b/doc/src/dump.rst index c76b8efbad..833575debc 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -154,12 +154,12 @@ of the atom configuration every N timesteps while the *movie* style combines and compresses them into a movie file; both are discussed in detail on the :doc:`dump image ` doc page. The timesteps on which dump output is written can also be controlled by a variable. -See the :doc:`dump\_modify every ` command. +See the :doc:`dump_modify every ` command. Only information for atoms in the specified group is dumped. The -:doc:`dump\_modify thresh and region and refresh ` commands +:doc:`dump_modify thresh and region and refresh ` commands can also alter what atoms are included. Not all styles support -these options; see details on the :doc:`dump\_modify ` doc +these options; see details on the :doc:`dump_modify ` doc page. As described below, the filename determines the kind of output (text @@ -172,16 +172,16 @@ or multiple smaller files). timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box. Re-neighbor timesteps will not typically coincide with the timesteps - dump snapshots are written. See the :doc:`dump\_modify pbc ` command if you with to force coordinates to be + dump snapshots are written. See the :doc:`dump_modify pbc ` command if you with to force coordinates to be strictly inside the simulation box. .. note:: - Unless the :doc:`dump\_modify sort ` option is + Unless the :doc:`dump_modify sort ` option is invoked, the lines of atom information written to dump files (typically one line per atom) will be in an indeterminate order for each snapshot. This is even true when running on a single processor, - if the :doc:`atom\_modify sort ` option is on, which it is + if the :doc:`atom_modify sort ` option is on, which it is by default. In this case atoms are re-ordered periodically during a simulation, due to spatial sorting. It is also true when running in parallel, because data for a single snapshot is collected from @@ -189,7 +189,7 @@ or multiple smaller files). For the *atom*\ , *custom*\ , *cfg*\ , and *local* styles, sorting is off by default. For the *dcd*\ , *xtc*\ , *xyz*\ , and *molfile* styles, sorting by -atom ID is on by default. See the :doc:`dump\_modify ` doc +atom ID is on by default. See the :doc:`dump_modify ` doc page for details. The *atom/gz*\ , *cfg/gz*\ , *custom/gz*\ , and *xyz/gz* styles are identical @@ -213,7 +213,7 @@ be inter-changeable. The one exception is how the filename is specified for the MPI-IO styles, as explained below. The precision of values output to text-based dump files can be -controlled by the :doc:`dump\_modify format ` command and +controlled by the :doc:`dump_modify format ` command and its options. @@ -222,7 +222,7 @@ its options. The *style* keyword determines what atom quantities are written to the file and in what format. Settings made via the -:doc:`dump\_modify ` command can also alter the format of +:doc:`dump_modify ` command can also alter the format of individual values and the file itself. The *atom*\ , *local*\ , and *custom* styles create files in a simple text @@ -288,7 +288,7 @@ the atom ID and atom type. By default, atom coords are written in a scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom is at a location 1/4 of the distance from xlo to xhi of the box boundaries. The format can be changed to unscaled coords via the -:doc:`dump\_modify ` settings. Image flags can also be +:doc:`dump_modify ` settings. Image flags can also be added for each atom via dump\_modify. Style *custom* allows you to specify a list of atom attributes to be @@ -310,7 +310,7 @@ of the possible dump local attributes is given below. Note that by using input from the :doc:`compute property/local ` command with dump local, it is possible to generate information on bonds, angles, etc that can be cut and pasted directly into a data file read by the -:doc:`read\_data ` command. +:doc:`read_data ` command. Style *cfg* has the same command syntax as style *custom* and writes extended CFG format files, as used by the @@ -323,7 +323,7 @@ since these quantities are needed to write the CFG files in the appropriate format (though the "mass" and "type" fields do not appear explicitly in the file). Any remaining attributes will be stored as "auxiliary properties" in the CFG files. Note that you will typically -want to use the :doc:`dump\_modify element ` command with +want to use the :doc:`dump_modify element ` command with CFG-formatted files, to associate element names with atom types, so that AtomEye can render atoms appropriately. When unwrapped coordinates *xsu*\ , *ysu*\ , and *zsu* are requested, the nominal AtomEye @@ -339,7 +339,7 @@ The *dcd* style writes DCD files, a standard atomic trajectory format used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD files are binary and thus may not be portable to different machines. The number of atoms per snapshot cannot change with the *dcd* style. -The *unwrap* option of the :doc:`dump\_modify ` command +The *unwrap* option of the :doc:`dump_modify ` command allows DCD coordinates to be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what @@ -351,12 +351,12 @@ The *xtc* style writes XTC files, a compressed trajectory format used by the GROMACS molecular dynamics package, and described `here `_. The precision used in XTC files can be adjusted via the -:doc:`dump\_modify ` command. The default value of 1000 +:doc:`dump_modify ` command. The default value of 1000 means that coordinates are stored to 1/1000 nanometer accuracy. XTC files are portable binary files written in the NFS XDR data format, so that any machine which supports XDR should be able to read them. The number of atoms per snapshot cannot change with the *xtc* style. -The *unwrap* option of the :doc:`dump\_modify ` command allows +The *unwrap* option of the :doc:`dump_modify ` command allows XTC coordinates to be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the @@ -369,7 +369,7 @@ coordinate format that many codes can read. Specifically it has a line with the number of atoms, then a comment line that is usually ignored followed by one line per atom with the atom type and the x-, y-, and z-coordinate of that atom. You can use the -:doc:`dump\_modify element ` option to change the output +:doc:`dump_modify element ` option to change the output from using the (numerical) atom type to an element name (or some other label). This will help many visualization programs to guess bonds and colors. @@ -387,15 +387,15 @@ timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be -changed via the :doc:`dump\_modify first ` command, which +changed via the :doc:`dump_modify first ` command, which can also be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by -using the :doc:`dump\_modify every ` command (not allowed -for *dcd* style). The :doc:`dump\_modify every ` command +using the :doc:`dump_modify every ` command (not allowed +for *dcd* style). The :doc:`dump_modify every ` command also allows a variable to be used to determine the sequence of timesteps on which dump files are written. In this mode a dump on the first timestep of a run will also not be written unless the -:doc:`dump\_modify first ` command is used. +:doc:`dump_modify first ` command is used. The specified filename determines how the dump file(s) is written. The default is to write one large text file, which is opened when the @@ -408,7 +408,7 @@ character appears in the filename, then one file per snapshot is written and the "\*" character is replaced with the timestep value. For example, tmp.dump.\* becomes tmp.dump.0, tmp.dump.10000, tmp.dump.20000, etc. This option is not available for the *dcd* and -*xtc* styles. Note that the :doc:`dump\_modify pad ` +*xtc* styles. Note that the :doc:`dump_modify pad ` command can be used to insure all timestep numbers are the same length (e.g. 00010), which can make it easier to read a series of dump files in order with some post-processing tools. @@ -423,7 +423,7 @@ support parallel I/O for output. This option is not available for the By default, P = the number of processors meaning one file per processor, but P can be set to a smaller value via the *nfile* or -*fileper* keywords of the :doc:`dump\_modify ` command. +*fileper* keywords of the :doc:`dump_modify ` command. These options can be the most efficient way of writing out dump files when running on large numbers of processors. @@ -448,7 +448,7 @@ Unlike MPI-IO restart files, which must be both written and read using MPI-IO, the dump files produced by these MPI-IO styles are identical in format to the files produced by their non-MPI-IO style counterparts. This means you can write a dump file using MPI-IO and -use the :doc:`read\_dump ` command or perform other +use the :doc:`read_dump ` command or perform other post-processing, just as if the dump file was not written using MPI-IO. @@ -529,7 +529,7 @@ bonds and angles. Note that computes which calculate global or per-atom quantities, as opposed to local quantities, cannot be output in a dump local command. -Instead, global quantities can be output by the :doc:`thermo\_style custom ` command, and per-atom quantities can be +Instead, global quantities can be output by the :doc:`thermo_style custom ` command, and per-atom quantities can be output by the dump custom command. If *c\_ID* is used as a attribute, then the local vector calculated by @@ -577,7 +577,7 @@ Nprocs-1) that currently owns the atom. *Procp1* is the proc ID+1, which can be convenient in place of a *type* attribute (1 to Ntypes) for coloring atoms in a visualization program. *Type* is the atom type (1 to Ntypes). *Element* is typically the chemical name of an -element, which you must assign to each type via the :doc:`dump\_modify element ` command. More generally, it can be any +element, which you must assign to each type via the :doc:`dump_modify element ` command. More generally, it can be any string you wish to associated with an atom type. *Mass* is the atom mass. *Vx*\ , *vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz*\ , and *q* are components of atom velocity and force and atomic charge. @@ -643,7 +643,7 @@ and coordination number of individual atoms. Note that computes which calculate global or local quantities, as opposed to per-atom quantities, cannot be output in a dump custom command. Instead, global quantities can be output by the -:doc:`thermo\_style custom ` command, and local quantities +:doc:`thermo_style custom ` command, and local quantities can be output by the dump local command. If *c\_ID* is used as a attribute, then the per-atom vector calculated @@ -718,7 +718,7 @@ Related commands :doc:`dump atom/adios `, :doc:`dump custom/adios `, :doc:`dump h5md `, :doc:`dump image `, -:doc:`dump molfile `, :doc:`dump\_modify `, +:doc:`dump molfile `, :doc:`dump_modify `, :doc:`undump ` Default diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index e3cb74e978..1cd2e81c9b 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -50,7 +50,7 @@ ADIOS-BP files are binary, portable and self-describing. **Use from write\_dump:** It is possible to use these dump styles with the -:doc:`write\_dump ` command. In this case, the sub-intervals +:doc:`write_dump ` command. In this case, the sub-intervals must not be set at all. The write\_dump command can be used to create a new file at each individual dump. @@ -84,7 +84,7 @@ See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` ---------- diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index 85a80e7d12..e0a22a846a 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -91,7 +91,7 @@ every N steps. **Use from write\_dump:** It is possible to use this dump style with the -:doc:`write\_dump ` command. In this case, the sub-intervals +:doc:`write_dump ` command. In this case, the sub-intervals must not be set at all. The write\_dump command can be used either to create a new file or to add current data to an existing dump file by using the *file\_from* keyword. @@ -137,7 +137,7 @@ provided by the HDF5 library. Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` ---------- diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 84be993724..938b11c356 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -104,7 +104,7 @@ Description Dump a high-quality rendered image of the atom configuration every N timesteps and save the images either as a sequence of JPEG or PNG or PPM files, or as a single movie file. The options for this command as -well as the :doc:`dump\_modify ` command control what is +well as the :doc:`dump_modify ` command control what is included in the image or movie and how it appears. A series of such images can easily be manually converted into an animated movie of your simulation or the process can be automated without writing the @@ -136,7 +136,7 @@ to see the full-size images: Only atoms in the specified group are rendered in the image. The -:doc:`dump\_modify region and thresh ` commands can also +:doc:`dump_modify region and thresh ` commands can also alter what atoms are included in the image. The filename suffix determines whether a JPEG, PNG, or PPM file is created with the *image* dump style. If the suffix is ".jpg" or @@ -153,7 +153,7 @@ Similarly, the format of the resulting movie is chosen with the and thus details have to be looked up in the FFmpeg documentation. Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie compression like bitrate and -framerate can be set using the :doc:`dump\_modify ` command. +framerate can be set using the :doc:`dump_modify ` command. To write out JPEG and PNG format files, you must build LAMMPS with support for the corresponding JPEG or PNG library. To convert images @@ -176,16 +176,16 @@ timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be -changed via the :doc:`dump\_modify first ` command, which +changed via the :doc:`dump_modify first ` command, which can be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by -using the :doc:`dump\_modify every ` command. +using the :doc:`dump_modify every ` command. Dump *image* filenames must contain a wildcard character "\*", so that one image file per snapshot is written. The "\*" character is replaced with the timestep value. For example, tmp.dump.\*.jpg becomes tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note -that the :doc:`dump\_modify pad ` command can be used to +that the :doc:`dump_modify pad ` command can be used to insure all timestep numbers are the same length (e.g. 00010), which can make it easier to convert a series of images into a movie in the correct ordering. @@ -219,11 +219,11 @@ to colors is as follows: * type 6 = cyan and repeats itself for types > 6. This mapping can be changed by the -:doc:`dump\_modify acolor ` command. +:doc:`dump_modify acolor ` command. If *type* is specified for the *diameter* setting then the diameter of each atom is determined by its atom type. By default all types have -diameter 1.0. This mapping can be changed by the :doc:`dump\_modify adiam ` command. +diameter 1.0. This mapping can be changed by the :doc:`dump_modify adiam ` command. If *element* is specified for the *color* and/or *diameter* setting, then the color and/or diameter of each atom is determined by which @@ -244,7 +244,7 @@ If "vx", for example, is used as the *color* setting, then the color of the atom will depend on the x-component of its velocity. The association of a per-atom value with a specific color is determined by a "color map", which can be specified via the -:doc:`dump\_modify ` command. The basic idea is that the +:doc:`dump_modify ` command. The basic idea is that the atom-attribute will be within a range of values, and every value within the range is mapped to a specific color. Depending on how the color map is defined, that mapping can take place via interpolation so @@ -255,7 +255,7 @@ If "vx", for example, is used as the *diameter* setting, then the atom will be rendered using the x-component of its velocity as the diameter. If the per-atom value <= 0.0, them the atom will not be drawn. Note that finite-size spherical particles, as defined by -:doc:`atom\_style sphere ` define a per-particle radius or +:doc:`atom_style sphere ` define a per-particle radius or diameter, which can be used as the *diameter* setting. @@ -291,9 +291,9 @@ The *bond* keyword allows to you to alter how bonds are drawn. A bond is only drawn if both atoms in the bond are being drawn due to being in the specified group and due to other selection criteria (e.g. region, threshold settings of the -:doc:`dump\_modify ` command). By default, bonds are drawn +:doc:`dump_modify ` command). By default, bonds are drawn if they are defined in the input data file as read by the -:doc:`read\_data ` command. Using *none* for both the bond +:doc:`read_data ` command. Using *none* for both the bond *color* and *width* value will turn off the drawing of all bonds. If *atom* is specified for the bond *color* value, then each bond is @@ -312,7 +312,7 @@ types to colors is as follows: * type 6 = cyan and repeats itself for bond types > 6. This mapping can be changed by -the :doc:`dump\_modify bcolor ` command. +the :doc:`dump_modify bcolor ` command. The bond *width* value can be a numeric value or *atom* or *type* (or *none* as indicated above). @@ -327,13 +327,13 @@ of the 2 atoms in the bond. If *type* is specified for the *width* value then the diameter of each bond is determined by its bond type. By default all types have -diameter 0.5. This mapping can be changed by the :doc:`dump\_modify bdiam ` command. +diameter 0.5. This mapping can be changed by the :doc:`dump_modify bdiam ` command. ---------- -The *line* keyword can be used when :doc:`atom\_style line ` +The *line* keyword can be used when :doc:`atom_style line ` is used to define particles as line segments, and will draw them as lines. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. The only setting @@ -349,7 +349,7 @@ mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump\_modify ` command. +change this via the :doc:`dump_modify ` command. The line *width* can only be a numeric value, which specifies that all lines will be drawn as cylinders with that diameter, e.g. 1.0, which @@ -360,7 +360,7 @@ e.g. Angstroms. ---------- -The *tri* keyword can be used when :doc:`atom\_style tri ` is +The *tri* keyword can be used when :doc:`atom_style tri ` is used to define particles as triangles, and will draw them as triangles or edges (3 lines) or both, depending on the setting for *tflag*\ . If edges are drawn, the *width* setting determines the diameters of the @@ -378,13 +378,13 @@ default the mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump\_modify ` command. +change this via the :doc:`dump_modify ` command. ---------- -The *body* keyword can be used when :doc:`atom\_style body ` +The *body* keyword can be used when :doc:`atom_style body ` is used to define body particles with internal state (e.g. sub-particles), and will drawn them in a manner specific to the body style. If this keyword is not used, such particles will be drawn @@ -413,7 +413,7 @@ particle. By default the mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump\_modify ` command. +change this via the :doc:`dump_modify ` command. ---------- @@ -439,7 +439,7 @@ the mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump\_modify ` command. +change this via the :doc:`dump_modify ` command. ---------- @@ -532,7 +532,7 @@ are rendered as thin cylinders in the image. If *no* is set, then the box boundaries are not drawn and the *diam* setting is ignored. If *yes* is set, the 12 edges of the box are drawn, with a diameter that is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for -2d). The color of the box boundaries can be set with the :doc:`dump\_modify boxcolor ` command. +2d). The color of the box boundaries can be set with the :doc:`dump_modify boxcolor ` command. The *axes* keyword determines if and how the coordinate axes are rendered as thin cylinders in the image. If *no* is set, then the @@ -551,7 +551,7 @@ set (default), then the sub-domain boundaries are not drawn and the *diam* setting is ignored. If *yes* is set, the 12 edges of each processor sub-domain are drawn, with a diameter that is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color -of the sub-domain boundaries can be set with the :doc:`dump\_modify boxcolor ` command. +of the sub-domain boundaries can be set with the :doc:`dump_modify boxcolor ` command. ---------- @@ -722,7 +722,7 @@ mp4). Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` Default """"""" diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 1aa09c6092..8d42a7acab 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -546,7 +546,7 @@ commands: The :doc:`compute displace/atom ` command calculates the displacement of each atom from its reference position. The "4" index is the scalar displacement; 1,2,3 are the xyz components -of the displacement. The :doc:`dump\_modify thresh ` +of the displacement. The :doc:`dump_modify thresh ` command will cause only atoms that have displaced more than 0.6 Angstroms to be output on a given snapshot (assuming metal units). However, note that when an atom is output, we also need to update the @@ -621,7 +621,7 @@ most effective when the typical magnitude of position data is between The *sort* keyword determines whether lines of per-atom output in a snapshot are sorted or not. A sort value of *off* means they will typically be written in indeterminate order, either in serial or -parallel. This is the case even in serial if the :doc:`atom\_modify sort ` option is turned on, which it is by default, to +parallel. This is the case even in serial if the :doc:`atom_modify sort ` option is turned on, which it is by default, to improve performance. A sort value of *id* means sort the output by atom ID. A sort value of N or -N means sort the output by the value in the Nth column of per-atom info in either ascending or descending @@ -647,7 +647,7 @@ performed. The *thermo* keyword only applies the dump *netcdf* style. It triggers writing of :doc:`thermo ` information to the dump file alongside per-atom data. The values included in the dump file are -identical to the values specified by :doc:`thermo\_style `. +identical to the values specified by :doc:`thermo_style `. ---------- diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst index 4c03def9b7..69347840b5 100644 --- a/doc/src/dump_molfile.rst +++ b/doc/src/dump_molfile.rst @@ -63,7 +63,7 @@ must be sorted, outside of the coordinates no change in atom properties The *format* keyword determines what format is used to write out the dump. For this to work, LAMMPS must be able to find and load a compatible molfile plugin that supports this format. Settings made via -the :doc:`dump\_modify ` command can alter per atom properties +the :doc:`dump_modify ` command can alter per atom properties like element names. The *path* keyword determines which in directories. This is a "path" @@ -71,7 +71,7 @@ like other search paths, i.e. it can contain multiple directories separated by a colon (or semi-colon on windows). This keyword is optional and default to ".", the current directory. -The *unwrap* option of the :doc:`dump\_modify ` command allows +The *unwrap* option of the :doc:`dump_modify ` command allows coordinates to be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the coordinate would be @@ -88,10 +88,10 @@ timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be -changed via the :doc:`dump\_modify first ` command, which can +changed via the :doc:`dump_modify first ` command, which can be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by using the -:doc:`dump\_modify every ` command. The :doc:`dump\_modify every ` command also allows a variable to be used to +:doc:`dump_modify every ` command. The :doc:`dump_modify every ` command also allows a variable to be used to determine the sequence of timesteps on which dump files are written. @@ -132,7 +132,7 @@ application itself. The plugins are installed in the directory: Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` Default """"""" diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst index f89faff0ca..9f98cd9824 100644 --- a/doc/src/dump_netcdf.rst +++ b/doc/src/dump_netcdf.rst @@ -20,7 +20,7 @@ Syntax * *netcdf* or *netcdf/mpiio* = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) * N = dump every this many timesteps * file = name of file to write dump info to -* args = list of atom attributes, same as for :doc:`dump\_style custom ` +* args = list of atom attributes, same as for :doc:`dump_style custom ` Examples """""""" @@ -59,7 +59,7 @@ all extensions of this dump style. In addition to per-atom data, :doc:`thermo ` data can be included in the dump file. The data included in the dump file is identical to the data specified -by :doc:`thermo\_style `. +by :doc:`thermo_style `. .. _netcdf-home: http://www.unidata.ucar.edu/software/netcdf/ @@ -89,7 +89,7 @@ more info. Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` .. _lws: http://lammps.sandia.gov diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index 2f229aaccc..6624820a4f 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -16,7 +16,7 @@ Syntax * vtk = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) * N = dump every this many timesteps * file = name of file to write dump info to -* args = same as arguments for :doc:`dump\_style custom ` +* args = same as arguments for :doc:`dump_style custom ` Examples """""""" @@ -34,20 +34,20 @@ Dump a snapshot of atom quantities to one or more files every N timesteps in a format readable by the `VTK visualization toolkit `_ or other visualization tools that use it, e.g. `ParaView `_. The timesteps on which dump output is written can also be controlled by a variable; see the -:doc:`dump\_modify every ` command for details. +:doc:`dump_modify every ` command for details. -This dump style is similar to :doc:`dump\_style custom ` but uses +This dump style is similar to :doc:`dump_style custom ` but uses the VTK library to write data to VTK simple legacy or XML format depending on the filename extension specified for the dump file. This can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*, respectively, for XML format; see the `VTK homepage `_ for a detailed description of these formats. Since this naming convention conflicts with the way binary output is usually specified (see below), the -:doc:`dump\_modify binary ` command allows setting of a +:doc:`dump_modify binary ` command allows setting of a binary option for this dump style explicitly. Only information for atoms in the specified group is dumped. The -:doc:`dump\_modify thresh and region ` commands can also +:doc:`dump_modify thresh and region ` commands can also alter what atoms are included; see details below. As described below, special characters ("\*", "%") in the filename @@ -62,17 +62,17 @@ determine the kind of output. .. warning:: - Unless the :doc:`dump\_modify sort ` option + Unless the :doc:`dump_modify sort ` option is invoked, the lines of atom information written to dump files will be in an indeterminate order for each snapshot. This is even true - when running on a single processor, if the :doc:`atom\_modify sort ` option is on, which it is by default. In this + when running on a single processor, if the :doc:`atom_modify sort ` option is on, which it is by default. In this case atoms are re-ordered periodically during a simulation, due to spatial sorting. It is also true when running in parallel, because data for a single snapshot is collected from multiple processors, each of which owns a subset of the atoms. For the *vtk* style, sorting is off by default. See the -:doc:`dump\_modify ` doc page for details. +:doc:`dump_modify ` doc page for details. ---------- @@ -91,7 +91,7 @@ hexahedrons in either legacy .vtk or .vtu XML format. Style *vtk* allows you to specify a list of atom attributes to be written to the dump file for each atom. The list of possible attributes -is the same as for the :doc:`dump\_style custom ` command; see +is the same as for the :doc:`dump_style custom ` command; see its doc page for a listing and an explanation of each attribute. .. note:: @@ -118,21 +118,21 @@ timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be -changed via the :doc:`dump\_modify first ` command, which +changed via the :doc:`dump_modify first ` command, which can also be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by -using the :doc:`dump\_modify every ` command. -The :doc:`dump\_modify every ` command +using the :doc:`dump_modify every ` command. +The :doc:`dump_modify every ` command also allows a variable to be used to determine the sequence of timesteps on which dump files are written. In this mode a dump on the first timestep of a run will also not be written unless the -:doc:`dump\_modify first ` command is used. +:doc:`dump_modify first ` command is used. Dump filenames can contain two wildcard characters. If a "\*" character appears in the filename, then one file per snapshot is written and the "\*" character is replaced with the timestep value. For example, tmp.dump\*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk, -tmp.dump20000.vtk, etc. Note that the :doc:`dump\_modify pad ` +tmp.dump20000.vtk, etc. Note that the :doc:`dump_modify pad ` command can be used to insure all timestep numbers are the same length (e.g. 00010), which can make it easier to read a series of dump files in order with some post-processing tools. @@ -146,7 +146,7 @@ mode of output on parallel machines that support parallel I/O for output. By default, P = the number of processors meaning one file per processor, but P can be set to a smaller value via the *nfile* or -*fileper* keywords of the :doc:`dump\_modify ` command. +*fileper* keywords of the :doc:`dump_modify ` command. These options can be the most efficient way of writing out dump files when running on large numbers of processors. @@ -185,7 +185,7 @@ Related commands """""""""""""""" :doc:`dump `, :doc:`dump image `, -:doc:`dump\_modify `, :doc:`undump ` +:doc:`dump_modify `, :doc:`undump ` Default """"""" diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 4d5cf59a39..723cbd4618 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -107,13 +107,13 @@ initial values after the run. The *pair* keyword enables various parameters of potentials defined by -the :doc:`pair\_style ` command to be changed, if the pair -style supports it. Note that the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands must be used in the usual manner +the :doc:`pair_style ` command to be changed, if the pair +style supports it. Note that the :doc:`pair_style ` and +:doc:`pair_coeff ` commands must be used in the usual manner to specify these parameters initially; the fix adapt command simply overrides the parameters. -The *pstyle* argument is the name of the pair style. If :doc:`pair\_style hybrid or hybrid/overlay ` is used, *pstyle* should be +The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay ` is used, *pstyle* should be a sub-style name. If there are multiple sub-styles using the same pair style, then *pstyle* should be specified as "style:N" where N is which instance of the pair style you wish to adapt, e.g. the first, @@ -213,9 +213,9 @@ meaning of these parameters: the pair\_\*.cpp file associated with the potential. Some parameters are global settings for the pair style, e.g. the -viscosity setting "mu" for :doc:`pair\_style lubricate `. +viscosity setting "mu" for :doc:`pair_style lubricate `. Other parameters apply to atom type pairs within the pair style, -e.g. the prefactor "a" for :doc:`pair\_style soft `. +e.g. the prefactor "a" for :doc:`pair_style soft `. Note that for many of the potentials, the parameter that can be varied is effectively a prefactor on the entire energy expression for the @@ -233,7 +233,7 @@ be specified to indicate which type pairs to apply it to. If a global parameter is specified, the *I* and *J* settings still need to be specified, but are ignored. -Similar to the :doc:`pair\_coeff command `, I and J can be +Similar to the :doc:`pair_coeff command `, I and J can be specified in one of two ways. Explicit numeric values can be used for each, as in the 1st example above. I <= J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values. @@ -248,9 +248,9 @@ all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). Note that only type pairs with I <= J are considered; if asterisks imply type pairs where J < I, they are ignored. -IMPROTANT NOTE: If :doc:`pair\_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will +IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will be a sub-style name. You must specify I,J arguments that correspond -to type pair values defined (via the :doc:`pair\_coeff ` +to type pair values defined (via the :doc:`pair_coeff ` command) for that sub-style. The *v\_name* argument for keyword *pair* is the name of an @@ -258,16 +258,16 @@ The *v\_name* argument for keyword *pair* is the name of an this fix is invoked to set the parameter to a new value. It should be specified as v\_name, where name is the variable name. Equal-style variables can specify formulas with various mathematical functions, -and include :doc:`thermo\_style ` command keywords for the +and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify parameters that change as a function of time or span consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the :doc:`run ` command and the -*elaplong* keyword of :doc:`thermo\_style custom ` for +*elaplong* keyword of :doc:`thermo_style custom ` for details. For example, these commands would change the prefactor coefficient of -the :doc:`pair\_style soft ` potential from 10.0 to 30.0 in a +the :doc:`pair_style soft ` potential from 10.0 to 30.0 in a linear fashion over the course of a simulation: @@ -309,7 +309,7 @@ working with fix\_adapt are The *kspace* keyword used the specified variable as a scale factor on the energy, forces, virial calculated by whatever K-Space solver is -defined by the :doc:`kspace\_style ` command. If the +defined by the :doc:`kspace_style ` command. If the variable has a value of 1.0, then the solver is unaltered. The *kspace* keyword works this way whether the *scale* keyword @@ -341,7 +341,7 @@ for all atoms in the fix group. by the *atom* keyword. If the atom parameter is *diameter* and per-atom density and per-atom -mass are defined for particles (e.g. :doc:`atom\_style granular `), then the mass of each particle is also +mass are defined for particles (e.g. :doc:`atom_style granular `), then the mass of each particle is also changed when the diameter changes (density is assumed to stay constant). @@ -361,7 +361,7 @@ over the course of a 1000-step simulation: **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 60c05ec796..2cc3a59191 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -111,13 +111,13 @@ the same values of the parameters. The *pair* keyword enables various parameters of potentials defined by -the :doc:`pair\_style ` command to be changed, if the pair -style supports it. Note that the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands must be used in the usual manner +the :doc:`pair_style ` command to be changed, if the pair +style supports it. Note that the :doc:`pair_style ` and +:doc:`pair_coeff ` commands must be used in the usual manner to specify these parameters initially; the fix adapt command simply overrides the parameters. -The *pstyle* argument is the name of the pair style. If :doc:`pair\_style hybrid or hybrid/overlay ` is used, *pstyle* should be +The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay ` is used, *pstyle* should be a sub-style name. For example, *pstyle* could be specified as "soft" or "lubricate". The *pparam* argument is the name of the parameter to change. This is the current list of pair styles and parameters that @@ -204,7 +204,7 @@ be specified to indicate which type pairs to apply it to. If a global parameter is specified, the *I* and *J* settings still need to be specified, but are ignored. -Similar to the :doc:`pair\_coeff command `, I and J can be +Similar to the :doc:`pair_coeff command `, I and J can be specified in one of two ways. Explicit numeric values can be used for each, as in the 1st example above. I <= J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values. @@ -219,9 +219,9 @@ all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). Note that only type pairs with I <= J are considered; if asterisks imply type pairs where J < I, they are ignored. -IMPROTANT NOTE: If :doc:`pair\_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will +IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will be a sub-style name. You must specify I,J arguments that correspond -to type pair values defined (via the :doc:`pair\_coeff ` +to type pair values defined (via the :doc:`pair_coeff ` command) for that sub-style. The *v\_name* argument for keyword *pair* is the name of an @@ -229,16 +229,16 @@ The *v\_name* argument for keyword *pair* is the name of an this fix is invoked to set the parameter to a new value. It should be specified as v\_name, where name is the variable name. Equal-style variables can specify formulas with various mathematical functions, -and include :doc:`thermo\_style ` command keywords for the +and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify parameters that change as a function of time or span consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the :doc:`run ` command and the -*elaplong* keyword of :doc:`thermo\_style custom ` for +*elaplong* keyword of :doc:`thermo_style custom ` for details. For example, these commands would change the prefactor coefficient of -the :doc:`pair\_style soft ` potential from 10.0 to 30.0 in a +the :doc:`pair_style soft ` potential from 10.0 to 30.0 in a linear fashion over the course of a simulation: @@ -253,7 +253,7 @@ linear fashion over the course of a simulation: The *kspace* keyword used the specified variable as a scale factor on the energy, forces, virial calculated by whatever K-Space solver is -defined by the :doc:`kspace\_style ` command. If the +defined by the :doc:`kspace_style ` command. If the variable has a value of 1.0, then the solver is unaltered. The *kspace* keyword works this way whether the *scale* keyword @@ -283,7 +283,7 @@ variables. The new value is assigned to the corresponding attribute for all atoms in the fix group. If the atom parameter is *diameter* and per-atom density and per-atom -mass are defined for particles (e.g. :doc:`atom\_style granular `), then the mass of each particle is also +mass are defined for particles (e.g. :doc:`atom_style granular `), then the mass of each particle is also changed when the diameter changes (density is assumed to stay constant). @@ -306,7 +306,7 @@ parameters on the outermost rRESPA level. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 91134eac12..971abdc682 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -59,7 +59,7 @@ will be evaluated each timestep, and its value(s) used to determine the force component. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent force field. @@ -145,7 +145,7 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" inferred by the added force to the system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious quantity but is needed so that the :doc:`minimize ` command can include the @@ -153,12 +153,12 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the added forces on atoms to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -184,7 +184,7 @@ the iteration count during the minimization. If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst index 26493624ec..75636d5abf 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -48,7 +48,7 @@ will be evaluated each timestep, and its value used to determine the torque component. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent torque. @@ -60,7 +60,7 @@ time. Thus it is easy to specify a time-dependent torque. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" inferred by the added forces to the system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious quantity but is needed so that the :doc:`minimize ` command can include the @@ -68,7 +68,7 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added forces. -The :doc:`fix\_modify ` *respa* option is supported by +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its torque. Default is the outermost level. diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst index 977e96a53a..29ef20342a 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -57,7 +57,7 @@ This fix creates atoms on a lattice, appended on the zhi edge of the system box. This can be useful when a shock or wave is propagating from zlo. This allows the system to grow with time to accommodate an expanding wave. A simulation box must already exist, which is -typically created via the :doc:`create\_box ` command. +typically created via the :doc:`create_box ` command. Before using this command, a lattice must also be defined using the :doc:`lattice ` command. @@ -94,7 +94,7 @@ define the lattice spacings. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index b765efb30c..2c2f474c93 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -122,7 +122,7 @@ Note coupling and post-processing can be combined in the same simulations using **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 +No information about this fix is written to :doc:`binary restart files `. The :doc:`fix_modify ` options relevant to this fix are listed below. 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 @@ -141,7 +141,7 @@ Thermal and two\_temperature (coupling) types use a Verlet time-integration algo Related commands """""""""""""""" -After specifying this fix in your input script, several other :doc:`fix\_modify ` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. +After specifying this fix in your input script, several other :doc:`fix_modify ` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. fix\_modify commands for setup: diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index e5851db353..420a490c15 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -141,7 +141,7 @@ include: :doc:`efield `, :doc:`gravity `, :doc:`temp/rescale `, and :doc:`wall fixes `. For that energy to be included in the total potential energy of the system (the quantity used when performing GCMC moves), -you MUST enable the :doc:`fix\_modify ` *energy* option for +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. @@ -150,17 +150,17 @@ specify if this should be done. 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 of exchange attempts and successes etc. See -the :doc:`read\_restart ` command for info on how to +the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. note:: For this to work correctly, the timestep must **not** be changed - after reading the restart with :doc:`reset\_timestep `. + after reading the restart with :doc:`reset_timestep `. The fix will try to detect it and stop with an error. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global vector of length 2, which can be accessed @@ -188,7 +188,7 @@ Related commands :doc:`fix nvt `, :doc:`neighbor `, :doc:`fix deposit `, :doc:`fix evaporate `, -:doc:`delete\_atoms `, :doc:`fix gcmc ` +:doc:`delete_atoms `, :doc:`fix gcmc ` Default """"""" diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 3a066ab55b..a9878887d8 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -162,7 +162,7 @@ per-atom quantities to time average. **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 +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 stored by this fix for access by various :doc:`output commands `. diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index ff317bf15e..92fe47bfb5 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -102,7 +102,7 @@ Use one or more per-atom vectors as inputs every few timesteps, sum the values over the atoms in each chunk at each timestep, then average the per-chunk values over longer timescales. The resulting chunk averages can be used by other :doc:`output commands ` such -as :doc:`thermo\_style custom `, and can also be written to +as :doc:`thermo_style custom `, and can also be written to a file. In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom @@ -474,7 +474,7 @@ dimensions. Those values are always in distance :doc:`units `. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global array of values which can be accessed by diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 9c7d27b761..c5b422ef6e 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -79,7 +79,7 @@ Use one or more global scalar values as inputs every few timesteps, calculate time correlations between them at varying time intervals, and average the correlation data over longer timescales. The resulting correlation values can be time integrated by -:doc:`variables ` or used by other :doc:`output commands ` such as :doc:`thermo\_style custom `, and can also be written to a file. See the +:doc:`variables ` or used by other :doc:`output commands ` such as :doc:`thermo_style custom `, and can also be written to a file. See the :doc:`fix ave/correlate/long ` command for an alternate method for computing correlation functions efficiently over very long time windows. @@ -332,7 +332,7 @@ included in the variable formula or via the *prefactor* keyword. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global array of values which can be accessed by diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 4a2e73d7df..176e4b51db 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -345,7 +345,7 @@ the histogram. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a global vector and global array which can be diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 3774379f19..39fa1746e4 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -76,7 +76,7 @@ Description Use one or more global values as inputs every few timesteps, and average them over longer timescales. The resulting averages can be used by other :doc:`output commands ` such as -:doc:`thermo\_style custom `, and can also be written to a +:doc:`thermo_style custom `, and can also be written to a file. Note that if no time averaging is done, this command can be used as a convenient way to simply output one or more global values to a file. @@ -321,7 +321,7 @@ appropriate fields from the fix ave/time command. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a global scalar or global vector or global array diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index f786c043c9..07d2e3b0f0 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -65,7 +65,7 @@ evaluated each timestep, and its value used to determine the average force. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent average force. @@ -103,7 +103,7 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 93c2a5b33c..db2bf9e64b 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -130,7 +130,7 @@ forced even if the current balance is perfect (1.0) be specifying a create a logical 3d grid cannot achieve perfect balance for many irregular distributions of particles. Likewise, if a portion of the system is a perfect lattice, e.g. the initial system is generated by - the :doc:`create\_atoms ` command, then "grid" methods may + the :doc:`create_atoms ` command, then "grid" methods may be unable to achieve exact balance. This is because entire lattice planes will be owned or not owned by a single processor. @@ -144,7 +144,7 @@ forced even if the current balance is perfect (1.0) be specifying a proportional to particle count, and changing the relative size and shape of processor sub-domains may lead to additional computational and communication overheads, e.g. in the PPPM solver used via the - :doc:`kspace\_style ` command. Thus you should benchmark + :doc:`kspace_style ` command. Thus you should benchmark the run times of a simulation before and after balancing. @@ -180,8 +180,8 @@ fashion so as to have equal numbers of particles (or weight) in each sub-box, as in the rightmost diagram above. The "grid" methods can be used with either of the -:doc:`comm\_style ` command options, *brick* or *tiled*\ . The -"tiling" methods can only be used with :doc:`comm\_style tiled `. +:doc:`comm_style ` command options, *brick* or *tiled*\ . The +"tiling" methods can only be used with :doc:`comm_style tiled `. When a "grid" method is specified, the current domain partitioning can be either a logical 3d grid or a tiled partitioning. In the former @@ -208,7 +208,7 @@ The *Nfreq* setting determines how often a re-balance is performed. If time a re-balance occurs, a reneighboring is triggered, so *Nfreq* should not be too small. If *Nfreq* = 0, then re-balancing will be done every time reneighboring normally occurs, as determined by the -the :doc:`neighbor ` and :doc:`neigh\_modify ` +the :doc:`neighbor ` and :doc:`neigh_modify ` command settings. On re-balance steps, re-balancing will only be attempted if the current @@ -377,7 +377,7 @@ each processor, instead of 4, and "SQUARES" replaced by "CUBES". **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which is the imbalance factor @@ -411,13 +411,13 @@ For 2d simulations, the *z* style cannot be used. Nor can a "z" appear in *dimstr* for the *shift* style. Balancing through recursive bisectioning (\ *rcb* style) requires -:doc:`comm\_style tiled ` +:doc:`comm_style tiled ` Related commands """""""""""""""" :doc:`group `, :doc:`processors `, :doc:`balance `, -:doc:`comm\_style ` +:doc:`comm_style ` .. _pizza: http://pizza.sandia.gov diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index fa7aba3c6b..57bd3d39a8 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -43,7 +43,7 @@ Break bonds between pairs of atoms as a simulation runs according to specified criteria. This can be used to model the dissolution of a polymer network due to stretching of the simulation box or other deformations. In this context, a bond means an interaction between a -pair of atoms computed by the :doc:`bond\_style ` command. +pair of atoms computed by the :doc:`bond_style ` command. Once the bond is broken it will be permanently deleted, as will all angle, dihedral, and improper interactions that bond is part of. @@ -100,7 +100,7 @@ neighbor lists must be immediately updated on the same timestep. This is to insure that any pairwise interactions that should be turned "on" due to a bond breaking, because they are no longer excluded by the presence of the bond and the settings of the -:doc:`special\_bonds ` command, will be immediately +:doc:`special_bonds ` command, will be immediately recognized. All of these operations increase the cost of a timestep. Thus you should be cautious about invoking this fix too frequently. @@ -123,7 +123,7 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes two statistics which it stores in a global vector of @@ -150,7 +150,7 @@ Related commands """""""""""""""" :doc:`fix bond/create `, :doc:`fix bond/react `, :doc:`fix bond/swap `, -:doc:`dump local `, :doc:`special\_bonds ` +:doc:`dump local `, :doc:`special_bonds ` Default """"""" diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index 9a11558e83..dbf1234582 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -57,7 +57,7 @@ Create bonds between pairs of atoms as a simulation runs according to specified criteria. This can be used to model cross-linking of polymers, the formation of a percolation network, etc. In this context, a bond means an interaction between a pair of atoms computed -by the :doc:`bond\_style ` command. Once the bond is created +by the :doc:`bond_style ` command. Once the bond is created it will be permanently in place. Optionally, the creation of a bond can also create angle, dihedral, and improper interactions that bond is part of. See the discussion of the *atype*\ , *dtype*\ , and *itype* @@ -92,7 +92,7 @@ a bond on this timestep, even if it has other possible bond partners. It is permissible to have *itype* = *jtype*\ . *Rmin* must be <= the pairwise cutoff distance between *itype* and *jtype* atoms, as defined -by the :doc:`pair\_style ` command. +by the :doc:`pair_style ` command. The *iparam* and *jparam* keywords can be used to limit the bonding functionality of the participating atoms. Each atom keeps track of @@ -106,7 +106,7 @@ The *newtype* value for *iparam* and *jparam* can be used to change the atom type of atom I or J when it reaches *maxbond* number of bonds of type *bondtype*\ . This means it can now interact in a pairwise fashion with other atoms in a different way by specifying different -:doc:`pair\_coeff ` coefficients. If you do not wish the +:doc:`pair_coeff ` coefficients. If you do not wish the atom type to change, simply specify *newtype* as *itype* or *jtype*\ . The *prob* keyword can also effect whether an eligible bond is @@ -132,10 +132,10 @@ of new bonds, angles, etc. molecule retain their original molecule IDs. If the *atype* keyword is used and if an angle potential is defined -via the :doc:`angle\_style ` command, then any new 3-body +via the :doc:`angle_style ` command, then any new 3-body interactions inferred by the creation of a bond will create new angles of type *angletype*\ , with parameters assigned by the corresponding -:doc:`angle\_coeff ` command. Likewise, the *dtype* and +:doc:`angle_coeff ` command. Likewise, the *dtype* and *itype* keywords will create new dihedrals and impropers of type *dihedraltype* and *impropertype*\ . @@ -149,8 +149,8 @@ of type *angletype*\ , with parameters assigned by the corresponding "extra bond per atom" parameter must be set to allow for it. Ditto for "extra angle per atom", "extra dihedral per atom", and "extra improper per atom" if angles, dihedrals, or impropers are being added - when bonds are created. See the :doc:`read\_data ` or - :doc:`create\_box ` command for more details. Note that a + when bonds are created. See the :doc:`read_data ` or + :doc:`create_box ` command for more details. Note that a data file with no atoms can be used if you wish to add non-bonded atoms via the :doc:`create atoms ` command, e.g. for a percolation simulation. @@ -165,8 +165,8 @@ of type *angletype*\ , with parameters assigned by the corresponding molecular topology of your system. The "extra special per atom" parameter must typically be set to allow for the new maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2 - ways to do this. See the :doc:`read\_data ` or - :doc:`create\_box ` commands for details. + ways to do this. See the :doc:`read_data ` or + :doc:`create_box ` commands for details. .. note:: @@ -174,20 +174,20 @@ of type *angletype*\ , with parameters assigned by the corresponding keywords, the list of topological neighbors is updated for atoms affected by the new bond. This in turn affects which neighbors are considered for pairwise interactions, using the weighting rules set by - the :doc:`special\_bonds ` command. Consider a new bond + the :doc:`special_bonds ` command. Consider a new bond created between atoms I,J. If J has a bonded neighbor K, then K becomes a 2nd neighbor of I. Even if the *atype* keyword is not used to create angle I-J-K, the pairwise interaction between I and K will be potentially turned off or weighted by the 1-3 weighting specified - by the :doc:`special\_bonds ` command. This is the case + by the :doc:`special_bonds ` command. This is the case even if the "angle yes" option was used with that command. The same is true for 3rd neighbors (1-4 interactions), the *dtype* keyword, and the "dihedral yes" option used with the - :doc:`special\_bonds ` command. + :doc:`special_bonds ` command. Note that even if your simulation starts with no bonds, you must -define a :doc:`bond\_style ` and use the -:doc:`bond\_coeff ` command to specify coefficients for the +define a :doc:`bond_style ` and use the +:doc:`bond_coeff ` command to specify coefficients for the *bondtype*\ . Similarly, if new atom types are specified by the *iparam* or *jparam* keywords, they must be within the range of atom types allowed by the simulation and pairwise coefficients must be @@ -201,7 +201,7 @@ created, neighbor lists must be immediately updated on the same timestep. This is to insure that any pairwise interactions that should be turned "off" due to a bond creation, because they are now excluded by the presence of the bond and the settings of the -:doc:`special\_bonds ` command, will be immediately +:doc:`special_bonds ` command, will be immediately recognized. All of these operations increase the cost of a timestep. Thus you should be cautious about invoking this fix too frequently. @@ -224,7 +224,7 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes two statistics which it stores in a global vector of @@ -251,7 +251,7 @@ Related commands """""""""""""""" :doc:`fix bond/break `, :doc:`fix bond/react `, :doc:`fix bond/swap `, -:doc:`dump local `, :doc:`special\_bonds ` +:doc:`dump local `, :doc:`special_bonds ` Default """"""" diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index b2866eb9c7..ec9533788e 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -248,7 +248,7 @@ A discussion of correctly handling this is also provided on the the existing system and reaction templates. As when inserting molecules, enough space for this increased topology/atom must be reserved by using the relevant "extra" keywords to the - :doc:`read\_data ` or :doc:`create\_box ` commands. + :doc:`read_data ` or :doc:`create_box ` commands. The map file is a text document with the following format: @@ -492,7 +492,7 @@ local command. Cumulative reaction counts for each reaction are written to :doc:`binary restart files `. These values are associated with the reaction name (react-ID). Additionally, internally-created per-atom properties are stored to allow for smooth restarts. None of the -:doc:`fix\_modify ` options are relevant to this fix. +:doc:`fix_modify ` options are relevant to this fix. This fix computes one statistic for each *react* argument that it stores in a global vector, of length 'number of react arguments', that @@ -524,7 +524,7 @@ Related commands :doc:`fix bond/create `, :doc:`fix bond/break `, :doc:`fix bond/swap `, -:doc:`dump local `, :doc:`special\_bonds ` +:doc:`dump local `, :doc:`special_bonds ` Default """"""" diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst index c4eb2a16b5..b341fea35b 100644 --- a/doc/src/fix_bond_swap.rst +++ b/doc/src/fix_bond_swap.rst @@ -41,7 +41,7 @@ gyration. It is designed for use with systems of :doc:`FENE ` or :doc:`harmonic ` bead-spring polymer chains where each polymer is a linear chain of monomers, but LAMMPS does not enforce this requirement, i.e. any -:doc:`bond\_style ` can be used. +:doc:`bond_style ` can be used. A schematic of the kinds of bond swaps that can occur is shown here: @@ -86,7 +86,7 @@ by this processor on this timestep. The criterion for matching molecule IDs is how bond swaps performed by this fix conserve chain length. To use this features you must setup the molecule IDs for your polymer chains in a certain way, typically -in the data file, read by the :doc:`read\_data ` command. +in the data file, read by the :doc:`read_data ` command. Consider a system of 6-mer chains. You have 2 choices. If the molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then swaps will conserve chain length. For a particular monomer there will @@ -134,11 +134,11 @@ appended and the group for the new compute is "all", so that the temperature of the entire system is used. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -157,7 +157,7 @@ each processor generates possible swaps independently of other processors. Thus if you repeat the same simulation on a different number of processors, the specific swaps performed will be different. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used to compute the temperature for the Boltzmann criterion. diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst index 315846a943..02e5f97736 100644 --- a/doc/src/fix_box_relax.rst +++ b/doc/src/fix_box_relax.rst @@ -67,7 +67,7 @@ varied together during the minimization. Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The :doc:`create\_box `, :doc:`read data `, and :doc:`read\_restart ` commands +dimensions (x,y,z,xy,xz,yz). The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -315,11 +315,11 @@ as the fix group. Also note that the pressure compute does not include a kinetic component. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -331,7 +331,7 @@ It also means that changing attributes of *thermo\_temp* or No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its temperature and pressure calculation, as described above. Note @@ -357,7 +357,7 @@ energy, plus the strain energy, if it exists, as described above. The energy values reported at the end of a minimization run under "Minimization stats" include this energy, and so differ from what LAMMPS normally reports as potential energy. This fix does not support -the :doc:`fix\_modify ` *energy* option, because that would +the :doc:`fix_modify ` *energy* option, because that would result in double-counting of the fix energy in the minimization energy. Instead, the fix energy can be explicitly added to the potential energy using one of these two variants: @@ -385,8 +385,8 @@ Only dimensions that are available can be adjusted by this fix. Non-periodic dimensions are not available. *z*\ , *xz*\ , and *yz*\ , are not available for 2D simulations. *xy*\ , *xz*\ , and *yz* are only available if the simulation domain is non-orthogonal. The -:doc:`create\_box `, :doc:`read data `, and -:doc:`read\_restart ` commands specify whether the +:doc:`create_box `, :doc:`read data `, and +:doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst index d935144cc0..01539b6d68 100644 --- a/doc/src/fix_client_md.rst +++ b/doc/src/fix_client_md.rst @@ -53,8 +53,8 @@ that LAMMPS exchanges with the server code is defined on the :doc:`server md `, :doc:`bond\_style `, or -:doc:`kspace\_style ` command. However it is possible for +:doc:`pair_style `, :doc:`bond_style `, or +:doc:`kspace_style ` command. However it is possible for a server code to only compute a portion of the full force-field, while LAMMPS computes the remaining part. Your LAMMPS script can also specify boundary conditions or force constraints in the usual way, @@ -74,11 +74,11 @@ LAMMPS and another code in tandem to perform a coupled simulation. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential energy computed by the server application to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the server application's contribution to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index abdf095959..70e1dd5987 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -76,7 +76,7 @@ remaining 5 columns are the atom IDs of the atoms in the two 4-atom dihedrals that overlap to create the CMAP 5-body interaction. Note that the "crossterm" and "CMAP" keywords for the header and body sections match those specified in the read\_data command following the -data file name; see the :doc:`read\_data ` doc page for +data file name; see the :doc:`read_data ` doc page for more details. A data file containing CMAP cross-terms can be generated from a PDB @@ -88,7 +88,7 @@ more information. The potential energy associated with CMAP interactions can be output as described below. It can also be included in the total potential energy of the system, as output by the -:doc:`thermo\_style ` command, if the :doc:`fix\_modify energy ` command is used, as in the example above. See +:doc:`thermo_style ` command, if the :doc:`fix_modify energy ` command is used, as in the example above. See the note below about how to include the CMAP energy when performing an :doc:`energy minimization `. @@ -98,16 +98,16 @@ the note below about how to include the CMAP energy when performing an **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 +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 restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" of the CMAP interactions system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interaction between atoms to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* @@ -128,15 +128,15 @@ invoked by the :doc:`minimize ` command. If you want the potential energy associated with the CMAP terms forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" To function as expected this fix command must be issued *before* a -:doc:`read\_data ` command but *after* a -:doc:`read\_restart ` command. +:doc:`read_data ` command but *after* a +:doc:`read_restart ` command. This fix can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more @@ -145,7 +145,7 @@ info. Related commands """""""""""""""" -:doc:`fix\_modify `, :doc:`read\_data ` +:doc:`fix_modify `, :doc:`read_data ` **Default:** none diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index bd29a394cb..eac0e21d76 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -74,7 +74,7 @@ no restriction to functionality by limiting the number of colvars fixes. The *input* keyword allows to specify a state file that would contain the restart information required in order to continue a calculation from a prerecorded state. Fix colvars records it state in :doc:`binary restart ` -files, so when using the :doc:`read\_restart ` command, +files, so when using the :doc:`read_restart ` command, this is usually not needed. The *output* keyword allows to specify the output prefix. All output @@ -103,7 +103,7 @@ This fix writes the current status of the colvars module into mode status file that is written by the colvars module itself and the kind of information in both files is identical. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change from the biasing force added by the fix to the system's potential energy as part of :doc:`thermodynamic output `. diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 906be7ca7c..55be294df8 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -194,7 +194,7 @@ equal-style versus internal-style variable interchangeably. **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 +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. This fix produces a global vector with 3 values which can be accessed diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index dc0b566678..fe1b0925d6 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -114,10 +114,10 @@ unspecified parameters can also be controlled by a :doc:`fix npt ` or :d The size and shape of the simulation box at the beginning of the simulation run were either specified by the -:doc:`create\_box ` or :doc:`read\_data ` or -:doc:`read\_restart ` command used to setup the simulation +:doc:`create_box ` or :doc:`read_data ` or +:doc:`read_restart ` command used to setup the simulation initially if it is the first run, or they are the values from the end -of the previous run. The :doc:`create\_box `, :doc:`read data `, and :doc:`read\_restart ` commands +of the previous run. The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. If fix deform changes the xy,xz,yz tilt factors, then the simulation box @@ -578,7 +578,7 @@ been previously used to define the lattice spacing. Note that the units choice also affects the *vel* style parameters since it is defined in terms of distance/time. Also note that the units keyword does not affect the *variable* style. You should use the *xlat*\ , -*ylat*\ , *zlat* keywords of the :doc:`thermo\_style ` +*ylat*\ , *zlat* keywords of the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. @@ -607,7 +607,7 @@ instructions on how to use the accelerated styles effectively. 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 ` -command. None of the :doc:`fix\_modify ` options are +command. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. @@ -630,7 +630,7 @@ xy) that is shrink-wrapped via the :doc:`boundary ` command. Related commands """""""""""""""" -:doc:`change\_box ` +:doc:`change_box ` Default """"""" diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 29b4381441..c076d80ed4 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -100,7 +100,7 @@ default group "all" and the group specified in the fix deposit command If you are computing temperature values which include inserted particles, you will want to use the -:doc:`compute\_modify ` dynamic option, which insures the +:doc:`compute_modify ` dynamic option, which insures the current number of atoms is used as a normalizing factor each time the temperature is computed. @@ -115,7 +115,7 @@ prevent this behavior. Note that if a shrink-wrap boundary is used, it is OK to insert the new particle outside the box, however the box will immediately be expanded to include the new particle. When simulating a sputtering experiment it is probably more realistic to -ignore those atoms using the :doc:`thermo\_modify ` +ignore those atoms using the :doc:`thermo_modify ` command with the *lost ignore* option and a fixed :doc:`boundary `. @@ -272,7 +272,7 @@ units of distance or velocity. If you are monitoring the temperature of a system where the atom count is changing due to adding particles, you typically should use - the :doc:`compute\_modify dynamic yes ` command for the + the :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. **Restart, fix\_modify, output, run start/stop, minimize info:** @@ -280,17 +280,17 @@ units of distance or velocity. 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 next timestep for deposition, etc. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. note:: For this to work correctly, the timestep must **not** be changed - after reading the restart with :doc:`reset\_timestep `. + after reading the restart with :doc:`reset_timestep `. The fix will try to detect it and stop with an error. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index e2cedd0d9f..09fc23ac66 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -39,10 +39,10 @@ the particle internal energy through a mesoparticle equation of state. An additional fix must be specified that defines the equation of state for each particle, e.g. :doc:`fix eos/cv `. -This fix must be used with the :doc:`pair\_style dpd/fdt/energy ` command. +This fix must be used with the :doc:`pair_style dpd/fdt/energy ` command. Note that numerous variants of DPD can be specified by choosing an -appropriate combination of the integrator and :doc:`pair\_style dpd/fdt/energy ` command. DPD under isoenergetic conditions +appropriate combination of the integrator and :doc:`pair_style dpd/fdt/energy ` command. DPD under isoenergetic conditions can be specified by using fix *dpd/energy*\ , fix *nve* and pair\_style *dpd/fdt/energy*\ . DPD under isoenthalpic conditions can be specified by using fix *dpd/energy*\ , fix *nph* and pair\_style @@ -85,7 +85,7 @@ LAMMPS was built with that package. See the :doc:`Build package This fix must be used with an additional fix that specifies time integration, e.g. :doc:`fix nve `. -The fix *dpd/energy* requires the *dpd* :doc:`atom\_style ` +The fix *dpd/energy* requires the *dpd* :doc:`atom_style ` to be used in order to properly account for the particle internal energies and temperature. diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 66895f2538..d23fbff1c9 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -72,7 +72,7 @@ cuboid domain to apply the source flux to. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -85,13 +85,13 @@ Restrictions This fix is part of the USER-MESO package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -Fix *edpd/source* must be used with the :doc:`pair\_style edpd ` command. Fix *tdpd/source* must be used with the -:doc:`pair\_style tdpd ` command. +Fix *edpd/source* must be used with the :doc:`pair_style edpd ` command. Fix *tdpd/source* must be used with the +:doc:`pair_style tdpd ` command. Related commands """""""""""""""" -:doc:`pair\_style edpd `, :doc:`pair\_style tdpd `, +:doc:`pair_style edpd `, :doc:`pair_style tdpd `, :doc:`compute edpd/temp/atom `, :doc:`compute tdpd/cc/atom ` **Default:** none diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst index 9490f58f01..bc1476301a 100644 --- a/doc/src/fix_drag.rst +++ b/doc/src/fix_drag.rst @@ -44,7 +44,7 @@ in the simulation. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst index 4a39c7abc8..d58d1c6d6a 100644 --- a/doc/src/fix_drude.rst +++ b/doc/src/fix_drude.rst @@ -44,12 +44,12 @@ Restrictions This fix should be invoked before any other commands that implement -the Drude oscillator model, such as :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair\_style thole `. +the Drude oscillator model, such as :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair_style thole `. Related commands """""""""""""""" -:doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair\_style thole ` +:doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair_style thole ` **Default:** None diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 58c3628dce..f54fce6a43 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -211,7 +211,7 @@ Related commands :doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`compute temp/drude `, -:doc:`pair\_style thole ` +:doc:`pair_style thole ` **Default:** none diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index b99161934f..ba34dee50b 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -81,11 +81,11 @@ outer loop (largest) timestep, which is the same timestep that the 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. +can be accessed by the :doc:`thermo_style time ` keyword. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index c5228a0cc3..faf4d9c81a 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -58,7 +58,7 @@ gradients of the field are required for the force and torque on dipoles. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent E-field. @@ -126,7 +126,7 @@ minimization will not converge properly. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" inferred by the added force due to the electric field to the system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious @@ -135,12 +135,12 @@ can include the forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force due to the electric field. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the added forces on atoms to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix adding its forces. Default is the outermost level. @@ -164,7 +164,7 @@ the iteration count during the minimization. If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst index 4c4487b11b..2a8a4c8f67 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -118,7 +118,7 @@ cool continuously. heat is added/subtracted less frequently but in larger portions. The resulting temperature profile will therefore be the same. -This fix will default to :doc:`fix\_heat ` (HEX algorithm) if +This fix will default to :doc:`fix_heat ` (HEX algorithm) if the keyword *hex* is specified. @@ -166,7 +166,7 @@ constraints will be satisfied. **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 +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 parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index 3329681333..6589d4b69d 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -68,7 +68,7 @@ its velocity and :math:`S_e` is the stopping power of the ion. :doc:`fix dt/reset `) and the repulsive ZBL potential (see :doc:`ZBL ` potential) or similar. Without these settings the interaction between the ion and the target atoms will be faulty. It is also - common to use in such simulations a thermostat (:doc:`fix\_nvt `) in + common to use in such simulations a thermostat (:doc:`fix_nvt `) in the borders of the simulation cell. .. note:: @@ -79,7 +79,7 @@ its velocity and :math:`S_e` is the stopping power of the ion. e.g. simulations of Swift Heavy Ions (energy per nucleon of 100 keV/amu or higher) or multiple projectiles. You could compensate energy loss by coupling bulk atoms with some thermostat or control heat transfer between electronic and - atomic subsystems with the two-temperature model (:doc:`fix\_ttm `). + atomic subsystems with the two-temperature model (:doc:`fix_ttm `). At low velocities the electronic stopping is negligible. The electronic friction is not applied to atoms whose kinetic energy is smaller than *Ecut*\ , @@ -141,7 +141,7 @@ to derive the stopping power. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` options are not supported. +The :doc:`fix_modify ` options are not supported. This fix computes a global scalar, which can be accessed by various :doc:`output commands `. The scalar is the total energy diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index bef732a82d..7c4934d223 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -60,7 +60,7 @@ instructions on how to use the accelerated styles effectively. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst index 850d0ecde3..7c309ec135 100644 --- a/doc/src/fix_eos_cv.rst +++ b/doc/src/fix_eos_cv.rst @@ -50,7 +50,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. Related commands diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst index 3953d31f2d..d1cb88edf4 100644 --- a/doc/src/fix_eos_table.rst +++ b/doc/src/fix_eos_table.rst @@ -113,7 +113,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. The equation of state must be a monotonically increasing function. diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index 622e24dd79..8b94ef9459 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -206,7 +206,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. The equation of state must be a monotonically increasing function. diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst index 24954ec3da..75c6b2bcbe 100644 --- a/doc/src/fix_evaporate.rst +++ b/doc/src/fix_evaporate.rst @@ -73,12 +73,12 @@ incur overhead due to the cost of building neighbor lists. If you are monitoring the temperature of a system where the atom count is changing due to evaporation, you typically should use the - :doc:`compute\_modify dynamic yes ` command for the + :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar, which can be accessed by various diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index fcd283ccc2..8e7ca5b2e1 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -144,7 +144,7 @@ insure this energy setting is used appropriately in a minimization. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" set by the external driver to the system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious quantity but is needed so that the :doc:`minimize ` command can include the @@ -152,7 +152,7 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interactions computed by the external program to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* @@ -171,7 +171,7 @@ invoked by the :doc:`minimize ` command. If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst index b914c23940..67e386c26f 100644 --- a/doc/src/fix_ffl.rst +++ b/doc/src/fix_ffl.rst @@ -95,7 +95,7 @@ This fix can ramp its target temperature over multiple runs, using the *start* and *stop* keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Langevin thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -119,7 +119,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair\_style dpd/tstat `, :doc:`fix gld `, :doc:`fix gle ` +:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat `, :doc:`fix gld `, :doc:`fix gle ` ---------- diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst index 50db945a37..b6765c25b4 100644 --- a/doc/src/fix_filter_corotate.rst +++ b/doc/src/fix_filter_corotate.rst @@ -44,7 +44,7 @@ method. In biomolecular simulations, it allows the usage of larger timesteps for long-range electrostatic interactions. For details, see :ref:`(Fath) `. -When using :doc:`run\_style respa ` for a biomolecular +When using :doc:`run_style respa ` for a biomolecular simulation with high-frequency covalent bonds, the outer time-step is restricted to below ~ 4fs due to resonance problems. This fix filters the outer stage of the respa and thus a larger (outer) time-step can @@ -60,7 +60,7 @@ is slightly modified only for the computation of long-range forces. A good cluster decomposition constitutes in building clusters which contain the fastest covalent bonds inside clusters. -If the clusters are chosen suitably, the :doc:`run\_style respa ` is stable for outer time-steps of at least 8fs. +If the clusters are chosen suitably, the :doc:`run_style respa ` is stable for outer time-steps of at least 8fs. ---------- @@ -68,7 +68,7 @@ If the clusters are chosen suitably, the :doc:`run\_style respa ` is **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 +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 stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used with the *start/stop* keywords of the :doc:`run ` command. These diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index fa1d65c999..728ef17387 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -93,7 +93,7 @@ fluctuating in time, the work cannot be computed from a potential. As a result, computing the work is slightly more computationally expensive than usual, so it is not performed by default. To invoke the work calculation, use the *energy* keyword. The -:doc:`fix\_modify ` *energy* option also invokes the work +:doc:`fix_modify ` *energy* option also invokes the work calculation, and overrides an *energy no* setting here. If neither *energy yes* or *fix\_modify energy yes* are set, the global scalar computed by the fix will return zero. @@ -109,7 +109,7 @@ If this fix is used in a simulation with the :doc:`rRESPA ` integrator, the applied acceleration must be computed and applied at the same rRESPA level as the interactions between the flowing fluid and the obstacle. The rRESPA level at which the acceleration is applied can be changed using -the :doc:`fix\_modify ` *respa* option discussed below. If the +the :doc:`fix_modify ` *respa* option discussed below. If the flowing fluid and the obstacle interact through multiple interactions that are computed at different rRESPA levels, then there must be a separate flow/gauss fix for each level. For example, if the flowing fluid and obstacle interact @@ -129,11 +129,11 @@ LAMMPS was built with that package. See the :doc:`Build package No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to subtract the work done from the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows the user to set at which level of the :doc:`rRESPA ` integrator the fix computes and adds the external acceleration. Default is the outermost level. diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index 773eacf509..cc67f969df 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -64,7 +64,7 @@ instructions on how to use the accelerated styles effectively. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global 3-vector of forces, which can be accessed @@ -91,7 +91,7 @@ this fix is applied. Related commands """""""""""""""" -:doc:`atom\_style sphere `, :doc:`fix setforce ` +:doc:`atom_style sphere `, :doc:`fix setforce ` **Default:** none diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index 9f64be8699..6b6af93fdc 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -343,7 +343,7 @@ include: :doc:`efield `, :doc:`gravity `, For that energy to be included in the total potential energy of the system (the quantity used when performing GCMC exchange and MC moves), you MUST enable -the :doc:`fix\_modify ` *energy* option for that fix. The +the :doc:`fix_modify ` *energy* option for that fix. The doc pages for individual :doc:`fix ` commands specify if this should be done. @@ -355,7 +355,7 @@ about simulating non-neutral systems with kspace on. Use of this fix typically will cause the number of atoms to fluctuate, therefore, you will want to use the -:doc:`compute\_modify dynamic/dof ` command to insure that the +:doc:`compute_modify dynamic/dof ` command to insure that the current number of atoms is used as a normalizing factor each time temperature is computed. A simple example of this is: @@ -403,17 +403,17 @@ adds all inserted atoms of the specified type to the 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 of MC step attempts and successes etc. See -the :doc:`read\_restart ` command for info on how to +the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. note:: For this to work correctly, the timestep must **not** be changed - after reading the restart with :doc:`reset\_timestep `. + after reading the restart with :doc:`reset_timestep `. The fix will try to detect it and stop with an error. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global vector of length 8, which can be accessed @@ -471,7 +471,7 @@ Related commands :doc:`fix atom/swap `, :doc:`fix nvt `, :doc:`neighbor `, :doc:`fix deposit `, :doc:`fix evaporate `, -:doc:`delete\_atoms ` +:doc:`delete_atoms ` Default """"""" diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index 03b5aa418b..4826ce07ff 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -137,7 +137,7 @@ do "exact" restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. @@ -158,7 +158,7 @@ Related commands """""""""""""""" :doc:`fix langevin `, :doc:`fix viscous `, -:doc:`pair\_style dpd/tstat ` +:doc:`pair_style dpd/tstat ` Default """"""" diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index ecb03618f5..53efdf91a5 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -121,7 +121,7 @@ This fix can ramp its target temperature over multiple runs, using the *start* and *stop* keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Langevin thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -150,7 +150,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair\_style dpd/tstat `, :doc:`fix gld ` +:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat `, :doc:`fix gld ` ---------- diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index e8aae5a910..87ed196a90 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -93,7 +93,7 @@ insure that the variable calculates a result in the appropriate units, e.g. force/mass or degrees. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent gravitational field. @@ -128,11 +128,11 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the gravitational potential energy of the system to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -153,7 +153,7 @@ Restrictions Related commands """""""""""""""" -:doc:`atom\_style sphere `, :doc:`fix addforce ` +:doc:`atom_style sphere `, :doc:`fix addforce ` **Default:** none diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index 598131a935..68e143b1ad 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -90,7 +90,7 @@ temperature changes. Replicas are easily added where needed. No information about this fix is written to :doc:`binary restart files `. -The :doc:`thermo\_modify ` *press* option is supported +The :doc:`thermo_modify ` *press* option is supported by this fix to add the rescaled kinetic pressure as part of :doc:`thermodynamic output `. @@ -104,7 +104,7 @@ LAMMPS was built with that package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`temper/grem `, :doc:`fix nvt `, :doc:`fix npt `, :doc:`thermo\_modify ` +:doc:`temper/grem `, :doc:`fix nvt `, :doc:`fix npt `, :doc:`thermo_modify ` **Default:** none diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 4eaa75abb8..e020ea7e26 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -128,8 +128,8 @@ If its value is *soft*\ , LAMMPS will exit the current run, but continue to execute subsequent commands in the input script. However, additional :doc:`run ` or :doc:`minimize ` commands will be skipped. For example, this allows a script to output the current -state of the system, e.g. via a :doc:`write\_dump ` or -:doc:`write\_restart ` command. +state of the system, e.g. via a :doc:`write_dump ` or +:doc:`write_restart ` command. If its value is *continue*\ , the behavior is the same as for *soft*\ , except subsequent :doc:`run ` or :doc:`minimize ` commands @@ -148,7 +148,7 @@ files. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst index 1972eb2b03..c96a88ee35 100644 --- a/doc/src/fix_heat.rst +++ b/doc/src/fix_heat.rst @@ -82,7 +82,7 @@ name. In this case, the variable will be evaluated each timestep, and its value(s) used to determine the flux. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent flux. @@ -114,7 +114,7 @@ by another fix - e.g. :doc:`fix nvt ` or :doc:`fix langevin `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index 7aa5891e25..579d6cc681 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -210,7 +210,7 @@ algorithm. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of the bias potential to the system's potential energy as part of :doc:`thermodynamic output `. diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 31c606380a..6758c747b6 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -249,7 +249,7 @@ well for many solid-state systems. atoms move (between quenched states) to be considered an "event". It is an argument to the "compute event/displace" command used to detect events. By default the ghost communication distance is set by the - pair\_style cutoff, which will typically be < *Dcut*\ . The :doc:`comm\_modify cutoff ` command should be used to override the ghost + pair\_style cutoff, which will typically be < *Dcut*\ . The :doc:`comm_modify cutoff ` command should be used to override the ghost cutoff explicitly, e.g. @@ -378,7 +378,7 @@ enabled by these keywords. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of the bias potential to the system's potential energy as part of :doc:`thermodynamic output `. @@ -475,7 +475,7 @@ the communication cutoff for ghosts is too close to *Dcut* leading to many not-found ghost atoms before the next event. This may lead to a reduced number of bonds being selected for biasing, since the code assumes those atoms are part of highly strained bonds. As explained -above, the :doc:`comm\_modify cutoff ` command can be used +above, the :doc:`comm_modify cutoff ` command can be used to set a longer cutoff. For value 22, no two bonds should be biased if they are within a diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index b688316546..75c5ccc741 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -150,7 +150,7 @@ screen output is active. **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 +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 quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index c130ede009..ea8aa28b41 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -110,12 +110,12 @@ will be evaluated each timestep, and its value used to define the indenter geometry. Note that equal-style variables can specify formulas with various -mathematical functions, and include :doc:`thermo\_style ` +mathematical functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify indenter properties that change as a function of time or span consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the -:doc:`run ` command and the *elaplong* keyword of :doc:`thermo\_style custom ` for details. +:doc:`run ` command and the *elaplong* keyword of :doc:`thermo_style custom ` for details. For example, if a spherical indenter's x-position is specified as v\_x, then this variable definition will keep it's center at a relative @@ -169,7 +169,7 @@ cylindrical indenter is scaled by the x lattice spacing. Note that the units keyword only affects indenter geometry parameters specified directly with numbers, not those specified as variables. In the latter case, you should use the *xlat*\ , *ylat*\ , *zlat* keywords of -the :doc:`thermo\_style ` command if you want to include +the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. The force constant *K* is not affected by the *units* keyword. It is @@ -177,7 +177,7 @@ always in force/distance\^2 units where force and distance are defined by the :doc:`units ` command. If you wish K to be scaled by the lattice spacing, you can define K with a variable whose formula contains *xlat*\ , *ylat*\ , *zlat* keywords of the -:doc:`thermo\_style ` command, e.g. +:doc:`thermo_style ` command, e.g. .. parsed-literal:: @@ -189,12 +189,12 @@ contains *xlat*\ , *ylat*\ , *zlat* keywords of the No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of interaction between atoms and the indenter to the system's potential energy as part of :doc:`thermodynamic output `. The energy of each particle interacting with the indenter is K/3 (r - R)\^3. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -214,7 +214,7 @@ check if you have done this. If you want the atom/indenter interaction energy to be included in the total potential energy of the system (the quantity being - minimized), you must enable the :doc:`fix\_modify ` *energy* + minimized), you must enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index d6f52084f5..429e831a11 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -74,11 +74,11 @@ will have the form: Fr is proportional to sqrt(Kb T m / (dt damp)) Fc is the conservative force computed via the usual inter-particle -interactions (:doc:`pair\_style `, -:doc:`bond\_style `, etc). +interactions (:doc:`pair_style `, +:doc:`bond_style `, etc). The Ff and Fr terms are added by this fix on a per-particle basis. -See the :doc:`pair\_style dpd/tstat ` command for a +See the :doc:`pair_style dpd/tstat ` command for a thermostatting option that adds similar terms on a pairwise basis to pairs of interacting particles. @@ -131,7 +131,7 @@ will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -145,7 +145,7 @@ with :doc:`compute commands ` that remove a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or removing the x-component of velocity from the calculation. This is not done by default, but only if the -:doc:`fix\_modify ` command is used to assign a temperature +:doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following @@ -304,13 +304,13 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Langevin thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. Note that use of this option requires setting the *tally* keyword to *yes*\ . @@ -337,7 +337,7 @@ with run\_style respa. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair\_style dpd/tstat ` +:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat ` Default """"""" diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index 16de2eba8b..32546f69b0 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -152,7 +152,7 @@ specify the Drude status of each atom type. .. note:: Ghost atoms need to know their velocity for this fix to act - correctly. You must use the :doc:`comm\_modify ` command to + correctly. You must use the :doc:`comm_modify ` command to enable this, e.g. @@ -174,7 +174,7 @@ the variable will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -182,7 +182,7 @@ Like other fixes that perform thermostatting, this fix can be used with :doc:`compute commands ` that remove a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms. This is not done by default, but only if the -:doc:`fix\_modify ` command is used to assign a temperature +:doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following @@ -283,7 +283,7 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by the @@ -302,7 +302,7 @@ Related commands :doc:`fix drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, -:doc:`pair\_style thole ` +:doc:`pair_style thole ` Default """"""" diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index 0de23c65ab..d9f00a76ea 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -62,7 +62,7 @@ each atom will have the form: Fr is proportional to sqrt(Kb T m / (dt damp)) Fc is the conservative force computed via the usual inter-particle -interactions (:doc:`pair\_style `). +interactions (:doc:`pair_style `). The Ff and Fr terms are added by this fix on a per-particle basis. @@ -78,13 +78,13 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Langevin thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. Note that use of this option requires setting the *tally* keyword to *yes*\ . diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index a13df3f40a..d30b911e7f 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -114,11 +114,11 @@ larger system sizes and longer time scales No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential energy computed by LATTE to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the LATTE DFTB contribution to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* @@ -139,7 +139,7 @@ energy minimization, invoked by the :doc:`minimize ` command. If you want the potential energy associated with the DFTB forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index cd177b7f32..c0d924078c 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -324,7 +324,7 @@ binary restart files, if requested, independent of the main LAMMPS :doc:`binary restart files `; no information about *lb\_fluid* is written to the main LAMMPS :doc:`binary restart files `. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index 2f1b953db3..cfc5c07d8d 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -56,7 +56,7 @@ dimension. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst index f490b82981..039e315be1 100644 --- a/doc/src/fix_lb_pc.rst +++ b/doc/src/fix_lb_pc.rst @@ -33,7 +33,7 @@ algorithm if the force coupling constant has been set by default. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst index ee962dfd75..36f33037bf 100644 --- a/doc/src/fix_lb_viscous.rst +++ b/doc/src/fix_lb_viscous.rst @@ -58,7 +58,7 @@ research. As described in the :doc:`fix viscous ` documentation: -"No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +"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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -67,7 +67,7 @@ the :doc:`run ` command. The forces due to this fix are imposed during an energy minimization, invoked by the :doc:`minimize ` command. This fix should only be used with damped dynamics minimizers that allow for -non-conservative forces. See the :doc:`min\_style ` command +non-conservative forces. See the :doc:`min_style ` command for details." Restrictions diff --git a/doc/src/fix_lineforce.rst b/doc/src/fix_lineforce.rst index ef365eb75c..e317348a5e 100644 --- a/doc/src/fix_lineforce.rst +++ b/doc/src/fix_lineforce.rst @@ -36,7 +36,7 @@ it should continue to move along the line thereafter. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst index 58f98762dc..5dfdd70150 100644 --- a/doc/src/fix_manifoldforce.rst +++ b/doc/src/fix_manifoldforce.rst @@ -38,7 +38,7 @@ adequately though. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_meso.rst b/doc/src/fix_meso.rst index 6be247101e..e28514f8ea 100644 --- a/doc/src/fix_meso.rst +++ b/doc/src/fix_meso.rst @@ -35,7 +35,7 @@ LAMMPS. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst index 79d9f499e5..62804aa75c 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -83,7 +83,7 @@ internal energy and extrapolated velocity are also updated. are stored by the fix in "unwrapped" form, by using the image flags associated with each particle. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of - the :doc:`read\_data ` command for a discussion of image flags + the :doc:`read_data ` command for a discussion of image flags and how they are set for each particle. You can reset the image flags (e.g. to 0) before invoking this fix by using the :doc:`set image ` command. @@ -220,7 +220,7 @@ spacings can be different in x,y,z. 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 -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -231,7 +231,7 @@ operation of the fix continues in an uninterrupted fashion. different value after reading a restart file, if you expect a fix move command to work in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a per-atom array which can be accessed by various @@ -252,7 +252,7 @@ This fix is part of the USER-SDPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store density and internal energy as -defined by the :doc:`atom\_style meso ` command. +defined by the :doc:`atom_style meso ` command. All particles in the group must be mesoscopic SPH/SDPD particles. @@ -260,7 +260,7 @@ Related commands """""""""""""""" :doc:`fix move `, :doc:`fix meso `, -:doc:`displace\_atoms ` +:doc:`displace_atoms ` Default """"""" diff --git a/doc/src/fix_meso_stationary.rst b/doc/src/fix_meso_stationary.rst index 5a39661cb6..5a7d53e55b 100644 --- a/doc/src/fix_meso_stationary.rst +++ b/doc/src/fix_meso_stationary.rst @@ -36,7 +36,7 @@ LAMMPS. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index ed9f82988e..baa31338ed 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -67,7 +67,7 @@ The *energy* keyword can be used with fixes that support it. *energy yes* adds a contribution to the potential energy of the system. The fix's global and per-atom energy is included in the calculation performed by the :doc:`compute pe ` or :doc:`compute pe/atom ` -commands. See the :doc:`thermo\_style ` command for info +commands. See the :doc:`thermo_style ` command for info on how potential energy is output. For fixes that tally a global energy, it can be printed by using the keyword f\_ID in the thermo\_style custom command, where ID is the fix-ID of the appropriate @@ -85,7 +85,7 @@ The *virial* keyword can be used with fixes that support it. system. The fix's global and per-atom virial is included in the calculation performed by the :doc:`compute pressure ` or :doc:`compute stress/atom ` -commands. See the :doc:`thermo\_style ` command for info +commands. See the :doc:`thermo_style ` command for info on how pressure is output. .. note:: @@ -129,7 +129,7 @@ normalized. Other thermostatting fixes, such as :doc:`fix nvt `, do not use the *dynamic/dof* keyword because they use a temperature - compute to calculate temperature. See the :doc:`compute\_modify dynamic/dof ` command for a similar way to insure + compute to calculate temperature. See the :doc:`compute_modify dynamic/dof ` command for a similar way to insure correct temperature normalization for those thermostats. The *bodyforces* keyword determines whether the forces and torques @@ -159,7 +159,7 @@ Restrictions Related commands """""""""""""""" -:doc:`fix `, :doc:`compute temp `, :doc:`compute pressure `, :doc:`thermo\_style ` +:doc:`fix `, :doc:`compute temp `, :doc:`compute pressure `, :doc:`thermo_style ` Default """"""" diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index e3ace5a60e..e8194143d6 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -94,7 +94,7 @@ instructions on how to use the accelerated styles effectively. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index 6994d9aa7c..036b156630 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -78,7 +78,7 @@ whose movement can influence nearby atoms. are stored by the fix in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of - the :doc:`read\_data ` command for a discussion of image flags + the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this fix by using the :doc:`set image ` command. @@ -159,7 +159,7 @@ around the axis in the direction of rotation. This style also sets the velocity of each atom to (omega cross Rperp) where omega is its angular velocity around the rotation axis and Rperp is a perpendicular vector from the rotation axis to the atom. If the -defined :doc:`atom\_style ` assigns an angular velocity or +defined :doc:`atom_style ` assigns an angular velocity or angular momentum or orientation to each atom (:doc:`atom styles ` sphere, ellipsoid, line, tri, body), then those properties are also updated appropriately to correspond to the atom's motion and rotation over time. @@ -219,7 +219,7 @@ spacings can be different in x,y,z. 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 -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -230,7 +230,7 @@ operation of the fix continues in an uninterrupted fashion. different value after reading a restart file, if you expect a fix move command to work in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a per-atom array which can be accessed by various @@ -251,7 +251,7 @@ Restrictions Related commands """""""""""""""" -:doc:`fix nve `, :doc:`displace\_atoms ` +:doc:`fix nve `, :doc:`displace_atoms ` **Default:** none diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst index 85fb9049c3..b22aedde7a 100644 --- a/doc/src/fix_msst.rst +++ b/doc/src/fix_msst.rst @@ -132,7 +132,7 @@ timestepping. DFTB+ will communicate its info to LAMMPS via that fix. **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 ` command +This fix writes the state of all internal variables 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 restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -142,11 +142,11 @@ scalar and global vector quantities computed by the fix. The scalar is the cumulative energy change due to the fix. This is also the energy added to the potential energy by the -:doc:`fix\_modify ` *energy* command. With this command, the +:doc:`fix_modify ` *energy* command. With this command, the thermo keyword *etotal* prints the conserved quantity of the MSST dynamic equations. This can be used to test if the MD timestep is sufficiently small for accurate integration of the dynamic -equations. See also :doc:`thermo\_style ` command. +equations. See also :doc:`thermo_style ` command. The global vector contains four values in this order: diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index 9c9471fd71..e42dc84115 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -62,15 +62,15 @@ standard velocity-Verlet (VV) scheme. For more details, see :ref:`Groot `. Fix *mvv/dpd* updates the position and velocity of each atom. It can -be used with the :doc:`pair\_style mdpd ` command or other +be used with the :doc:`pair_style mdpd ` command or other pair styles such as :doc:`pair dpd `. Fix *mvv/edpd* updates the per-atom temperature, in addition to -position and velocity, and must be used with the :doc:`pair\_style edpd ` command. +position and velocity, and must be used with the :doc:`pair_style edpd ` command. Fix *mvv/tdpd* updates the per-atom chemical concentration, in addition to position and velocity, and must be used with the -:doc:`pair\_style tdpd ` command. +:doc:`pair_style tdpd ` command. ---------- @@ -78,7 +78,7 @@ addition to position and velocity, and must be used with the **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -94,8 +94,8 @@ LAMMPS was built with that package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`pair\_style mdpd `, :doc:`pair\_style edpd `, -:doc:`pair\_style tdpd ` +:doc:`pair_style mdpd `, :doc:`pair_style edpd `, +:doc:`pair_style tdpd ` Default """"""" diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 5dded81f55..4d84e5d0b6 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -219,7 +219,7 @@ target energy. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst index 5b316f0009..859ae5ad79 100644 --- a/doc/src/fix_neb_spin.rst +++ b/doc/src/fix_neb_spin.rst @@ -48,7 +48,7 @@ See this reference for more explanation about their expression. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -69,7 +69,7 @@ page for more info. Related commands """""""""""""""" -:doc:`neb\_spin ` +:doc:`neb_spin ` Default """"""" diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 0f75125058..50abc247a1 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -181,7 +181,7 @@ Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The :doc:`create\_box `, :doc:`read data `, and :doc:`read\_restart ` commands +dimensions (x,y,z,xy,xz,yz). The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -389,7 +389,7 @@ If the *update* keyword is used with the *dipole* value, then the orientation of the dipole moment of each particle is also updated during the time integration. This option should be used for models where a dipole moment is assigned to finite-size particles, -e.g. spheroids via use of the :doc:`atom\_style hybrid sphere dipole ` command. +e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole ` command. The default dipole orientation integrator can be changed to the Dullweber-Leimkuhler-McLachlan integration scheme @@ -478,12 +478,12 @@ commands for details. Note that the IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID + underscore + "press". Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of these fix's temperature or pressure via the -:doc:`compute\_modify ` command. Or you can print this +:doc:`compute_modify ` command. Or you can print this temperature or pressure during thermodynamic output via the -:doc:`thermo\_style custom ` command using the appropriate +:doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -493,7 +493,7 @@ temperature after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not -done by default, but only if the :doc:`fix\_modify ` command +done by default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -577,11 +577,11 @@ instructions on how to use the accelerated styles effectively. These fixes writes the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by these fixes. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure, as described above. @@ -602,7 +602,7 @@ compute temperature on a subset of atoms. specified by the *press* keyword will be unaffected by the *temp* setting. -The :doc:`fix\_modify ` *energy* option is supported by these +The :doc:`fix_modify ` *energy* option is supported by these fixes to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -663,8 +663,8 @@ Restrictions periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the simulation domain is triclinic and the 2nd dimension in the keyword (\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be -barostatted for 2D simulations. The :doc:`create\_box `, -:doc:`read data `, and :doc:`read\_restart ` +barostatted for 2D simulations. The :doc:`create_box `, +:doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -690,8 +690,8 @@ over time or the atom count becomes very small. Related commands """""""""""""""" -:doc:`fix nve `, :doc:`fix\_modify `, -:doc:`run\_style ` +:doc:`fix nve `, :doc:`fix_modify `, +:doc:`run_style ` Default """"""" diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index cf6a65352f..58ed3e41cd 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -138,7 +138,7 @@ Related commands """""""""""""""" :doc:`fix nvt `, :doc:`fix nph `, :doc:`fix npt `, -:doc:`fix\_modify `, :doc:`run\_style ` +:doc:`fix_modify `, :doc:`run_style ` Default """"""" diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 35110d9cce..7c15f5ffcb 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -187,7 +187,7 @@ or fix\_ID + underscore + "press". **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 +as well as the cumulative strain applied, 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 restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -199,7 +199,7 @@ uninterrupted fashion. not contain the cumulative applied strain, will this keyword be necessary. -This fix can be used with the :doc:`fix\_modify ` *temp* and +This fix can be used with the :doc:`fix_modify ` *temp* and *press* options. The temperature and pressure computes used must be of type *temp/uef* and *pressure/uef*\ . @@ -217,7 +217,7 @@ was built with that package. See the :doc:`Build package ` doc pa Due to requirements of the boundary conditions, when the *strain* keyword is set to zero (or unset), the initial simulation box must be cubic and have style triclinic. If the box is initially of type ortho, -use :doc:`change\_box ` before invoking the fix. +use :doc:`change_box ` before invoking the fix. .. note:: diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index cea1ee71b3..88d8052a5a 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -77,11 +77,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -109,12 +109,12 @@ instructions on how to use the accelerated styles effectively. **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 ` +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 reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -123,7 +123,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -144,7 +144,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point @@ -154,7 +154,7 @@ shape attribute. Related commands """""""""""""""" -:doc:`fix nph `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix\_modify ` +:doc:`fix nph `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nph_body.rst b/doc/src/fix_nph_body.rst index 8ce3009700..25416bfa11 100644 --- a/doc/src/fix_nph_body.rst +++ b/doc/src/fix_nph_body.rst @@ -74,11 +74,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -106,12 +106,12 @@ instructions on how to use the accelerated styles effectively. **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 ` +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 reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -120,7 +120,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -141,13 +141,13 @@ This fix is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. Related commands """""""""""""""" -:doc:`fix nph `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix npt\_body `, :doc:`fix\_modify ` +:doc:`fix nph `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix npt\_body `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index af45b6babc..de8fb71944 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -90,11 +90,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -122,12 +122,12 @@ instructions on how to use the accelerated styles effectively. **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 ` +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 reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -136,7 +136,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -154,7 +154,7 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres. They cannot @@ -167,7 +167,7 @@ Related commands """""""""""""""" :doc:`fix nph `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_sphere `, :doc:`fix npt\_sphere `, -:doc:`fix\_modify ` +:doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index be0a28b8b4..070192207f 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -143,11 +143,11 @@ the new computes is "all" since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -182,18 +182,18 @@ instructions on how to use the accelerated styles effectively. This fix writes the values of E0, V0, and P0, as well as the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *e0*\ , *v0* and *p0* keywords +The :doc:`fix_modify ` *e0*\ , *v0* and *p0* keywords can be used to define the values of E0, V0, and P0. Note the the values for *e0* and *v0* are extensive, and so must correspond to the total energy and volume of the entire system, not energy and volume per atom. If any of these quantities are not specified, then the instantaneous value in the system at the start of the simulation is used. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by these fixes. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure, as described above. @@ -202,7 +202,7 @@ temperature should be consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by these +The :doc:`fix_modify ` *energy* option is supported by these fixes to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. Either way, this energy is \*not\* @@ -236,7 +236,7 @@ plus the additional ones mentioned above. Related commands """""""""""""""" -:doc:`fix msst `, :doc:`fix npt `, :doc:`fix\_modify ` +:doc:`fix msst `, :doc:`fix npt `, :doc:`fix_modify ` Default """"""" diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index a728128aa3..ee3a81892e 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -85,11 +85,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -99,7 +99,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -133,11 +133,11 @@ instructions on how to use the accelerated styles effectively. This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -146,7 +146,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -169,7 +169,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point @@ -179,7 +179,7 @@ shape attribute. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix\_modify ` +:doc:`fix npt `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_npt_body.rst b/doc/src/fix_npt_body.rst index 64ae261e31..bfc743d923 100644 --- a/doc/src/fix_npt_body.rst +++ b/doc/src/fix_npt_body.rst @@ -82,11 +82,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -96,7 +96,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -130,11 +130,11 @@ instructions on how to use the accelerated styles effectively. This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -143,7 +143,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -166,13 +166,13 @@ This fix is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix\_modify ` +:doc:`fix npt `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index 9d0e04b0c0..3a660c5c4f 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -136,7 +136,7 @@ Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The :doc:`create\_box `, :doc:`read data `, and :doc:`read\_restart ` commands +dimensions (x,y,z,xy,xz,yz). The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -411,12 +411,12 @@ commands for details. Note that the IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID + underscore + "press". Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of these fix's temperature or pressure via the -:doc:`compute\_modify ` command. Or you can print this +:doc:`compute_modify ` command. Or you can print this temperature or pressure during thermodynamic output via the -:doc:`thermo\_style custom ` command using the appropriate +:doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -426,7 +426,7 @@ temperature after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not -done by default, but only if the :doc:`fix\_modify ` command +done by default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -476,11 +476,11 @@ of the underlying non-Hamiltonian equations of motion. This fix writes the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure, as described above. @@ -501,7 +501,7 @@ compute temperature on a subset of atoms. specified by the *press* keyword will be unaffected by the *temp* setting. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -565,8 +565,8 @@ LAMMPS was built with that package. See the :doc:`Build package periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the simulation domain is triclinic and the 2nd dimension in the keyword (\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be -barostatted for 2D simulations. The :doc:`create\_box `, -:doc:`read data `, and :doc:`read\_restart ` +barostatted for 2D simulations. The :doc:`create_box `, +:doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -625,8 +625,8 @@ over time or the atom count becomes very small. Related commands """""""""""""""" -:doc:`fix nve `, :doc:`fix\_modify `, -:doc:`run\_style ` +:doc:`fix nve `, :doc:`fix_modify `, +:doc:`run_style ` Default """"""" diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index 9fe7b93633..0c4b79d616 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -98,11 +98,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -112,7 +112,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -146,11 +146,11 @@ instructions on how to use the accelerated styles effectively. This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -159,7 +159,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -179,7 +179,7 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres. They cannot @@ -191,7 +191,7 @@ defined by the :doc:`dimension ` keyword. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_sphere `, :doc:`fix npt\_asphere `, :doc:`fix\_modify ` +:doc:`fix npt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_sphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index bae6f8a95c..9c8b5dcf33 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -67,7 +67,7 @@ instructions on how to use the accelerated styles effectively. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index 4ac734c468..688792058d 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -38,7 +38,7 @@ assumes point particles and only updates their position and velocity. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -78,7 +78,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point diff --git a/doc/src/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst index 309928f582..b175b769e8 100644 --- a/doc/src/fix_nve_asphere_noforce.rst +++ b/doc/src/fix_nve_asphere_noforce.rst @@ -30,7 +30,7 @@ angular momenta are used to update their positions and orientation. This is useful as an implicit time integrator for Fast Lubrication Dynamics, since the velocity and angular momentum are updated by the -:doc:`pair\_style lubricuteU ` command. +:doc:`pair_style lubricuteU ` command. ---------- @@ -38,7 +38,7 @@ Dynamics, since the velocity and angular momentum are updated by the **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -52,7 +52,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst index e44f78c25c..8aeb6969b2 100644 --- a/doc/src/fix_nve_awpmd.rst +++ b/doc/src/fix_nve_awpmd.rst @@ -39,7 +39,7 @@ the electron wave functions are also updated. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_body.rst b/doc/src/fix_nve_body.rst index 1d75b3ac34..5410ddb8ee 100644 --- a/doc/src/fix_nve_body.rst +++ b/doc/src/fix_nve_body.rst @@ -36,7 +36,7 @@ assumes point particles and only updates their position and velocity. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -50,7 +50,7 @@ This fix is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. All particles in the group must be body particles. They cannot be diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index 3143db968f..6b210b7150 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -68,8 +68,8 @@ The total force on each atom will have the form: Fr is proportional to sqrt(Kb T m / (dt damp)) Fc is the conservative force computed via the usual inter-particle -interactions (:doc:`pair\_style `, -:doc:`bond\_style `, etc). +interactions (:doc:`pair_style `, +:doc:`bond_style `, etc). The Ff and Fr terms are implicitly taken into account by this fix on a per-particle basis. @@ -146,7 +146,7 @@ See the :doc:`Build package ` doc page for more info. 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 ` +: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 diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst index a7346f1ed2..a1d10cb484 100644 --- a/doc/src/fix_nve_eff.rst +++ b/doc/src/fix_nve_eff.rst @@ -34,7 +34,7 @@ of electrons are also updated. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_limit.rst b/doc/src/fix_nve_limit.rst index f637db54d1..684016959b 100644 --- a/doc/src/fix_nve_limit.rst +++ b/doc/src/fix_nve_limit.rst @@ -42,7 +42,7 @@ in a single timestep. *Xmax* is specified in distance units; see the consistent with the neighbor skin distance and the frequency of neighbor list re-building, so that pairwise interactions are not missed on successive timesteps as atoms move. See the -:doc:`neighbor ` and :doc:`neigh\_modify ` commands +:doc:`neighbor ` and :doc:`neigh_modify ` commands for details. Note that if a velocity reset occurs the integrator will not conserve @@ -64,7 +64,7 @@ very large for overlapped configurations. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various @@ -88,7 +88,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nve/noforce `, -:doc:`pair\_style soft ` +:doc:`pair_style soft ` **Default:** none diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst index 8f77e8481e..e92f529542 100644 --- a/doc/src/fix_nve_line.rst +++ b/doc/src/fix_nve_line.rst @@ -36,7 +36,7 @@ assumes point particles and only updates their position and velocity. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -50,7 +50,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that particles be line segments as defined by the -:doc:`atom\_style line ` command. +:doc:`atom_style line ` command. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index 5836dc005c..f4215f2abe 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -78,7 +78,7 @@ conserved. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst index 07caefca16..bacc4a9908 100644 --- a/doc/src/fix_nve_noforce.rst +++ b/doc/src/fix_nve_noforce.rst @@ -41,7 +41,7 @@ fcm() group function to compute the total force on the group of atoms. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index 1789a9e119..855ea0f916 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -57,7 +57,7 @@ If the *update* keyword is used with the *dipole* value, then the orientation of the dipole moment of each particle is also updated during the time integration. This option should be used for models where a dipole moment is assigned to finite-size particles, -e.g. spheroids via use of the :doc:`atom\_style hybrid sphere dipole ` command. +e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole ` command. The default dipole orientation integrator can be changed to the Dullweber-Leimkuhler-McLachlan integration scheme @@ -100,7 +100,7 @@ instructions on how to use the accelerated styles effectively. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -111,9 +111,9 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. If the *dipole* keyword is used, then they must also store a -dipole moment as defined by the :doc:`atom\_style dipole ` +dipole moment as defined by the :doc:`atom_style dipole ` command. All particles in the group must be finite-size spheres. They cannot diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst index 5f1b1a648f..65f235bd3f 100644 --- a/doc/src/fix_nve_spin.rst +++ b/doc/src/fix_nve_spin.rst @@ -82,7 +82,7 @@ instead of "array" is also valid. Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`fix nve ` +:doc:`atom_style spin `, :doc:`fix nve ` Default """"""" diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst index 4e71a69c5a..c5e5aa99d6 100644 --- a/doc/src/fix_nve_tri.rst +++ b/doc/src/fix_nve_tri.rst @@ -37,7 +37,7 @@ assumes point particles and only updates their position and velocity. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -51,7 +51,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that particles be triangles as defined by the -:doc:`atom\_style tri ` command. +:doc:`atom_style tri ` command. Related commands """""""""""""""" diff --git a/doc/src/fix_nvk.rst b/doc/src/fix_nvk.rst index c153ab6ff2..a3f3928339 100644 --- a/doc/src/fix_nvk.rst +++ b/doc/src/fix_nvk.rst @@ -45,7 +45,7 @@ energy prior to this fix. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index 9df4c9e84f..a3ad145405 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -66,11 +66,11 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -80,7 +80,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -112,17 +112,17 @@ instructions on how to use the accelerated styles effectively. **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 ` +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 reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -143,7 +143,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point @@ -153,7 +153,7 @@ shape attribute. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix\_modify ` +:doc:`fix nvt `, :doc:`fix nve\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst index f94c1850da..92819b26ca 100644 --- a/doc/src/fix_nvt_body.rst +++ b/doc/src/fix_nvt_body.rst @@ -63,11 +63,11 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -77,7 +77,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -109,17 +109,17 @@ instructions on how to use the accelerated styles effectively. **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 ` +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 reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -140,13 +140,13 @@ This fix is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve\_body `, :doc:`fix npt\_body `, :doc:`fix\_modify ` +:doc:`fix nvt `, :doc:`fix nve\_body `, :doc:`fix npt\_body `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index 4b9c063caf..438c11fe7e 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -54,7 +54,7 @@ parameters, see the :doc:`Howto manifold ` doc page. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst index aa4197e19b..cd8f529c83 100644 --- a/doc/src/fix_nvt_sllod.rst +++ b/doc/src/fix_nvt_sllod.rst @@ -98,11 +98,11 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -112,7 +112,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -144,17 +144,17 @@ instructions on how to use the accelerated styles effectively. **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 ` +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 reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -179,7 +179,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix langevin `, -:doc:`fix\_modify `, :doc:`compute temp/deform ` +:doc:`fix_modify `, :doc:`compute temp/deform ` Default """"""" diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst index 0e8b005176..f1dc60c88f 100644 --- a/doc/src/fix_nvt_sllod_eff.rst +++ b/doc/src/fix_nvt_sllod_eff.rst @@ -42,17 +42,17 @@ velocity. **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 ` +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 reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -79,7 +79,7 @@ equilibration. Related commands """""""""""""""" -:doc:`fix nve/eff `, :doc:`fix nvt/eff `, :doc:`fix langevin/eff `, :doc:`fix nvt/sllod `, :doc:`fix\_modify `, :doc:`compute temp/deform/eff ` +:doc:`fix nve/eff `, :doc:`fix nvt/eff `, :doc:`fix langevin/eff `, :doc:`fix nvt/sllod `, :doc:`fix_modify `, :doc:`compute temp/deform/eff ` Default """"""" diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index eedf21f69b..3275114a03 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -80,11 +80,11 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -94,7 +94,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -126,17 +126,17 @@ instructions on how to use the accelerated styles effectively. **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 ` +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 reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -154,7 +154,7 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres. They cannot @@ -166,7 +166,7 @@ defined by the :doc:`dimension ` keyword. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_sphere `, :doc:`fix\_modify ` +:doc:`fix nvt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_sphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst index 9d1f40ef5f..cc57989a53 100644 --- a/doc/src/fix_oneway.rst +++ b/doc/src/fix_oneway.rst @@ -46,7 +46,7 @@ membrane, or as an implementation of Maxwell's demon. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index dcce12eb91..7ac297b064 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -130,12 +130,12 @@ writing the orientation files is given in :ref:`(Wicaksono2) ` No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential energy of atom interactions with the grain boundary driving force to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by these +The :doc:`fix_modify ` *respa* option is supported by these fixes. This allows to set at which level of the :doc:`r-RESPA ` integrator a fix is adding its forces. Default is the outermost level. @@ -164,7 +164,7 @@ This fix should only be used with fcc or bcc lattices. Related commands """""""""""""""" -:doc:`fix\_modify ` +:doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index ca71595664..f331f3ebb4 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -164,7 +164,7 @@ corresponding reciprocal lattice. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to change the temperature compute from thermo\_temp to the one that reflects the true temperature of atoms in the group. @@ -200,7 +200,7 @@ Related commands """""""""""""""" :doc:`compute msd `, -:doc:`dynamical\_matrix ` +:doc:`dynamical_matrix ` Default """"""" diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index 2639150bd4..cdbdf33d2b 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -161,7 +161,7 @@ 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. A PIMD simulation can be initialized with a single data file read via -the :doc:`read\_data ` command. However, this means all +the :doc:`read_data ` command. However, this means all quasi-beads in a ring polymer will have identical positions and velocities, resulting in identical trajectories for all quasi-beads. To avoid this, users can simply initialize velocities with different diff --git a/doc/src/fix_planeforce.rst b/doc/src/fix_planeforce.rst index 1cac0f8be8..2a406f5da5 100644 --- a/doc/src/fix_planeforce.rst +++ b/doc/src/fix_planeforce.rst @@ -36,7 +36,7 @@ should continue to move in the plane thereafter. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index 93a3ac0638..26f66d4ac7 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -90,7 +90,7 @@ dependent bias potentials that were accumulated in previous calculations will be read in when the RESTART command is included in the PLUMED input. -The :doc:`fix\_modify ` *energy* option is not supported by +The :doc:`fix_modify ` *energy* option is not supported by this fix. Nothing is computed by this fix that can be accessed by any of the diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index 816568b537..da690030f6 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -115,7 +115,7 @@ off, and there is only a single fix poems defined. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *bodyforces* option is supported by +The :doc:`fix_modify ` *bodyforces* option is supported by this fix style to set whether per-body forces and torques are computed early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage, respectively. @@ -136,8 +136,8 @@ built and linked with LAMMPS. See the :doc:`Build package ` doc Related commands """""""""""""""" -:doc:`fix rigid `, :doc:`delete\_bonds `, -:doc:`neigh\_modify ` exclude +:doc:`fix rigid `, :doc:`delete_bonds `, +:doc:`neigh_modify ` exclude **Default:** none diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index 8deeb6e885..dab9fa601d 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -154,7 +154,7 @@ many timesteps until the desired # of particles has been inserted. If you are monitoring the temperature of a system where the particle count is changing due to adding particles, you typically - should use the :doc:`compute\_modify dynamic yes ` + should use the :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. @@ -220,7 +220,7 @@ successively higher height over time. The *ignore* option is useful when running a simulation that used line segment (2d) or triangle (3d) particles, typically to define boundaries for spherical granular particles to interact with. See the -:doc:`atom\_style line or tri ` command for details. Lines +:doc:`atom_style line or tri ` command for details. Lines and triangles store their size, and if the size is large it may overlap (in a spherical sense) with the insertion region, even if the line/triangle is oriented such that there is no actual overlap. This @@ -249,7 +249,7 @@ place. However, in a statistical sense, a restarted simulation should produce the same behavior if you adjust the fix pour parameters appropriately. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 2c84eaa304..b81d0a8bf8 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -142,7 +142,7 @@ Those styles can be combined within one single command line. By default, the energy associated to this fix is not added to the potential energy of the system. -The :doc:`fix\_modify ` *energy* option is supported by this fix +The :doc:`fix_modify ` *energy* option is supported by this fix to add this magnetic potential energy to the potential energy of the system, @@ -167,7 +167,7 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin ` +:doc:`atom_style spin ` **Default:** diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst index 4237d06228..17338048b0 100644 --- a/doc/src/fix_press_berendsen.rst +++ b/doc/src/fix_press_berendsen.rst @@ -197,11 +197,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID as the fix group. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -209,7 +209,7 @@ It also means that changing attributes of *thermo\_temp* or No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its temperature and pressure calculations. If you do this, note @@ -237,7 +237,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nph `, :doc:`fix npt `, :doc:`fix temp/berendsen `, -:doc:`fix\_modify ` +:doc:`fix_modify ` Default """"""" diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst index 865d3d9741..72d231a15c 100644 --- a/doc/src/fix_print.rst +++ b/doc/src/fix_print.rst @@ -97,7 +97,7 @@ where ID is replaced with the fix-ID. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 645bc13452..f13c6239cd 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -53,8 +53,8 @@ about atoms and to use during a simulation. The specified *group-ID* is ignored by this fix. The atom style used for a simulation defines a set of per-atom -properties, as explained on the :doc:`atom\_style ` and -:doc:`read\_data ` doc pages. The latter command allows these +properties, as explained on the :doc:`atom_style ` and +:doc:`read_data ` doc pages. The latter command allows these properties to be defined for each atom in the system when a data file is read. This fix will augment the set of properties with new custom ones. This can be useful in several scenarios. @@ -113,7 +113,7 @@ new properties are also defined for the ghost atoms. If you use this command with the *mol*\ , *q* or *rmass* vectors, then you most likely want to set *ghost* yes, since these properties - are stored with ghost atoms if you use an :doc:`atom\_style ` + are stored with ghost atoms if you use an :doc:`atom_style ` that defines them, and many LAMMPS operations that use molecule IDs or charge, such as neighbor lists and pair styles, will expect ghost atoms to have these values. LAMMPS will issue a warning it you define @@ -142,14 +142,14 @@ new properties are also defined for the ghost atoms. This fix is one of a small number that can be defined in an input script before the simulation box is created or atoms are defined. -This is so it can be used with the :doc:`read\_data ` command +This is so it can be used with the :doc:`read_data ` command as described below. Per-atom properties that are defined by the :doc:`atom style ` are initialized when atoms are created, e.g. by -the :doc:`read\_data ` or :doc:`create\_atoms ` +the :doc:`read_data ` or :doc:`create_atoms ` commands. The per-atom properties defined by this fix are not. So you need to initialize them explicitly. This can be done by the -:doc:`read\_data ` command, using its *fix* keyword and +:doc:`read_data ` command, using its *fix* keyword and passing it the fix-ID of this fix. Thus these commands: @@ -258,7 +258,7 @@ this to using per-atom masses: set type 1 mass 15.9994 set type 2 mass 1.008 -When writing out the system data with the :doc:`write\_data ` +When writing out the system data with the :doc:`write_data ` command, there will be a new section named with the fix-ID (i.e. *Isotopes* in this case). Alternatively, you can take an existing data file and just add this *Isotopes* section with @@ -312,12 +312,12 @@ instructions on how to use the accelerated styles effectively. **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 ` +simulation is restarted. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -330,7 +330,7 @@ Restrictions Related commands """""""""""""""" -:doc:`read\_data `, :doc:`set `, :doc:`compute property/atom ` +:doc:`read_data `, :doc:`set `, :doc:`compute property/atom ` Default """"""" diff --git a/doc/src/fix_python_move.rst b/doc/src/fix_python_move.rst index 0d59cf82c0..e188c096af 100644 --- a/doc/src/fix_python_move.rst +++ b/doc/src/fix_python_move.rst @@ -91,7 +91,7 @@ Examples for how to do this are in the *examples/python* folder. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index 84ab2abc91..6156c65041 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -176,9 +176,9 @@ vector contains five values in this order: To print these quantities to the log file with descriptive column headers, the following LAMMPS commands are suggested. Here the -:doc:`fix\_modify ` energy command is also enabled to allow +:doc:`fix_modify ` energy command is also enabled to allow the thermo keyword *etotal* to print the quantity etot. See -also the :doc:`thermo\_style ` command. +also the :doc:`thermo_style ` command. .. parsed-literal:: @@ -195,7 +195,7 @@ also the :doc:`thermo\_style ` command. The global scalar under the entry f\_fix\_id is the quantity of thermo energy as an extra part of etot. This global scalar and the vector of 5 quantities can be accessed by various :doc:`output commands `. It is worth noting that the temp keyword -under the :doc:`thermo\_style ` command print the +under the :doc:`thermo_style ` command print the instantaneous classical temperature Tcl as described in the command :doc:`fix qtb `. diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 8875c22af6..77ce447fed 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -137,7 +137,7 @@ point charges, but uses a shielded Coulomb potential to describe the interaction between a pair of charged particles. Interaction through the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field ` paper. The shielding accounts for charge overlap between charged particles at small separation. This style is the same -as :doc:`fix qeq/reax `, and can be used with :doc:`pair\_style reax/c `. Only the *chi*\ , *eta*\ , and *gamma* +as :doc:`fix qeq/reax `, and can be used with :doc:`pair_style reax/c `. Only the *chi*\ , *eta*\ , and *gamma* parameters from the *qfile* file are used. When using the string *reax/c* as filename, these parameters are extracted directly from an active *reax/c* pair style. This style solves partial diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index 35eb514a75..b5da7142fa 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -97,7 +97,7 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is performing charge equilibration. Default is the outermost level. @@ -121,7 +121,7 @@ This fix command currently only supports :doc:`pair style *comb*\ `. Related commands """""""""""""""" -:doc:`pair\_style comb ` +:doc:`pair_style comb ` Default """"""" diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst index 4371e7a1a1..e39c0eb590 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -39,7 +39,7 @@ Description Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) `. It is typically used in conjunction with the ReaxFF force field model as -implemented in the :doc:`pair\_style reax/c ` command, but +implemented in the :doc:`pair_style reax/c ` command, but it can be used with any potential in LAMMPS, so long as it defines and uses charges on each atom. The :doc:`fix qeq/comb ` command should be used to perform charge equilibration with the :doc:`COMB potential `. For more technical details about the @@ -50,7 +50,7 @@ The QEq method minimizes the electrostatic energy of the system by adjusting the partial charge on individual atoms based on interactions with their neighbors. It requires some parameters for each atom type. If the *params* setting above is the word "reax/c", then these are -extracted from the :doc:`pair\_style reax/c ` command and +extracted from the :doc:`pair_style reax/c ` command and the ReaxFF force field file it reads in. If a file name is specified for *params*\ , then the parameters are taken from the specified file and the file must contain one line for each atom type. The latter @@ -122,7 +122,7 @@ be used for periodic cell dimensions less than 10 angstroms. Related commands """""""""""""""" -:doc:`pair\_style reax/c ` +:doc:`pair_style reax/c ` **Default:** none diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index ee08cd1d15..6166efbada 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -45,7 +45,7 @@ description of the QM/MM interface code itself in lib/qmmm/README. **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 +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 quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index b6c15a2dd3..fcd788cff0 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -31,7 +31,7 @@ Description """"""""""" Write out the bond information computed by the ReaxFF potential specified -by :doc:`pair\_style reax/c ` in the exact same format as the +by :doc:`pair_style reax/c ` in the exact same format as the original stand-alone ReaxFF code of Adri van Duin. The bond information is written to *filename* on timesteps that are multiples of *Nevery*\ , including timestep 0. For time-averaged chemical species analysis, @@ -64,7 +64,7 @@ version, but will also take longer to write. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -101,7 +101,7 @@ Restrictions """""""""""" -The fix reax/c/bonds command requires that the :doc:`pair\_style reax/c ` is invoked. This fix is part of the +The fix reax/c/bonds command requires that the :doc:`pair_style reax/c ` is invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -112,7 +112,7 @@ To write gzipped bond files, you must compile LAMMPS with the Related commands """""""""""""""" -:doc:`pair\_style reax/c `, :doc:`fix reax/c/species ` +:doc:`pair_style reax/c `, :doc:`fix reax/c/species ` **Default:** none diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index 210f6fe5cc..ebcae065ee 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -49,7 +49,7 @@ Description """"""""""" Write out the chemical species information computed by the ReaxFF -potential specified by :doc:`pair\_style reax/c `. +potential specified by :doc:`pair_style reax/c `. Bond-order values (either averaged or instantaneous, depending on value of *Nrepeat*\ ) are used to determine chemical bonds. Every *Nfreq* timesteps, chemical species information is written to @@ -122,7 +122,7 @@ average bond-order for the species analysis output on timestep 100. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes both a global vector of length 2 and a per-atom @@ -174,7 +174,7 @@ Restrictions """""""""""" -The "fix reax/c/species" currently only works with :doc:`pair\_style reax/c ` and it requires that the :doc:`pair\_style reax/c ` be invoked. This fix is part of the +The "fix reax/c/species" currently only works with :doc:`pair_style reax/c ` and it requires that the :doc:`pair_style reax/c ` be invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -189,7 +189,7 @@ It should be possible to extend it to other reactive pair\_styles (such as Related commands """""""""""""""" -:doc:`pair\_style reax/c `, :doc:`fix reax/c/bonds ` +:doc:`pair_style reax/c `, :doc:`fix reax/c/bonds ` Default """"""" diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst index 0a33bbaea3..d6895b0874 100644 --- a/doc/src/fix_recenter.rst +++ b/doc/src/fix_recenter.rst @@ -99,7 +99,7 @@ velocities with zero aggregate linear and/or angular momentum. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various @@ -124,7 +124,7 @@ This fix should not be used with an x,y,z setting that causes a large shift in the system on the 1st timestep, due to the requested COM being very different from the initial COM. This could cause atoms to be lost, especially in parallel. Instead, use the -:doc:`displace\_atoms ` command, which can be used to +:doc:`displace_atoms ` command, which can be used to move atoms a large distance. Related commands diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index 0fc0ccee77..04d7a01c07 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -53,7 +53,7 @@ Restrain the motion of the specified sets of atoms by making them part of a bond or angle or dihedral interaction whose strength can vary over time during a simulation. This is functionally similar to creating a bond or angle or dihedral for the same atoms in a data -file, as specified by the :doc:`read\_data ` command, albeit +file, as specified by the :doc:`read_data ` command, albeit with a time-varying pre-factor coefficient, and except for exclusion rules, as explained below. @@ -68,9 +68,9 @@ data file. Adding a bond/angle/dihedral with this command does not apply the exclusion rules and weighting factors specified by the - :doc:`special\_bonds ` command to atoms in the restraint + :doc:`special_bonds ` command to atoms in the restraint that are now bonded (1-2,1-3,1-4 neighbors) as a result. If they are - close enough to interact in a :doc:`pair\_style ` sense + close enough to interact in a :doc:`pair_style ` sense (non-bonded interaction), then the bond/angle/dihedral restraint interaction will simply be superposed on top of that interaction. @@ -131,7 +131,7 @@ as the following may be useful: The *bond* keyword applies a bond restraint to the specified atoms -using the same functional form used by the :doc:`bond\_style harmonic ` command. The potential associated with +using the same functional form used by the :doc:`bond_style harmonic ` command. The potential associated with the restraint is .. math:: @@ -152,7 +152,7 @@ is included in :math:`K`. The *angle* keyword applies an angle restraint to the specified atoms -using the same functional form used by the :doc:`angle\_style harmonic ` command. The potential associated with +using the same functional form used by the :doc:`angle_style harmonic ` command. The potential associated with the restraint is .. math:: @@ -173,7 +173,7 @@ factor is included in :math:`K`. The *dihedral* keyword applies a dihedral restraint to the specified atoms using a simplified form of the function used by the -:doc:`dihedral\_style charmm ` command. The potential +:doc:`dihedral_style charmm ` command. The potential associated with the restraint is .. math:: @@ -201,11 +201,11 @@ current dihedral angle :math:`\phi` is equal to :math:`\phi_0`. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential energy associated with this fix to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -214,7 +214,7 @@ integrator the fix is adding its forces. Default is the outermost level. If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. This fix computes a global scalar and a global vector of length 3, which can be accessed by various :doc:`output commands `. diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst index 7f18b03966..25acb09f0b 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -51,7 +51,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`thermo\_style ` +:doc:`thermo_style ` **Default:** none diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 1f16d33a19..9e9c65dd19 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -204,8 +204,8 @@ processors when ghost atom info is accumulated. large enough to span the distance between the atom that owns the body and every other atom in the body. This distance value is printed out when the rigid bodies are defined. If the - :doc:`pair\_style ` cutoff plus neighbor skin does not span - this distance, then you should use the :doc:`comm\_modify cutoff ` command with a setting epsilon larger than + :doc:`pair_style ` cutoff plus neighbor skin does not span + this distance, then you should use the :doc:`comm_modify cutoff ` command with a setting epsilon larger than the distance. Which of the two variants is faster for a particular problem is hard @@ -254,7 +254,7 @@ differences may accumulate to produce divergent trajectories. could displace the atoms in a body or add a large velocity to each atom in a body to make it move in a desired direction before a 2nd run is performed, using the :doc:`set ` or - :doc:`displace\_atoms ` or :doc:`velocity ` + :doc:`displace_atoms ` or :doc:`velocity ` commands. But these commands will not affect the internal attributes of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no* (or using the *infile* option, which implies *reinit* *no*\ ) the position @@ -353,7 +353,7 @@ settings from the final keyword are used. For computational efficiency, you may wish to turn off pairwise and bond interactions within each rigid body, as they no longer - contribute to the motion. The :doc:`neigh\_modify exclude ` and :doc:`delete\_bonds ` + contribute to the motion. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` commands are used to do this. If the rigid bodies have strongly overlapping atoms, you may need to turn off these interactions to avoid numerical problems due to large equal/opposite intra-body forces @@ -370,7 +370,7 @@ is more expensive. The constituent particles within a rigid body can be point particles (the default in LAMMPS) or finite-size particles, such as spheres or -ellipsoids or line segments or triangles. See the :doc:`atom\_style sphere and ellipsoid and line and tri ` commands for more +ellipsoids or line segments or triangles. See the :doc:`atom_style sphere and ellipsoid and line and tri ` commands for more details on these kinds of particles. Finite-size particles contribute differently to the moment of inertia of a rigid body than do point particles. Finite-size particles can also experience torque (e.g. due @@ -380,7 +380,7 @@ orientation. These contributions are accounted for by these fixes. Forces between particles within a body do not contribute to the external force or torque on the body. Thus for computational efficiency, you may wish to turn off pairwise and bond interactions -between particles within each rigid body. The :doc:`neigh\_modify exclude ` and :doc:`delete\_bonds ` +between particles within each rigid body. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` commands are used to do this. For finite-size particles this also means the particles can be highly overlapped when creating the rigid body. @@ -792,27 +792,27 @@ with rigid body information each time a restart file is written, as explained above for the *infile* keyword. For the 2 NVT rigid styles, the state of the Nose/Hoover thermostat is written to :doc:`binary restart files `. Ditto for the 4 NPT and NPH rigid styles, and the state of the Nose/Hoover barostat. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *energy* option is supported by the 6 +The :doc:`fix_modify ` *energy* option is supported by the 6 NVT, NPT, NPH rigid styles to add the energy change induced by the thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to keeping the objects rigid to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by the 4 NPT and NPH rigid styles to change the computes used to calculate the instantaneous pressure tensor. Note that the 2 NVT rigid fixes do not use any external compute to compute instantaneous temperature. -The :doc:`fix\_modify ` *bodyforces* option is supported by +The :doc:`fix_modify ` *bodyforces* option is supported by all rigid styles to set whether per-body forces and torques are computed early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage or the timestep, respectively. @@ -906,7 +906,7 @@ example: Related commands """""""""""""""" -:doc:`delete\_bonds `, :doc:`neigh\_modify ` +:doc:`delete_bonds `, :doc:`neigh_modify ` exclude, :doc:`fix shake ` Default diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index c7835e83fb..964d414c70 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -112,7 +112,7 @@ internal energy and extrapolated velocity are also updated. could displace the particles in a body or add a large velocity to each particle in a body to make it move in a desired direction before a 2nd run is performed, using the :doc:`set ` or - :doc:`displace\_atoms ` or :doc:`velocity ` + :doc:`displace_atoms ` or :doc:`velocity ` commands. But these commands will not affect the internal attributes of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no* (or using the *infile* option, which implies *reinit* *no*\ ) the position @@ -306,7 +306,7 @@ If the *infile* keyword is used, an auxiliary file is written out with rigid body information each time a restart file is written, as explained above for the *infile* keyword. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global array of values which can be accessed by @@ -362,7 +362,7 @@ package. It is only enabled if LAMMPS was built with both packages. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store density and internal energy as -defined by the :doc:`atom\_style meso ` command. +defined by the :doc:`atom_style meso ` command. All particles in the group must be mesoscopic SPH/SDPD particles. @@ -370,7 +370,7 @@ Related commands """""""""""""""" :doc:`fix meso/move `, :doc:`fix rigid `, -:doc:`neigh\_modify exclude ` +:doc:`neigh_modify exclude ` Default """"""" diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index b9df24f5a9..79809b7fc6 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -193,7 +193,7 @@ define the thermodynamic properties of each species. Furthermore, the number of species molecules (i.e., concentration) can be specified either with the :doc:`set ` command using the "d\_" prefix or by reading directly the concentrations from a data file. For the latter -case, the :doc:`read\_data ` command with the fix keyword +case, the :doc:`read_data ` command with the fix keyword should be specified, where the fix-ID will be the "fix rx`ID with a `_ suffix, e.g. fix foo all rx reaction.file ... @@ -232,7 +232,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. This command can only be used with a constant energy or constant diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst index 8b11f71e62..2aa3960efb 100644 --- a/doc/src/fix_saed_vtk.rst +++ b/doc/src/fix_saed_vtk.rst @@ -179,7 +179,7 @@ output. This option can only be used with the *ave running* setting. **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 +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 parameter of this fix can be used with the *start/stop* keywords of @@ -190,12 +190,12 @@ Restrictions The attributes for fix\_saed\_vtk must match the values assigned in the -associated :doc:`compute\_saed ` command. +associated :doc:`compute_saed ` command. Related commands """""""""""""""" -:doc:`compute\_saed ` +:doc:`compute_saed ` Default """"""" diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index a01fb7dc00..39a51e0f7b 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -64,7 +64,7 @@ will be evaluated each timestep, and its value used to determine the force component. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent force field. @@ -125,7 +125,7 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *respa* option is supported by +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is setting the forces to the desired values; on all other levels, the force is set to 0.0 for the atoms in the fix group, diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 28a50e6754..ce875b18cf 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -211,12 +211,12 @@ LAMMPS closely follows (:ref:`Andersen (1983) `). **Restart, fix\_modify, output, run start/stop, minimize info:** -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to keeping the constraints to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* -No information about these fixes is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +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 stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used with the *start/stop* keywords of the :doc:`run ` command. These diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index b1f3cb0745..20bd2273d4 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -38,12 +38,12 @@ the deterministic integration of the conservative force. Further details regarding the method are provided in :ref:`(Lisal) ` and :ref:`(Larentzos1) `. -The fix *shardlow* must be used with the :doc:`pair\_style dpd/fdt ` or :doc:`pair\_style dpd/fdt/energy ` command to properly initialize the +The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt ` or :doc:`pair_style dpd/fdt/energy ` command to properly initialize the fluctuation-dissipation theorem parameter(s) sigma (and kappa, if necessary). Note that numerous variants of DPD can be specified by choosing an -appropriate combination of the integrator and :doc:`pair\_style dpd/fdt ` command. DPD under isothermal conditions can +appropriate combination of the integrator and :doc:`pair_style dpd/fdt ` command. DPD under isothermal conditions can be specified by using fix *shardlow*\ , fix *nve* and pair\_style *dpd/fdt*\ . DPD under isoenergetic conditions can be specified by using fix *shardlow*\ , fix *nve* and pair\_style *dpd/fdt/energy*\ . DPD @@ -100,7 +100,7 @@ requested. Related commands """""""""""""""" -:doc:`pair\_style dpd/fdt `, :doc:`fix eos/cv ` +:doc:`pair_style dpd/fdt `, :doc:`fix eos/cv ` **Default:** none diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index 7473cb07a9..e9ea27e61f 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -107,16 +107,16 @@ pulling path. The fix stores the direction of the spring, current pulling target distance and the running PMF to :doc:`binary restart files `. -See the :doc:`read\_restart ` command for info on how to +See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the added forces on atoms to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index 6a8eb80ade..22cf1dff53 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -53,7 +53,7 @@ will be evaluated each timestep, and its value used to determine the force component. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent velocity field. @@ -72,7 +72,7 @@ specified geometric :doc:`region ` in order to have its velocity set by **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 +None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global 3-vector of forces, which can be accessed diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst index 2d874e4b23..c3621cab3f 100644 --- a/doc/src/fix_spring.rst +++ b/doc/src/fix_spring.rst @@ -105,11 +105,11 @@ last example holds the ion a distance 5 away from the pore axis No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy stored in the spring to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -140,7 +140,7 @@ invoked by the :doc:`minimize ` command. If you want the spring energy to be included in the total potential energy of the system (the quantity being minimized), you - MUST enable the :doc:`fix\_modify ` *energy* option for this + MUST enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst index 9f6182df8e..d645519add 100644 --- a/doc/src/fix_spring_chunk.rst +++ b/doc/src/fix_spring_chunk.rst @@ -54,11 +54,11 @@ atom. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy stored in all the springs to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -78,7 +78,7 @@ invoked by the :doc:`minimize ` command. If you want the spring energies to be included in the total potential energy of the system (the quantity being minimized), you - MUST enable the :doc:`fix\_modify ` *energy* option for this + MUST enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst index b2573483e0..59007b6cb6 100644 --- a/doc/src/fix_spring_rg.rst +++ b/doc/src/fix_spring_rg.rst @@ -57,13 +57,13 @@ the time the fix is specified, and that value is used as the target. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. diff --git a/doc/src/fix_spring_self.rst b/doc/src/fix_spring_self.rst index d061c96eba..d9720f0e7c 100644 --- a/doc/src/fix_spring_self.rst +++ b/doc/src/fix_spring_self.rst @@ -47,15 +47,15 @@ plane, respectively. 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 +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy stored in the per-atom springs to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -75,7 +75,7 @@ invoked by the :doc:`minimize ` command. If you want the per-atom spring energy to be included in the total potential energy of the system (the quantity being minimized), - you MUST enable the :doc:`fix\_modify ` *energy* option for + you MUST enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 51c1b25930..6232c345a1 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -333,12 +333,12 @@ one of the operations and off for the other. Three other input script commands will largely overcome this effect, speeding up an SRD simulation by a significant amount. These are the -:doc:`atom\_modify first `, :doc:`neigh\_modify include `, and :doc:`comm\_modify group ` +:doc:`atom_modify first `, :doc:`neigh_modify include `, and :doc:`comm_modify group ` commands. Each takes a group-ID as an argument, which in this case should be the group-ID of the big solute particles. -Additionally, when a :doc:`pair\_style ` for big/big particle -interactions is specified, the :doc:`pair\_coeff ` command +Additionally, when a :doc:`pair_style ` for big/big particle +interactions is specified, the :doc:`pair_coeff ` command should be used to turn off big/SRD interactions, e.g. by setting their epsilon or cutoff length to 0.0. @@ -352,7 +352,7 @@ particles. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix tabulates several SRD statistics which are stored in a vector diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst index 4578f39f87..5d96ee26fe 100644 --- a/doc/src/fix_store_force.rst +++ b/doc/src/fix_store_force.rst @@ -53,7 +53,7 @@ potentially modify the force on each atom. Examples of such fixes are **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a per-atom array which can be accessed by various diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index 131ba5d0b1..15cad5bc81 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -110,12 +110,12 @@ group. **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 ` +simulation is restarted. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. If a single input is specified, this fix produces a per-atom vector. diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index 8d0959cd96..f378d5dac7 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/doc/src/fix_temp_berendsen.rst @@ -64,7 +64,7 @@ its value used to determine the target temperature. zero temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -97,11 +97,11 @@ that the ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -111,7 +111,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -127,13 +127,13 @@ thermal degrees of freedom, and the bias is added back in. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of :doc:`thermodynamic output `. @@ -164,7 +164,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix langevin `, -:doc:`fix\_modify `, :doc:`compute temp `, +:doc:`fix_modify `, :doc:`compute temp `, :doc:`fix press/berendsen ` **Default:** none diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 6494c9e981..27aabaab1d 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -74,7 +74,7 @@ name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -107,11 +107,11 @@ that the ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -121,7 +121,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -137,7 +137,7 @@ thermal degrees of freedom, and the bias is added back in. No information about these fixes are written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by these +The :doc:`fix_modify ` *temp* option is supported by these fixes. You can use it to assign a temperature :doc:`compute ` you have defined to these fixes which will be used in its thermostatting procedure, as described above. For consistency, the group used by @@ -172,7 +172,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix langevin `, -:doc:`fix\_modify `, :doc:`compute temp `, +:doc:`fix_modify `, :doc:`compute temp `, :doc:`fix temp/berendsen ` **Default:** none diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index 80f03a3018..13858f6043 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -64,7 +64,7 @@ name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -104,11 +104,11 @@ ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -118,7 +118,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -134,13 +134,13 @@ thermal degrees of freedom, and the bias is added back in. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of :doc:`thermodynamic output `. @@ -163,7 +163,7 @@ Related commands """""""""""""""" :doc:`fix langevin `, :doc:`fix nvt `, -:doc:`fix\_modify ` +:doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst index e60459a29b..ef7cf8f42a 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/doc/src/fix_temp_rescale_eff.rst @@ -41,13 +41,13 @@ particles. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of :doc:`thermodynamic output `. @@ -72,7 +72,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix langevin/eff `, :doc:`fix nvt/eff `, :doc:`fix\_modify `, +:doc:`fix langevin/eff `, :doc:`fix nvt/eff `, :doc:`fix_modify `, :doc:`fix temp rescale `, **Default:** none diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst index ab407ba7b1..a5d37136ef 100644 --- a/doc/src/fix_tfmc.rst +++ b/doc/src/fix_tfmc.rst @@ -126,7 +126,7 @@ rotational component of the tfMC displacements after every iteration. No information about this fix is written to :doc:`binary restart files `. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix is not invoked during :doc:`energy minimization `. diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index 05552c1b37..9682adf76a 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/doc/src/fix_thermal_conductivity.rst @@ -115,7 +115,7 @@ fluid, in appropriate units. See the :ref:`Muller-Plathe paper **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst index ed31733196..416ab877ab 100644 --- a/doc/src/fix_tmd.rst +++ b/doc/src/fix_tmd.rst @@ -61,7 +61,7 @@ the atoms to follow. If image flags are included with the atoms, the 1st 3 lo/hi lines must appear in the file. If image flags are not included, the 1st 3 lines should not appear. The 3 lines contain the simulation box dimensions for the atom coordinates, in the same format -as in a LAMMPS data file (see the :doc:`read\_data ` command). +as in a LAMMPS data file (see the :doc:`read_data ` command). The remaining lines each contain an atom ID and its target x,y,z coordinates. The atom lines (all or none of them) can optionally be @@ -94,7 +94,7 @@ For more information about TMD, see :ref:`(Schlitter1) ` and **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 +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 by this fix for access by various :doc:`output commands `. diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index b6bc43ecd3..8833e0f471 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -285,7 +285,7 @@ ignored. The lines with the even numbers are treated as follows: **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 +exchange between the subsystems 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 restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -296,7 +296,7 @@ fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -None of the :doc:`fix\_modify ` options are relevant to these +None of the :doc:`fix_modify ` options are relevant to these fixes. Both fixes compute 2 output quantities stored in a vector of length 2, diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index 1dc6c2befd..8424418988 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -70,11 +70,11 @@ to use this fix only to discover the optimal parameter set for a given setup that can then be used on subsequent production runs. This fix starts with kspace parameters that are set by the user with the -:doc:`kspace\_style ` and :doc:`kspace\_modify ` +:doc:`kspace_style ` and :doc:`kspace_modify ` commands. The prescribed accuracy will be maintained by this fix throughout the simulation. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No parameter of this fix can be used with the *start/stop* keywords of @@ -96,9 +96,9 @@ TIP4P water support, or long-range point dipole support. Related commands """""""""""""""" -:doc:`kspace\_style `, :doc:`boundary ` -:doc:`kspace\_modify `, :doc:`pair\_style lj/cut/coul/long `, :doc:`pair\_style lj/charmm/coul/long `, :doc:`pair\_style lj/long `, :doc:`pair\_style lj/long/coul/long `, -:doc:`pair\_style buck/coul/long ` +:doc:`kspace_style `, :doc:`boundary ` +:doc:`kspace_modify `, :doc:`pair_style lj/cut/coul/long `, :doc:`pair_style lj/charmm/coul/long `, :doc:`pair_style lj/long `, :doc:`pair_style lj/long/coul/long `, +:doc:`pair_style buck/coul/long ` Default """"""" diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 3d7fb85274..a2c7c87cd5 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -134,7 +134,7 @@ quantities to be stored by fix vector. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a global vector or global array which can be diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index 637551b1e4..27250f2c85 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -120,7 +120,7 @@ box orthogonal; thus it does not suffer from this limitation. **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst index 247600db93..0c8338048a 100644 --- a/doc/src/fix_viscous.rst +++ b/doc/src/fix_viscous.rst @@ -89,20 +89,20 @@ easily be used as a thermostat. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is modifying forces. Default is the outermost level. The forces due to this fix are imposed during an energy minimization, invoked by the :doc:`minimize ` command. This fix should only be used with damped dynamics minimizers that allow for -non-conservative forces. See the :doc:`min\_style ` command +non-conservative forces. See the :doc:`min_style ` command for details. Restrictions diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index b31ee4a663..a14cf423b0 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -118,7 +118,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: :align: center For style *wall/colloid*\ , the energy E is given by an integrated form -of the :doc:`pair\_style colloid ` potential: +of the :doc:`pair_style colloid ` potential: .. image:: Eqs/fix_wall_colloid.jpg :align: center @@ -157,7 +157,7 @@ where name is an :doc:`equal-style variable ` name. In this case the variable is evaluated each timestep and the result becomes the current position of the reflecting wall. Equal-style variables can specify formulas with various mathematical functions, and include -:doc:`thermo\_style ` command keywords for the simulation +:doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent wall position. See examples below. @@ -213,7 +213,7 @@ specified as v\_name, where name is the variable name. As with a variable wall position, the variable is evaluated each timestep and the result becomes the current epsilon or sigma of the wall. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent wall interaction. @@ -247,7 +247,7 @@ define the lattice spacings. The *fld* keyword can be used with a *yes* setting to invoke the wall constraint before pairwise interactions are computed. This allows an -implicit FLD model using :doc:`pair\_style lubricateU ` +implicit FLD model using :doc:`pair_style lubricateU ` to include the wall force in its calculations. If the setting is *no*\ , wall forces are imposed after pairwise interactions, in the usual manner. @@ -321,15 +321,15 @@ perturbation on the particles: No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of interaction between atoms and each wall to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -353,7 +353,7 @@ invoked by the :doc:`minimize ` command. If you want the atom/wall interaction energy to be included in the total potential energy of the system (the quantity being - minimized), you MUST enable the :doc:`fix\_modify ` *energy* + minimized), you MUST enable the :doc:`fix_modify ` *energy* option for this fix. diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 840338db5c..2ecbb2e911 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -56,7 +56,7 @@ the :doc:`Howto body ` doc page for more details on using body particles. The parameters *k\_n*, *c\_n*, *c\_t* have the same meaning and units as -those specified with the :doc:`pair\_style body/rounded/polygon ` command. +those specified with the :doc:`pair_style body/rounded/polygon ` command. The *wallstyle* can be planar or cylindrical. The 2 planar options specify a pair of walls in a dimension. Wall positions are given by @@ -91,7 +91,7 @@ to the derivative of this expression. **Restart, fix\_modify, output, run start/stop, minimize info:** -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -109,7 +109,7 @@ Any dimension (xy) that has a wall must be non-periodic. Related commands """""""""""""""" -:doc:`atom\_style body `, :doc:`pair\_style body/rounded/polygon ` +:doc:`atom_style body `, :doc:`pair_style body/rounded/polygon ` **Default:** none diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index 6c3e3f5e6d..fd58c16c44 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -56,7 +56,7 @@ the :doc:`Howto body ` doc page for more details on using body particles. The parameters *k\_n*, *c\_n*, *c\_t* have the same meaning and units as -those specified with the :doc:`pair\_style body/rounded/polyhedron ` command. +those specified with the :doc:`pair_style body/rounded/polyhedron ` command. The *wallstyle* can be planar or cylindrical. The 3 planar options specify a pair of walls in a dimension. Wall positions are given by @@ -90,7 +90,7 @@ to the derivative of this expression. **Restart, fix\_modify, output, run start/stop, minimize info:** -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -108,7 +108,7 @@ Any dimension (xyz) that has a wall must be non-periodic. Related commands """""""""""""""" -:doc:`atom\_style body `, :doc:`pair\_style body/rounded/polyhedron ` +:doc:`atom_style body `, :doc:`pair_style body/rounded/polyhedron ` **Default:** none diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index 559f1958d9..873811110c 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -116,7 +116,7 @@ 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. This fix requires that atoms be ellipsoids as defined by the -:doc:`atom\_style ellipsoid ` command. +:doc:`atom_style ellipsoid ` command. Related commands """""""""""""""" diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 5c9c476a44..0db5a3e5ac 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -83,12 +83,12 @@ close enough to touch it. The nature of the wall/particle interactions are determined by the *fstyle* setting. It can be any of the styles defined by the -:doc:`pair\_style gran/\* ` or the more general `pair\_style granular `_ commands. Currently the options are +:doc:`pair_style gran/\* ` or the more general `pair\_style granular `_ commands. Currently the options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and *granular* with all the possible options of the associated *pair\_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the -corresponding equation on the :doc:`pair\_style gran/\* ` and +corresponding equation on the :doc:`pair_style gran/\* ` and :doc:`pair\_style\_granular ` doc pages, in the limit of one of the two particles going to infinite radius and mass (flat wall). Specifically, delta = radius - r = overlap of particle with @@ -97,16 +97,16 @@ RiRj/Ri+Rj is set to the radius of the particle. The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag* have the same meaning and units as those specified with the -:doc:`pair\_style gran/\* ` commands. This means a NULL can be +:doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma\_t* as described on that page. If a NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7 *Kn*\ . If a NULL is used for *gamma\_t*, then a default value is used where *gamma\_t* = 1/2 *gamma\_n*. All the model choices for cohesion, tangential friction, rolling -friction and twisting friction supported by the :doc:`pair\_style granular ` through its *pair\_coeff* command are also +friction and twisting friction supported by the :doc:`pair_style granular ` through its *pair\_coeff* command are also supported for walls. These are discussed in greater detail on the doc -page for :doc:`pair\_style granular `. +page for :doc:`pair_style granular `. Note that you can choose a different force styles and/or different values for the wall/particle coefficients than for particle/particle @@ -115,7 +115,7 @@ material. .. note:: - As discussed on the doc page for :doc:`pair\_style gran/\* `, versions of LAMMPS before 9Jan09 used a + As discussed on the doc page for :doc:`pair_style gran/\* `, versions of LAMMPS before 9Jan09 used a different equation for Hertzian interactions. This means Hertizian wall/particle interactions have also changed. They now include a sqrt(radius) term which was not present before. Also the previous @@ -128,7 +128,7 @@ material. Kt, gamma\_n, and gamma\_s should be set sqrt(2.0) larger than they were previously. -The effective mass *m\_eff* in the formulas listed on the :doc:`pair\_style granular ` doc page is the mass of the particle for +The effective mass *m\_eff* in the formulas listed on the :doc:`pair_style granular ` doc page is the mass of the particle for particle/wall interactions (mass of wall is infinite). If the particle is part of a rigid body, its mass is replaced by the mass of the rigid body in those formulas. This is determined by searching for @@ -180,12 +180,12 @@ the wall at whatever *radius* has been defined. This fix writes the shear friction state of atoms interacting with the wall to :doc:`binary restart files `, so that a simulation can continue correctly if granular potentials with shear "history" effects -are being used. See the :doc:`read\_restart ` command for +are being used. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -205,8 +205,8 @@ Related commands :doc:`fix move `, :doc:`fix wall/gran/region `, -:doc:`pair\_style gran/\* ` -:doc:`pair\_style granular ` +:doc:`pair_style gran/\* ` +:doc:`pair_style granular ` **Default:** none diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index cdd6c7445b..3ca17aa440 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -81,7 +81,7 @@ wall exerts on the particle is along the direction between that point and the particle center, which is the direction normal to the surface at that point. Note that if the region surface is comprised of multiple "faces", then each face can exert a force on the particle if -it is close enough. E.g. for :doc:`region\_style block `, a +it is close enough. E.g. for :doc:`region_style block `, a particle in the interior, near a corner of the block, could feel wall forces from 1, 2, or 3 faces of the block. @@ -154,12 +154,12 @@ corresponding manner. The nature of the wall/particle interactions are determined by the *fstyle* setting. It can be any of the styles defined by the -:doc:`pair\_style gran/\* ` or the more general `pair\_style granular `_ commands. Currently the options are +:doc:`pair_style gran/\* ` or the more general `pair\_style granular `_ commands. Currently the options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and *granular* with all the possible options of the associated *pair\_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the -corresponding equation on the :doc:`pair\_style gran/\* ` and +corresponding equation on the :doc:`pair_style gran/\* ` and :doc:`pair\_style\_granular ` doc pages, but the effective radius is calculated using the radius of the particle and the radius of curvature of the wall at the contact point. @@ -175,16 +175,16 @@ particle. The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag* have the same meaning and units as those specified with the -:doc:`pair\_style gran/\* ` commands. This means a NULL can be +:doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma\_t* as described on that page. If a NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7 *Kn*\ . If a NULL is used for *gamma\_t*, then a default value is used where *gamma\_t* = 1/2 *gamma\_n*. All the model choices for cohesion, tangential friction, rolling -friction and twisting friction supported by the :doc:`pair\_style granular ` through its *pair\_coeff* command are also +friction and twisting friction supported by the :doc:`pair_style granular ` through its *pair\_coeff* command are also supported for walls. These are discussed in greater detail on the doc -page for :doc:`pair\_style granular `. +page for :doc:`pair_style granular `. Note that you can choose a different force styles and/or different values for the 6 wall/particle coefficients than for particle/particle @@ -197,7 +197,7 @@ 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 correctly if granular potentials with shear "history" effects are being used. This fix also includes info about a moving region in the -restart file. See the :doc:`read\_restart ` command for +restart file. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -205,7 +205,7 @@ uninterrupted fashion. .. note:: Information about region definitions is NOT included in restart - files, as discussed on the :doc:`read\_restart ` doc page. + files, as discussed on the :doc:`read_restart ` doc page. So you must re-define your region and if it is a moving region, define its motion attributes in a way that is consistent with the simulation that wrote the restart file. In particular, if you want to change the @@ -219,7 +219,7 @@ uninterrupted fashion. use the same fix ID for fix wall/gran/region, but assign it a region with a different region ID. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -235,10 +235,10 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix\_move `, +:doc:`fix_move `, :doc:`fix wall/gran `, :doc:`fix wall/region `, -:doc:`pair\_style granular `, +:doc:`pair_style granular `, :doc:`region ` **Default:** none diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index c38057915b..863fb2bd86 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -98,7 +98,7 @@ define the lattice spacings. **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 +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 by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 464ae3b4a5..c6807eee94 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -59,7 +59,7 @@ put back inside the face by the same delta, and the sign of the corresponding component of its velocity is flipped. When used in conjunction with :doc:`fix nve ` and -:doc:`run\_style verlet `, the resultant time-integration +:doc:`run_style verlet `, the resultant time-integration algorithm is equivalent to the primitive splitting algorithm (PSA) described by :ref:`Bond `. Because each reflection event divides the corresponding timestep asymmetrically, energy conservation @@ -83,7 +83,7 @@ where name is an :doc:`equal-style variable ` name. In this case the variable is evaluated each timestep and the result becomes the current position of the reflecting wall. Equal-style variables can specify formulas with various mathematical functions, and include -:doc:`thermo\_style ` command keywords for the simulation +:doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent wall position. @@ -177,7 +177,7 @@ instructions on how to use the accelerated styles effectively. **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 +`. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index 36b2dffde9..069221df9d 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -56,7 +56,7 @@ particle is along the direction between that point and the particle, which is the direction normal to the surface at that point. Note that if the region surface is comprised of multiple "faces", then each face can exert a force on the particle if it is close enough. E.g. for -:doc:`region\_style block `, a particle in the interior, near a +:doc:`region_style block `, a particle in the interior, near a corner of the block, could feel wall forces from 1, 2, or 3 faces of the block. @@ -146,7 +146,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: :align: center For style *colloid*\ , the energy E is given by an integrated form of -the :doc:`pair\_style colloid ` potential: +the :doc:`pair_style colloid ` potential: .. image:: Eqs/fix_wall_colloid.jpg :align: center @@ -178,15 +178,15 @@ For a full description of these wall styles, see fix\_style No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of interaction between atoms and the wall to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -207,7 +207,7 @@ invoked by the :doc:`minimize ` command. If you want the atom/wall interaction energy to be included in the total potential energy of the system (the quantity being - minimized), you MUST enable the :doc:`fix\_modify ` *energy* + minimized), you MUST enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index c302539f3c..8a4fd22176 100644 --- a/doc/src/fix_wall_srd.rst +++ b/doc/src/fix_wall_srd.rst @@ -93,7 +93,7 @@ where name is an :doc:`equal-style variable ` name. In this case the variable is evaluated each timestep and the result becomes the current position of the reflecting wall. Equal-style variables can specify formulas with various mathematical functions, and include -:doc:`thermo\_style ` command keywords for the simulation +:doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent wall position. @@ -190,7 +190,7 @@ perturbation on the particles: **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 +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global array of values which can be accessed by diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst index bf1e884cda..90268a2c90 100644 --- a/doc/src/hyper.rst +++ b/doc/src/hyper.rst @@ -115,9 +115,9 @@ is performed by quenching the system and comparing the resulting atom coordinates to the coordinates from the previous basin. A quench is an energy minimization and is performed by whichever -algorithm has been defined by the :doc:`min\_style ` command. +algorithm has been defined by the :doc:`min_style ` command. Minimization parameters may be set via the -:doc:`min\_modify ` command and by the *min* keyword of the +:doc:`min_modify ` command and by the *min* keyword of the hyper command. The latter are the settings that would be used with the :doc:`minimize ` command. Note that typically, you do not need to perform a highly-converged minimization to detect a transition diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst index d6f23e761c..ed120acb58 100644 --- a/doc/src/improper_class2.rst +++ b/doc/src/improper_class2.rst @@ -39,7 +39,7 @@ where Ei is the improper term and Eaa is an angle-angle term. The 3 X terms in Ei are an average over 3 out-of-plane angles. The 4 atoms in an improper quadruplet (listed in the data file read by -the :doc:`read\_data ` command) are ordered I,J,K,L. X\_IJKL +the :doc:`read_data ` command) are ordered I,J,K,L. X\_IJKL refers to the angle between the plane of I,J,K and the plane of J,K,L, and the bond JK lies in both planes. Similarly for X\_KJLI and X\_LJIK. Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X @@ -60,9 +60,9 @@ this is not required. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. Coefficients for the Ei and Eaa formulas must be defined for each -improper type via the :doc:`improper\_coeff ` command as +improper type via the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. These are the 2 coefficients for the Ei formula: @@ -74,7 +74,7 @@ X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian\^2. For the Eaa formula, each line in a -:doc:`improper\_coeff ` command in the input script lists +:doc:`improper_coeff ` command in the input script lists 7 coefficients, the first of which is "aa" to indicate they are AngleAngle coefficients. In a data file, these coefficients should be listed under a "AngleAngle Coeffs" heading and you must leave out the @@ -128,7 +128,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_coeff.rst b/doc/src/improper_coeff.rst index b71469523f..3c50f9bf58 100644 --- a/doc/src/improper_coeff.rst +++ b/doc/src/improper_coeff.rst @@ -30,7 +30,7 @@ Description Specify the improper force field coefficients for one or more improper types. The number and meaning of the coefficients depends on the improper style. Improper coefficients can also be set in the data -file read by the :doc:`read\_data ` command or in a restart +file read by the :doc:`read_data ` command or in a restart file. N can be specified in one of two ways. An explicit numeric value can @@ -65,7 +65,7 @@ corresponds to the 1st example above would be listed as 1 300.0 0.0 -The :doc:`improper\_style class2 ` is an exception to +The :doc:`improper_style class2 ` is an exception to this rule, in that an additional argument is used in the input script to allow specification of the cross-term coefficients. See its doc page for details. @@ -75,7 +75,7 @@ page for details. The list of all improper styles defined in LAMMPS is given on the -:doc:`improper\_style ` doc page. They are also listed +:doc:`improper_style ` doc page. They are also listed in more compact form on the :ref:`Commands improper ` doc page. On either of those pages, click on the style to display the formula it @@ -91,8 +91,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. An improper style must be defined before any improper coefficients are set, either in the input script or in a data file. @@ -100,7 +100,7 @@ set, either in the input script or in a data file. Related commands """""""""""""""" -:doc:`improper\_style ` +:doc:`improper_style ` **Default:** none diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index 803f6d9e6a..b8f0c33c29 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -35,7 +35,7 @@ where x is the improper angle, x0 is its equilibrium value, and K is a prefactor. If the 4 atoms in an improper quadruplet (listed in the data file read -by the :doc:`read\_data ` command) are ordered I,J,K,L then X +by the :doc:`read_data ` command) are ordered I,J,K,L then X is the angle between the plane of I,J,K and the plane of J,K,L. Alternatively, you can think of atoms J,K,L as being in a plane, and atom I above the plane, and X as a measure of how far out-of-plane I @@ -47,9 +47,9 @@ linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined between the 4 atoms. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -92,7 +92,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index 43cd36f60a..e661d3b84a 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -37,11 +37,11 @@ The *cvff* improper style uses the potential where phi is the improper dihedral angle. If the 4 atoms in an improper quadruplet (listed in the data file read -by the :doc:`read\_data ` command) are ordered I,J,K,L then +by the :doc:`read_data ` command) are ordered I,J,K,L then the improper dihedral angle is between the plane of I,J,K and the plane of J,K,L. Note that because this is effectively a dihedral angle, the formula for this improper style is the same as for -:doc:`dihedral\_style harmonic `. +:doc:`dihedral_style harmonic `. Note that defining 4 atoms to interact in this way, does not mean that bonds necessarily exist between I-J, J-K, or K-L, as they would in a @@ -49,9 +49,9 @@ linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined between the 4 atoms. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -95,7 +95,7 @@ for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst index 4efc9a2261..72643a05bd 100644 --- a/doc/src/improper_distance.rst +++ b/doc/src/improper_distance.rst @@ -27,7 +27,7 @@ The *distance* improper style uses the potential where d is the distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet -(listed in the data file read by the :doc:`read\_data ` +(listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the I-atom is assumed to be the central atom. @@ -61,7 +61,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst index 8fb74129ec..dcbdfbc656 100644 --- a/doc/src/improper_distharm.rst +++ b/doc/src/improper_distharm.rst @@ -27,7 +27,7 @@ The *distharm* improper style uses the potential where d is the oriented distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet -(listed in the data file read by the :doc:`read\_data ` +(listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the L-atom is assumed to be the central atom. Note that this is different from the convention used in the improper\_style distance. The distance d is oriented and can take @@ -55,7 +55,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 227b02d275..23988a49ad 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -40,9 +40,9 @@ and omega is the angle between the IL axis and the IJK plane: If all parameter (see below) is not zero, the all the three possible angles will taken in account. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -88,7 +88,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index 6eb205f8e7..d3332c816c 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -41,7 +41,7 @@ where X is the improper angle, X0 is its equilibrium value, and K is a prefactor. Note that the usual 1/2 factor is included in K. If the 4 atoms in an improper quadruplet (listed in the data file read -by the :doc:`read\_data ` command) are ordered I,J,K,L then X +by the :doc:`read_data ` command) are ordered I,J,K,L then X is the angle between the plane of I,J,K and the plane of J,K,L. Alternatively, you can think of atoms J,K,L as being in a plane, and atom I above the plane, and X as a measure of how far out-of-plane I @@ -53,9 +53,9 @@ linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined between the 4 atoms. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy/radian\^2) @@ -101,7 +101,7 @@ for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst index 7272cb2abc..5b170749cc 100644 --- a/doc/src/improper_hybrid.rst +++ b/doc/src/improper_hybrid.rst @@ -32,7 +32,7 @@ example, impropers in a polymer flow (of improper type 1) could be computed with a *harmonic* potential and impropers in the wall boundary (of improper type 2) could be computed with a *cvff* potential. The assignment of improper type to style is made via the -:doc:`improper\_coeff ` command or in the data file. +:doc:`improper_coeff ` command or in the data file. In the improper\_coeff command, the first coefficient sets the improper style and the remaining coefficients are those appropriate to that @@ -73,7 +73,7 @@ restart file, you need to re-specify improper\_coeff commands. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst index 11832d2754..ecdcad7136 100644 --- a/doc/src/improper_inversion_harmonic.rst +++ b/doc/src/improper_inversion_harmonic.rst @@ -37,13 +37,13 @@ the IL axis and the IJK plane omega looks as follows: :align: center Note that the *inversion/harmonic* angle term evaluation differs to -the :doc:`improper\_umbrella ` due to the cyclic +the :doc:`improper_umbrella ` due to the cyclic evaluation of all possible angles omega. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -68,7 +68,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_none.rst b/doc/src/improper_none.rst index 83622b4f11..b348f3aab2 100644 --- a/doc/src/improper_none.rst +++ b/doc/src/improper_none.rst @@ -24,9 +24,9 @@ Description Using an improper style of none means improper forces and energies are not computed, even if quadruplets of improper atoms were listed in the -data file read by the :doc:`read\_data ` command. +data file read by the :doc:`read_data ` command. -See the :doc:`improper\_style zero ` command for a way to +See the :doc:`improper_style zero ` command for a way to calculate improper statistics, but compute no improper interactions. Restrictions @@ -36,7 +36,7 @@ Restrictions Related commands """""""""""""""" -:doc:`improper\_style zero ` +:doc:`improper_style zero ` **Default:** none diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index 374b64fcd7..6cc14ea15a 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -35,7 +35,7 @@ where K is a prefactor, theta is the angle formed by the atoms specified by (i,j,k,l) indices and theta0 its equilibrium value. If the 4 atoms in an improper quadruplet (listed in the data file read -by the :doc:`read\_data ` command) are ordered i,j,k,l then +by the :doc:`read_data ` command) are ordered i,j,k,l then theta\_\ *ijl* is the angle between atoms i,j and l, theta\_\ *ijk* is the angle between atoms i,j and k, theta\_\ *kjl* is the angle between atoms j,k, and l. @@ -51,9 +51,9 @@ data file four atoms: i, j, k and l are specified with i,j and l lying on the backbone of the chain and k specifying the chirality of j. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -96,7 +96,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` .. _Destree: diff --git a/doc/src/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst index 94e9c12fca..f54e610c80 100644 --- a/doc/src/improper_sqdistharm.rst +++ b/doc/src/improper_sqdistharm.rst @@ -27,7 +27,7 @@ The *sqdistharm* improper style uses the potential where d is the distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet -(listed in the data file read by the :doc:`read\_data ` +(listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the L-atom is assumed to be the central atom. Note that this is different from the convention used in the improper\_style distance. @@ -56,7 +56,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst index e49818981a..ee8b75ed3f 100644 --- a/doc/src/improper_style.rst +++ b/doc/src/improper_style.rst @@ -29,7 +29,7 @@ Description Set the formula(s) LAMMPS uses to compute improper interactions between quadruplets of atoms, which remain in force for the duration of the simulation. The list of improper quadruplets is read in by a -:doc:`read\_data ` or :doc:`read\_restart ` command +:doc:`read_data ` or :doc:`read_restart ` command from a data or restart file. Note that the ordering of the 4 atoms in an improper quadruplet determines the definition of the improper angle used in the formula for each style. See the doc pages of @@ -39,14 +39,14 @@ Hybrid models where impropers are computed using different improper potentials can be setup using the *hybrid* improper style. The coefficients associated with an improper style can be specified in -a data or restart file or via the :doc:`improper\_coeff ` +a data or restart file or via the :doc:`improper_coeff ` command. All improper potentials store their coefficient data in binary restart files which means improper\_style and -:doc:`improper\_coeff ` commands do not need to be +:doc:`improper_coeff ` commands do not need to be re-specified in an input script that restarts a simulation. See the -:doc:`read\_restart ` command for details on how to do +:doc:`read_restart ` command for details on how to do this. The one exception is that improper\_style *hybrid* only stores the list of sub-styles in the restart file; improper coefficients need to be re-specified. @@ -54,7 +54,7 @@ to be re-specified. .. note:: When both an improper and pair style is defined, the - :doc:`special\_bonds ` command often needs to be used to + :doc:`special_bonds ` command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise exist between a group of 4 bonded atoms. @@ -64,12 +64,12 @@ to be re-specified. Here is an alphabetic list of improper styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients -specified by the associated :doc:`improper\_coeff ` +specified by the associated :doc:`improper_coeff ` command. Click on the style to display the formula it computes, any additional arguments specified in the improper\_style command, and coefficients -specified by the associated :doc:`improper\_coeff ` +specified by the associated :doc:`improper_coeff ` command. There are also additional accelerated pair styles included in the @@ -112,7 +112,7 @@ individual improper potentials tell if it is part of a package. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` Default """"""" diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst index 785d3ce7dd..66f3112fe7 100644 --- a/doc/src/improper_umbrella.rst +++ b/doc/src/improper_umbrella.rst @@ -46,9 +46,9 @@ in between. See :ref:`(Mayo) ` for a description of the DREIDING force field. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -91,7 +91,7 @@ for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_zero.rst b/doc/src/improper_zero.rst index 145146e6f6..5714749596 100644 --- a/doc/src/improper_zero.rst +++ b/doc/src/improper_zero.rst @@ -30,7 +30,7 @@ accessible to other commands. As an example, the :doc:`compute improper/local ` command can be used to compute the chi values for the list of quadruplets of improper atoms -listed in the data file read by the :doc:`read\_data ` +listed in the data file read by the :doc:`read_data ` command. If no improper style is defined, this command cannot be used. @@ -38,7 +38,7 @@ The optional *nocoeff* flag allows to read data files with a ImproperCoeff section for any improper style. Similarly, any improper\_coeff commands will only be checked for the improper type number and the rest ignored. -Note that the :doc:`improper\_coeff ` command must be +Note that the :doc:`improper_coeff ` command must be used for all improper types, though no additional values are specified. @@ -48,7 +48,7 @@ Restrictions **Related commands:** none -:doc:`improper\_style none ` +:doc:`improper_style none ` **Default:** none diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index 9f0b5a6775..ea2f768e7c 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -195,7 +195,7 @@ the simulation box is created (normally at the top of the file). This command sets the OpenKIM IM that will be used and may issue additional commands changing LAMMPS default settings that are required for using the selected IM (such as :doc:`units ` or -:doc:`atom\_style `). If needed, those settings can be overridden, +:doc:`atom_style `). If needed, those settings can be overridden, however, typically a script containing a *kim\_init* command would not include *units* and *atom\_style* commands. @@ -216,7 +216,7 @@ printed to help diagnose any incompatible changes to input script or command syntax between the two LAMMPS versions. Based on the selected model *kim\_init* may modify the -:doc:`atom\_style `. +:doc:`atom_style `. Some SMs have requirements for this setting. If this is the case, then *atom\_style* will be set to the required style. Otherwise, the value is left unchanged (which in the absence of an *atom\_style* command in the input script @@ -316,7 +316,7 @@ will work correctly for any IM for Al (KIM PM or SM) selected by the Care must be taken to apply unit conversion to dimensional variables read in from a file. For example, if a configuration of atoms is read in from a -dump file using the :doc:`read\_dump ` command, the following can +dump file using the :doc:`read_dump ` command, the following can be done to convert the box and all atomic positions to the correct units: @@ -345,7 +345,7 @@ OpenKIM IM Execution (*kim\_interactions*) The second and final step in using an OpenKIM IM is to execute the *kim\_interactions* command. This command must be preceded by a *kim\_init* command and a command that defines the number of atom types *N* (such as -:doc:`create\_box `). +:doc:`create_box `). The *kim\_interactions* command has one argument *typeargs*\ . This argument contains either a list of *N* chemical species, which defines a mapping between atom types in LAMMPS to the available species in the OpenKIM IM, or the @@ -374,7 +374,7 @@ Alternatively, for a model with a fixed mapping the command would be: The *kim\_interactions* command performs all the necessary steps to set up the OpenKIM IM selected in the *kim\_init* command. The specific actions depend on whether the IM is a KIM PM or a KIM SM. For a KIM PM, -a :doc:`pair\_style kim ` command is executed followed by +a :doc:`pair_style kim ` command is executed followed by the appropriate *pair\_coeff* command. For example, for the Ercolessi and Adams (1994) KIM PM for Al set by the following commands: @@ -894,7 +894,7 @@ must be installed. Related commands """""""""""""""" -:doc:`pair\_style kim ` +:doc:`pair_style kim ` ---------- diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index 5f4dad4dcd..c79b9ceb09 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -72,7 +72,7 @@ Description """"""""""" Set parameters used by the kspace solvers defined by the -:doc:`kspace\_style ` command. Not all parameters are +:doc:`kspace_style ` command. Not all parameters are relevant to all kspace styles. @@ -92,12 +92,12 @@ collective operations and adequate hardware. The *compute* keyword allows Kspace computations to be turned off, -even though a :doc:`kspace\_style ` is defined. This is +even though a :doc:`kspace_style ` is defined. This is not useful for running a real simulation, but can be useful for debugging purposes or for computing only partial forces that do not include the Kspace contribution. You can also do this by simply not -defining a :doc:`kspace\_style `, but a Kspace-compatible -:doc:`pair\_style ` requires a kspace style to be defined. +defining a :doc:`kspace_style `, but a Kspace-compatible +:doc:`pair_style ` requires a kspace style to be defined. This keyword gives you that option. @@ -179,7 +179,7 @@ are different. The *force* keyword overrides the relative accuracy parameter set by -the :doc:`kspace\_style ` command with an absolute +the :doc:`kspace_style ` command with an absolute accuracy. The accuracy determines the RMS error in per-atom forces calculated by the long-range solver and is thus specified in force units. A negative value for the accuracy setting means to use the @@ -272,7 +272,7 @@ MSM. The *mix/disp* keyword selects the mixing rule for the dispersion coefficients. With *pair*\ , the dispersion coefficients of unlike -types are computed as indicated with :doc:`pair\_modify `. +types are computed as indicated with :doc:`pair_modify `. With *geom*\ , geometric mixing is enforced on the dispersion coefficients in the kspace coefficients. When using the arithmetic mixing rule, this will speed-up the simulations but introduces some @@ -361,10 +361,10 @@ or with suffix kspace/pair styles of MSM, like OMP or GPU. The *scafacos* keyword is used for settings that are passed to the -ScaFaCoS library when using :doc:`kspace\_style scafacos `. +ScaFaCoS library when using :doc:`kspace_style scafacos `. The *tolerance* option affects how the *accuracy* specified with the -:doc:`kspace\_style ` command is interpreted by ScaFaCoS. +:doc:`kspace_style ` command is interpreted by ScaFaCoS. The following values may be used: * energy = absolute accuracy in total Coulombic energy @@ -394,7 +394,7 @@ field\_rel tolerance types set a tolerance based on the electric field values computed by ScaFaCoS. Since per-atom forces are derived from the per-atom electric field, this effectively sets a tolerance on the forces, similar to other LAMMPS KSpace styles, as explained on the -:doc:`kspace\_style ` doc page. +:doc:`kspace_style ` doc page. Note that not all ScaFaCoS solvers support all tolerance types. These are the allowed values for each method: @@ -444,7 +444,7 @@ boundaries can be set using :doc:`boundary ` (the slab approximation in not needed). The *slab* keyword is not currently supported by Ewald or PPPM when using a triclinic simulation cell. The slab correction has also been extended to point dipole interactions -:ref:`(Klapp) ` in :doc:`kspace\_style ` *ewald/disp*\ , +:ref:`(Klapp) ` in :doc:`kspace_style ` *ewald/disp*\ , *ewald/dipole*\ , and *pppm/dipole*\ . .. note:: @@ -488,7 +488,7 @@ Restrictions Related commands """""""""""""""" -:doc:`kspace\_style `, :doc:`boundary ` +:doc:`kspace_style `, :doc:`boundary ` Default """"""" diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 32179f8be0..013c39ef61 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -212,7 +212,7 @@ that Lennard-Jones or Buckingham potentials can be used without a cutoff, i.e. they become full long-range potentials. For these styles, you will possibly want to adjust the default choice -of parameters by using the :doc:`kspace\_modify ` command. +of parameters by using the :doc:`kspace_modify ` command. This can be done by either choosing the Ewald and grid parameters, or by specifying separate accuracies for the real and kspace calculations. When not making any settings, the simulation will stop @@ -256,7 +256,7 @@ angstroms instead of 10 angstroms) provides better MSM accuracy for both the real space and grid computed forces. Currently calculation of the full pressure tensor in MSM is expensive. -Using the :doc:`kspace\_modify ` *pressure/scalar yes* +Using the :doc:`kspace_modify ` *pressure/scalar yes* command provides a less expensive way to compute the scalar pressure (Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example, to run an isotropic barostat. If the full pressure tensor is needed, @@ -320,9 +320,9 @@ ScaFaCoS library the *accuracy* is treated as a tolerance level (either absolute or relative) for the chosen quantity, where the quantity can be either the Columic field values, the per-atom Columic energy or the total Columic energy. To select from these options, see -the :doc:`kspace\_modify scafacos accuracy ` doc page. +the :doc:`kspace_modify scafacos accuracy ` doc page. -The :doc:`kspace\_modify scafacos ` command also explains +The :doc:`kspace_modify scafacos ` command also explains other ScaFaCoS options currently exposed to LAMMPS. @@ -346,7 +346,7 @@ Note that style *pppm* only computes the grid size at the beginning of a simulation, so if the length or triclinic tilt of the simulation cell increases dramatically during the course of the simulation, the accuracy of the simulation may degrade. Likewise, if the -:doc:`kspace\_modify slab ` option is used with +:doc:`kspace_modify slab ` option is used with shrink-wrap boundaries in the z-dimension, and the box size changes dramatically in z. For example, for a triclinic system with all three tilt factors set to the maximum limit, the PPPM grid should be @@ -359,7 +359,7 @@ works because the grid size is re-computed at the beginning of each run. Another way to ensure the described accuracy requirement is met is to run a short simulation at the maximum expected tilt or length, note the required grid size, and then use the -:doc:`kspace\_modify ` *mesh* command to manually set the +:doc:`kspace_modify ` *mesh* command to manually set the PPPM grid size to this value for the long run. The simulation then will be "too accurate" for some portion of the run. @@ -378,7 +378,7 @@ or *ewald/dipole* are estimated using equations 33 and 46 of :ref:`(Wang) `. The RMS force errors for *pppm/dipole* are estimated using the equations in :ref:`(Cerda) `. -See the :doc:`kspace\_modify ` command for additional +See the :doc:`kspace_modify ` command for additional options of the K-space solvers that can be set, including a *force* option for setting an absolute RMS error in forces, as opposed to a relative RMS error. @@ -441,7 +441,7 @@ the :doc:`boundary ` command). For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions. The only exception is if the slab option is set with -:doc:`kspace\_modify `, in which case the xy dimensions +:doc:`kspace_modify `, in which case the xy dimensions must be periodic and the z dimension must be non-periodic. The scafacos KSpace style will only be enabled if LAMMPS is built with @@ -451,7 +451,7 @@ doc page for more info. The use of ScaFaCos in LAMMPS does not yet support molecular charged systems where the short-range Coulombic interactions between atoms in the same bond/angle/dihedral are weighted by the -:doc:`special\_bonds ` command. Likewise it does not +:doc:`special_bonds ` command. Likewise it does not support the "TIP4P water style" where a fictitious charge site is introduced in each water molecule. Finally, the methods *p3m* and *ewald* do not support computing the @@ -460,7 +460,7 @@ virial, so this contribution is not included. Related commands """""""""""""""" -:doc:`kspace\_modify `, :doc:`pair\_style lj/cut/coul/long `, :doc:`pair\_style lj/charmm/coul/long `, :doc:`pair\_style lj/long/coul/long `, :doc:`pair\_style buck/coul/long ` +:doc:`kspace_modify `, :doc:`pair_style lj/cut/coul/long `, :doc:`pair_style lj/charmm/coul/long `, :doc:`pair_style lj/long/coul/long `, :doc:`pair_style buck/coul/long ` Default """"""" diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index bf5dec5453..a26060d7c0 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -61,13 +61,13 @@ of the lattice command can be used to define a wide variety of crystallographic lattices. A lattice is used by LAMMPS in two ways. First, the -:doc:`create\_atoms ` command creates atoms on the lattice +:doc:`create_atoms ` command creates atoms on the lattice points inside the simulation box. Note that the -:doc:`create\_atoms ` command allows different atom types +:doc:`create_atoms ` command allows different atom types to be assigned to different basis atoms of the lattice. Second, the lattice spacing in the x,y,z dimensions implied by the lattice, can be used by other commands as distance units -(e.g. :doc:`create\_box `, :doc:`region ` and +(e.g. :doc:`create_box `, :doc:`region ` and :doc:`velocity `), which are often convenient to use when the underlying problem geometry is atoms on a lattice. @@ -89,7 +89,7 @@ Note that the lattice command can be used multiple times in an input script. Each time it is invoked, the lattice attributes are re-defined and are used for all subsequent commands (that use lattice attributes). For example, a sequence of lattice, -:doc:`region `, and :doc:`create\_atoms ` commands +:doc:`region `, and :doc:`create_atoms ` commands can be repeated multiple times to build a poly-crystalline model with different geometric regions populated with atoms in different lattice orientations. @@ -99,7 +99,7 @@ orientations. A lattice of style *none* does not define a unit cell and basis set, -so it cannot be used with the :doc:`create\_atoms ` +so it cannot be used with the :doc:`create_atoms ` command. However it does define a lattice spacing via the specified scale parameter. As explained above the lattice spacings in x,y,z can be used by other commands as distance units. No additional @@ -242,7 +242,7 @@ factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and of the periodicity of the lattice in that direction. Thus, if you create an orthogonal periodic simulation box whose size in a dimension is a multiple of the lattice spacing, and then fill it with atoms via - the :doc:`create\_atoms ` command, you will NOT necessarily + the :doc:`create_atoms ` command, you will NOT necessarily create a periodic system. I.e. atoms may overlap incorrectly at the faces of the simulation box. @@ -314,7 +314,7 @@ The *a1,a2,a3,basis* keywords can only be used with style *custom*\ . Related commands """""""""""""""" -:doc:`dimension `, :doc:`create\_atoms `, +:doc:`dimension `, :doc:`create_atoms `, :doc:`region ` Default diff --git a/doc/src/mass.rst b/doc/src/mass.rst index 05cef2e3b2..0431b8f65b 100644 --- a/doc/src/mass.rst +++ b/doc/src/mass.rst @@ -28,7 +28,7 @@ Description """"""""""" Set the mass for all atoms of one or more atom types. Per-type mass -values can also be set in the :doc:`read\_data ` data file +values can also be set in the :doc:`read_data ` data file using the "Masses" keyword. See the :doc:`units ` command for what mass units to use. @@ -57,12 +57,12 @@ Note that the mass command can only be used if the :doc:`atom style Currently, all but the *sphere* and *ellipsoid* and *peri* styles do. They require mass to be set for individual particles, not types. Per-atom masses are defined in the data file read by the -:doc:`read\_data ` command, or set to default values by the -:doc:`create\_atoms ` command. Per-atom masses can also be +:doc:`read_data ` command, or set to default values by the +:doc:`create_atoms ` command. Per-atom masses can also be set to new values by the :doc:`set mass ` or :doc:`set density ` commands. -Also note that :doc:`pair\_style eam ` and :doc:`pair\_style bop ` commands define the masses of atom types in their +Also note that :doc:`pair_style eam ` and :doc:`pair_style bop ` commands define the masses of atom types in their respective potential files, in which case the mass command is normally not used. @@ -77,8 +77,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. All masses must be defined before a simulation is run. They must also all be defined before a :doc:`velocity ` or :doc:`fix shake ` command is used. diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index 6b25a1d32d..b90354deb0 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -43,7 +43,7 @@ Description """"""""""" This command sets parameters that affect the energy minimization -algorithms selected by the :doc:`min\_style ` command. The +algorithms selected by the :doc:`min_style ` command. The various settings may affect the convergence rate and overall number of force evaluations required by a minimization, so users can experiment with these parameters to tune their minimizations. @@ -107,13 +107,13 @@ For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force norm is replaced by the spin-torque norm. Keywords *alpha\_damp* and *discrete\_factor* only make sense when -a :doc:`min\_spin ` command is declared. +a :doc:`min_spin ` command is declared. Keyword *alpha\_damp* defines an analog of a magnetic Gilbert damping. It defines a relaxation rate toward an equilibrium for a given magnetic system. Keyword *discrete\_factor* defines a discretization factor for the adaptive timestep used in the *spin* minimization. -See :doc:`min\_spin ` for more information about those +See :doc:`min_spin ` for more information about those quantities. The choice of a line search algorithm for the *spin/cg* and @@ -138,7 +138,7 @@ See :doc:`neb/spin ` for more explanation. Related commands """""""""""""""" -:doc:`min\_style `, :doc:`minimize ` +:doc:`min_style `, :doc:`minimize ` Default """"""" diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 1535a1067f..96053fda98 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -43,7 +43,7 @@ timestep, according to: with lambda a damping coefficient (similar to a Gilbert damping). Lambda can be defined by setting the *alpha\_damp* keyword with the -:doc:`min\_modify ` command. +:doc:`min_modify ` command. The minimization procedure solves this equation using an adaptive timestep. The value of this timestep is defined @@ -59,12 +59,12 @@ spin/neb calculation is performed). Kappa defines a discretization factor *discrete\_factor* for the definition of this timestep. -*discrete\_factor* can be defined with the :doc:`min\_modify ` +*discrete\_factor* can be defined with the :doc:`min_modify ` command. Style *spin/cg* defines an orthogonal spin optimization (OSO) combined to a conjugate gradient (CG) algorithm. -The :doc:`min\_modify ` command can be used to +The :doc:`min_modify ` command can be used to couple the *spin/cg* to a line search procedure, and to modify the discretization factor *discrete\_factor*. By default, style *spin/cg* does not employ the line search procedure @@ -80,7 +80,7 @@ The default value for Kappa is 10. The *spin\_cubic* line search can improve the convergence of the *spin/lbfgs* algorithm. -The :doc:`min\_modify ` command can be used to +The :doc:`min_modify ` command can be used to activate the line search procedure, and to modify the discretization factor *discrete\_factor*. @@ -108,8 +108,8 @@ freedom for a frozen lattice configuration. Related commands """""""""""""""" -:doc:`min\_style `, :doc:`minimize `, -:doc:`min\_modify ` +:doc:`min_style `, :doc:`minimize `, +:doc:`min_modify ` Default """"""" diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst index 91accc7967..b9e896df3e 100644 --- a/doc/src/min_style.rst +++ b/doc/src/min_style.rst @@ -46,7 +46,7 @@ derivative. When close to an energy minimum, the algorithm behaves like a Newton method and exhibits a quadratic convergence rate to high accuracy. In most cases the behavior of *hftn* is similar to *cg*\ , but it offers an alternative if *cg* seems to perform poorly. This -style is not affected by the :doc:`min\_modify ` command. +style is not affected by the :doc:`min_modify ` command. Style *sd* is a steepest descent algorithm. At each iteration, the search direction is set to the downhill direction corresponding to the @@ -135,7 +135,7 @@ Restrictions Related commands """""""""""""""" -:doc:`min\_modify `, :doc:`minimize `, :doc:`neb ` +:doc:`min_modify `, :doc:`minimize `, :doc:`neb ` Default """"""" diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index 668759401e..d9aba3eda0 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -39,8 +39,8 @@ configuration should approximate a critical point for the objective function (see below), which may or may not be a local minimum. The minimization algorithm used is set by the -:doc:`min\_style ` command. Other options are set by the -:doc:`min\_modify ` command. Minimize commands can be +:doc:`min_style ` command. Other options are set by the +:doc:`min_modify ` command. Minimize commands can be interspersed with :doc:`run ` commands to alternate between relaxation and dynamics. The minimizers bound the distance atoms move in one iteration, so that you can relax systems with highly overlapped @@ -50,7 +50,7 @@ other. Alternate means of relaxing a system are to run dynamics with a small or :doc:`limited timestep `. Or dynamics can be run using :doc:`fix viscous ` to impose a damping force that -slowly drains all kinetic energy from the system. The :doc:`pair\_style soft ` potential can be used to un-overlap atoms while +slowly drains all kinetic energy from the system. The :doc:`pair_style soft ` potential can be used to un-overlap atoms while running dynamics. Note that you can minimize some atoms in the system while holding the @@ -155,7 +155,7 @@ During a minimization, the outer iteration count is treated as a timestep. Output is triggered by this timestep, e.g. thermodynamic output or dump and restart files. -Using the :doc:`thermo\_style custom ` command with the +Using the :doc:`thermo_style custom ` command with the *fmax* or *fnorm* keywords can be useful for monitoring the progress of the minimization. Note that these outputs will be calculated only from forces on the atoms, and will not include any extra degrees of @@ -228,14 +228,14 @@ The iterations and force evaluation values are what is checked by the Note that a cutoff Lennard-Jones potential (and others) can be shifted so that its energy is 0.0 at the cutoff via the -:doc:`pair\_modify ` command. See the doc pages for +:doc:`pair_modify ` command. See the doc pages for individual :doc:`pair styles ` for details. Note that Coulombic potentials always have a cutoff, unless versions with a -long-range component are used (e.g. :doc:`pair\_style lj/cut/coul/long `). The CHARMM potentials go to 0.0 at -the cutoff (e.g. :doc:`pair\_style lj/charmm/coul/charmm `), -as do the GROMACS potentials (e.g. :doc:`pair\_style lj/gromacs `). +long-range component are used (e.g. :doc:`pair_style lj/cut/coul/long `). The CHARMM potentials go to 0.0 at +the cutoff (e.g. :doc:`pair_style lj/charmm/coul/charmm `), +as do the GROMACS potentials (e.g. :doc:`pair_style lj/gromacs `). -If a soft potential (:doc:`pair\_style soft `) is used the +If a soft potential (:doc:`pair_style soft `) is used the Astop value is used for the prefactor (no time dependence). The :doc:`fix box/relax ` command can be used to apply an @@ -266,7 +266,7 @@ that can be used include: Some fixes which are invoked during minimization have an associated potential energy. For that energy to be included in the total potential energy of the system (the quantity being minimized), - you MUST enable the :doc:`fix\_modify ` *energy* option for + 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. @@ -321,7 +321,7 @@ algorithm. is not an error to have it defined, but the energy minimization will not keep the defined body(s) rigid during the minimization. Note that if bonds, angles, etc internal to a rigid body have been turned off -(e.g. via :doc:`neigh\_modify exclude `), they will not +(e.g. via :doc:`neigh_modify exclude `), they will not contribute to the potential energy which is probably not what is desired. @@ -333,8 +333,8 @@ system will not fully relax. Related commands """""""""""""""" -:doc:`min\_modify `, :doc:`min\_style `, -:doc:`run\_style ` +:doc:`min_modify `, :doc:`min_style `, +:doc:`run_style ` **Default:** none diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index e4a8a40468..6a36636d9c 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -64,8 +64,8 @@ templates include: * :doc:`fix rigid/small ` * :doc:`fix shake ` * :doc:`fix gcmc ` -* :doc:`create\_atoms ` -* :doc:`atom\_style template ` +* :doc:`create_atoms ` +* :doc:`atom_style template ` The ID of a molecule template can only contain alphanumeric characters and underscores. @@ -73,7 +73,7 @@ and underscores. A single template can contain multiple molecules, listed one per file. Some of the commands listed above currently use only the first molecule in the template, and will issue a warning if the template -contains multiple molecules. The :doc:`atom\_style template ` command allows multiple-molecule templates +contains multiple molecules. The :doc:`atom_style template ` command allows multiple-molecule templates to define a system with more than one templated molecule. Each filename can be followed by optional keywords which are applied @@ -109,16 +109,16 @@ molecule (header keyword = inertia). to your simulation, via one or more of the commands listed above. Since this topology-related information requires that suitable storage is reserved when LAMMPS creates the simulation box (e.g. when using - the :doc:`create\_box ` command or the - :doc:`read\_data ` command) suitable space has to be reserved + the :doc:`create_box ` command or the + :doc:`read_data ` command) suitable space has to be reserved so you do not overflow those pre-allocated data structures when adding - molecules later. Both the :doc:`create\_box ` command and - the :doc:`read\_data ` command have "extra" options which + molecules later. Both the :doc:`create_box ` command and + the :doc:`read_data ` command have "extra" options which insure space is allocated for storing topology info for molecules that are added later. The format of an individual molecule file is similar but -(not identical) to the data file read by the :doc:`read\_data ` +(not identical) to the data file read by the :doc:`read_data ` commands, and is as follows. A molecule file has a header and a body. The header appears first. @@ -182,7 +182,7 @@ details below). This is optional since if these sections are not included, LAMMPS will auto-generate this information. Note that LAMMPS uses this info to properly exclude or weight bonded pairwise interactions between bonded atoms. See the -:doc:`special\_bonds ` command for more details. One +:doc:`special_bonds ` command for more details. One reason to list the special bond info explicitly is for the :doc:`thermalized Drude oscillator model ` which treats the bonds between nuclear cores and Drude electrons in a different manner. @@ -350,7 +350,7 @@ the doc pages for individual styles for details. N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of this atom within the topology of the molecule. See the -:doc:`special\_bonds ` doc page for more discussion of +:doc:`special_bonds ` doc page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds section must also appear. @@ -373,7 +373,7 @@ A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3, Natoms, where Natoms = # of atoms in the molecule. The first N1 values should be the 1-2 neighbors, the next N2 should be the 1-3 neighbors, the last N3 should be the 1-4 neighbors. No atom ID should -appear more than once. See the :doc:`special\_bonds ` doc +appear more than once. See the :doc:`special_bonds ` doc page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bond Counts section must also appear. @@ -498,8 +498,8 @@ Restrictions This command must come after the simulation box is define by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. Related commands """""""""""""""" diff --git a/doc/src/neb.rst b/doc/src/neb.rst index ef14739301..713179b02c 100644 --- a/doc/src/neb.rst +++ b/doc/src/neb.rst @@ -171,8 +171,8 @@ For a *file-style* setting of *none*\ , no filename is specified. Each replica is assumed to already be in its initial configuration at the time the neb command is issued. This allows each replica to define its own configuration by reading a replica-specific data or restart or -dump file, via the :doc:`read\_data `, -:doc:`read\_restart `, or :doc:`read\_dump ` +dump file, via the :doc:`read_data `, +:doc:`read_restart `, or :doc:`read_dump ` commands. The replica-specific names of these files can be specified as in the discussion above for the *each* file-style. Also see the section below for how a NEB calculation can produce restart files, so @@ -192,7 +192,7 @@ that a long calculation can be restarted if needed. A NEB calculation proceeds in two stages, each of which is a minimization procedure, performed via damped dynamics. To enable this, you must first define a damped dynamics -:doc:`min\_style `, such as *quickmin* or *fire*\ . The *cg*\ , +:doc:`min_style `, such as *quickmin* or *fire*\ . The *cg*\ , *sd*\ , and *hftn* styles cannot be used, since they perform iterative line searches in their inner loop, which cannot be easily synchronized across multiple replicas. @@ -254,7 +254,7 @@ A few other settings in your input script are required or advised to perform a NEB calculation. See the NOTE about the choice of timestep at the beginning of this doc page. -An atom map must be defined which it is not by default for :doc:`atom\_style atomic ` problems. The :doc:`atom\_modify map ` command can be used to do this. +An atom map must be defined which it is not by default for :doc:`atom_style atomic ` problems. The :doc:`atom_modify map ` command can be used to do this. The minimizers in LAMMPS operate on all atoms in your system, even non-NEB atoms, as defined above. To prevent non-NEB atoms from moving diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 161348e97c..74c46ff58e 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -171,8 +171,8 @@ For a *file-style* setting of *none*\ , no filename is specified. Each replica is assumed to already be in its initial configuration at the time the neb command is issued. This allows each replica to define its own configuration by reading a replica-specific data or restart or -dump file, via the :doc:`read\_data `, -:doc:`read\_restart `, or :doc:`read\_dump ` +dump file, via the :doc:`read_data `, +:doc:`read_restart `, or :doc:`read_dump ` commands. The replica-specific names of these files can be specified as in the discussion above for the *each* file-style. Also see the section below for how a NEB calculation can produce restart files, so @@ -192,9 +192,9 @@ that a long calculation can be restarted if needed. A NEB calculation proceeds in two stages, each of which is a minimization procedure. To enable this, you must first define a -:doc:`min\_style `, using either the *spin*\ , +:doc:`min_style `, using either the *spin*\ , *spin/cg*\ , or *spin/lbfgs* style (see -:doc:`min\_spin ` for more information). +:doc:`min_spin ` for more information). The other styles cannot be used, since they relax the lattice degrees of freedom instead of the spins. @@ -253,7 +253,7 @@ profile of the transition along the MEP. ---------- -An atom map must be defined which it is not by default for :doc:`atom\_style atomic ` problems. The :doc:`atom\_modify map ` command can be used to do this. +An atom map must be defined which it is not by default for :doc:`atom_style atomic ` problems. The :doc:`atom_modify map ` command can be used to do this. An initial value can be defined for the timestep. Although, the *spin* minimization algorithm is an adaptive timestep methodology, so that diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 9035690a00..2ab119193c 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -92,7 +92,7 @@ move far enough that the neighbor list should be rebuilt, e.g. running a simulation of a cold crystal. Note that it is not that expensive to check if neighbor lists should be rebuilt. -When the rRESPA integrator is used (see the :doc:`run\_style ` +When the rRESPA integrator is used (see the :doc:`run_style ` command), the *every* and *delay* parameters refer to the longest (outermost) timestep. @@ -107,7 +107,7 @@ nearby periodic images. The only way this should happen is if the pairwise cutoff is so short that atoms that are part of the same interaction are not communicated as ghost atoms. This is an unusual model (e.g. no pair interactions at all) and the problem can be fixed -by use of the :doc:`comm\_modify cutoff ` command. Note +by use of the :doc:`comm_modify cutoff ` command. Note that to save time, the default *cluster* setting is *no*\ , so that this check is not performed. @@ -116,7 +116,7 @@ atoms in the specified group. This can be useful for models where a large portion of the simulation is particles that do not interact with other particles or with each other via pairwise interactions. The group specified with this option must also be specified via the -:doc:`atom\_modify first ` command. Note that specifying +:doc:`atom_modify first ` command. Note that specifying "all" as the group-ID effectively turns off the *include* option. The *exclude* option turns off pairwise interactions between certain @@ -150,20 +150,20 @@ The other exclude options are more expensive if specified multiple times; they require one check for each time they have been specified. Note that the exclude options only affect pairwise interactions; see -the :doc:`delete\_bonds ` command for information on +the :doc:`delete_bonds ` command for information on turning off bond interactions. .. note:: Excluding pairwise interactions will not work correctly when also using a long-range solver via the - :doc:`kspace\_style ` command. LAMMPS will give a warning + :doc:`kspace_style ` command. LAMMPS will give a warning to this effect. This is because the short-range pairwise interaction needs to subtract off a term from the total energy for pairs whose short-range interaction is excluded, to compensate for how the long-range solver treats the interaction. This is done correctly for pairwise interactions that are excluded (or weighted) via the - :doc:`special\_bonds ` command. But it is not done for + :doc:`special_bonds ` command. But it is not done for interactions that are excluded via these neigh\_modify exclude options. The *page* and *one* options affect how memory is allocated for the @@ -219,7 +219,7 @@ space. Related commands """""""""""""""" -:doc:`neighbor `, :doc:`delete\_bonds ` +:doc:`neighbor `, :doc:`delete_bonds ` Default """"""" diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index ae21232609..3869723202 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -37,7 +37,7 @@ default values below. The *skin* distance is also used to determine how often atoms migrate to new processors if the *check* option of the -:doc:`neigh\_modify ` command is set to *yes*\ . Atoms are +:doc:`neigh_modify ` command is set to *yes*\ . Atoms are migrated (communicated) to new processors on the same timestep that neighbor lists are re-built. @@ -59,10 +59,10 @@ other type pairs have a much shorter cutoff. For style *multi* the bin size is set to 1/2 of the shortest cutoff distance and multiple sets of bins are defined to search over for different atom types. This imposes some extra setup overhead, but the searches themselves -may be much faster for the short-cutoff cases. See the :doc:`comm\_modify mode multi ` command for a communication option +may be much faster for the short-cutoff cases. See the :doc:`comm_modify mode multi ` command for a communication option that may also be beneficial for simulations of this kind. -The :doc:`neigh\_modify ` command has additional options +The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are stored in the list. @@ -77,8 +77,8 @@ Restrictions Related commands """""""""""""""" -:doc:`neigh\_modify `, :doc:`units `, -:doc:`comm\_modify ` +:doc:`neigh_modify `, :doc:`units `, +:doc:`comm_modify ` Default """"""" diff --git a/doc/src/newton.rst b/doc/src/newton.rst index 6c1f600224..eb7a2250c7 100644 --- a/doc/src/newton.rst +++ b/doc/src/newton.rst @@ -46,7 +46,7 @@ processor. LAMMPS should produce the same answers for any newton flag settings, except for round-off issues. -With :doc:`run\_style ` *respa* and only bonded interactions +With :doc:`run_style ` *respa* and only bonded interactions (bond, angle, etc) computed in the innermost timestep, it may be faster to turn newton *off* for bonded interactions, to avoid extra communication in the innermost loop. @@ -56,13 +56,13 @@ Restrictions The newton bond setting cannot be changed after the simulation box is -defined by a :doc:`read\_data ` or -:doc:`create\_box ` command. +defined by a :doc:`read_data ` or +:doc:`create_box ` command. Related commands """""""""""""""" -:doc:`run\_style ` respa +:doc:`run_style ` respa Default """"""" diff --git a/doc/src/package.rst b/doc/src/package.rst index 06cebea6c4..368caf63fb 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -387,7 +387,7 @@ process. LAMMPS will generate a warning in the case that more threads are used than available in SMT hardware on a node. If the PPPM solver from the USER-INTEL package is not used, then the LRT setting is ignored and no extra threads are generated. Enabling LRT will replace -the :doc:`run\_style ` with the *verlet/lrt/intel* style that +the :doc:`run_style ` with the *verlet/lrt/intel* style that is identical to the default *verlet* style aside from supporting the LRT feature. This feature requires setting the pre-processor flag -DLMP\_INTEL\_USELRT in the makefile when compiling LAMMPS. @@ -483,7 +483,7 @@ CPUs a value of *on* is the default since it can often be faster, just as it is for non-accelerated pair styles The *binsize* keyword sets the size of bins used to bin atoms in -neighbor list builds. The same value can be set by the :doc:`neigh\_modify binsize ` command. Making it an option in the package +neighbor list builds. The same value can be set by the :doc:`neigh_modify binsize ` command. Making it an option in the package kokkos command allows it to be set from the command line. The default value for CPUs is 0.0, which means the LAMMPS default will be used, which is bins = 1/2 the size of the pairwise cutoff + neighbor skin @@ -622,7 +622,7 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. The gpu style of this command can only be invoked if LAMMPS was built with the GPU package. See the :doc:`Build package ` doc diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index 36311f738d..b6fba9e960 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -54,7 +54,7 @@ command to specify them. Note that ADP potentials obtained from NIST must be converted into the extended DYNAMO *setfl* format discussed below. * The OpenKIM Project at https://openkim.org/browse/models/by-type provides - ADP potentials that can be used directly in LAMMPS with the :doc:`kim\_commands interface `. + ADP potentials that can be used directly in LAMMPS with the :doc:`kim_commands interface `. ---------- @@ -68,7 +68,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of extended *setfl* elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways to +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, the potentials/AlCu.adp file, included in the @@ -99,7 +99,7 @@ that will be used with other potentials. have an ".adp" suffix. A DYNAMO *setfl* file extended for ADP is formatted as follows. Basically it is the standard *setfl* format with additional tabulated functions u and w added to the file after -the tabulated pair potentials. See the :doc:`pair\_eam ` +the tabulated pair potentials. See the :doc:`pair_eam ` command for further details on the *setfl* format. * lines 1,2,3 = comments (ignored) @@ -159,7 +159,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, no special mixing rules are needed, since the ADP potential files specify alloy interactions explicitly. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in tabulated potential files. @@ -167,7 +167,7 @@ Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -184,7 +184,7 @@ if LAMMPS was built with that package. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_eam ` +:doc:`pair_coeff `, :doc:`pair_eam ` **Default:** none diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index 96bcf5eccd..d7088a7eae 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -51,7 +51,7 @@ pair\_coeff command, where N is the number of LAMMPS atom types: * filename * N element names = mapping of AGNI elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the force field file. An AGNI force field is fully specified by the filename which contains the @@ -85,7 +85,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -93,7 +93,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -125,7 +125,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index 66dc56c7a6..2a742d8ee2 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -147,7 +147,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of AIREBO elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want @@ -228,7 +228,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` mix, shift, table, and tail options. These pair styles do not write their information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -236,7 +236,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -259,7 +259,7 @@ doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_atm.rst b/doc/src/pair_atm.rst index 1f22ca01c3..7043de0041 100644 --- a/doc/src/pair_atm.rst +++ b/doc/src/pair_atm.rst @@ -53,7 +53,7 @@ the same for all those permutations of the atom types of I,J,K and needs to be specified only once, as discussed below. The *atm* potential is typically used in combination with a two-body -potential using the :doc:`pair\_style hybrid/overlay ` +potential using the :doc:`pair_style hybrid/overlay ` command as in the example above. The potential for a triplet of atom is calculated only if all 3 @@ -63,9 +63,9 @@ cutoff\_triple\^3 is required, which excludes from calculation the triplets with small contribution to the interaction. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the restart files read by the -:doc:`read\_restart ` commands: +:doc:`read_restart ` commands: * K = atom type of the third atom (1 to Ntypes) * nu = prefactor (energy/distance\^9 units) @@ -147,18 +147,18 @@ combinations, else an error will result. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair styles do not support the :doc:`pair\_modify ` +This pair styles do not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. However, if the *atm* potential is used in combination with other -potentials using the :doc:`pair\_style hybrid/overlay ` +potentials using the :doc:`pair_style hybrid/overlay ` command then pair\_coeff commands need to be re-specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -175,7 +175,7 @@ if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst index 0076f50684..ecf6cc7c30 100644 --- a/doc/src/pair_awpmd.rst +++ b/doc/src/pair_awpmd.rst @@ -84,13 +84,13 @@ details needed. If the *flex\_press* keyword is used, then a contribution from the electrons is added to the total virial and pressure of the system. -This potential is designed to be used with :doc:`atom\_style wavepacket ` definitions, in order to handle the +This potential is designed to be used with :doc:`atom_style wavepacket ` definitions, in order to handle the description of systems with interacting nuclei and explicit electrons. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutoff (distance units) @@ -105,14 +105,14 @@ specified in the pair\_style command is used. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The :doc:`pair\_modify ` mix, shift, table, and tail options +The :doc:`pair_modify ` mix, shift, table, and tail options are not relevant for this pair style. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -126,7 +126,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` Default """"""" diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index 96f6d5d3f5..15bd126ac2 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -40,9 +40,9 @@ includes truncation at a cutoff distance Rc. :align: center The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. * A (energy units) @@ -86,20 +86,20 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. -This pair style does not support the :doc:`pair\_modify ` shift +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -113,7 +113,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_body_nparticle.rst b/doc/src/pair_body_nparticle.rst index 5d6b2a500b..1ebb6a3b47 100644 --- a/doc/src/pair_body_nparticle.rst +++ b/doc/src/pair_body_nparticle.rst @@ -74,9 +74,9 @@ where Rc is the cutoff. As explained above, an interaction involving one or two body sub-particles may be computed even for r > Rc. For style *body*\ , the following coefficients must be defined for each -pair of atoms types via the :doc:`pair\_coeff ` command as in +pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (energy units) @@ -97,13 +97,13 @@ and cutoff distance for all of this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -118,12 +118,12 @@ This style is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Defining particles to be bodies so they participate in body/body or -body/particle interactions requires the use of the :doc:`atom\_style body ` command. +body/particle interactions requires the use of the :doc:`atom_style body ` command. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix rigid ` +:doc:`pair_coeff `, :doc:`fix rigid ` **Default:** none diff --git a/doc/src/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst index 237a792344..7fee589b9f 100644 --- a/doc/src/pair_body_rounded_polygon.rst +++ b/doc/src/pair_body_rounded_polygon.rst @@ -95,8 +95,8 @@ that gross sliding takes place as soon as two particles are in contact. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, -or in the data file read by the :doc:`read\_data ` command: +via the :doc:`pair_coeff ` command as in the examples above, +or in the data file read by the :doc:`read_data ` command: * k\_n (energy/distance\^2 units) * k\_na (energy/distance\^2 units) @@ -107,14 +107,14 @@ above for force versus surface separation, for \delta\_n < 0 and 0 < **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -130,7 +130,7 @@ for pair interactions. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst index 1334756908..010e346f30 100644 --- a/doc/src/pair_body_rounded_polyhedron.rst +++ b/doc/src/pair_body_rounded_polyhedron.rst @@ -90,8 +90,8 @@ that gross sliding takes place as soon as two particles are in contact. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, -or in the data file read by the :doc:`read\_data ` command: +via the :doc:`pair_coeff ` command as in the examples above, +or in the data file read by the :doc:`read_data ` command: * k\_n (energy/distance\^2 units) * k\_na (energy/distance\^2 units) @@ -102,14 +102,14 @@ above for force versus surface separation, for \delta\_n < 0 and 0 < **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -125,7 +125,7 @@ for pair interactions. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index 75446ded3c..3c45e2cf2f 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -105,7 +105,7 @@ incorporation of dihedral angles effects. potentials with hydrogen, you will likely want to set the mass of H atoms to be 10x or 20x larger to avoid having to use a tiny timestep. You can do this by using the :doc:`mass ` command after using the - :doc:`pair\_coeff ` command to read the BOP potential + :doc:`pair_coeff ` command to read the BOP potential file. One option can be specified as a keyword with the pair\_style command. @@ -388,7 +388,7 @@ The rest of the table has the same structure as the previous section (see above) **Mixing, shift, table tail correction, restart**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -396,7 +396,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -422,7 +422,7 @@ appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` Default """"""" diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 3a9191cfd7..7aeed58d48 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -111,7 +111,7 @@ ionic-pair dependent length parameter, and Rc is the cutoff. The styles with *coul/long* or *coul/msm* add a Coulombic term as described for the :doc:`lj/cut ` pair styles. An additional damping factor is applied to the Coulombic term so it can be used in -conjunction with the :doc:`kspace\_style ` command and its +conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* of *msm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in @@ -132,9 +132,9 @@ damped shifted force model as in the :doc:`coul/dsf ` style. Note that these potentials are related to the :doc:`Buckingham potential `. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy units) @@ -185,12 +185,12 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These styles support the :doc:`pair\_modify ` shift option +These styles support the :doc:`pair_modify ` shift option for the energy of the exp(), 1/r\^6, and 1/r\^8 portion of the pair interaction. The *born/coul/long* pair style supports the -:doc:`pair\_modify ` table option to tabulate the +:doc:`pair_modify ` table option to tabulate the short-range portion of the long-range Coulombic interaction. These styles support the pair\_modify tail option for adding long-range @@ -200,7 +200,7 @@ Thess styles writes thei information to binary :doc:`restart ` files, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. -These styles can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. They do not support the *inner*\ , +These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -217,7 +217,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package `, :doc:`pair\_style buck ` +:doc:`pair_coeff `, :doc:`pair_style buck ` **Default:** none diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index a05043d141..4286818c74 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -49,7 +49,7 @@ torques on finite-size spherical particles. The former requires monodisperse spherical particles; the latter allows for polydisperse spherical particles. -These pair styles are designed to be used with either the :doc:`pair\_style lubricate ` or :doc:`pair\_style lubricateU ` commands to provide thermostatting +These pair styles are designed to be used with either the :doc:`pair_style lubricate ` or :doc:`pair_style lubricateU ` commands to provide thermostatting when dissipative lubrication forces are acting. Thus the parameters *mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , and *cutoff* should be specified consistent with the settings in the lubrication pair styles. @@ -67,9 +67,9 @@ used, or both must be defined. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutinner (distance units) @@ -111,13 +111,13 @@ For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -125,7 +125,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -147,7 +147,7 @@ Only spherical particles are allowed for pair\_style brownian/poly. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style lubricate `, :doc:`pair\_style lubricateU ` +:doc:`pair_coeff `, :doc:`pair_style lubricate `, :doc:`pair_style lubricateU ` Default """"""" diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 7c559001b8..c3b5458ba1 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -119,7 +119,7 @@ The styles with *coul/cut* or *coul/long* or *coul/msm* add a Coulombic term as described for the :doc:`lj/cut ` pair styles. For *buck/coul/long* and *buc/coul/msm*\ , an additional damping factor is applied to the Coulombic term so it can be used in conjunction with -the :doc:`kspace\_style ` command and its *ewald* or *pppm* +the :doc:`kspace_style ` command and its *ewald* or *pppm* or *msm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. @@ -138,12 +138,12 @@ Note that these potentials are related to the :doc:`Born-Mayer-Huggins potential cutoff. The additional Coulombic term can be cutoff or long-range (no cutoff) depending on whether the style name includes coul/cut or coul/long or coul/msm. If you wish the C/r\^6 term to be long-range - (no cutoff), then see the :doc:`pair\_style buck/long/coul/long ` command. + (no cutoff), then see the :doc:`pair_style buck/long/coul/long ` command. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (energy units) @@ -199,11 +199,11 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These styles support the :doc:`pair\_modify ` shift option +These styles support the :doc:`pair_modify ` shift option for the energy of the exp() and 1/r\^6 portion of the pair interaction. The *buck/coul/long* pair style supports the -:doc:`pair\_modify ` table option to tabulate the +:doc:`pair_modify ` table option to tabulate the short-range portion of the long-range Coulombic interaction. These styles support the pair\_modify tail option for adding long-range @@ -213,7 +213,7 @@ pair interaction. These styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. -These styles can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. They do not support the *inner*\ , +These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -226,7 +226,7 @@ only enabled if LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style born ` +:doc:`pair_coeff `, :doc:`pair_style born ` **Default:** none diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 94351f5152..3bf9fa53a2 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -92,7 +92,7 @@ via the damped shifted force model described in :ref:`(Fennell) ` approximating an Ewald sum similar to the :doc:`pair coul/dsf ` styles. In *buck6d/coul/gauss/long* an additional damping factor is applied to the Coulombic term so it can be used in conjunction with the -:doc:`kspace\_style ` command and its *ewald* or *pppm* +:doc:`kspace_style ` command and its *ewald* or *pppm* options. The Coulombic cutoff in this case separates the real and reciprocal space evaluation of the Ewald sum. @@ -101,9 +101,9 @@ terms. If two cutoffs are specified, the first is used as the cutoff for the vdW terms, and the second is the cutoff for the Coulombic term. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (energy units) @@ -126,7 +126,7 @@ is used. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These styles do not support the :doc:`pair\_modify ` shift +These styles do not support the :doc:`pair_modify ` shift option for the energy. Instead the smoothing function should be applied by setting the global smoothing parameter to a value < 1.0. @@ -143,7 +143,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index 3871e554ce..332f15b4f9 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -70,16 +70,16 @@ potential. If *flag\_buck* is set to *long*\ , no cutoff is used on the Buckingham 1/r\^6 dispersion term. The long-range portion can be calculated by -using the :doc:`kspace\_style ewald/disp or pppm/disp ` +using the :doc:`kspace_style ewald/disp or pppm/disp ` commands. The specified Buckingham cutoff then determines which portion of the Buckingham interactions are computed directly by the pair potential versus which part is computed in reciprocal space via the Kspace style. If *flag\_buck* is set to *cut*\ , the Buckingham -interactions are simply cutoff, as with :doc:`pair\_style buck `. +interactions are simply cutoff, as with :doc:`pair_style buck `. If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic interactions. The long-range portion can calculated by using any of -several :doc:`kspace\_style ` command options such as +several :doc:`kspace_style ` command options such as *pppm* or *ewald*\ . Note that if *flag\_buck* is also set to long, then the *ewald/disp* or *pppm/disp* Kspace style needs to be used to perform the long-range calculations for both the Buckingham and @@ -87,9 +87,9 @@ Coulombic interactions. If *flag\_coul* is set to *off*\ , Coulombic interactions are not computed. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (energy units) @@ -143,15 +143,15 @@ instructions on how to use the accelerated styles effectively. This pair styles does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the exp() and 1/r\^6 portion of the pair interaction, assuming *flag\_buck* is *cut*\ . -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the Buckingham portion of the pair interaction. -This pair style supports the :doc:`pair\_modify ` table and +This pair style supports the :doc:`pair_modify ` table and table/disp options since they can tabulate the short-range portion of the long-range Coulombic and dispersion interactions. @@ -159,9 +159,9 @@ This pair style write its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* -keywords of the :doc:`run\_style respa ` command, meaning the +keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the :doc:`run\_style ` command for +the rRESPA hierarchy. See the :doc:`run_style ` command for details. @@ -178,7 +178,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index cd3e5dbc70..16a9a80223 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -145,7 +145,7 @@ artifacts. The newer *charmmfsw* or *charmmfsh* styles were released in March 2017. We recommend they be used instead of the older *charmm* - styles. This includes the newer :doc:`dihedral\_style charmmfsw ` command. Eventually code from the new + styles. This includes the newer :doc:`dihedral_style charmmfsw ` command. Eventually code from the new styles will propagate into the related pair styles (e.g. implicit, accelerator, free energy variants). @@ -194,7 +194,7 @@ formulas as style *lj/charmm/coul/charmm* and style *lj/charmmfsw/coul/long* computes the same formulas as style *lj/charmmfsw/coul/charmmfsh*\ , except that an additional damping factor is applied to the Coulombic term, so it can be used in -conjunction with the :doc:`kspace\_style ` command and its +conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* or *msm* option. Only one Coulombic cutoff is specified for these styles; if only 2 arguments are used in the pair\_style command, then the outer LJ cutoff is used as the single @@ -204,9 +204,9 @@ directly; interactions outside that distance are computed in reciprocal space. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -260,16 +260,16 @@ usual settings for the CHARMM force field. See the "pair\_modify" command for details. None of the *lj/charmm* or *lj/charmmfsw* pair styles support the -:doc:`pair\_modify ` shift option, since the Lennard-Jones +:doc:`pair_modify ` shift option, since the Lennard-Jones portion of the pair interaction is smoothed to 0.0 at the cutoff. The *lj/charmm/coul/long* and *lj/charmmfsw/coul/long* styles support -the :doc:`pair\_modify ` table option since they can +the :doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. None of the *lj/charmm* or *lj/charmmfsw* pair styles support the -:doc:`pair\_modify ` tail option for adding long-range tail +:doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since the Lennard-Jones portion of the pair interaction is smoothed to 0.0 at the cutoff. @@ -280,10 +280,10 @@ that reads a restart file. The *lj/charmm/coul/long* and *lj/charmmfsw/coul/long* pair styles support the use of the *inner*\ , *middle*\ , and *outer* keywords of the -:doc:`run\_style respa ` command, meaning the pairwise forces +:doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of -run\_style respa. See the :doc:`run\_style ` command for +run\_style respa. See the :doc:`run_style ` command for details. @@ -303,7 +303,7 @@ page for more info. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 985e6688f3..01c442176f 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -93,9 +93,9 @@ Coulombic term as described for the :doc:`lj/cut ` pair styles. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -123,7 +123,7 @@ specified in the pair\_style command. If the pair\_coeff command is not used to define coefficients for a particular I != J type pair, the mixing rule for epsilon and sigma for all class2 potentials is to use the *sixthpower* formulas documented -by the :doc:`pair\_modify ` command. The :doc:`pair\_modify mix ` setting is thus ignored for class2 potentials +by the :doc:`pair_modify ` command. The :doc:`pair_modify mix ` setting is thus ignored for class2 potentials for epsilon and sigma. However it is still followed for mixing the cutoff distance. @@ -172,15 +172,15 @@ command (default = geometric). See the "pair\_modify" command for details. All of the lj/class2 pair styles support the -:doc:`pair\_modify ` shift option for the energy of the +:doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction. The *lj/class2/coul/long* pair style does not support the -:doc:`pair\_modify ` table option since a tabulation +:doc:`pair_modify ` table option since a tabulation capability has not yet been added to this potential. All of the lj/class2 pair styles support the -:doc:`pair\_modify ` tail option for adding a long-range +:doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the Lennard-Jones portion of the pair interaction. @@ -188,10 +188,10 @@ All of the lj/class2 pair styles write their information to :doc:`binary restart not need to be specified in an input script that reads a restart file. Only the *lj/class2* and *lj/class2/coul/long* pair styles support the use of the -*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run\_style respa ` command, meaning the pairwise forces can be +*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of run\_style respa. -See the :doc:`run\_style ` command for details. +See the :doc:`run_style ` command for details. Restrictions """""""""""" @@ -203,7 +203,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_fep\_soft ` +:doc:`pair_coeff `, :doc:`pair\_fep\_soft ` **Default:** none diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 424b8c3242..a7eac2b6e6 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -34,7 +34,7 @@ Description Specify the pairwise force field coefficients for one or more pairs of atom types. The number and meaning of the coefficients depends on the pair style. Pair coefficients can also be set in the data file read -by the :doc:`read\_data ` command or in a restart file. +by the :doc:`read_data ` command or in a restart file. I and J can be specified in one of two ways. Explicit numeric values can be used for each, as in the 1st example above. I <= J is @@ -80,7 +80,7 @@ as For many potentials, if coefficients for type pairs with I != J are not set explicitly by a pair\_coeff command, the values are inferred from the I,I and J,J settings by mixing rules; see the -:doc:`pair\_modify ` command for a discussion. Details on +:doc:`pair_modify ` command for a discussion. Details on this option as it pertains to individual potentials are described on the doc page for the potential. @@ -132,7 +132,7 @@ Windows: The alphabetic list of pair styles defined in LAMMPS is given on the -:doc:`pair\_style ` doc page. They are also listed in more +:doc:`pair_style ` doc page. They are also listed in more compact form on the :doc:`Commands pair ` doc page. Click on the style to display the formula it computes and its @@ -147,15 +147,15 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. Related commands """""""""""""""" -:doc:`pair\_style `, :doc:`pair\_modify `, -:doc:`read\_data `, :doc:`read\_restart `, -:doc:`pair\_write ` +:doc:`pair_style `, :doc:`pair_modify `, +:doc:`read_data `, :doc:`read_restart `, +:doc:`pair_write ` **Default:** none diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index fb9c92989f..3893d2113a 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -69,14 +69,14 @@ Lennard-Jones formula with A\_ss set appropriately, which results from letting both particle sizes go to zero. -When used in combination with :doc:`pair\_style yukawa/colloid `, the two terms become the so-called +When used in combination with :doc:`pair_style yukawa/colloid `, the two terms become the so-called DLVO potential, which combines electrostatic repulsion and van der Waals attraction. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy units) @@ -132,7 +132,7 @@ colloid-solvent cutoff in this case. widely different particles sizes (e.g. sigma=10 colloids in a background sigma=1 LJ fluid), you will likely want to use these commands for efficiency: :doc:`neighbor multi ` and - :doc:`comm\_modify multi `. + :doc:`comm_modify multi `. ---------- @@ -168,13 +168,13 @@ is an energy value mixed like a LJ epsilon. D1 and d2 are distance values and are mixed like sigma. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -182,7 +182,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -197,7 +197,7 @@ This style is part of the COLLOID package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Normally, this pair style should be used with finite-size particles -which have a diameter, e.g. see the :doc:`atom\_style sphere ` command. However, this is not a requirement, +which have a diameter, e.g. see the :doc:`atom_style sphere ` command. However, this is not a requirement, since the only definition of particle size is via the pair\_coeff parameters for each type. In other words, the physical radius of the particle is ignored. Thus you should insure that the d1,d2 parameters @@ -210,7 +210,7 @@ only per-type polydispersity is enabled via the pair\_coeff parameters. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index ece536a011..0dc15dcd89 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -112,7 +112,7 @@ file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be automatically loaded if carbon atom is detected in LAMMPS input structure. This file must be in your working directory or in the directory pointed to by the environment variable LAMMPS\_POTENTIALS, as -described on the :doc:`pair\_coeff ` command doc page. +described on the :doc:`pair_coeff ` command doc page. Keyword *polar* indicates whether the force field includes the atomic polarization. Since the equilibration of the polarization @@ -155,7 +155,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -These pair styles does not support the :doc:`pair\_modify ` +These pair styles does not support the :doc:`pair_modify ` shift, table, and tail options. These pair styles do not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -163,7 +163,7 @@ need to re-specify the pair\_style, pair\_coeff, and :doc:`fix qeq/comb ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -190,7 +190,7 @@ doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_style `, :doc:`pair\_coeff `, +:doc:`pair_style `, :doc:`pair_coeff `, :doc:`fix qeq/comb ` **Default:** none diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index f08ddc38e0..4031a9741c 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -94,7 +94,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -111,8 +111,8 @@ enabled if LAMMPS is build with that package. See the :doc:`Build package `, -:doc:`pair\_style lj/cut ` +:doc:`pair_coeff `, +:doc:`pair_style lj/cut ` **Default:** none diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index fda9ae4069..735b52cb6e 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -209,9 +209,9 @@ of the Streitz-Mintmire potential, as described in :ref:`this paper `, as a Slater 1\ *s* orbital. More details can be found in the referenced paper. To fully reproduce the published Streitz-Mintmire potential, which is a variable charge potential, style *coul/streitz* must be -used with :doc:`pair\_style eam/alloy ` (or some other +used with :doc:`pair_style eam/alloy ` (or some other short-range potential that has been parameterized appropriately) via -the :doc:`pair\_style hybrid/overlay ` command. Likewise, +the :doc:`pair_style hybrid/overlay ` command. Likewise, charge equilibration must be performed via the :doc:`fix qeq/slater ` command. For example: @@ -235,7 +235,7 @@ be computed via an Ewald summation. For example: kspace_style ewald 1e-6 Keyword *ewald* does not need a damping parameter, but a -:doc:`kspace\_style ` must be defined, which can be style +:doc:`kspace_style ` must be defined, which can be style *ewald* or *pppm*\ . The Ewald method was used in Streitz and Mintmire's original paper, but a Wolf summation offers a speed-up in some cases. @@ -264,7 +264,7 @@ Streitz-Mintmire parameterization for the material being modeled. Styles *coul/long* and *coul/msm* compute the same Coulombic interactions as style *coul/cut* except that an additional damping factor is applied so it can be used in conjunction with the -:doc:`kspace\_style ` command and its *ewald* or *pppm* +:doc:`kspace_style ` command and its *ewald* or *pppm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. @@ -303,16 +303,16 @@ your model. Note that these potentials are designed to be combined with other pair -potentials via the :doc:`pair\_style hybrid/overlay ` +potentials via the :doc:`pair_style hybrid/overlay ` command. This is because they have no repulsive core. Hence if they are used by themselves, there will be no repulsion to keep two oppositely charged particles from moving arbitrarily close to each other. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutoff (distance units) @@ -358,14 +358,14 @@ For atom type pairs I,J and I != J, the cutoff distance for the *coul/cut* style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -The :doc:`pair\_modify ` shift option is not relevant +The :doc:`pair_modify ` shift option is not relevant for these pair styles. -The *coul/long* style supports the :doc:`pair\_modify ` +The *coul/long* style supports the :doc:`pair_modify ` table option for tabulation of the short-range portion of the long-range Coulombic interaction. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -373,7 +373,7 @@ These pair styles write their information to :doc:`binary restart files ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -392,7 +392,7 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style, hybrid/overlay `, :doc:`kspace\_style ` +:doc:`pair_coeff `, :doc:`pair\_style, hybrid/overlay `, :doc:`kspace_style ` **Default:** none diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index 2e86ab41b4..0d98a22dc7 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -58,9 +58,9 @@ and in combination with coul/cut or coul/long. It is also usually combined with gauss/cut, see :ref:`(Lenart) ` or :ref:`(Jusufi) `. The following coefficients must be defined for each pair of atom -types via the :doc:`pair\_coeff ` command as in the example +types via the :doc:`pair_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (no units) @@ -78,19 +78,19 @@ The global cutoff (r\_c) specified in the pair\_style command is used. This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the Gauss-potential portion of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -103,8 +103,8 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` -:doc:`pair\_style gauss/cut ` +:doc:`pair_coeff ` +:doc:`pair_style gauss/cut ` **Default:** none diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index c6d306b2eb..dff5869649 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -50,9 +50,9 @@ eliminates the short-range singularity of the classical mono-polar electrostatic interaction expression :ref:`(Maaravi) `. The shielding parameter *lambda* (1/distance units) must be defined for -each pair of atom types via the :doc:`pair\_coeff ` command as +each pair of atom types via the :doc:`pair_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` commands: +:doc:`read_data ` or :doc:`read_restart ` commands: The global cutoff (r\_c) specified in the pair\_style command is used. @@ -65,15 +65,15 @@ The global cutoff (r\_c) specified in the pair\_style command is used. This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs. -The :doc:`pair\_modify ` *table* option is not relevant +The :doc:`pair_modify ` *table* option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` *tail* option for adding long-range tail corrections to energy and pressure. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -86,8 +86,8 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` -:doc:`pair\_style ilp/graphene/hbn ` +:doc:`pair_coeff ` +:doc:`pair_style ilp/graphene/hbn ` **Default:** tap\_flag = 1 diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index 3667aa6e2f..000f8df3eb 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -111,26 +111,26 @@ the model as implemented in LAMMPS. All the styles are identical to the corresponding pair style without the "/cs" in the name: -* :doc:`pair\_style born/coul/dsf ` -* :doc:`pair\_style born/coul/long ` -* :doc:`pair\_style born/coul/wolf ` -* :doc:`pair\_style buck/coul/long ` -* :doc:`pair\_style coul/long ` -* :doc:`pair\_style coul/wolf ` -* :doc:`pair\_style lj/cut/coul/long ` +* :doc:`pair_style born/coul/dsf ` +* :doc:`pair_style born/coul/long ` +* :doc:`pair_style born/coul/wolf ` +* :doc:`pair_style buck/coul/long ` +* :doc:`pair_style coul/long ` +* :doc:`pair_style coul/wolf ` +* :doc:`pair_style lj/cut/coul/long ` except that they correctly treat the special case where the distance between two charged core and shell atoms in the same core/shell pair approach r = 0.0. Styles with a "/long" in the name are used with a long-range solver -for Coulombic interactions via the :doc:`kspace\_style ` +for Coulombic interactions via the :doc:`kspace_style ` command. They require special treatment of the short-range Coulombic interactions within the cor/shell model. Specifically, the short-range Coulomb interaction between a core and its shell should be turned off using the -:doc:`special\_bonds ` command by setting the 1-2 weight +:doc:`special_bonds ` command by setting the 1-2 weight to 0.0, which works because the core and shell atoms are bonded to each other. This induces a long-range correction approximation which fails at small distances (~< 10e-8). Therefore, the Coulomb term which @@ -196,8 +196,8 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package `, :doc:`pair\_style born `, -:doc:`pair\_style buck ` +:doc:`pair_coeff `, :doc:`pair_style born `, +:doc:`pair_style buck ` **Default:** none diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index fc7de92900..9b9d969215 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -154,8 +154,8 @@ Style *lj/cut/dipole/long* computes long-range point-dipole interactions as discussed in :ref:`(Toukmaji) `. Dipole-dipole, dipole-charge, and charge-charge interactions are all supported, along with the standard 12/6 Lennard-Jones interactions, which are computed -with a cutoff. A :doc:`kspace\_style ` must be defined to -use this pair style. Currently, only :doc:`kspace\_style ewald/disp ` support long-range point-dipole +with a cutoff. A :doc:`kspace_style ` must be defined to +use this pair style. Currently, only :doc:`kspace_style ewald/disp ` support long-range point-dipole interactions. Style *lj/long/dipole/long* also computes point-dipole interactions as @@ -166,16 +166,16 @@ can be cutoff or long-ranged. For style *lj/long/dipole/long*\ , if *flag\_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6 dispersion term. The long-range -portion is calculated by using the :doc:`kspace\_style ewald\_disp ` command. The specified LJ cutoff then +portion is calculated by using the :doc:`kspace_style ewald\_disp ` command. The specified LJ cutoff then determines which portion of the LJ interactions are computed directly by the pair potential versus which part is computed in reciprocal space via the Kspace style. If *flag\_lj* is set to *cut*\ , the LJ -interactions are simply cutoff, as with :doc:`pair\_style lj/cut `. If *flag\_lj* is set to *off*\ , LJ interactions +interactions are simply cutoff, as with :doc:`pair_style lj/cut `. If *flag\_lj* is set to *off*\ , LJ interactions are not computed at all. If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic or dipole interactions. The long-range portion is calculated by using -*ewald\_disp* of the :doc:`kspace\_style ` command. If +*ewald\_disp* of the :doc:`kspace_style ` command. If *flag\_coul* is set to *off*\ , Coulombic and dipole interactions are not computed at all. @@ -183,16 +183,16 @@ Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere up dipole moments. The *omega* option on the :doc:`fix langevin ` command can be used to thermostat the rotational motion. The :doc:`compute temp/sphere ` command can be used to monitor the temperature, since it includes -rotational degrees of freedom. The :doc:`atom\_style hybrid dipole sphere ` command should be used since +rotational degrees of freedom. The :doc:`atom_style hybrid dipole sphere ` command should be used since it defines the point dipoles and their rotational state. The magnitude and orientation of the dipole moment for each particle can be defined by the :doc:`set ` command or in the "Atoms" section -of the data file read in by the :doc:`read\_data ` command. +of the data file read in by the :doc:`read_data ` command. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -245,14 +245,14 @@ is an energy value mixed like a LJ epsilon. D1 and d2 are distance values and are mixed like sigma. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction; such energy goes to zero at the cutoff by construction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -260,7 +260,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -280,7 +280,7 @@ currently supported. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`set `, :doc:`read\_data `, +:doc:`pair_coeff `, :doc:`set `, :doc:`read_data `, :doc:`fix nve/sphere `, :doc:`fix nvt/sphere ` **Default:** none diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 439e41d93b..aceef23179 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -61,7 +61,7 @@ field. This pair-wise thermostat can be used in conjunction with any :doc:`pair style `, and in leiu of per-particle thermostats like :doc:`fix langevin ` or ensemble thermostats like Nose Hoover as implemented by :doc:`fix nvt `. To use -*dpd/tstat* as a thermostat for another pair style, use the :doc:`pair\_style hybrid/overlay ` command to compute both the desired +*dpd/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. For style *dpd*\ , the force on atom I due to atom J is given as a sum @@ -91,9 +91,9 @@ all 3 terms. For style *dpd/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. For style *dpd*\ , the following coefficients must be defined for each -pair of atoms types via the :doc:`pair\_coeff ` command as in +pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (force units) @@ -102,11 +102,11 @@ commands: The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that sigma is set equal to sqrt(2 T gamma), -where T is the temperature set by the :doc:`pair\_style ` +where T is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. For style *dpd/tstat*\ , the coefficients defined for each pair of -atoms types via the :doc:`pair\_coeff ` command is the same, +atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. The GPU-accelerated versions of these styles are implemented based on @@ -115,7 +115,7 @@ the work of :ref:`(Afshar) ` and :ref:`(Phillips) `. .. note:: If you are modeling DPD polymer chains, you may want to use the - :doc:`pair\_style srp ` command in conjunction with these pair + :doc:`pair_style srp ` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. @@ -156,15 +156,15 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative Fc term is already shifted to be 0.0 at the cutoff distance Rc. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for these pair styles. -These pair style do not support the :doc:`pair\_modify ` +These pair style do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -178,7 +178,7 @@ be the same as they would have been if the original simulation had continued past the restart time. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. The *dpd/tstat* style can ramp its target temperature over multiple @@ -195,26 +195,26 @@ Restrictions The default frequency for rebuilding neighbor lists is every 10 steps -(see the :doc:`neigh\_modify ` command). This may be too +(see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpd* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of "dangerous" reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. -These pair styles requires you to use the :doc:`comm\_modify vel yes ` command so that velocities are stored by ghost +These pair styles requires you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the -:doc:`read\_restart ` command, though they should provide +:doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the -:doc:`read\_restart ` command for more details. +:doc:`read_restart ` command for more details. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair\_style srp ` +:doc:`pair_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair_style srp ` **Default:** none diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index c0d4f8c0c4..91de642ddb 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -75,9 +75,9 @@ For style *dpd/fdt*\ , the fluctuation-dissipation theorem defines gamma to be set equal to sigma\*sigma/(2 T), where T is the set point temperature specified as a pair style parameter in the above examples. The following coefficients must be defined for each pair of atoms types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` commands: +:doc:`read_data ` or :doc:`read_restart ` commands: * A (force units) * sigma (force\*time\^(1/2) units) @@ -108,9 +108,9 @@ variance that is used to compute the internal conductive energy. The fluctuation-dissipation theorem defines alpha\*alpha to be set equal to 2\*kB\*kappa, where kappa is the mesoparticle thermal conductivity parameter. The following coefficients must be defined for -each pair of atoms types via the :doc:`pair\_coeff ` +each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files -read by the :doc:`read\_data ` or :doc:`read\_restart ` +read by the :doc:`read_data ` or :doc:`read_restart ` commands: * A (force units) @@ -174,17 +174,17 @@ These commands are part of the USER-DPD package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Pair styles *dpd/fdt* and *dpd/fdt/energy* require use of the -:doc:`comm\_modify vel yes ` option so that velocities are +:doc:`comm_modify vel yes ` option so that velocities are stored by ghost atoms. -Pair style *dpd/fdt/energy* requires :doc:`atom\_style dpd ` +Pair style *dpd/fdt/energy* requires :doc:`atom_style dpd ` to be used in order to properly account for the particle internal energies and temperatures. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix shardlow ` +:doc:`pair_coeff `, :doc:`fix shardlow ` **Default:** none diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst index 270afb8dbd..abc65900a0 100644 --- a/doc/src/pair_drip.rst +++ b/doc/src/pair_drip.rst @@ -67,13 +67,13 @@ potentials (e.g. 2 Angstrom for :doc:`REBO `) is much smaller than the equilibrium layer distance of graphene layers (about 3.4 Angstrom). If you want, you can enforce this by assigning different atom types to atoms in different layers, and apply an intralayer potential to one atom type. -See :doc:`pair\_hybrid ` for details. +See :doc:`pair_hybrid ` for details. ---------- -The :doc:`pair\_coeff ` command for DRIP takes *4+N* arguments, where +The :doc:`pair_coeff ` command for DRIP takes *4+N* arguments, where *N* is the number of LAMMPS atom types. The fist three arguments must be fixed to be *\* \* drip*, the fourth argument is the path to the DRIP parameter file, and the remaining N arguments specifying the mapping between element in the @@ -139,10 +139,10 @@ simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_style lebedeva\_z `, -:doc:`pair\_style kolmogorov/crespi/z `, -:doc:`pair\_style kolmogorov/crespi/full `, -:doc:`pair\_style ilp/graphene/hbn `. +:doc:`pair_style lebedeva\_z `, +:doc:`pair_style kolmogorov/crespi/z `, +:doc:`pair_style kolmogorov/crespi/full `, +:doc:`pair_style ilp/graphene/hbn `. ---------- diff --git a/doc/src/pair_dsmc.rst b/doc/src/pair_dsmc.rst index 38093d00e8..1b76efd3a2 100644 --- a/doc/src/pair_dsmc.rst +++ b/doc/src/pair_dsmc.rst @@ -48,9 +48,9 @@ There is no pairwise energy or virial contributions associated with this pair style. The following coefficient must be defined for each pair of atoms types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * sigma (area units, i.e. distance-squared) @@ -118,13 +118,13 @@ as in the following: This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -138,7 +138,7 @@ be the same as they would have been if the original simulation had continued past the restart time. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -155,9 +155,9 @@ was built with that package. See the :doc:`Build package ` doc p Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nve/noforce `, -:doc:`neigh\_modify `, :doc:`neighbor `, -:doc:`comm\_modify ` +:doc:`pair_coeff `, :doc:`fix nve/noforce `, +:doc:`neigh_modify `, :doc:`neighbor `, +:doc:`comm_modify ` **Default:** none diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index 73afdd7f53..320090b8ca 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -111,7 +111,7 @@ See the examples/USER/e3b directory for a complete example script. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. Thus, you @@ -143,7 +143,7 @@ The *preset* keyword currently only works with real, metal, si, and cgs :doc:`un Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`compute pair ` +:doc:`pair_coeff `, :doc:`compute pair ` Default """"""" diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index b367f00eb5..0f6840bbe4 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -114,7 +114,7 @@ within the cutoff distance. The cutoff distance and the tabulated values of the functionals F, rho, and phi are listed in one or more files which are specified by -the :doc:`pair\_coeff ` command. These are ASCII text files +the :doc:`pair_coeff ` command. These are ASCII text files in a DYNAMO-style format which is described below. DYNAMO was the original serial EAM MD code, written by the EAM originators. Several DYNAMO potential files for different metals are included in the @@ -185,7 +185,7 @@ Thus the following command will read the cuu3 potential file and use the tabulated Cu values for F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs -1,2 and 2,1 are ignored). See the :doc:`pair\_coeff ` doc +1,2 and 2,1 are ignored). See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms. Different single-element files can be assigned to different atom types @@ -242,7 +242,7 @@ where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms. Style *eam/alloy* computes pairwise interactions using the same formula as style *eam*\ . However the associated -:doc:`pair\_coeff ` command reads a DYNAMO *setfl* file +:doc:`pair_coeff ` command reads a DYNAMO *setfl* file instead of a *funcfl* file. *Setfl* files can be used to model a single-element or alloy system. In the alloy case, as explained above, *setfl* files contain explicit tabulated values for alloy @@ -267,7 +267,7 @@ where N is the number of LAMMPS atom types: As an example, the potentials/NiAlH\_jea.eam.alloy file is a *setfl* file which has tabulated EAM values for 3 elements and their alloy -interactions: Ni, Al, and H. See the :doc:`pair\_coeff ` doc +interactions: Ni, Al, and H. See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Ni, and the 4th to be Al, you would use the following pair\_coeff @@ -380,7 +380,7 @@ so that different elements can contribute differently to the total electron density at an atomic site depending on the identity of the element at that atomic site. -The associated :doc:`pair\_coeff ` command for style *eam/fs* +The associated :doc:`pair_coeff ` command for style *eam/fs* reads a DYNAMO *setfl* file that has been extended to include additional rho\_alpha\_beta arrays of tabulated values. A discussion of how FS EAM differs from conventional EAM alloy potentials is given in @@ -400,7 +400,7 @@ same as for style *eam/alloy*\ , e.g. pair_coeff \* \* NiAlH_jea.eam.fs Ni Ni Ni Al where there are N additional arguments after the filename, where N is -the number of LAMMPS atom types. See the :doc:`pair\_coeff ` +the number of LAMMPS atom types. See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. The N values determine the mapping of LAMMPS atom types to EAM elements in the file, as described above for style *eam/alloy*\ . As @@ -477,7 +477,7 @@ two different element types, mixing is performed by LAMMPS as described above with the individual styles. You never need to specify a pair\_coeff command with I != J arguments for the eam styles. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The eam pair styles do not write their information to :doc:`binary restart files `, since it is stored in tabulated potential files. @@ -485,7 +485,7 @@ Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. The eam pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -502,7 +502,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index a976baaf61..68b54a16fe 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -56,7 +56,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of EDIP elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file Si.edip has EDIP values for Si. @@ -139,7 +139,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -147,7 +147,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -174,7 +174,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index 438ced6785..235090cd39 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -126,7 +126,7 @@ r\_ij to the distances between electrons. For additional details see The overall electrostatics energy is given in Hartree units of energy by default and can be modified by an energy-conversion constant, -according to the units chosen (see :doc:`electron\_units `). The +according to the units chosen (see :doc:`electron_units `). The cutoff Rc, given in Bohrs (by default), truncates the interaction distance. The recommended cutoff for this pair style should follow the minimum image criterion, i.e. half of the minimum unit cell @@ -135,18 +135,18 @@ length. Style *eff/long* (not yet available) computes the same interactions as style *eff/cut* except that an additional damping factor is applied so it can be used in conjunction with the -:doc:`kspace\_style ` command and its *ewald* or *pppm* +:doc:`kspace_style ` command and its *ewald* or *pppm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. -This potential is designed to be used with :doc:`atom\_style electron ` definitions, in order to handle the +This potential is designed to be used with :doc:`atom_style electron ` definitions, in order to handle the description of systems with interacting nuclei and explicit electrons. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutoff (distance units) @@ -156,7 +156,7 @@ For *eff/cut*\ , the cutoff coefficient is optional. If it is not used in the pair\_style command is used. For *eff/long* (not yet available) no cutoff will be specified for an -individual I,J type pair via the :doc:`pair\_coeff ` command. +individual I,J type pair via the :doc:`pair_coeff ` command. All type pairs use the same global cutoff specified in the pair\_style command. @@ -283,14 +283,14 @@ For atom type pairs I,J and I != J, the cutoff distance for the *eff/cut* style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -The :doc:`pair\_modify ` shift option is not relevant for +The :doc:`pair_modify ` shift option is not relevant for these pair styles. The *eff/long* (not yet available) style supports the -:doc:`pair\_modify ` table option for tabulation of the +:doc:`pair_modify ` table option for tabulation of the short-range portion of the long-range Coulombic interaction. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -298,7 +298,7 @@ These pair styles write their information to :doc:`binary restart files ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -316,16 +316,16 @@ more info. These pair styles require that particles store electron attributes such as radius, radial velocity, and radial force, as defined by the -:doc:`atom\_style `. The *electron* atom style does all of +:doc:`atom_style `. The *electron* atom style does all of this. -Thes pair styles require you to use the :doc:`comm\_modify vel yes ` command so that velocities are stored by ghost +Thes pair styles require you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` Default """"""" diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index 001f314443..bdaa8733bb 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -63,7 +63,7 @@ atoms in the atomic pair. .. note:: Even though the EIM potential is treating atoms as charged ions, - you should not use a LAMMPS :doc:`atom\_style ` that stores a + you should not use a LAMMPS :doc:`atom_style ` that stores a charge on each atom and thus requires you to assign a charge to each atom, e.g. the *charge* or *full* atom styles. This is because the EIM potential infers the charge on an atom from the equation above for @@ -74,7 +74,7 @@ atoms in the atomic pair. All the EIM parameters are listed in a potential file which is -specified by the :doc:`pair\_coeff ` command. This is an +specified by the :doc:`pair_coeff ` command. This is an ASCII text file in a format described below. The "ffield.eim" file included in the "potentials" directory of the LAMMPS distribution currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I. @@ -97,7 +97,7 @@ command, where N is the number of LAMMPS atom types: * EIM potential file * N element names = mapping of EIM elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example like one of those above, suppose you want to model a @@ -183,7 +183,7 @@ LAMMPS was built with that package. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index d8262e0712..01ef5ad9d1 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -50,7 +50,7 @@ where the *epsilon* parameter determines the depth of the potential minimum located at *Rm*\ , and *alpha* determines the softness of the repulsion. The coefficients must be defined for each species in a given particle -type via the :doc:`pair\_coeff ` command as in the examples +type via the :doc:`pair_coeff ` command as in the examples above, where the first argument is the filename that includes the exponential-6 parameters for each species. The file includes the species tag followed by the *alpha*\ , *epsilon* and *Rm* @@ -161,7 +161,7 @@ comprise the gas mixture. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` shift option +This style does not support the :doc:`pair_modify ` shift option for the energy of the exp() and 1/r\^6 portion of the pair interaction. This style does not support the pair\_modify tail option for adding long-range @@ -204,7 +204,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** fractional weighting diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index 90dbfeb612..d1e64ae5df 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -212,7 +212,7 @@ order to avoid singularities in potential energy and forces when sites are created or annihilated and can overlap :ref:`(Beutler) `. The parameters n, alpha\_LJ and alpha\_C are set in the -:doc:`pair\_style ` command, before the cutoffs. Usual choices for the +:doc:`pair_style ` command, before the cutoffs. Usual choices for the exponent are n = 2 or n = 1. For the remaining coefficients alpha\_LJ = 0.5 and alpha\_C = 10 Angstrom\^2 are appropriate choices. Plots of the 12/6 LJ and Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1. @@ -223,9 +223,9 @@ Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1. For the *lj/cut/coul/cut/soft* or *lj/cut/coul/long/soft* pair styles, as well as for the equivalent *class2* versions, the following coefficients must be -defined for each pair of atoms types via the :doc:`pair\_coeff ` +defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by -the :doc:`read\_data ` or :doc:`read\_restart ` commands, or +the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -246,31 +246,31 @@ specified. Style *lj/cut/tip4p/long/soft* implements a soft-core version of the TIP4P water model. The usage of the TIP4P pair style is documented in the -:doc:`pair\_lj ` styles. In the soft version the parameters n, alpha\_LJ -and alpha\_C are set in the :doc:`pair\_style ` command, after the +:doc:`pair_lj ` styles. In the soft version the parameters n, alpha\_LJ +and alpha\_C are set in the :doc:`pair_style ` command, after the specific parameters of the TIP4P water model and before the cutoffs. The activation parameter lambda is supplied as an argument of the -:doc:`pair\_coeff ` command, after epsilon and sigma and before the +:doc:`pair_coeff ` command, after epsilon and sigma and before the optional cutoffs. Style *lj/charmm/coul/long/soft* implements a soft-core version of the modified 12-6 LJ potential used in CHARMM and documented in the :doc:`pair\_lj\_charmm ` style. In the soft version the parameters n, -alpha\_LJ and alpha\_C are set in the :doc:`pair\_style ` command, before +alpha\_LJ and alpha\_C are set in the :doc:`pair_style ` command, before the global cutoffs. The activation parameter lambda is introduced as an argument -of the :doc:`pair\_coeff ` command, after epsilon and sigma and +of the :doc:`pair_coeff ` command, after epsilon and sigma and before the optional eps14 and sigma14. Style *lj/class2/soft* implements a soft-core version of the 9-6 potential in :doc:`pair\_class2 `. In the soft version the parameters n, alpha\_LJ -and alpha\_C are set in the :doc:`pair\_style ` command, before the +and alpha\_C are set in the :doc:`pair_style ` command, before the global cutoffs. The activation parameter lambda is introduced as an argument of -the the :doc:`pair\_coeff ` command, after epsilon and sigma and before +the the :doc:`pair_coeff ` command, after epsilon and sigma and before the optional cutoffs. The *coul/cut/soft*\ , *coul/long/soft* and *tip4p/long/soft* sub-styles are designed to be combined with other pair potentials via the -:doc:`pair\_style hybrid/overlay ` command. This is because +:doc:`pair_style hybrid/overlay ` command. This is because they have no repulsive core. Hence, if used by themselves, there will be no repulsion to keep two oppositely charged particles from overlapping each other. In this case, if lambda = 1, a singularity may @@ -299,13 +299,13 @@ in several water models). related styles; use the lambda parameter instead to activate/deactivate interactions, or use epsilon = 0 and sigma = 1. Alternatively, when sites do not interact though the Lennard-Jones term the *coul/long/soft* or similar sub-style - can be used via the :doc:`pair\_style hybrid/overlay ` command. + can be used via the :doc:`pair_style hybrid/overlay ` command. ---------- -The *morse/soft* variant modifies the :doc:`pair\_morse ` style at +The *morse/soft* variant modifies the :doc:`pair_morse ` style at short range to have a soft core. The functional form differs from that of the *lj/soft* styles, and is instead given by: @@ -357,20 +357,20 @@ distance for these pair style can be mixed. The default mix value is *geometric* for 12-6 styles. The mixing rule for epsilon and sigma for *lj/class2/soft* 9-6 potentials is to use the -*sixthpower* formulas. The :doc:`pair\_modify mix ` setting is thus +*sixthpower* formulas. The :doc:`pair_modify mix ` setting is thus ignored for class2 potentials for epsilon and sigma. However it is still -followed for mixing the cutoff distance. See the :doc:`pair\_modify ` +followed for mixing the cutoff distance. See the :doc:`pair_modify ` command for details. The *morse/soft* pair style does not support mixing. Thus, coefficients for all LJ pairs must be specified explicitly. -All of the pair styles with soft core support the :doc:`pair\_modify ` +All of the pair styles with soft core support the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction. The different versions of the *lj/cut/soft* pair styles support the -:doc:`pair\_modify ` tail option for adding a long-range tail +:doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure for the Lennard-Jones portion of the pair interaction. @@ -387,7 +387,7 @@ interaction. other approximations, namely that the system is homogeneous (local density equal the average density) beyond the cutoff. -The *morse/soft* pair style does not support the :doc:`pair\_modify ` +The *morse/soft* pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. All of these pair styles write information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be @@ -411,7 +411,7 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix adapt `, +:doc:`pair_coeff `, :doc:`fix adapt `, :doc:`fix adapt/fep `, :doc:`compute fep ` **Default:** none diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index e5252afe2b..cb687ff487 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -51,9 +51,9 @@ between an atom and its corresponding tether site which will typically be a frozen atom in the simulation. Rc is the cutoff. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (energy units) @@ -79,9 +79,9 @@ barrier is located at r\_mh and has a width of sigma\_h. The prefactor determines the height of the potential barrier. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the example above, +via the :doc:`pair_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * H (energy \* distance units) @@ -146,22 +146,22 @@ before mixing, and converted back after mixing This way, if either particle is repulsive (if Ai<0 or Aj<0), then the default interaction between both particles will be repulsive. -The *gauss* style does not support the :doc:`pair\_modify ` +The *gauss* style does not support the :doc:`pair_modify ` shift option. There is no effect due to the Gaussian well beyond the cutoff; hence reasonable cutoffs need to be specified. -The *gauss/cut* style supports the :doc:`pair\_modify ` shift +The *gauss/cut* style supports the :doc:`pair_modify ` shift option for the energy of the Gauss-potential portion of the pair interaction. -The :doc:`pair\_modify ` table and tail options are not +The :doc:`pair_modify ` table and tail options are not relevant for these pair styles. These pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. The *gauss* pair style tallies an "occupancy" count of how many Gaussian-well @@ -192,8 +192,8 @@ enabled if LAMMPS is build with that package. See the :doc:`Build package `, -:doc:`pair\_style coul/diel ` +:doc:`pair_coeff `, +:doc:`pair_style coul/diel ` **Default:** none diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 47b7b5564e..8db0e6edc2 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -71,13 +71,13 @@ listed below and in `this supplementary document `_ Use of this pair style requires the NVE, NVT, or NPT fixes with the *asphere* extension (e.g. :doc:`fix nve/asphere `) in -order to integrate particle rotation. Additionally, :doc:`atom\_style ellipsoid ` should be used since it defines the +order to integrate particle rotation. Additionally, :doc:`atom_style ellipsoid ` should be used since it defines the rotational state and the size and shape of each ellipsoidal particle. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon = well depth (energy units) @@ -96,7 +96,7 @@ cutoff specified in the pair\_style command is used. It is typical with the Gay-Berne potential to define *sigma* as the minimum of the 3 shape diameters of the particles involved in an I,I interaction, though this is not required. Note that this is a -different meaning for *sigma* than the :doc:`pair\_style resquared ` potential uses. +different meaning for *sigma* than the :doc:`pair_style resquared ` potential uses. The epsilon\_i and epsilon\_j coefficients are actually defined for atom types, not for pairs of atom types. Thus, in a series of pair\_coeff @@ -114,7 +114,7 @@ J, you should insure they are consistent with their values in other pair\_coeff commands, since only the last setting will be in effect. Note that if this potential is being used as a sub-style of -:doc:`pair\_style hybrid `, and there is no "pair\_coeff I I" +:doc:`pair_style hybrid `, and there is no "pair\_coeff I I" setting made for Gay-Berne for a particular type I (because I-I interactions are computed by another hybrid pair potential), then you still need to insure the epsilon a,b,c coefficients are assigned to @@ -171,16 +171,16 @@ For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair styles supports the :doc:`pair\_modify ` shift +This pair styles supports the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction, but only for sphere-sphere interactions. There is no shifting performed for ellipsoidal interactions due to the anisotropic dependence of the interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -188,7 +188,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -204,12 +204,12 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package `. It also require they store a per-type +:doc:`atom_style `. It also require they store a per-type :doc:`shape `. The particles cannot store a per-particle diameter. This pair style requires that atoms be ellipsoids as defined by the -:doc:`atom\_style ellipsoid ` command. +:doc:`atom_style ellipsoid ` command. Particles acted on by the potential can be finite-size aspherical or spherical particles, or point particles. Spherical particles have all @@ -224,8 +224,8 @@ ratio ellipsoids are used. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nve/asphere `, -:doc:`compute temp/asphere `, :doc:`pair\_style resquared ` +:doc:`pair_coeff `, :doc:`fix nve/asphere `, +:doc:`compute temp/asphere `, :doc:`pair_style resquared ` **Default:** none diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 7f03519f35..20ab3b3cab 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -184,9 +184,9 @@ This is determined by searching for a :doc:`fix rigid ` command (or its variants). For granular styles there are no additional coefficients to set for -each pair of atom types via the :doc:`pair\_coeff ` command. +each pair of atom types via the :doc:`pair_coeff ` command. All settings are global and are made via the pair\_style command. -However you must still use the :doc:`pair\_coeff ` for all +However you must still use the :doc:`pair_coeff ` for all pairs of granular atom types. For example the command @@ -196,7 +196,7 @@ pairs of granular atom types. For example the command should be used if all atoms in the simulation interact via a granular potential (i.e. one of the pair styles above is used). If a granular -potential is used as a sub-style of :doc:`pair\_style hybrid `, then specific atom types can be used in the +potential is used as a sub-style of :doc:`pair_style hybrid `, then specific atom types can be used in the pair\_coeff command to determine which atoms interact via a granular potential. @@ -228,14 +228,14 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The :doc:`pair\_modify ` mix, shift, table, and tail options +The :doc:`pair_modify ` mix, shift, table, and tail options are not relevant for granular pair styles. These pair styles write their information to :doc:`binary restart files `, so a pair\_style command does not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. The single() function of these pair styles returns 0.0 for the energy @@ -265,23 +265,23 @@ All the granular pair styles are part of the GRANULAR package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. These pair styles require that atoms store torque and angular velocity -(omega) as defined by the :doc:`atom\_style `. They also +(omega) as defined by the :doc:`atom_style `. They also require a per-particle radius is stored. The *sphere* atom style does all of this. -This pair style requires you to use the :doc:`comm\_modify vel yes ` command so that velocities are stored by ghost +This pair style requires you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the -:doc:`read\_restart ` command, though they should provide +:doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the -:doc:`read\_restart ` command for more details. +:doc:`read_restart ` command for more details. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index 294bec9b8c..a22e6b233a 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -50,10 +50,10 @@ and torques are the sum of various models selected for the normal, tangential, rolling and twisting modes of motion. All model choices and parameters are entered in the -:doc:`pair\_coeff ` command, as described below. Unlike +:doc:`pair_coeff ` command, as described below. Unlike e.g. :doc:`pair gran/hooke `, coefficient values are not global, but can be set to different values for different combinations -of particle types, as determined by the :doc:`pair\_coeff ` +of particle types, as determined by the :doc:`pair_coeff ` command. If the contact model choice is the same for two particle types, the mixing for the cross-coefficients can be carried out automatically. This is shown in the last example, where model @@ -674,7 +674,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The :doc:`pair\_modify ` mix, shift, table, and tail options +The :doc:`pair_modify ` mix, shift, table, and tail options are not relevant for granular pair styles. Mixing of coefficients is carried out using geometric averaging for @@ -711,7 +711,7 @@ These pair styles write their information to :doc:`binary restart files ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. The single() function of these pair styles returns 0.0 for the energy @@ -743,23 +743,23 @@ All the granular pair styles are part of the GRANULAR package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. These pair styles require that atoms store torque and angular velocity -(omega) as defined by the :doc:`atom\_style `. They also +(omega) as defined by the :doc:`atom_style `. They also require a per-particle radius is stored. The *sphere* atom style does all of this. -This pair style requires you to use the :doc:`comm\_modify vel yes ` command so that velocities are stored by ghost +This pair style requires you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the -:doc:`read\_restart ` command, though they should provide +:doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the -:doc:`read\_restart ` command for more details. +:doc:`read_restart ` command for more details. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` :doc:`pair gran/\* ` Default diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index 9bc803bc55..d80e8a794b 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -86,9 +86,9 @@ the pair\_style command. The inner LJ cutoff must be > 0, but the inner Coulombic cutoff can be >= 0. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -143,15 +143,15 @@ The default mix value is *geometric*\ . See the "pair\_modify" command for details. None of the GROMACS pair styles support the -:doc:`pair\_modify ` shift option, since the Lennard-Jones +:doc:`pair_modify ` shift option, since the Lennard-Jones portion of the pair interaction is already smoothed to 0.0 at the cutoff. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. None of the GROMACS pair styles support the -:doc:`pair\_modify ` tail option for adding long-range tail +:doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since there are no corrections for a potential that goes to 0.0 at the cutoff. @@ -159,7 +159,7 @@ All of the GROMACS pair styles write their information to :doc:`binary restart f not need to be specified in an input script that reads a restart file. All of the GROMACS pair styles can only be used via the *pair* -keyword of the :doc:`run\_style respa ` command. They do not +keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -173,7 +173,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index d1c89eaee8..cb17e581e1 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -52,7 +52,7 @@ command, where N is the number of LAMMPS atom types: * filename * N element names = mapping of GW elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.gw has Gao-Weber values for Si and C. @@ -90,7 +90,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -98,7 +98,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -124,7 +124,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index f87f0c45e2..e202cb4293 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -64,9 +64,9 @@ These 3-body interactions can be defined for pairs of acceptor and donor atoms, based on atom types. For each donor/acceptor atom pair, the 3rd atom in the interaction is a hydrogen permanently bonded to the donor atom, e.g. in a bond list read in from a data file via the -:doc:`read\_data ` command. The atom types of possible +:doc:`read_data ` command. The atom types of possible hydrogen atoms for each donor/acceptor type pair are specified by the -:doc:`pair\_coeff ` command (see below). +:doc:`pair_coeff ` command (see below). Style *hbond/dreiding/lj* is the original DREIDING potential of :ref:`(Mayo) `. It uses a LJ 12/10 functional for the Donor-Acceptor @@ -84,16 +84,16 @@ on the DREIDING force field. Because the Dreiding hydrogen bond potential is only one portion of an overall force field which typically includes other pairwise - interactions, it is common to use it as a sub-style in a :doc:`pair\_style hybrid/overlay ` command, where another pair style + interactions, it is common to use it as a sub-style in a :doc:`pair_style hybrid/overlay ` command, where another pair style provides the repulsive core interaction between pairs of atoms, e.g. a 1/r\^12 Lennard-Jones repulsion. .. note:: - When using the hbond/dreiding pair styles with :doc:`pair\_style hybrid/overlay `, you should explicitly define pair + When using the hbond/dreiding pair styles with :doc:`pair_style hybrid/overlay `, you should explicitly define pair interactions between the donor atom and acceptor atoms, (as well as between these atoms and ALL other atoms in your system). Whenever - :doc:`pair\_style hybrid/overlay ` is used, ordinary mixing + :doc:`pair_style hybrid/overlay ` is used, ordinary mixing rules are not applied to atoms like the donor and acceptor atoms because they are typically referenced in multiple pair styles. Neglecting to do this can cause difficult-to-detect physics problems. @@ -110,20 +110,20 @@ on the DREIDING force field. The following coefficients must be defined for pairs of eligible -donor/acceptor types via the :doc:`pair\_coeff ` command as +donor/acceptor types via the :doc:`pair_coeff ` command as in the examples above. .. note:: Unlike other pair styles and their associated - :doc:`pair\_coeff ` commands, you do not need to specify + :doc:`pair_coeff ` commands, you do not need to specify pair\_coeff settings for all possible I,J type pairs. Only I,J type pairs for atoms which act as joint donors/acceptors need to be specified; all other type pairs are assumed to be inactive. .. note:: - A :doc:`pair\_coeff ` command can be specified multiple + A :doc:`pair_coeff ` command can be specified multiple times for the same donor/acceptor type pair. This enables multiple hydrogen types to be assigned to the same donor/acceptor type pair. For other pair\_styles, if the pair\_coeff command is re-used for the @@ -160,14 +160,14 @@ follows: A single hydrogen atom type K can be specified, or a wild-card asterisk can be used in place of or in conjunction with the K arguments to select multiple types as hydrogen atoms. This takes the form -"\*" or "\*n" or "n\*" or "m\*n". See the :doc:`pair\_coeff ` +"\*" or "\*n" or "n\*" or "m\*n". See the :doc:`pair_coeff ` command doc page for details. If the donor flag is *i*\ , then the atom of type I in the pair\_coeff command is treated as the donor, and J is the acceptor. If the donor flag is *j*\ , then the atom of type J in the pair\_coeff command is treated as the donor and I is the donor. This option is required -because the :doc:`pair\_coeff ` command requires that I <= J. +because the :doc:`pair_coeff ` command requires that I <= J. Epsilon and sigma are settings for the hydrogen bond potential based on a Lennard-Jones functional form. Note that sigma is defined as the @@ -214,13 +214,13 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. You must explicitly identify each donor/acceptor type pair. -These styles do not support the :doc:`pair\_modify ` shift +These styles do not support the :doc:`pair_modify ` shift option for the energy of the interactions. -The :doc:`pair\_modify ` table option is not relevant for +The :doc:`pair_modify ` table option is not relevant for these pair styles. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -228,7 +228,7 @@ These pair styles do not write their information to :doc:`binary restart files < re-specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. These pair styles tally a count of how many hydrogen bonding @@ -258,7 +258,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 3ee9c19428..2ede99b35a 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -46,7 +46,7 @@ pair styles in one simulation. With the *hybrid* style, exactly one pair style is assigned to each pair of atom types. With the *hybrid/overlay* style, one or more pair styles can be assigned to each pair of atom types. The assignment of pair styles to type pairs -is made via the :doc:`pair\_coeff ` command. +is made via the :doc:`pair_coeff ` command. Here are two examples of hybrid simulations. The *hybrid* style could be used for a simulation of a metal droplet on a LJ surface. The @@ -122,7 +122,7 @@ with Tersoff, and the cross-interactions with Lennard-Jones: pair_coeff 1 2 lj/cut 1.0 1.5 If pair coefficients are specified in the data file read via the -:doc:`read\_data ` command, then the same rule applies. +:doc:`read_data ` command, then the same rule applies. E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for each line in the "Pair Coeffs" section, e.g. @@ -135,7 +135,7 @@ each line in the "Pair Coeffs" section, e.g. ... Note that the pair\_coeff command for some potentials such as -:doc:`pair\_style eam/alloy ` includes a mapping specification +:doc:`pair_style eam/alloy ` includes a mapping specification of elements to all atom types, which in the hybrid case, can include atom types not assigned to the *eam/alloy* potential. The NULL keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO, @@ -170,20 +170,20 @@ commands are the same: pair_coeff 2 2 lj/cut 1.5 0.8 Coefficients must be defined for each pair of atoms types via the -:doc:`pair\_coeff ` command as described above, or in the -data file or restart files read by the :doc:`read\_data ` or -:doc:`read\_restart ` commands, or by mixing as described +:doc:`pair_coeff ` command as described above, or in the +data file or restart files read by the :doc:`read_data ` or +:doc:`read_restart ` commands, or by mixing as described below. For both the *hybrid* and *hybrid/overlay* styles, every atom type pair I,J (where I <= J) must be assigned to at least one sub-style via -the :doc:`pair\_coeff ` command as in the examples above, or -in the data file read by the :doc:`read\_data `, or by mixing +the :doc:`pair_coeff ` command as in the examples above, or +in the data file read by the :doc:`read_data `, or by mixing as described below. If you want there to be no interactions between a particular pair of atom types, you have 3 choices. You can assign the type pair to some -sub-style and use the :doc:`neigh\_modify exclude type ` +sub-style and use the :doc:`neigh_modify exclude type ` command. You can assign it to some sub-style and set the coefficients so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ potential). Or, for *hybrid* and *hybrid/overlay* simulations, you @@ -205,7 +205,7 @@ If an assignment to *none* is made in a simulation with the *hybrid/overlay* pair style, it wipes out all previous assignments of that atom type pair to sub-styles. -Note that you may need to use an :doc:`atom\_style ` hybrid +Note that you may need to use an :doc:`atom_style ` hybrid command in your input script, if atoms in the simulation will need attributes from several atom styles, due to using multiple pair potentials. @@ -218,8 +218,8 @@ Different force fields (e.g. CHARMM vs AMBER) may have different rules for applying weightings that change the strength of pairwise interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 neighbors in the molecular bond topology, as normally set by the -:doc:`special\_bonds ` command. Different weights can be -assigned to different pair hybrid sub-styles via the :doc:`pair\_modify special ` command. This allows multiple force fields +:doc:`special_bonds ` command. Different weights can be +assigned to different pair hybrid sub-styles via the :doc:`pair_modify special ` command. This allows multiple force fields to be used in a model of a hybrid system, however, there is no consistent approach to determine parameters automatically for the interactions between the two force fields, this is only recommended when particles @@ -261,12 +261,12 @@ effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA: pair_modify pair tersoff special lj/coul 1.0 1.0 1.0 For use with the various :doc:`compute \*/tally ` -computes, the :doc:`pair\_modify compute/tally ` +computes, the :doc:`pair_modify compute/tally ` command can be used to selectively turn off processing of the compute tally styles, for example, if those pair styles (e.g. many-body styles) do not support this feature. -See the :doc:`pair\_modify ` doc page for details on +See the :doc:`pair_modify ` doc page for details on the specific syntax, requirements and restrictions. @@ -288,7 +288,7 @@ individual sub-style can be accessed and output via the :doc:`compute pair ` command, using "\* \*" to include +single :doc:`pair_coeff ` command, using "\* \*" to include all types and the NULL keywords described above to exclude specific types not assigned to that potential. If types 1,3,4 were assigned in that way (but not type 2), this means that all many-body interactions @@ -309,7 +309,7 @@ to think of excluding an interaction between a particular pair of atoms when the potential computes 3-body or 4-body interactions. However, you can still use the pair\_coeff none setting or the -:doc:`neigh\_modify exclude ` command to exclude certain +:doc:`neigh_modify exclude ` command to exclude certain type pairs from the neighbor list that will be passed to a many-body sub-style. This will alter the calculations made by a many-body potential, since it builds its list of 3-body, 4-body, etc @@ -390,7 +390,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : Any pair potential settings made via the -:doc:`pair\_modify ` command are passed along to all +:doc:`pair_modify ` command are passed along to all sub-styles of the hybrid potential. For atom type pairs I,J and I != J, if the sub-style assigned to I,I @@ -405,19 +405,19 @@ sub-style. See the "pair\_modify" command for details of mixing rules. See the See the doc page for the sub-style to see if allows for mixing. -The hybrid pair styles supports the :doc:`pair\_modify ` +The hybrid pair styles supports the :doc:`pair_modify ` shift, table, and tail options for an I,J pair interaction, if the associated sub-style supports it. For the hybrid pair styles, the list of sub-styles and their -respective settings are written to :doc:`binary restart files `, so a :doc:`pair\_style ` command does +respective settings are written to :doc:`binary restart files `, so a :doc:`pair_style ` command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart file. Thus, pair\_coeff commands need to be re-specified in the restart input script. These pair styles support the use of the *inner*\ , *middle*\ , and -*outer* keywords of the :doc:`run\_style respa ` command, if +*outer* keywords of the :doc:`run_style respa ` command, if their sub-styles do. Restrictions @@ -425,7 +425,7 @@ Restrictions When using a long-range Coulombic solver (via the -:doc:`kspace\_style ` command) with a hybrid pair\_style, +:doc:`kspace_style ` command) with a hybrid pair\_style, one or more sub-styles will be of the "long" variety, e.g. *lj/cut/coul/long* or *buck/coul/long*\ . You must insure that the short-range Coulombic cutoff used by each of these long pair styles is @@ -434,7 +434,7 @@ the same or else LAMMPS will generate an error. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index b18ebb341b..74937bd0fb 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -146,14 +146,14 @@ units, if your simulation does not use *metal* units. Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_none `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style drip `, -:doc:`pair\_style pair\_kolmogorov\_crespi\_z `, -:doc:`pair\_style pair\_kolmogorov\_crespi\_full `, -:doc:`pair\_style pair\_lebedeva\_z `, -:doc:`pair\_style pair\_coul\_shield `. +:doc:`pair_coeff `, +:doc:`pair_none `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style drip `, +:doc:`pair_style pair\_kolmogorov\_crespi\_z `, +:doc:`pair_style pair\_kolmogorov\_crespi\_full `, +:doc:`pair_style pair\_lebedeva\_z `, +:doc:`pair_style pair\_coul\_shield `. **Default:** tap\_flag = 1 diff --git a/doc/src/pair_kim.rst b/doc/src/pair_kim.rst index 768ac3fa9b..56232a3e92 100644 --- a/doc/src/pair_kim.rst +++ b/doc/src/pair_kim.rst @@ -29,14 +29,14 @@ This pair style is a wrapper on the `Open Knowledgebase of Interatomic Models (O potentials to enable their use in LAMMPS scripts. The preferred interface for using interatomic models archived in -OpenKIM is the :doc:`kim\_commands interface `. That +OpenKIM is the :doc:`kim_commands interface `. That interface supports both "KIM Portable Models" (PMs) that conform to the KIM API Portable Model Interface (PMI) and can be used by any simulation code that conforms to the KIM API/PMI, and "KIM Simulator Models" that are natively implemented within a single simulation code (like LAMMPS) and can only be used with it. The *pair\_style kim* command is limited to KIM PMs. It is -used by the :doc:`kim\_commands interface ` as needed. +used by the :doc:`kim_commands interface ` as needed. .. note:: @@ -49,7 +49,7 @@ used by the :doc:`kim\_commands interface ` as needed. The argument *model* is the name of the KIM PM. For potentials archived in OpenKIM -this is the extended KIM ID (see :doc:`kim\_commands ` +this is the extended KIM ID (see :doc:`kim_commands ` for details). LAMMPS can invoke any KIM PM, however there can be incompatibilities (for example due to unit matching issues). In the event of an incompatibility, the code will terminate with @@ -97,7 +97,7 @@ in *examples/kim*\ . **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since KIM stores the potential parameters. @@ -105,7 +105,7 @@ Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -117,7 +117,7 @@ Restrictions This pair style is part of the KIM package. See details on -restrictions in :doc:`kim\_commands `. +restrictions in :doc:`kim_commands `. This current version of pair\_style kim is compatible with the kim-api package version 2.0.0 and higher. @@ -125,7 +125,7 @@ kim-api package version 2.0.0 and higher. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`kim\_commands ` +:doc:`pair_coeff `, :doc:`kim_commands ` **Default:** none diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index 1faf271497..a9dcbcbda9 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -134,13 +134,13 @@ units. Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_none `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style drip `, -:doc:`pair\_style pair\_lebedeva\_z `, -:doc:`pair\_style kolmogorov/crespi/z `, -:doc:`pair\_style ilp/graphene/hbn `. +:doc:`pair_coeff `, +:doc:`pair_none `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style drip `, +:doc:`pair_style pair\_lebedeva\_z `, +:doc:`pair_style kolmogorov/crespi/z `, +:doc:`pair_style ilp/graphene/hbn `. **Default:** tap\_flag = 0 diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index a1e6c1afad..f9c116e15a 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -63,13 +63,13 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_none `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style drip `, -:doc:`pair\_style ilp/graphene/hbn `. -:doc:`pair\_style kolmogorov/crespi/full `, -:doc:`pair\_style lebedeva/z ` +:doc:`pair_coeff `, +:doc:`pair_none `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style drip `, +:doc:`pair_style ilp/graphene/hbn `. +:doc:`pair_style kolmogorov/crespi/full `, +:doc:`pair_style lebedeva/z ` **Default:** none diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst index 8f667bf918..49a0ba0a4b 100644 --- a/doc/src/pair_lcbop.rst +++ b/doc/src/pair_lcbop.rst @@ -36,7 +36,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of LCBOP elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want @@ -65,7 +65,7 @@ carefully. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -73,7 +73,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -95,7 +95,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_airebo `, :doc:`pair\_coeff ` +:doc:`pair_airebo `, :doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst index 78e21ca616..08a88450b5 100644 --- a/doc/src/pair_lebedeva_z.rst +++ b/doc/src/pair_lebedeva_z.rst @@ -57,13 +57,13 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_style none `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style drip `, -:doc:`pair\_style ilp/graphene/hbd `, -:doc:`pair\_style kolmogorov/crespi/z `, -:doc:`pair\_style kolmogorov/crespi/full `. +:doc:`pair_coeff `, +:doc:`pair_style none `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style drip `, +:doc:`pair_style ilp/graphene/hbd `, +:doc:`pair_style kolmogorov/crespi/z `, +:doc:`pair_style kolmogorov/crespi/full `. **Default:** none diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst index e8b1a9850f..3b7af38fd1 100644 --- a/doc/src/pair_line_lj.rst +++ b/doc/src/pair_line_lj.rst @@ -33,7 +33,7 @@ explained below. Interactions between two line segments, each with N1 and N2 spherical particles, are calculated as the pairwise sum of N1\*N2 Lennard-Jones interactions. Interactions between a line segment with N spherical particles and a point particle are treated as the -pairwise sum of N Lennard-Jones interactions. See the :doc:`pair\_style lj/cut ` doc page for the definition of Lennard-Jones +pairwise sum of N Lennard-Jones interactions. See the :doc:`pair_style lj/cut ` doc page for the definition of Lennard-Jones interactions. The set of non-overlapping spherical sub-particles that represent a @@ -79,9 +79,9 @@ the pair of particles to be included in the neighbor list. are using and the sub-particle cutoff settings. For style *line/lj*\ , the following coefficients must be defined for -each pair of atom types via the :doc:`pair\_coeff ` command +each pair of atom types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by -the :doc:`read\_data ` or :doc:`read\_restart ` +the :doc:`read_data ` or :doc:`read_restart ` commands: * sizeI (distance units) @@ -122,13 +122,13 @@ cutoff is used. For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -144,12 +144,12 @@ LAMMPS was built with that package. See the :doc:`Build package Defining particles to be line segments so they participate in line/line or line/particle interactions requires the use the -:doc:`atom\_style line ` command. +:doc:`atom_style line ` command. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style tri/lj ` +:doc:`pair_coeff `, :doc:`pair_style tri/lj ` **Default:** none diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst index b74070c4d3..2dd5ec44de 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -122,17 +122,17 @@ Note that the usual 1/2 factor is included in :math:`K`. This pair style does not support mixing since all parameters are explicit for each pair. -The :doc:`pair\_modify ` shift option is supported by this +The :doc:`pair_modify ` shift option is supported by this pair style. -The :doc:`pair\_modify ` table and tail options are not +The :doc:`pair_modify ` table and tail options are not relevant for this pair style. This pair style does not write its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -159,10 +159,10 @@ LAMMPS is build with that package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style lj/cut `, -:doc:`pair\_style morse `, -:doc:`bond\_style harmonic ` +:doc:`pair_coeff `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style lj/cut `, +:doc:`pair_style morse `, +:doc:`bond_style harmonic ` **Default:** none diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index cfc56ecb5e..3fa1cb0bca 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -258,7 +258,7 @@ setting *alpha* to a small non-zero value. Styles *lj/cut/coul/long* and *lj/cut/coul/msm* compute the same Coulombic interactions as style *lj/cut/coul/cut* except that an additional damping factor is applied to the Coulombic term so it can -be used in conjunction with the :doc:`kspace\_style ` +be used in conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are @@ -314,9 +314,9 @@ your model. For all of the *lj/cut* pair styles, the following coefficients must be defined for each pair of atoms types via the -:doc:`pair\_coeff ` command as in the examples above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands, or by mixing as +:doc:`pair_coeff ` command as in the examples above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -385,15 +385,15 @@ The default mix value is *geometric*\ . See the "pair\_modify" command for details. All of the *lj/cut* pair styles support the -:doc:`pair\_modify ` shift option for the energy of the +:doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction. The *lj/cut/coul/long* and *lj/cut/tip4p/long* pair styles support the -:doc:`pair\_modify ` table option since they can tabulate +:doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. All of the *lj/cut* pair styles support the -:doc:`pair\_modify ` tail option for adding a long-range +:doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure for the Lennard-Jones portion of the pair interaction. @@ -401,10 +401,10 @@ All of the *lj/cut* pair styles write their information to :doc:`binary restart not need to be specified in an input script that reads a restart file. The *lj/cut* and *lj/cut/coul/long* pair styles support the use of the -*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run\_style respa ` command, meaning the pairwise forces can be +*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of run\_style respa. -See the :doc:`run\_style ` command for details. +See the :doc:`run_style ` command for details. ---------- @@ -423,7 +423,7 @@ more info. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 814eac69f9..e71627a364 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -41,9 +41,9 @@ of the standard 12/6 potential, given by Rc is the cutoff. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -86,13 +86,13 @@ and cutoff distance for all of the lj/cut pair styles can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style supports the :doc:`pair\_modify ` tail +This pair style supports the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the pair interaction. @@ -100,9 +100,9 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* -keywords of the :doc:`run\_style respa ` command, meaning the +keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the :doc:`run\_style ` command for +the rRESPA hierarchy. See the :doc:`run_style ` command for details. @@ -116,7 +116,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index e03e70cb6b..dcfcc7167c 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -54,9 +54,9 @@ This potential is commonly used to study the shock mechanics of FCC solids, as in Ravelo et al. :ref:`(Ravelo) `. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the example above, +via the :doc:`pair_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -101,15 +101,15 @@ The default mix value is *geometric*\ . See the "pair\_modify" command for details. The lj/cubic pair style does not support the -:doc:`pair\_modify ` shift option, +:doc:`pair_modify ` shift option, since pair interaction is already smoothed to 0.0 at the cutoff. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. The lj/cubic pair style does not support the -:doc:`pair\_modify ` tail option for adding long-range tail +:doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since there are no corrections for a potential that goes to 0.0 at the cutoff. @@ -117,7 +117,7 @@ The lj/cubic pair style writes its information to :doc:`binary restart files ` command. It does not +keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -131,7 +131,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 45a56219c4..606cead480 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -59,9 +59,9 @@ actual force cutoff is the sum of cutoff + delta. For all of the *lj/expand* pair styles, the following coefficients must be defined for each pair of atoms types via the -:doc:`pair\_coeff ` command as in the examples above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands, or by mixing as +:doc:`pair_coeff ` command as in the examples above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -112,13 +112,13 @@ coefficients are mixed according to the pair\_modify mix value. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style supports the :doc:`pair\_modify ` tail +This pair style supports the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the pair interaction. @@ -126,7 +126,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -140,7 +140,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index c6f17e2eb8..40d5688a33 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -125,16 +125,16 @@ calculation, so you can test the trade-off for your model. If *flag\_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6 dispersion term. The long-range portion can be calculated by using -the :doc:`kspace\_style ewald/disp or pppm/disp ` commands. +the :doc:`kspace_style ewald/disp or pppm/disp ` commands. The specified LJ cutoff then determines which portion of the LJ interactions are computed directly by the pair potential versus which part is computed in reciprocal space via the Kspace style. If *flag\_lj* is set to *cut*\ , the LJ interactions are simply cutoff, as -with :doc:`pair\_style lj/cut `. +with :doc:`pair_style lj/cut `. If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic interactions. The long-range portion can calculated by using any of -several :doc:`kspace\_style ` command options such as +several :doc:`kspace_style ` command options such as *pppm* or *ewald*\ . Note that if *flag\_lj* is also set to long, then the *ewald/disp* or *pppm/disp* Kspace style needs to be used to perform the long-range calculations for both the LJ and Coulombic @@ -142,9 +142,9 @@ interactions. If *flag\_coul* is set to *off*\ , Coulombic interactions are not computed. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -216,15 +216,15 @@ and cutoff distance for all of the lj/long pair styles can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -These pair styles support the :doc:`pair\_modify ` shift +These pair styles support the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction, assuming *flag\_lj* is *cut*\ . -These pair styles support the :doc:`pair\_modify ` table and +These pair styles support the :doc:`pair_modify ` table and table/disp options since they can tabulate the short-range portion of the long-range Coulombic and dispersion interactions. -Thes pair styles do not support the :doc:`pair\_modify ` +Thes pair styles do not support the :doc:`pair_modify ` tail option for adding a long-range tail correction to the Lennard-Jones portion of the energy and pressure. @@ -232,10 +232,10 @@ These pair styles write their information to :doc:`binary restart files ` +*middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the -:doc:`run\_style ` command for details. +:doc:`run_style ` command for details. ---------- @@ -251,7 +251,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index 6120faa24a..4b3c206ef5 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -50,12 +50,12 @@ and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0. in its values and 1st derivative. This can lead to poor energy conservation and may require the use of a thermostat. Plot the energy and force resulting from this formula via the - :doc:`pair\_write ` command to see the effect. + :doc:`pair_write ` command to see the effect. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -101,13 +101,13 @@ coefficients are mixed according to the pair\_modify mix option. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since the energy of the pair interaction is smoothed to 0.0 at the cutoff. @@ -116,7 +116,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -130,7 +130,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair lj/smooth/linear ` +:doc:`pair_coeff `, :doc:`pair lj/smooth/linear ` **Default:** none diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index 13dc334719..d400552ca1 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -39,9 +39,9 @@ continuously to zero at the cutoff Rc :ref:`(Toxvaerd) `: :align: center The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -83,14 +83,14 @@ For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance can be mixed. The default mix value is geometric. See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction, since it goes to 0.0 at the cutoff by construction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since the energy of the pair interaction is smoothed to 0.0 at the cutoff. @@ -99,7 +99,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -113,7 +113,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair lj/smooth ` +:doc:`pair_coeff `, :doc:`pair lj/smooth ` **Default:** none diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index dd4040c595..3a885784a3 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -59,16 +59,16 @@ where qi and qj are the charges on the 2 atoms, epsilon is the dielectric constant which can be set by the :doc:`dielectric ` command, gamma\_i and gamma\_j are the widths of the Gaussian charge distribution and erf() is the error-function. -This style has to be used in conjunction with the :doc:`kspace\_style ` command +This style has to be used in conjunction with the :doc:`kspace_style ` command If one cutoff is specified it is used for both the vdW and Coulomb terms. If two cutoffs are specified, the first is used as the cutoff for the vdW terms, and the second is the cutoff for the Coulombic term. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (energy) @@ -94,7 +94,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst index 2a9d4068b7..7cea5ef807 100644 --- a/doc/src/pair_local_density.rst +++ b/doc/src/pair_local_density.rst @@ -201,7 +201,7 @@ types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha, beta) means that alpha is the central atom to which the LD potential is applied and beta is the neighbor atom which contributes to the LD potential on alpha). -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The local/density pair style does not write its information to :doc:`binary restart files `, since it is stored in tabulated potential files. @@ -222,7 +222,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index b9033be48d..c6aa16fe00 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -98,7 +98,7 @@ as long as *flagVF* is set to 1 (default). When using the FLD terms, these pair styles are designed to be used with explicit time integration and a correspondingly small timestep. Thus either :doc:`fix nve/sphere ` or :doc:`fix nve/asphere ` should be used for time integration. - To perform implicit FLD, see the :doc:`pair\_style lubricateU ` command. + To perform implicit FLD, see the :doc:`pair_style lubricateU ` command. Style *lubricate* requires monodisperse spherical particles; style *lubricate/poly* allows for polydisperse spherical particles. @@ -129,7 +129,7 @@ boundaries. Since lubrication forces are dissipative, it is usually desirable to thermostat the system at a constant temperature. If Brownian motion (at a constant temperature) is desired, it can be set using the -:doc:`pair\_style brownian ` command. These pair styles +:doc:`pair_style brownian ` command. These pair styles and the brownian style should use consistent parameters for *mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ . @@ -138,9 +138,9 @@ and the brownian style should use consistent parameters for *mu*\ , The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutinner (distance units) @@ -182,13 +182,13 @@ For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -196,7 +196,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -216,15 +216,15 @@ lubricate. Only spherical particles are allowed for pair\_style lubricate/poly. These pair styles will not restart exactly when using the -:doc:`read\_restart ` command, though they should provide +:doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the -:doc:`read\_restart ` command for more details. +:doc:`read_restart ` command for more details. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style lubricateU ` +:doc:`pair_coeff `, :doc:`pair_style lubricateU ` Default """"""" diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index bf0a39c56e..b50eb18467 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -105,8 +105,8 @@ computed. When using these styles, the these pair styles are designed to be used with implicit time integration and a correspondingly larger timestep. Thus either :doc:`fix nve/noforce ` should - be used for spherical particles defined via :doc:`atom\_style sphere ` or :doc:`fix nve/asphere/noforce ` should be used for - spherical particles defined via :doc:`atom\_style ellipsoid `. This is because the velocity and angular + be used for spherical particles defined via :doc:`atom_style sphere ` or :doc:`fix nve/asphere/noforce ` should be used for + spherical particles defined via :doc:`atom_style ellipsoid `. This is because the velocity and angular momentum of each particle is set by the pair style, and should not be reset by the time integration fix. @@ -134,7 +134,7 @@ fix wall command. Since lubrication forces are dissipative, it is usually desirable to thermostat the system at a constant temperature. If Brownian motion (at a constant temperature) is desired, it can be set using the -:doc:`pair\_style brownian ` command. These pair styles +:doc:`pair_style brownian ` command. These pair styles and the brownian style should use consistent parameters for *mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ . @@ -143,9 +143,9 @@ and the brownian style should use consistent parameters for *mu*\ , The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutinner (distance units) @@ -165,13 +165,13 @@ For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -179,7 +179,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -212,7 +212,7 @@ velocity-gradient direction. In this case, one must use :doc:`fix deform `, :doc:`pair\_style lubricate ` +:doc:`pair_coeff `, :doc:`pair_style lubricate ` Default """"""" diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 181b7929a7..4174a516d3 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -90,7 +90,7 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form: Either the first two or all of the following coefficients must be defined for each pair of atoms types via the pair\_coeff command as in the examples above, or in the data file read by the -:doc:`read\_data `. The two cutoffs default to the global +:doc:`read_data `. The two cutoffs default to the global values and epsilon and sigma can also be determined by mixing as described below: @@ -152,13 +152,13 @@ support mixing, so all I,J pairs of coefficients must be specified explicitly. None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports -the :doc:`pair\_modify ` shift option or long-range +the :doc:`pair_modify ` shift option or long-range tail corrections to pressure and energy. These styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. -These styles can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. They do not support the *inner*\ , +These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -176,7 +176,7 @@ page for more info. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index 68ccc829c9..d8cf53a66d 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -56,7 +56,7 @@ element. The cutoffs and the coefficients for these spline functions are listed in a parameter file which is specified by the -:doc:`pair\_coeff ` command. Parameter files for different +:doc:`pair_coeff ` command. Parameter files for different elements are included in the "potentials" directory of the LAMMPS distribution and have a ".meam.spline" file suffix. All of these files are parameterized in terms of LAMMPS :doc:`metal units `. @@ -79,7 +79,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of spline-based MEAM elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine the Ti.meam.spline file has values for Ti (old style). If @@ -143,7 +143,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The *meam/spline* pair style does not write its information to :doc:`binary restart files `, since it is stored in an external @@ -151,7 +151,7 @@ potential parameter file. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. The *meam/spline* pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -172,7 +172,7 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style meam/c ` +:doc:`pair_coeff `, :doc:`pair_style meam/c ` **Default:** none diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index 9331b5f36a..847ce797a1 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -41,7 +41,7 @@ Phi, F, G, U, rho, f, and g are represented by cubic splines. The cutoffs and the coefficients for these spline functions are listed in a parameter file which is specified by the -:doc:`pair\_coeff ` command. Parameter files for different +:doc:`pair_coeff ` command. Parameter files for different elements are included in the "potentials" directory of the LAMMPS distribution and have a ".meam.sw.spline" file suffix. All of these files are parameterized in terms of LAMMPS :doc:`metal units `. @@ -64,7 +64,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of spline-based MEAM+SW elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine the Ti.meam.sw.spline file has values for Ti. @@ -100,7 +100,7 @@ in the examples/USER/misc/meam\_sw\_spline directory. The pair style does not support multiple element types or mixing. It has been designed for pure elements only. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The *meam/sw/spline* pair style does not write its information to @@ -109,7 +109,7 @@ potential parameter file. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. The *meam/sw/spline* pair style can only be used via the *pair* -keyword of the :doc:`run\_style respa ` command. They do not +keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -130,8 +130,8 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style meam/c `, -:doc:`pair\_style meam/spline ` +:doc:`pair_coeff `, :doc:`pair_style meam/c `, +:doc:`pair_style meam/spline ` **Default:** none diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index ac858ce24b..0240e683da 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -58,7 +58,7 @@ computation of the embedding and pair energies, as implemented in LAMMPS, are given in :ref:`(Gullet) ` and references therein. The various parameters in the MEAM formulas are listed in two files -which are specified by the :doc:`pair\_coeff ` command. +which are specified by the :doc:`pair_coeff ` command. These are ASCII text files in a format consistent with other MD codes that implement MEAM potentials, such as the serial DYNAMO code and Warp. Several MEAM potential files with parameters for different @@ -81,7 +81,7 @@ command, where N is the number of LAMMPS atom types: * MEAM parameter file * N element names = mapping of MEAM elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential files. As an example, the potentials/library.meam file has generic MEAM @@ -382,7 +382,7 @@ two different element types, mixing is performed by LAMMPS with user-specifiable parameters as described above. You never need to specify a pair\_coeff command with I != J arguments for this style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -390,7 +390,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -415,8 +415,8 @@ limit on the number of atoms types. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style eam `, -:doc:`pair\_style meam/spline ` +:doc:`pair_coeff `, :doc:`pair_style eam `, +:doc:`pair_style meam/spline ` **Default:** none diff --git a/doc/src/pair_meso.rst b/doc/src/pair_meso.rst index b4a945409d..d645c4ab03 100644 --- a/doc/src/pair_meso.rst +++ b/doc/src/pair_meso.rst @@ -99,7 +99,7 @@ with υ being the kinematic viscosity. For more details, see Eq.(15) in :ref:`(Li2014\_JCP) `. The following coefficients must be defined in eDPD system for each -pair of atom types via the :doc:`pair\_coeff ` command as in +pair of atom types via the :doc:`pair_coeff ` command as in the examples above. * A (force units) @@ -133,7 +133,7 @@ The *mdpd/rhosum* style computes the local particle mass density rho for mDPD particles by kernel function interpolation. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above. +via the :doc:`pair_coeff ` command as in the examples above. * cutoff (distance units) @@ -157,7 +157,7 @@ term with B > 0 is the density-dependent repulsive force within an interaction range rd. The following coefficients must be defined for each pair of atom types via the -:doc:`pair\_coeff ` command as in the examples above. +:doc:`pair_coeff ` command as in the examples above. * A (force units) * B (force units) @@ -201,7 +201,7 @@ a tDPD particle m. For more details, see :ref:`(Li2015\_JCP) `. The following coefficients must be defined for each pair of atom types via the -:doc:`pair\_coeff ` command as in the examples above. +:doc:`pair_coeff ` command as in the examples above. * A (force units) * gamma (force/velocity units) @@ -272,7 +272,7 @@ The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not support -the :doc:`pair\_modify ` shift, table, and tail options. +the :doc:`pair_modify ` shift, table, and tail options. The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not write information to :doc:`binary restart files `. Thus, you need @@ -291,7 +291,7 @@ more info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix mvv/dpd `, +:doc:`pair_coeff `, :doc:`fix mvv/dpd `, :doc:`fix mvv/edpd `, :doc:`fix mvv/tdpd `, :doc:`fix edpd/source `, :doc:`fix tdpd/source `, :doc:`compute edpd/temp/atom `, diff --git a/doc/src/pair_mesocnt.rst b/doc/src/pair_mesocnt.rst index 30de8a07aa..566a6125c1 100644 --- a/doc/src/pair_mesocnt.rst +++ b/doc/src/pair_mesocnt.rst @@ -51,7 +51,7 @@ original papers :ref:`(Volkov1) ` and :ref:`(Volkov2) `. The potential requires tabulated data provided in a single ASCII -text file specified in the :doc:`pair\_coeff ` command. +text file specified in the :doc:`pair_coeff ` command. The first line of the file provides a time stamp and general information. The second line lists four integers giving the number of data points provided in the subsequent four @@ -105,7 +105,7 @@ Communications. This pair style does not support mixing. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The *mesocnt* pair style do not write their information to :doc:`binary restart files `, @@ -114,7 +114,7 @@ Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -134,7 +134,7 @@ This pair potential requires the :doc:`newton ` setting to be Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 1c43d47b00..0981502635 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -64,7 +64,7 @@ algorithms have been developed independently by Glosli The *mgpt* pair style calculates forces, energies, and the total energy per atom, E\_tot/N, using the Oppelstrup matrix-MGPT algorithm. Input potential and control data are entered through the -:doc:`pair\_coeff ` command. Each material treated requires +:doc:`pair_coeff ` command. Each material treated requires input parmin and potin potential files, as shown in the above examples, as well as specification by the user of the initial atomic volume Omega through pair\_coeff. At the beginning of a time step in @@ -83,7 +83,7 @@ time step, and then respecified at the new value of Omega. In all simulations, Omega must remain within the defined volume range for E\_vol and the potentials for the given material. -The default option volpress yes in the :doc:`pair\_coeff ` +The default option volpress yes in the :doc:`pair_coeff ` command includes all volume derivatives of E\_tot required to calculate the stress tensor and pressure correctly. The option volpress no disregards the pressure contribution resulting from the volume term @@ -109,7 +109,7 @@ routines. For x-86 machines, there is a provided Makefile.mgptfast which enables the fast algebra routines, i.e. build LAMMPS with "make mgptfast". The user will be informed in the output files of the matrix kernels in use. To further improve speed, on x86 the option -precision single can be added to the :doc:`pair\_coeff ` +precision single can be added to the :doc:`pair_coeff ` command line, which improves speed (up to a factor of two) at the cost of doing matrix calculations with 7 digit precision instead of the default 16. For consistency the default option can be specified @@ -151,7 +151,7 @@ before proceeding to more complex simulations. **Mixing, shift, table tail correction, restart**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -159,7 +159,7 @@ needs to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -201,12 +201,12 @@ such cases will be added over time. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` Default """"""" -The options defaults for the :doc:`pair\_coeff ` command are +The options defaults for the :doc:`pair_coeff ` command are volpress yes, nbody 1234, and precision double. diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index ba94830475..a516bdd3c0 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -45,9 +45,9 @@ Note that for 12/6 exponents, C is equal to 4 and the formula is the same as the standard Lennard-Jones potential. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -72,10 +72,10 @@ exponents for different atoms will be calculated following the same mixing rule defined for distances. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -This pair style supports the :doc:`pair\_modify ` tail +This pair style supports the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the pair interaction. @@ -83,9 +83,9 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* -keywords of the :doc:`run\_style respa ` command, meaning the +keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the :doc:`run\_style ` command for +the rRESPA hierarchy. See the :doc:`run_style ` command for details. @@ -99,7 +99,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index 3f3a7cbc72..f100f9202d 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -59,16 +59,16 @@ where qi and qj are the charges on the 2 atoms, epsilon is the dielectric constant which can be set by the :doc:`dielectric ` command, gamma\_i and gamma\_j are the widths of the Gaussian charge distribution and erf() is the error-function. -This style has to be used in conjunction with the :doc:`kspace\_style ` command +This style has to be used in conjunction with the :doc:`kspace_style ` command If one cutoff is specified it is used for both the vdW and Coulomb terms. If two cutoffs are specified, the first is used as the cutoff for the vdW terms, and the second is the cutoff for the Coulombic term. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (energy) @@ -96,7 +96,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index b45a50573a..dee1390234 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -66,7 +66,7 @@ following parameters will only be modified for the specified sub-style. If the sub-style is defined multiple times, then an additional numeric argument *N* must also be specified, which is a number from 1 to M where M is the number of times the sub-style was -listed in the :doc:`pair\_style hybrid ` command. The extra +listed in the :doc:`pair_style hybrid ` command. The extra number indicates which instance of the sub-style the remaining keywords will be applied to. Note that if the *pair* keyword is not used, and the pair style is *hybrid* or *hybrid/overlay*\ , then all the @@ -75,7 +75,7 @@ specified keywords will be applied to all sub-styles. The *special* and *compute/tally* keywords can **only** be used in conjunction with the *pair* keyword and must directly follow it. *special* allows to override the -:doc:`special\_bonds ` settings for the specified sub-style. +:doc:`special_bonds ` settings for the specified sub-style. *compute/tally* allows to disable or enable registering :doc:`compute \*/tally ` computes for a given sub-style. More details are given below. @@ -93,7 +93,7 @@ In each case, the cutoff distance is mixed the same way as sigma. Note that not all pair styles support mixing. Also, some mix options are not available for certain pair styles. See the doc page for individual pair styles for those restrictions. Note also that the -:doc:`pair\_coeff ` command also can be to directly set +:doc:`pair_coeff ` command also can be to directly set coefficients for a specific I != J pairing, in which case no mixing is performed. @@ -168,7 +168,7 @@ These corrections are bookkeeping terms which do not affect dynamics, unless a constant-pressure simulation is being performed. See the doc page for individual styles to see which support this option. These corrections are included in the calculation and printing of -thermodynamic quantities (see the :doc:`thermo\_style ` +thermodynamic quantities (see the :doc:`thermo_style ` command). Their effect will also be included in constant NPT or NPH simulations where the pressure influences the simulation box dimensions (e.g. the :doc:`fix npt ` and :doc:`fix nph ` @@ -214,19 +214,19 @@ including the following: The *compute* keyword allows pairwise computations to be turned off, -even though a :doc:`pair\_style ` is defined. This is not +even though a :doc:`pair_style ` is defined. This is not useful for running a real simulation, but can be useful for debugging purposes or for performing a :doc:`rerun ` simulation, when you only wish to compute partial forces that do not include the pairwise contribution. Two examples are as follows. First, this option allows you to perform -a simulation with :doc:`pair\_style hybrid ` with only a +a simulation with :doc:`pair_style hybrid ` with only a subset of the hybrid sub-styles enabled. Second, this option allows you to perform a simulation with only long-range interactions but no short-range pairwise interactions. Doing this by simply not defining a pair style will not work, because the -:doc:`kspace\_style ` command requires a Kspace-compatible +:doc:`kspace_style ` command requires a Kspace-compatible pair style be defined. The *nofdotr* keyword allows to disable an optimization that computes @@ -240,7 +240,7 @@ than from summing forces between individual pairs of atoms. The *special* keyword allows to override the 1-2, 1-3, and 1-4 exclusion settings for individual sub-styles of a :doc:`hybrid pair style `. It requires 4 arguments similar -to the :doc:`special\_bonds ` command, *which* and +to the :doc:`special_bonds ` command, *which* and wt1,wt2,wt3. The *which* argument can be *lj* to change the Lennard-Jones settings, *coul* to change the Coulombic settings, or *lj/coul* to change both to the same set of 3 values. The wt1,wt2,wt3 @@ -254,7 +254,7 @@ it will cause an error. .. note:: The global settings specified by the - :doc:`special\_bonds ` command affect the construction of + :doc:`special_bonds ` command affect the construction of neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors) exclude those pairs from the neighbor list entirely. Weights of 1.0 store the neighbor with no weighting applied. Thus only global values @@ -289,8 +289,8 @@ USER-INTEL package. Related commands """""""""""""""" -:doc:`pair\_style `, :doc:`pair\_style hybrid `, -pair\_coeff"_pair\_coeff.html, :doc:`thermo\_style `, +:doc:`pair_style `, :doc:`pair_style hybrid `, +pair\_coeff"_pair\_coeff.html, :doc:`thermo_style `, :doc:`compute \*/tally ` Default diff --git a/doc/src/pair_momb.rst b/doc/src/pair_momb.rst index e318d285a3..0bc3e41310 100644 --- a/doc/src/pair_momb.rst +++ b/doc/src/pair_momb.rst @@ -40,9 +40,9 @@ dispersion in density functional theory calculations. :align: center For the *momb* pair style, the following coefficients must be defined -for each pair of atoms types via the :doc:`pair\_coeff ` +for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files -read by the :doc:`read\_data ` as described below: +read by the :doc:`read_data ` as described below: * D0 (energy units) * alpha (1/distance units) @@ -64,7 +64,7 @@ LAMMPS is built with that package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style morse ` +:doc:`pair_coeff `, :doc:`pair_style morse ` **Default:** none diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 61f2e08904..ac1c106b06 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -62,9 +62,9 @@ Style *morse* computes pairwise interactions with the formula Rc is the cutoff. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * D0 (energy units) @@ -129,13 +129,13 @@ instructions on how to use the accelerated styles effectively. None of these pair styles support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -All of these pair styles support the :doc:`pair\_modify ` +All of these pair styles support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table options is not relevant for +The :doc:`pair_modify ` table options is not relevant for the Morse pair styles. -None of these pair styles support the :doc:`pair\_modify ` +None of these pair styles support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -143,7 +143,7 @@ All of these pair styles write their information to :doc:`binary restart files < to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -160,7 +160,7 @@ built with the USER-MISC package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_fep\_soft ` +:doc:`pair_coeff `, :doc:`pair\_fep\_soft ` **Default:** none diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index cd2032c799..512ce07bd7 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -70,7 +70,7 @@ table values from which the density-dependent energy and force are computed by linear interpolation. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * filename @@ -117,7 +117,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair\_style multi/lucy ` command. +specified in the :doc:`pair_style multi/lucy ` command. Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It @@ -174,7 +174,7 @@ one that matches the specified keyword. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -The :doc:`pair\_modify ` shift, table, and tail options are +The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. This pair style writes the settings for the "pair\_style multi/lucy" command @@ -185,7 +185,7 @@ file, since it is tabulated in the potential files. Thus, pair\_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -202,7 +202,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index 977309e311..7a7f5cbb47 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -83,7 +83,7 @@ table values from which the density-dependent energy and force are computed by linear interpolation. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * filename @@ -145,7 +145,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair\_style multi/lucy/rx ` +specified in the :doc:`pair_style multi/lucy/rx ` command. Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as @@ -203,7 +203,7 @@ one that matches the specified keyword. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -The :doc:`pair\_modify ` shift, table, and tail options are +The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. This pair style writes the settings for the "pair\_style multi/lucy/rx" command @@ -214,7 +214,7 @@ file, since it is tabulated in the potential files. Thus, pair\_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -253,7 +253,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** fractional weighting diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index ef00dec25a..bc26e9b5ae 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -43,7 +43,7 @@ number of LAMMPS atom types: * filename * N element names = mapping of elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.nb3b.harmonic has potential values @@ -109,7 +109,7 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index e188ce1d1f..d0ef9efdf5 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -88,7 +88,7 @@ cutoffs for the NM and Coulombic terms respectively. Styles *nm/cut/coul/long* compute the same Coulombic interactions as style *nm/cut/coul/cut* except that an additional damping factor is applied to the Coulombic term so it can -be used in conjunction with the :doc:`kspace\_style ` +be used in conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are @@ -96,9 +96,9 @@ computed in reciprocal space. For all of the *nm* pair styles, the following coefficients must be defined for each pair of atoms types -via the :doc:`pair\_coeff ` command as in the +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. * E0 (energy units) @@ -131,14 +131,14 @@ These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. All of the *nm* pair styles supports the -:doc:`pair\_modify ` shift option for the energy of the pair +:doc:`pair_modify ` shift option for the energy of the pair interaction. The *nm/cut/coul/long* pair styles support the -:doc:`pair\_modify ` table option since they can tabulate +:doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. -All of the *nm* pair styles support the :doc:`pair\_modify ` +All of the *nm* pair styles support the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure for the NM portion of the pair interaction. @@ -146,7 +146,7 @@ All of the *nm* pair styles write their information to :doc:`binary restart file to be specified in an input script that reads a restart file. All of the *nm* pair styles can only be used via the *pair* keyword of -the :doc:`run\_style respa ` command. They do not support the +the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -181,7 +181,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_none.rst b/doc/src/pair_none.rst index 080bb1168a..04a763b8e0 100644 --- a/doc/src/pair_none.rst +++ b/doc/src/pair_none.rst @@ -38,7 +38,7 @@ distance is small, then these data structures can consume a large amount of memory. So you should either set the neighbor style to *nsq* or set the skin distance to a larger value. -See the :doc:`pair\_style zero ` for a way to trigger the +See the :doc:`pair_style zero ` for a way to trigger the building of a neighbor lists, but compute no pairwise interactions. Restrictions @@ -48,7 +48,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_style zero ` +:doc:`pair_style zero ` **Default:** none diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index 727f19c327..2f6be35608 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -82,7 +82,7 @@ for a detailed description of the oxDNA force field. These pair styles have to be used together with the related oxDNA bond style *oxdna/fene* for the connectivity of the phosphate backbone (see also documentation of - :doc:`bond\_style oxdna/fene `). Most of the coefficients + :doc:`bond_style oxdna/fene `). Most of the coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first four coefficients after *oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example) and the first coefficient after *oxdna/hbond* (seq=seqdep in the above example). @@ -118,9 +118,9 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`bond\_style oxdna/fene `, :doc:`pair\_coeff `, -:doc:`bond\_style oxdna2/fene `, :doc:`pair\_style oxdna2/excv `, -:doc:`bond\_style oxrna2/fene `, :doc:`pair\_style oxrna2/excv `, +:doc:`bond_style oxdna/fene `, :doc:`pair_coeff `, +:doc:`bond_style oxdna2/fene `, :doc:`pair_style oxdna2/excv `, +:doc:`bond_style oxrna2/fene `, :doc:`pair_style oxrna2/excv `, :doc:`fix nve/dotc/langevin ` **Default:** none diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 77052da666..c57eb86c1d 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -90,7 +90,7 @@ and :ref:`(Ouldridge) ` for a detailed description of the oxDNA2 fo These pair styles have to be used together with the related oxDNA2 bond style *oxdna2/fene* for the connectivity of the phosphate backbone (see also documentation of - :doc:`bond\_style oxdna2/fene `). Most of the coefficients + :doc:`bond_style oxdna2/fene `). Most of the coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example), the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients @@ -124,9 +124,9 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`bond\_style oxdna2/fene `, :doc:`pair\_coeff `, -:doc:`bond\_style oxdna/fene `, :doc:`pair\_style oxdna/excv `, -:doc:`bond\_style oxrna2/fene `, :doc:`pair\_style oxrna2/excv `, +:doc:`bond_style oxdna2/fene `, :doc:`pair_coeff `, +:doc:`bond_style oxdna/fene `, :doc:`pair_style oxdna/excv `, +:doc:`bond_style oxrna2/fene `, :doc:`pair_style oxrna2/excv `, :doc:`fix nve/dotc/langevin ` **Default:** none diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 3cc6e7f4a6..38e77e3368 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -91,7 +91,7 @@ and :ref:`(Ouldridge) ` for a detailed description of the oxRNA2 fo These pair styles have to be used together with the related oxDNA2 bond style *oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of - :doc:`bond\_style oxrna2/fene `). Most of the coefficients + :doc:`bond_style oxrna2/fene `). Most of the coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example), the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients @@ -125,9 +125,9 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`bond\_style oxrna2/fene `, :doc:`pair\_coeff `, -:doc:`bond\_style oxdna/fene `, :doc:`pair\_style oxdna/excv `, -:doc:`bond\_style oxdna2/fene `, :doc:`pair\_style oxdna2/excv `, +:doc:`bond_style oxrna2/fene `, :doc:`pair_coeff `, +:doc:`bond_style oxdna/fene `, :doc:`pair_style oxdna/excv `, +:doc:`bond_style oxdna2/fene `, :doc:`pair_style oxdna2/excv `, :doc:`fix nve/dotc/langevin ` **Default:** diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index 284f3de32a..c618aeccca 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -81,9 +81,9 @@ regarding the VES and EPS models in LAMMPS you can contact R. Rahman (rezwanur.rahman at utsa.edu). The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below. For the *peri/pmb* style: @@ -177,17 +177,17 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` shift option. -The :doc:`pair\_modify ` table and tail options are not +The :doc:`pair_modify ` table and tail options are not relevant for these pair styles. These pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -204,7 +204,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index e9ab595011..ff522ae6b0 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -205,7 +205,7 @@ for the F(X) functions. **Mixing, shift, table tail correction, restart**\ : -This pair styles does not support the :doc:`pair\_modify ` +This pair styles does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write their information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -238,7 +238,7 @@ files. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` ---------- diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index 53480ff286..a962bdb7ca 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -38,7 +38,7 @@ interpreted language, however, the performance of this pair style is going to be significantly slower (often between 20x and 100x) than corresponding compiled code. This penalty can be significantly reduced through generating tabulations from the python code through the -:doc:`pair\_write ` command, which is supported by this style. +:doc:`pair_write ` command, which is supported by this style. Only a single pair\_coeff command is used with the *python* pair style which specifies a python class inside a python module or file that @@ -177,7 +177,7 @@ the *LJCutMelt* example, here are the two functions: computation pair-wise interactions quite significantly. However, this can be largely worked around through using the python pair style not for the actual simulation, but to generate tabulated potentials on the - fly using the :doc:`pair\_write ` command. Please see below + fly using the :doc:`pair_write ` command. Please see below for an example LAMMPS input of how to build a table file: @@ -219,7 +219,7 @@ energy computation can be correctly performed for all pairs of atom types as they are mapped to the atom type labels inside the python potential class. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -227,7 +227,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -244,7 +244,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_write `, +:doc:`pair_coeff `, :doc:`pair_write `, :doc:`pair style table ` **Default:** none diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index 3e953afebc..293d76443e 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -44,7 +44,7 @@ number of LAMMPS atom types: * QUIP initialization string * N atomic numbers = mapping of QUIP elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. A QUIP potential is fully specified by the filename which contains the @@ -62,7 +62,7 @@ directory. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -70,7 +70,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -84,7 +84,7 @@ QUIP potentials are parameterized in electron-volts and Angstroms and therefore should be used with LAMMPS metal :doc:`units `. QUIP potentials are generally not designed to work with the scaling -factors set by the :doc:`special\_bonds ` command. The +factors set by the :doc:`special_bonds ` command. The recommended setting in molecular systems is to include all interactions, i.e. to use *special\_bonds lj/coul 1.0 1.0 1.0*. Scaling factors > 0.0 will be ignored and treated as 1.0. The only exception @@ -98,7 +98,7 @@ required. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` ---------- diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index b670711e8c..6040b78a77 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -116,8 +116,8 @@ Examples using *pair\_style reax/c* are provided in the examples/reax sub-directory. Use of this pair style requires that a charge be defined for every -atom. See the :doc:`atom\_style ` and -:doc:`read\_data ` commands for details on how to specify +atom. See the :doc:`atom_style ` and +:doc:`read_data ` commands for details on how to specify charges. The ReaxFF parameter files provided were created using a charge @@ -309,7 +309,7 @@ angle\_info: 1 prints angles in the trajectory file (default = 0) **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -317,7 +317,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -362,7 +362,7 @@ appropriate units if your simulation doesn't use "real" units. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix qeq/reax `, :doc:`fix reax/c/bonds `, :doc:`fix reax/c/species ` +:doc:`pair_coeff `, :doc:`fix qeq/reax `, :doc:`fix reax/c/bonds `, :doc:`fix reax/c/species ` Default """"""" diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 2ddf7fb24d..b996ae1189 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -44,13 +44,13 @@ in `this supplementary document `_. Use of this pair style requires the NVE, NVT, or NPT fixes with the *asphere* extension (e.g. :doc:`fix nve/asphere `) in -order to integrate particle rotation. Additionally, :doc:`atom\_style ellipsoid ` should be used since it defines the +order to integrate particle rotation. Additionally, :doc:`atom_style ellipsoid ` should be used since it defines the rotational state and the size and shape of each ellipsoidal particle. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A12 = Energy Prefactor/Hamaker constant (energy units) @@ -113,7 +113,7 @@ When one of both of the interacting particles are ellipsoids, then *sigma* specifies the diameter of the continuous distribution of constituent particles within each ellipsoid used to model the RE-squared potential. Note that this is a different meaning for -*sigma* than the :doc:`pair\_style gayberne ` potential +*sigma* than the :doc:`pair_style gayberne ` potential uses. The epsilon\_i and epsilon\_j coefficients are defined for atom types, @@ -132,7 +132,7 @@ J, you should insure they are consistent with their values in other pair\_coeff commands. Note that if this potential is being used as a sub-style of -:doc:`pair\_style hybrid `, and there is no "pair\_coeff I I" +:doc:`pair_style hybrid `, and there is no "pair\_coeff I I" setting made for RE-squared for a particular type I (because I-I interactions are computed by another hybrid pair potential), then you still need to insure the epsilon a,b,c coefficients are assigned to @@ -188,16 +188,16 @@ equation for the Hamaker constant presented here. Mixing of sigma and epsilon followed by calculation of the energy prefactors using the equations above is recommended. -This pair styles supports the :doc:`pair\_modify ` shift +This pair styles supports the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction, but only for sphere-sphere interactions. There is no shifting performed for ellipsoidal interactions due to the anisotropic dependence of the interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -205,8 +205,8 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords of the :doc:`run\_style command `. +:doc:`run_style respa ` command. It does not support the +*inner*\ , *middle*\ , *outer* keywords of the :doc:`run_style command `. ---------- @@ -220,7 +220,7 @@ This style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This pair style requires that atoms be ellipsoids as defined by the -:doc:`atom\_style ellipsoid ` command. +:doc:`atom_style ellipsoid ` command. Particles acted on by the potential can be finite-size aspherical or spherical particles, or point particles. Spherical particles have all @@ -233,8 +233,8 @@ less accurate when high-aspect ratio ellipsoids are used. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nve/asphere `, -:doc:`compute temp/asphere `, :doc:`pair\_style gayberne ` +:doc:`pair_coeff `, :doc:`fix nve/asphere `, +:doc:`compute temp/asphere `, :doc:`pair_style gayberne ` **Default:** none diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 17694067c8..1ad9bd9c59 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -78,16 +78,16 @@ as required for the SDK Coarse-grained MD parameterization discussed in Style *lj/sdk/coul/long* computes the adds Coulombic interactions with an additional damping factor applied so it can be used in -conjunction with the :doc:`kspace\_style ` command and +conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* or *pppm/cg* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cg\_type (lj9\_6, lj12\_4, or lj12\_6) @@ -147,18 +147,18 @@ command. Defining then in a data file is also not supported, due to limitations of that file format. All of the lj/sdk pair styles support the -:doc:`pair\_modify ` shift option for the energy of the +:doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction. The *lj/sdk/coul/long* pair styles support the -:doc:`pair\_modify ` table option since they can tabulate +:doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. All of the lj/sdk pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. The lj/sdk and lj/cut/coul/long pair styles do not support -the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run\_style respa ` command. +the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command. ---------- @@ -177,7 +177,7 @@ doc page for more info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`angle\_style sdk ` +:doc:`pair_coeff `, :doc:`angle_style sdk ` **Default:** none diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst index ec4ada108b..5d970d382d 100644 --- a/doc/src/pair_sdpd_taitwater_isothermal.rst +++ b/doc/src/pair_sdpd_taitwater_isothermal.rst @@ -72,7 +72,7 @@ to formulas described in :ref:`(Espanol and Revenga) `. different MPI tasks have distinct seeds. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * rho0 reference density (mass/volume units) @@ -88,13 +88,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions diff --git a/doc/src/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst index 5af530aabb..a7b004830f 100644 --- a/doc/src/pair_smd_hertz.rst +++ b/doc/src/pair_smd_hertz.rst @@ -59,7 +59,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst index 02343b678f..20fbbf86dc 100644 --- a/doc/src/pair_smd_tlsph.rst +++ b/doc/src/pair_smd_tlsph.rst @@ -75,7 +75,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 07b08a95f2..e531a7a2ec 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -60,7 +60,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index cd97a799a3..f09f2d829e 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -90,7 +90,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index cb57f6ba98..14f836bd52 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -191,7 +191,7 @@ For each cations (metal): 7) Charge initialization mode: -* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Qinit*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Qinit*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create\_atom"#create\_atom command or the charge specified in the file structure using :doc:`read\_data ` command. +* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Qinit*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Qinit*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create\_atom"#create\_atom command or the charge specified in the file structure using :doc:`read_data ` command. * Divided line 8) Mode for the electronegativity equalization (Qeq) @@ -217,7 +217,7 @@ For each cations (metal): **Mixing, shift, table, tail correction, restart, rRESPA info:** -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -225,7 +225,7 @@ needs to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 1b0fb0f385..d1137eb586 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -93,7 +93,7 @@ LAMMPS mapping list. The name of the SNAP parameter file usually ends in the ".snapparam" extension. It contains a small number of parameters that define the overall form of the SNAP potential. -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for these files. Quite commonly, @@ -171,7 +171,7 @@ two different element types, mixing is performed by LAMMPS with user-specifiable parameters as described above. You never need to specify a pair\_coeff command with I != J arguments for this style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -179,7 +179,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index 9e81b26c10..384f7e1cc3 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -50,9 +50,9 @@ interactions over time. Rc is the cutoff. See the :doc:`fix nve/limit ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy units) @@ -63,7 +63,7 @@ cutoff is used. .. note:: - The syntax for :doc:`pair\_coeff ` with a single A + The syntax for :doc:`pair_coeff ` with a single A coeff is different in the current version of LAMMPS than in older versions which took two values, Astart and Astop, to ramp between them. This functionality is now available in a more general form @@ -124,17 +124,17 @@ distance for this pair style can be mixed. A is always mixed via a mix value. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option, since the pair interaction goes to 0.0 at the cutoff. -The :doc:`pair\_modify ` table and tail options are not +The :doc:`pair_modify ` table and tail options are not relevant for this pair style. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -148,7 +148,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nve/limit `, :doc:`fix adapt ` +:doc:`pair_coeff `, :doc:`fix nve/limit `, :doc:`fix adapt ` **Default:** none diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst index 741cfe4368..6e468aaf1d 100644 --- a/doc/src/pair_sph_heatconduction.rst +++ b/doc/src/pair_sph_heatconduction.rst @@ -30,7 +30,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * D diffusion coefficient (length\^2/time units) @@ -45,13 +45,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -64,7 +64,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst index 9267186e7d..bd21a3cf5b 100644 --- a/doc/src/pair_sph_idealgas.rst +++ b/doc/src/pair_sph_idealgas.rst @@ -38,7 +38,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * nu artificial viscosity (no units) @@ -53,13 +53,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -72,7 +72,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst index cf9d145121..1911e4f1b8 100644 --- a/doc/src/pair_sph_lj.rst +++ b/doc/src/pair_sph_lj.rst @@ -34,7 +34,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * nu artificial viscosity (no units) @@ -49,13 +49,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -71,7 +71,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst index 2ba1ad010a..65a0840ef5 100644 --- a/doc/src/pair_sph_rhosum.rst +++ b/doc/src/pair_sph_rhosum.rst @@ -32,7 +32,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * h (distance units) @@ -46,13 +46,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -65,7 +65,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/taitwater +:doc:`pair_coeff `, pair\_sph/taitwater **Default:** none diff --git a/doc/src/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst index ede4d4b115..3bb085b5bd 100644 --- a/doc/src/pair_sph_taitwater.rst +++ b/doc/src/pair_sph_taitwater.rst @@ -39,7 +39,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * rho0 reference density (mass/volume units) @@ -56,13 +56,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -75,7 +75,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst index 8637faf188..91f79a1ac5 100644 --- a/doc/src/pair_sph_taitwater_morris.rst +++ b/doc/src/pair_sph_taitwater_morris.rst @@ -38,7 +38,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * rho0 reference density (mass/volume units) @@ -55,13 +55,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -74,7 +74,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index 87a3f7e424..8b2112e34a 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -52,18 +52,18 @@ is the direction vector between the two particles. Style *spin/dipole/long* computes long-range magnetic dipole-dipole interaction. -A :doc:`kspace\_style ` must be defined to -use this pair style. Currently, :doc:`kspace\_style ewald/dipole/spin ` and :doc:`kspace\_style pppm/dipole/spin ` support long-range magnetic +A :doc:`kspace_style ` must be defined to +use this pair style. Currently, :doc:`kspace_style ewald/dipole/spin ` and :doc:`kspace_style pppm/dipole/spin ` support long-range magnetic dipole-dipole interactions. ---------- -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -85,7 +85,7 @@ currently supported. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`kspace\_style ` +:doc:`pair_coeff `, :doc:`kspace_style ` :doc:`fix nve/spin ` **Default:** none diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 166885d29d..98205e8d6e 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -55,9 +55,9 @@ More details about the derivation of these torques/forces are reported in :ref:`(Tranchida) `. For the *spin/dmi* pair style, the following coefficients must be defined for -each pair of atoms types via the :doc:`pair\_coeff ` command as in +each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` commands, and +:doc:`read_data ` or :doc:`read_restart ` commands, and set in the following order: * rc (distance units) @@ -85,8 +85,8 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`pair\_coeff `, -:doc:`pair\_eam `, +:doc:`atom_style spin `, :doc:`pair_coeff `, +:doc:`pair_eam `, **Default:** none diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index 3bbbed421b..b232649f95 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -72,9 +72,9 @@ More details about the derivation of these torques/forces are reported in :ref:`(Tranchida) `. For the *spin/exchange* pair style, the following coefficients must be defined -for each pair of atoms types via the :doc:`pair\_coeff ` command as in +for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` commands, and +:doc:`read_data ` or :doc:`read_restart ` commands, and set in the following order: * :math:`R_c` (distance units) @@ -104,8 +104,8 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`pair\_coeff `, -:doc:`pair\_eam `, +:doc:`atom_style spin `, :doc:`pair_coeff `, +:doc:`pair_eam `, **Default:** diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 679e13e628..bd5ff51650 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -67,8 +67,8 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`pair\_coeff `, -:doc:`pair\_spin\_exchange `, :doc:`pair\_eam `, +:doc:`atom_style spin `, :doc:`pair_coeff `, +:doc:`pair\_spin\_exchange `, :doc:`pair_eam `, **Default:** none diff --git a/doc/src/pair_spin_neel.rst b/doc/src/pair_spin_neel.rst index ecdb8f30f6..872b40d522 100644 --- a/doc/src/pair_spin_neel.rst +++ b/doc/src/pair_spin_neel.rst @@ -91,8 +91,8 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`pair\_coeff `, -:doc:`pair\_eam `, +:doc:`atom_style spin `, :doc:`pair_coeff `, +:doc:`pair_eam `, **Default:** diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index 1b4e6d3031..057b09e427 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -75,9 +75,9 @@ closest approach of bond *i* and *j*\ . The *mid* option takes *L* as 0.5 for each interaction as described in :ref:`(Sirk) `. The following coefficients must be defined via the -:doc:`pair\_coeff ` command as in the examples above, or in -the data file or restart file read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`pair_coeff ` command as in the examples above, or in +the data file or restart file read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * *C* (force units) * *rc* (distance units) @@ -93,15 +93,15 @@ is used. Any actual existing particles with this atom type will be deleted at the beginning of a run. This means you must specify the number of types in your system accordingly; usually to be one larger than what - would normally be the case, e.g. via the :doc:`create\_box ` + would normally be the case, e.g. via the :doc:`create_box ` or by changing the header in your :doc:`data file `. The fictitious "bond particles" are inserted at the beginning of the run, and serve as placeholders that define the position of the bonds. This allows neighbor lists to be constructed and pairwise interactions to be computed in almost the same way as is done for actual particles. - Because bonds interact only with other bonds, :doc:`pair\_style hybrid ` should be used to turn off interactions + Because bonds interact only with other bonds, :doc:`pair_style hybrid ` should be used to turn off interactions between atom type *bptype* and all other types of atoms. An error - will be flagged if :doc:`pair\_style hybrid ` is not used. + will be flagged if :doc:`pair_style hybrid ` is not used. The optional *exclude* keyword determines if forces are computed between first neighbor (directly connected) bonds. For a setting of @@ -111,7 +111,7 @@ distance calculation because the minimum distance between directly connected bonds is zero. Pair style *srp* turns off normalization of thermodynamic properties -by particle number, as if the command :doc:`thermo\_modify norm no ` had been issued. +by particle number, as if the command :doc:`thermo_modify norm no ` had been issued. The pairwise energy associated with style *srp* is shifted to be zero at the cutoff distance *rc*\ . @@ -124,23 +124,23 @@ at the cutoff distance *rc*\ . This pair styles does not support mixing. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy term is already shifted to be 0.0 at the cutoff distance *rc*\ . -The :doc:`pair\_modify ` table option is not relevant for +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes global and per-atom information to :doc:`binary restart files `. Pair srp should be used with :doc:`pair\_style hybrid `, thus the pair\_coeff commands need to be +This pair style writes global and per-atom information to :doc:`binary restart files `. Pair srp should be used with :doc:`pair_style hybrid `, thus the pair\_coeff commands need to be specified in the input script when reading a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -155,7 +155,7 @@ This pair style is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. -This pair style must be used with :doc:`pair\_style hybrid `. +This pair style must be used with :doc:`pair_style hybrid `. This pair style requires the :doc:`newton ` command to be *on* for non-bonded interactions. @@ -165,7 +165,7 @@ This pair style is not compatible with :doc:`rigid body integrators ` Related commands """""""""""""""" -:doc:`pair\_style hybrid `, :doc:`pair\_coeff `, +:doc:`pair_style hybrid `, :doc:`pair_coeff `, :doc:`pair dpd ` Default diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index ae09daf919..abd551cffb 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -55,7 +55,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of SW elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.sw has Stillinger-Weber values for @@ -192,7 +192,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -200,7 +200,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -226,7 +226,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 202832dfe7..9607f2ab77 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -78,7 +78,7 @@ to index into the table via a fast bit-mapping technique due to adjacent table values. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * filename @@ -95,12 +95,12 @@ table. The format of this file is described below. If your tabulated potential(s) are designed to be used as the short-range part of one of the long-range solvers specified by the -:doc:`kspace\_style ` command, then you must use one or +:doc:`kspace_style ` command, then you must use one or more of the optional keywords listed above for the pair\_style command. These are *ewald* or *pppm* or *msm* or *dispersion* or *tip4p*\ . This is so LAMMPS can insure the short-range potential and long-range solver are compatible with each other, as it does for other -short-range pair styles, such as :doc:`pair\_style lj/cut/coul/long `. Note that it is up to you to insure +short-range pair styles, such as :doc:`pair_style lj/cut/coul/long `. Note that it is up to you to insure the tabulated values for each pair of atom types has the correct functional form to be compatible with the matching long-range solver. @@ -113,7 +113,7 @@ best effect: * Vary the number of table points; you may need to use more than you think to get good resolution. -* Always use the :doc:`pair\_write ` command to produce a plot +* Always use the :doc:`pair_write ` command to produce a plot of what the final interpolated potential looks like. This can show up interpolation "features" you may not like. * Start with the linear style; it's the style least likely to have problems. @@ -158,7 +158,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair\_style table ` command. Let +specified in the :doc:`pair_style table ` command. Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It @@ -200,7 +200,7 @@ If used, the parameter "BITMAP" is also followed by 2 values *rlo* and *rhi*\ . These values, along with the "N" value determine the ordering of the N lines that follow and what distance is associated with each. This ordering is complex, so it is not documented here, since this -file is typically produced by the :doc:`pair\_write ` command +file is typically produced by the :doc:`pair_write ` command with its *bitmap* option. When the table is in BITMAP format, the "N" parameter in the file must be equal to 2\^M where M is the value specified in the pair\_style command. Also, a cutoff parameter cannot @@ -256,7 +256,7 @@ instructions on how to use the accelerated styles effectively. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -The :doc:`pair\_modify ` shift, table, and tail options are +The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. This pair style writes the settings for the "pair\_style table" command @@ -267,7 +267,7 @@ file, since it is tabulated in the potential files. Thus, pair\_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -281,7 +281,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_write ` +:doc:`pair_coeff `, :doc:`pair_write ` **Default:** none diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index e04f12e715..616dbb3da0 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -42,7 +42,7 @@ one CG particle can interact with a species in a neighboring CG particle through a site-site interaction potential model. Style *table/rx* creates interpolation tables of length *N* from pair potential and force values listed in a file(s) as a function of -distance. The files are read by the :doc:`pair\_coeff ` +distance. The files are read by the :doc:`pair_coeff ` command. The interpolation tables are created by fitting cubic splines to the @@ -69,7 +69,7 @@ table via a fast bit-mapping technique :ref:`(Wolff) ` and a linear interpolation is performed between adjacent table values. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * filename @@ -108,7 +108,7 @@ best effect: * Vary the number of table points; you may need to use more than you think to get good resolution. -* Always use the :doc:`pair\_write ` command to produce a plot +* Always use the :doc:`pair_write ` command to produce a plot of what the final interpolated potential looks like. This can show up interpolation "features" you may not like. * Start with the linear style; it's the style least likely to have problems. @@ -152,7 +152,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair\_style table/rx ` command. Let +specified in the :doc:`pair_style table/rx ` command. Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It @@ -184,7 +184,7 @@ If used, the parameter "BITMAP" is also followed by 2 values *rlo* and *rhi*\ . These values, along with the "N" value determine the ordering of the N lines that follow and what distance is associated with each. This ordering is complex, so it is not documented here, since this -file is typically produced by the :doc:`pair\_write ` command +file is typically produced by the :doc:`pair_write ` command with its *bitmap* option. When the table is in BITMAP format, the "N" parameter in the file must be equal to 2\^M where M is the value specified in the pair\_style command. Also, a cutoff parameter cannot @@ -218,7 +218,7 @@ one that matches the specified keyword. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -The :doc:`pair\_modify ` shift, table, and tail options are +The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. This pair style writes the settings for the "pair\_style table/rx" command @@ -229,7 +229,7 @@ file, since it is tabulated in the potential files. Thus, pair\_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -268,7 +268,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** fractional weighting diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 773ee649df..071fc6c084 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -72,7 +72,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of Tersoff elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine the SiC.tersoff file has Tersoff values for Si @@ -227,7 +227,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -235,7 +235,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -261,7 +261,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index 15cce523f7..d0ba8770be 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -173,7 +173,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -181,7 +181,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -207,7 +207,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index fecc22c31a..4b9fc25918 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -70,7 +70,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of Tersoff/ZBL elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values @@ -231,7 +231,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -239,7 +239,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -266,7 +266,7 @@ units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 8f4bac0182..9f8cb67714 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -103,14 +103,14 @@ is not applied to the full charge of the core particle :math:`q_i`, but only to the :math:`-q_{D,i}` part of it. The interactions between core charges are subject to the weighting -factors set by the :doc:`special\_bonds ` command. The +factors set by the :doc:`special_bonds ` command. The interactions between Drude particles and core charges or non-polarizable atoms are also subject to these weighting factors. The Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from their respective cores. For pair\_style *thole*\ , the following coefficients must be defined for -each pair of atoms types via the :doc:`pair\_coeff ` command +each pair of atoms types via the :doc:`pair_coeff ` command as in the example above. * alpha (distance units\^3) @@ -123,7 +123,7 @@ command are used. In order to specify a cutoff (third argument) a damp parameter (second argument) must also be specified. For pair style *lj/cut/thole/long*\ , the following coefficients must be -defined for each pair of atoms types via the :doc:`pair\_coeff ` +defined for each pair of atoms types via the :doc:`pair_coeff ` command. * epsilon (energy units) @@ -194,7 +194,7 @@ Related commands """""""""""""""" :doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude ` -:doc:`pair\_style lj/cut/coul/long ` +:doc:`pair_style lj/cut/coul/long ` **Default:** none diff --git a/doc/src/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst index 350f9c0617..b9590a02a8 100644 --- a/doc/src/pair_tri_lj.rst +++ b/doc/src/pair_tri_lj.rst @@ -32,7 +32,7 @@ Interactions between two triangles, each with N1 and N2 spherical particles, are calculated as the pairwise sum of N1\*N2 Lennard-Jones interactions. Interactions between a triangle with N spherical particles and a point particle are treated as the pairwise sum of N -Lennard-Jones interactions. See the :doc:`pair\_style lj/cut ` +Lennard-Jones interactions. See the :doc:`pair_style lj/cut ` doc page for the definition of Lennard-Jones interactions. The cutoff distance for an interaction between 2 triangles, or between @@ -69,9 +69,9 @@ means that any specified sigma\_IJ values (for I != J) are effectively ignored. For style *tri/lj*\ , the following coefficients must be defined for -each pair of atoms types via the :doc:`pair\_coeff ` command +each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by -the :doc:`read\_data ` or :doc:`read\_restart ` +the :doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (energy units) @@ -92,13 +92,13 @@ and cutoff distance for all of this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -113,12 +113,12 @@ This style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Defining particles to be triangles so they participate in tri/tri or -tri/particle interactions requires the use the :doc:`atom\_style tri ` command. +tri/particle interactions requires the use the :doc:`atom_style tri ` command. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style line/lj ` +:doc:`pair_coeff `, :doc:`pair_style line/lj ` **Default:** none diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index 318762bb4b..1656720fd1 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -50,9 +50,9 @@ to control the softness of the interactions :ref:`(Paula Leite2017) `. This model is useful as a reference system for fluid-phase free-energy calculations :ref:`(Paula Leite2016) `. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -112,18 +112,18 @@ distance for this pair style can be mixed. A is always mixed via a mix value. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style support the :doc:`pair\_modify ` shift option for the energy of the pair interaction. +This pair style support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table and tail are not relevant for this +The :doc:`pair_modify ` table and tail are not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` tail option for adding long-range tail corrections to energy and pressure. +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -137,7 +137,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix adapt ` +:doc:`pair_coeff `, :doc:`fix adapt ` **Default:** none diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index c4c8a6c9f5..58baf53143 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -95,7 +95,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of Vashishta elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.vashishta has parameters for @@ -220,7 +220,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -228,7 +228,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -254,7 +254,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 17be08f29a..eff77b4d68 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -40,7 +40,7 @@ file. The energy and force values are computed at distances from inner to outer for 2 interacting atoms of type itype and jtype, using the -appropriate :doc:`pair\_coeff ` coefficients. If the style +appropriate :doc:`pair_coeff ` coefficients. If the style is *r*\ , then N distances are used, evenly spaced in r; if the style is *rsq*\ , N distances are used, evenly spaced in r\^2. @@ -49,7 +49,7 @@ values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. If the style is *bitmap*\ , then 2\^N values are written to the file in a format and order consistent with how they are read in by the -:doc:`pair\_coeff ` command for pair style *table*\ . For +:doc:`pair_coeff ` command for pair style *table*\ . For reasonable accuracy in a bitmapped table, choose N >= 12, an *inner* value that is smaller than the distance of closest approach of 2 atoms, and an *outer* value <= cutoff of the potential. @@ -59,7 +59,7 @@ of the pair of interacting atoms can optionally be specified. If not specified, values of Qi = Qj = 1.0 are used. The file is written in the format used as input for the -:doc:`pair\_style ` *table* option with *keyword* as the +:doc:`pair_style ` *table* option with *keyword* as the section name. Each line written to the file lists an index number (1-N), a distance (in distance units), an energy (in energy units), and a force (in force units). @@ -80,8 +80,8 @@ pairwise portion of the potential, not the embedding portion. Related commands """""""""""""""" -:doc:`pair\_style table `, -:doc:`pair\_style `, :doc:`pair\_coeff ` +:doc:`pair_style table `, +:doc:`pair_style `, :doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 14cec88d2e..a4a96b15c3 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -44,9 +44,9 @@ Style *yukawa* computes pairwise interactions with the formula Rc is the cutoff. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy\*distance units) @@ -88,13 +88,13 @@ distance for this pair style can be mixed. A is an energy value mixed like a LJ epsilon. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -102,7 +102,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -116,7 +116,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index b46f8fc704..74fa1e7e78 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -41,7 +41,7 @@ Style *yukawa/colloid* computes pairwise interactions with the formula where Ri and Rj are the radii of the two particles and Rc is the cutoff. -In contrast to :doc:`pair\_style yukawa `, this functional +In contrast to :doc:`pair_style yukawa `, this functional form arises from the Coulombic interaction between two colloid particles, screened due to the presence of an electrolyte, see the book by :ref:`Safran ` for a derivation in the context of DLVO @@ -52,14 +52,14 @@ This potential applies to nearby particle pairs for which the Derjagin approximation holds, meaning h << Ri + Rj, where h is the surface-to-surface separation of the two particles. -When used in combination with :doc:`pair\_style colloid `, +When used in combination with :doc:`pair_style colloid `, the two terms become the so-called DLVO potential, which combines electrostatic repulsion and van der Waals attraction. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy/distance units) @@ -68,7 +68,7 @@ commands, or by mixing as described below: The prefactor A is determined from the relationship between surface charge and surface potential due to the presence of electrolyte. Note that the A for this potential style has different units than the A -used in :doc:`pair\_style yukawa `. For low surface +used in :doc:`pair_style yukawa `. For low surface potentials, i.e. less than about 25 mV, A can be written as: @@ -120,13 +120,13 @@ distance for this pair style can be mixed. A is an energy value mixed like a LJ epsilon. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -134,7 +134,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -149,7 +149,7 @@ This style is part of the COLLOID package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This pair style requires that atoms be finite-size spheres with a -diameter, as defined by the :doc:`atom\_style sphere ` +diameter, as defined by the :doc:`atom_style sphere ` command. Per-particle polydispersity is not yet supported by this pair style; @@ -160,7 +160,7 @@ diameter. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index 6bb485ee8a..4d08418ce8 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -49,11 +49,11 @@ energy due to a pair of atoms at a distance r\_ij is given by: where e is the electron charge, epsilon\_0 is the electrical permittivity of vacuum, and Z\_i and Z\_j are the nuclear charges of the two atoms. The switching function S(r) is identical to that used by -:doc:`pair\_style lj/gromacs `. Here, the inner and outer +:doc:`pair_style lj/gromacs `. Here, the inner and outer cutoff are the same for all pairs of atom types. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the LAMMPS data file. * Z\_i (atomic number for first atom type, e.g. 13.0 for aluminum) @@ -115,17 +115,17 @@ with :doc:`hybrid/overlay ` and pairs are assigned to more than one sub-style, the mixing rule is not used and each pair of types interacting with the ZBL sub-style must be included in a pair\_coeff command. -The :doc:`pair\_modify ` mix option has no effect on +The :doc:`pair_modify ` mix option has no effect on the mixing behavior -The ZBL pair style does not support the :doc:`pair\_modify ` +The ZBL pair style does not support the :doc:`pair_modify ` shift option, since the ZBL interaction is already smoothed to 0.0 at the cutoff. -The :doc:`pair\_modify ` table option is not relevant for +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since there are no corrections for a potential that goes to 0.0 at the cutoff. @@ -134,7 +134,7 @@ This pair style does not write information to :doc:`binary restart files ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -148,7 +148,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_zero.rst b/doc/src/pair_zero.rst index 6afafc2017..18afdbf355 100644 --- a/doc/src/pair_zero.rst +++ b/doc/src/pair_zero.rst @@ -38,7 +38,7 @@ to enumerate pairs of atoms within some cutoff distance, but when pairwise forces are not otherwise needed. Examples are the :doc:`fix bond/create `, :doc:`compute rdf `, :doc:`compute voronoi/atom ` commands. -Note that the :doc:`comm\_modify cutoff ` command can be +Note that the :doc:`comm_modify cutoff ` command can be used to insure communication of ghost atoms even when a pair style is not defined, but it will not trigger neighbor list generation. @@ -48,9 +48,9 @@ will only be checked for the atom type numbers and the rest ignored. In this case, only the global cutoff will be used. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutoff (distance units) @@ -69,14 +69,14 @@ pair coefficient is ignored. The cutoff distance for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , -and *outer* keywords of the :doc:`run\_style respa ` command. +and *outer* keywords of the :doc:`run_style respa ` command. ---------- @@ -89,7 +89,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_style none ` +:doc:`pair_style none ` **Default:** none diff --git a/doc/src/partition.rst b/doc/src/partition.rst index e238e7c60d..7ee6d76f3c 100644 --- a/doc/src/partition.rst +++ b/doc/src/partition.rst @@ -72,7 +72,7 @@ Restrictions Related commands """""""""""""""" -:doc:`run\_style verlet/split ` +:doc:`run_style verlet/split ` **Default:** none diff --git a/doc/src/prd.rst b/doc/src/prd.rst index 5ea3db6121..a53f8d561e 100644 --- a/doc/src/prd.rst +++ b/doc/src/prd.rst @@ -145,9 +145,9 @@ The first time through the PRD loop, the "previous basin" is the set of quenched coordinates from the initial state of the system. A quench is an energy minimization and is performed by whichever -algorithm has been defined by the :doc:`min\_style ` command. +algorithm has been defined by the :doc:`min_style ` command. Minimization parameters may be set via the -:doc:`min\_modify ` command and by the *min* keyword of the +:doc:`min_modify ` command and by the *min* keyword of the PRD command. The latter are the settings that would be used with the :doc:`minimize ` command. Note that typically, you do not need to perform a highly-converged minimization to detect a transition @@ -337,8 +337,8 @@ Related commands """""""""""""""" :doc:`compute event/displace `, -:doc:`min\_modify `, :doc:`min\_style `, -:doc:`run\_style `, :doc:`minimize `, +:doc:`min_modify `, :doc:`min_style `, +:doc:`run_style `, :doc:`minimize `, :doc:`velocity `, :doc:`temper `, :doc:`neb `, :doc:`tad `, :doc:`hyper ` diff --git a/doc/src/processors.rst b/doc/src/processors.rst index a13b44330c..6f593ffc6a 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -107,11 +107,11 @@ different processor grids for different partitions, e.g. This command only affects the initial regular 3d grid created when the simulation box is first specified via a - :doc:`create\_box ` or :doc:`read\_data ` or - :doc:`read\_restart ` command. Or if the simulation box is + :doc:`create_box ` or :doc:`read_data ` or + :doc:`read_restart ` command. Or if the simulation box is re-created via the :doc:`replicate ` command. The same regular grid is initially created, regardless of which - :doc:`comm\_style ` command is in effect. + :doc:`comm_style ` command is in effect. If load-balancing is never invoked via the :doc:`balance ` or :doc:`fix balance ` commands, then the initial regular grid @@ -120,7 +120,7 @@ the methods invoked by those commands retain the logical topology of the initial 3d grid, and the mapping of processors to the grid specified by the processors command. However the grid spacings in different dimensions may change, so that processors own sub-domains of -different sizes. If the :doc:`comm\_style tiled ` command is +different sizes. If the :doc:`comm_style tiled ` command is used, methods invoked by the balancing commands may discard the 3d grid of processors and tile the simulation domain with sub-domains of different sizes and shapes which no longer have a logical 3d @@ -274,7 +274,7 @@ styles are not supported, so an *xyz* style is used in their place. The *part* keyword affects the factorization of P into Px,Py,Pz. It can be useful when running in multi-partition mode, e.g. with the -:doc:`run\_style verlet/split ` command. It specifies a +:doc:`run_style verlet/split ` command. It specifies a dependency between a sending partition *Psend* and a receiving partition *Precv* which is enforced when each is setting up their own mapping of their processors to the simulation box. Each of *Psend* @@ -292,7 +292,7 @@ constraint. The nature of the constraint is determined by the For a *cstyle* of *multiple*\ , each dimension of the sender's processor grid is required to be an integer multiple of the corresponding dimension in the receiver's processor grid. This is a requirement of -the :doc:`run\_style verlet/split ` command. +the :doc:`run_style verlet/split ` command. For example, assume the sending partition creates a 4x6x10 grid = 240 processor grid. If the receiving partition is running on 80 @@ -358,7 +358,7 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. It can be used before a restart file is read to change the 3d processor grid from what is specified in the restart file. diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 798f95e5ec..59ce92ca34 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -68,8 +68,8 @@ Description Read in a data file containing information LAMMPS needs to run a simulation. The file can be ASCII text or a gzipped text file (detected by a .gz suffix). This is one of 3 ways to specify initial -atom coordinates; see the :doc:`read\_restart ` and -:doc:`create\_atoms ` commands for alternative methods. +atom coordinates; see the :doc:`read_restart ` and +:doc:`create_atoms ` commands for alternative methods. Also see the explanation of the :doc:`-restart command-line switch ` which can convert a restart file to a data file. @@ -83,7 +83,7 @@ specified group-ID. The group will be created if it does not already exist. This is useful if you are reading multiple data files and wish to put sets of atoms into different groups so they can be operated on later. E.g. a group of added atoms can be moved to new positions via -the :doc:`displace\_atoms ` command. Note that atoms +the :doc:`displace_atoms ` command. Note that atoms read from the data file are also always added to the "all" group. The :doc:`group ` command discusses atom groups, as used in LAMMPS. @@ -107,7 +107,7 @@ contained in individual data files. For example one data file could contain fluid in a confined domain; a second could contain wall atoms, and the second file could be read a third time to create a wall on the other side of the fluid. The third set of atoms could be rotated to -an opposing direction using the :doc:`displace\_atoms ` +an opposing direction using the :doc:`displace_atoms ` command, after the third read\_data command is used. The *add*\ , *offset*\ , *shift*\ , *extra*\ , and *group* keywords are @@ -116,7 +116,7 @@ useful in this context. If a simulation box does not yet exist, the *add* keyword cannot be used; the read\_data command is being used for the first time. If a simulation box does exist, due to using the -:doc:`create\_box ` command, or a previous read\_data command, +:doc:`create_box ` command, or a previous read\_data command, then the *add* keyword must be used. .. note:: @@ -175,9 +175,9 @@ for a 2d simulation. This is a mechanism for adding structured collections of atoms at different locations within the simulation box, to build up a complex geometry. It is up to you to insure atoms do not end up overlapping unphysically which would lead to bad dynamics. -Note that the :doc:`displace\_atoms ` command can be used +Note that the :doc:`displace_atoms ` command can be used to move a subset of atoms after they have been read from a data file. -Likewise, the :doc:`delete\_atoms ` command can be used to +Likewise, the :doc:`delete_atoms ` command can be used to remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are also added to the simulation box information (xlo, xhi, ylo, yhi, zlo, zhi) in the data file to shift its boundaries. E.g. xlo\_new = xlo + @@ -212,7 +212,7 @@ interactions in your input script to have a complete pairwise interaction model. An alternative to using the *extra* keywords with the read\_data -command, is to use the :doc:`create\_box ` command to +command, is to use the :doc:`create_box ` command to initialize the simulation box and all the various type limits you need via its *extra* keywords. Then use the read\_data command one or more times to populate the system with atoms, bonds, angles, etc, using the @@ -408,7 +408,7 @@ molecules defined in the data file. Using this header flag is deprecated; please use the *extra/special/per/atom* keyword instead. Using this setting will pre-allocate space in the LAMMPS data structures for storing these neighbors. See the -:doc:`special\_bonds ` and :doc:`molecule ` doc +:doc:`special_bonds ` and :doc:`molecule ` doc pages for more discussion of 1-2,1-3,1-4 neighbors. .. note:: @@ -421,7 +421,7 @@ pages for more discussion of 1-2,1-3,1-4 neighbors. If they appear in later data files, they are ignored. The "ellipsoids" and "lines" and "triangles" and "bodies" settings are -only used with :doc:`atom\_style ellipsoid or line or tri or body ` and specify how many of the atoms are +only used with :doc:`atom_style ellipsoid or line or tri or body ` and specify how many of the atoms are finite-size ellipsoids or lines or triangles or bodies; the remainder are point particles. See the discussion of ellipsoidflag and the *Ellipsoids* section below. See the discussion of lineflag and the @@ -431,7 +431,7 @@ are point particles. See the discussion of ellipsoidflag and the .. note:: - For :doc:`atom\_style template `, the molecular + For :doc:`atom_style template `, the molecular topology (bonds,angles,etc) is contained in the molecule templates read-in by the :doc:`molecule ` command. This means you cannot set the *bonds*\ , *angles*\ , etc header keywords in the data @@ -466,8 +466,8 @@ For example, these lines: Atoms # sphere Pair Coeffs # lj/cut -will check if the currently-defined :doc:`atom\_style ` is -*sphere*\ , and the current :doc:`pair\_style ` is *lj/cut*\ . +will check if the currently-defined :doc:`atom_style ` is +*sphere*\ , and the current :doc:`pair_style ` is *lj/cut*\ . If not, LAMMPS will issue a warning to indicate that the data file section likely does not contain the correct number or type of parameters expected for the currently-defined style. @@ -508,9 +508,9 @@ Atoms section: The number and meaning of the coefficients are specific to the defined -angle style. See the :doc:`angle\_style ` and -:doc:`angle\_coeff ` commands for details. Coefficients can -also be set via the :doc:`angle\_coeff ` command in the +angle style. See the :doc:`angle_style ` and +:doc:`angle_coeff ` commands for details. Coefficients can +also be set via the :doc:`angle_coeff ` command in the input script. @@ -702,7 +702,7 @@ in dump files. Normally, it is a unique value from 1 to Natoms for each atom. Unique values larger than Natoms can be used, but they will cause extra memory to be allocated on each processor, if an atom map array is used, but not if an atom map hash is used; see the -:doc:`atom\_modify ` command for details. If an atom map is +:doc:`atom_modify ` command for details. If an atom map is not used (e.g. an atomic system with no bonds), and you don't care if unique atom IDs appear in dump files, then the atom-IDs can all be set to 0. @@ -723,7 +723,7 @@ triangle, or body in the corresponding *Ellipsoids*\ , *Lines*\ , *Triangles*\ , or *Bodies* section. The *template-index* and *template-atom* are only defined used by -:doc:`atom\_style template `. In this case the +:doc:`atom_style template `. In this case the :doc:`molecule ` command is used to define a molecule template which contains one or more molecules. If an atom belongs to one of those molecules, its *template-index* and *template-atom* are both set @@ -757,7 +757,7 @@ discs (not 3d spheres), by changing their moment of inertia. For atom\_style hybrid, following the 5 initial values (ID,type,x,y,z), specific values for each sub-style must be listed. The order of the sub-styles is the same as they were listed in the -:doc:`atom\_style ` command. The sub-style specific values +:doc:`atom_style ` command. The sub-style specific values are those that are not the 5 standard ones (ID,type,x,y,z). For example, for the "charge" sub-style, a "q" value would appear. For the "full" sub-style, a "molecule-ID" and "q" would appear. These are @@ -875,7 +875,7 @@ script. -The *Bodies* section must appear if :doc:`atom\_style body ` +The *Bodies* section must appear if :doc:`atom_style body ` is used and any atoms listed in the *Atoms* section have a bodyflag = 1. The number of bodies should be specified in the header section via the "bodies" keyword. @@ -883,7 +883,7 @@ the "bodies" keyword. Each body can have a variable number of integer and/or floating-point values. The number and meaning of the values is defined by the body style, as described in the :doc:`Howto body ` doc page. The -body style is given as an argument to the :doc:`atom\_style body ` command. +body style is given as an argument to the :doc:`atom_style body ` command. The Ninteger and Ndouble values determine how many integer and floating-point values are specified for this particle. Ninteger and @@ -919,9 +919,9 @@ The *Bodies* section must appear after the *Atoms* section. The number and meaning of the coefficients are specific to the defined -bond style. See the :doc:`bond\_style ` and -:doc:`bond\_coeff ` commands for details. Coefficients can -also be set via the :doc:`bond\_coeff ` command in the input +bond style. See the :doc:`bond_style ` and +:doc:`bond_coeff ` commands for details. Coefficients can +also be set via the :doc:`bond_coeff ` command in the input script. @@ -1021,10 +1021,10 @@ in this section must be integers (1, not 1.0). The number and meaning of the coefficients are specific to the defined -dihedral style. See the :doc:`dihedral\_style ` and -:doc:`dihedral\_coeff ` commands for details. +dihedral style. See the :doc:`dihedral_style ` and +:doc:`dihedral_coeff ` commands for details. Coefficients can also be set via the -:doc:`dihedral\_coeff ` command in the input script. +:doc:`dihedral_coeff ` command in the input script. ---------- @@ -1076,7 +1076,7 @@ section must be integers (1, not 1.0). -The *Ellipsoids* section must appear if :doc:`atom\_style ellipsoid ` is used and any atoms are listed in the +The *Ellipsoids* section must appear if :doc:`atom_style ellipsoid ` is used and any atoms are listed in the *Atoms* section with an ellipsoidflag = 1. The number of ellipsoids should be specified in the header section via the "ellipsoids" keyword. @@ -1138,10 +1138,10 @@ The *Ellipsoids* section must appear after the *Atoms* section. The number and meaning of the coefficients are specific to the defined -improper style. See the :doc:`improper\_style ` and -:doc:`improper\_coeff ` commands for details. +improper style. See the :doc:`improper_style ` and +:doc:`improper_coeff ` commands for details. Coefficients can also be set via the -:doc:`improper\_coeff ` command in the input script. +:doc:`improper_coeff ` command in the input script. ---------- @@ -1196,7 +1196,7 @@ values in this section must be integers (1, not 1.0). -The *Lines* section must appear if :doc:`atom\_style line ` +The *Lines* section must appear if :doc:`atom_style line ` is used and any atoms are listed in the *Atoms* section with a lineflag = 1. The number of lines should be specified in the header section via the "lines" keyword. @@ -1235,7 +1235,7 @@ The *Lines* section must appear after the *Atoms* section. This defines the mass of each atom type. This can also be set via the :doc:`mass ` command in the input script. This section cannot be used for atom styles that define a mass for individual atoms - -e.g. :doc:`atom\_style sphere `. +e.g. :doc:`atom_style sphere `. ---------- @@ -1276,12 +1276,12 @@ e.g. :doc:`atom\_style sphere `. The number and meaning of the coefficients are specific to the defined -pair style. See the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands for details. Since pair +pair style. See the :doc:`pair_style ` and +:doc:`pair_coeff ` commands for details. Since pair coefficients for types I != J are not specified, these will be generated automatically by the pair style's mixing rule. See the -individual pair\_style doc pages and the :doc:`pair\_modify mix ` command for details. Pair coefficients can also -be set via the :doc:`pair\_coeff ` command in the input +individual pair\_style doc pages and the :doc:`pair_modify mix ` command for details. Pair coefficients can also +be set via the :doc:`pair_coeff ` command in the input script. @@ -1310,12 +1310,12 @@ script. This section must have N\*(N+1)/2 lines where N = # of atom types. The number and meaning of the coefficients are specific to the defined -pair style. See the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands for details. Since pair +pair style. See the :doc:`pair_style ` and +:doc:`pair_coeff ` commands for details. Since pair coefficients for types I != J are all specified, these values will turn off the default mixing rule defined by the pair style. See the -individual pair\_style doc pages and the :doc:`pair\_modify mix ` command for details. Pair coefficients can also -be set via the :doc:`pair\_coeff ` command in the input +individual pair\_style doc pages and the :doc:`pair_modify mix ` command for details. Pair coefficients can also +be set via the :doc:`pair_coeff ` command in the input script. @@ -1342,7 +1342,7 @@ script. -The *Triangles* section must appear if :doc:`atom\_style tri ` is used and any atoms are listed in the *Atoms* +The *Triangles* section must appear if :doc:`atom_style tri ` is used and any atoms are listed in the *Atoms* section with a triangleflag = 1. The number of lines should be specified in the header section via the "triangles" keyword. @@ -1394,7 +1394,7 @@ Wz are in units of angular velocity (radians/time). For atom\_style hybrid, following the 4 initial values (ID,vx,vy,vz), specific values for each sub-style must be listed. The order of the sub-styles is the same as they were listed in the -:doc:`atom\_style ` command. The sub-style specific values +:doc:`atom_style ` command. The sub-style specific values are those that are not the 5 standard ones (ID,vx,vy,vz). For example, for the "sphere" sub-style, "wx", "wy", "wz" values would appear. These are listed in the same order they appear as listed @@ -1431,8 +1431,8 @@ doc page for details. Related commands """""""""""""""" -:doc:`read\_dump `, :doc:`read\_restart `, -:doc:`create\_atoms `, :doc:`write\_data ` +:doc:`read_dump `, :doc:`read_restart `, +:doc:`create_atoms `, :doc:`write_data ` Default """"""" diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index de81a98276..030d55f25a 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -78,15 +78,15 @@ Read atom information from a dump file to overwrite the current atom coordinates, and optionally the atom velocities and image flags and the simulation box dimensions. This is useful for restarting a run from a particular snapshot in a dump file. See the -:doc:`read\_restart ` and :doc:`read\_data ` +:doc:`read_restart ` and :doc:`read_data ` commands for alternative methods to do this. Also see the :doc:`rerun ` command for a means of reading multiple snapshots from a dump file. Note that a simulation box must already be defined before using the read\_dump command. This can be done by the -:doc:`create\_box `, :doc:`read\_data `, or -:doc:`read\_restart ` commands. The read\_dump command can +:doc:`create_box `, :doc:`read_data `, or +:doc:`read_restart ` commands. The read\_dump command can reset the simulation box dimensions, as explained below. Also note that reading per-atom information from a dump snapshot is @@ -95,7 +95,7 @@ explained below. Other atom properties, which may be necessary to run a valid simulation, such as atom charge, or bond topology information for a molecular system, are not read from (or even contained in) dump files. Thus this auxiliary information should be defined in the usual -way, e.g. in a data file read in by a :doc:`read\_data ` +way, e.g. in a data file read in by a :doc:`read_data ` command, before using the read\_dump command, or by the :doc:`set ` command, after the dump snapshot is read. @@ -247,7 +247,7 @@ supported. The dump file does not store atom IDs, so these are assigned consecutively to the atoms as they appear in the dump file, starting from 1. Thus you should insure that order of atoms is consistent from snapshot to snapshot in the XYZ dump file. See -the :doc:`dump\_modify sort ` command if the XYZ dump file +the :doc:`dump_modify sort ` command if the XYZ dump file was written by LAMMPS. For dump files in *molfile* format, the *x*\ , *y*\ , *z*\ , *vx*\ , *vy*\ , and @@ -257,7 +257,7 @@ velocities. The molfile dump files do not store atom IDs, so these are assigned consecutively to the atoms as they appear in the dump file, starting from 1. Thus you should insure that order of atoms are consistent from snapshot to snapshot in the molfile dump file. -See the :doc:`dump\_modify sort ` command if the dump file +See the :doc:`dump_modify sort ` command if the dump file was written by LAMMPS. The *adios* format supports all fields that the *native* format supports @@ -282,7 +282,7 @@ for how this is done, determined by the specified fields and optional keywords. The timestep of the snapshot becomes the current timestep for the -simulation. See the :doc:`reset\_timestep ` command if +simulation. See the :doc:`reset_timestep ` command if you wish to change this after the dump snapshot is read. If the *box* keyword is specified with a *yes* value, then the current @@ -312,7 +312,7 @@ added to the system. They are simply ignored. If a *yes* value is specified, the atoms with new IDs are added to the system but their atom IDs are not preserved. Instead, after all the atoms are added, new IDs are assigned to them in the same manner as is -described for the :doc:`create\_atoms ` command. Basically +described for the :doc:`create_atoms ` command. Basically the largest existing atom ID in the system is identified, and all the added atoms are assigned IDs that consecutively follow the largest ID. @@ -328,7 +328,7 @@ type, so this value must appear in the dump file. Any other attributes (e.g. charge or particle diameter for spherical particles) will be set to default values, the same as if the -:doc:`create\_atoms ` command were used. +:doc:`create_atoms ` command were used. ---------- @@ -406,7 +406,7 @@ Related commands :doc:`dump `, :doc:`dump molfile `, :doc:`dump adios `, -:doc:`read\_data `, :doc:`read\_restart `, +:doc:`read_data `, :doc:`read_restart `, :doc:`rerun ` Default diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index 44210a3a70..321b533acb 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -44,7 +44,7 @@ changed by the :doc:`balance ` or :doc:`fix balance ` comm .. note:: Normally, restart files are written by the - :doc:`restart ` or :doc:`write\_restart ` commands + :doc:`restart ` or :doc:`write_restart ` commands so that all atoms in the restart file are inside the simulation box. If this is not the case, the read\_restart command will print an error that atoms were "lost" when the file is read. This error should be @@ -86,7 +86,7 @@ Because restart files are binary, they may not be portable to other machines. In this case, you can use the :doc:`-restart command-line switch ` to convert a restart file to a data file. Similar to how restart files are written (see the -:doc:`write\_restart ` and :doc:`restart ` +:doc:`write_restart ` and :doc:`restart ` commands), the restart filename can contain two wild-card characters. If a "\*" appears in the filename, the directory is searched for all filenames that match the pattern where "\*" is replaced with a timestep @@ -98,7 +98,7 @@ the run command so it doesn't need to be changed either. If a "%" character appears in the restart filename, LAMMPS expects a set of multiple files to exist. The :doc:`restart ` and -:doc:`write\_restart ` commands explain how such sets are +:doc:`write_restart ` commands explain how such sets are created. Read\_restart will first read a filename where "%" is replaced by "base". This file tells LAMMPS how many processors created the set and how many files are in it. Read\_restart then reads @@ -110,7 +110,7 @@ processors that created the restart file. Note that P could be the total number of processors in the previous simulation, or some subset of those processors, if the *fileper* or *nfile* options were used when the restart file was written; see the -:doc:`restart ` and :doc:`write\_restart ` commands +:doc:`restart ` and :doc:`write_restart ` commands for details. The processors in the current LAMMPS simulation share the work of reading these files; each reads a roughly equal subset of the files. The number of processors which created the set can be @@ -146,8 +146,8 @@ these settings after the restart file is read. * :doc:`units ` * :doc:`newton bond ` (see discussion of newton command below) -* :doc:`atom style ` and :doc:`atom\_modify ` settings id, map, sort -* :doc:`comm style ` and :doc:`comm\_modify ` settings mode, cutoff, vel +* :doc:`atom style ` and :doc:`atom_modify ` settings id, map, sort +* :doc:`comm style ` and :doc:`comm_modify ` settings mode, cutoff, vel * :doc:`timestep ` * simulation box size and shape and :doc:`boundary ` settings * atom :doc:`group ` definitions @@ -155,8 +155,8 @@ these settings after the restart file is read. * per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc) * force field styles (:doc:`pair `, :doc:`bond `, :doc:`angle `, etc) * force field coefficients (:doc:`pair `, :doc:`bond `, :doc:`angle `, etc) in some cases (see below) -* :doc:`pair\_modify ` settings, except the compute option -* :doc:`special\_bonds ` settings +* :doc:`pair_modify ` settings, except the compute option +* :doc:`special_bonds ` settings Here is a list of information not stored in a restart file, which means you must re-issue these commands in your input script, after @@ -167,8 +167,8 @@ reading the restart file. * :doc:`compute ` commands (see below) * :doc:`variable ` commands * :doc:`region ` commands -* :doc:`neighbor list ` criteria including :doc:`neigh\_modify ` settings -* :doc:`kspace\_style ` and :doc:`kspace\_modify ` settings +* :doc:`neighbor list ` criteria including :doc:`neigh_modify ` settings +* :doc:`kspace_style ` and :doc:`kspace_modify ` settings * info for :doc:`thermodynamic `, :doc:`dump `, or :doc:`restart ` output The :doc:`newton ` command has two settings, one for pairwise @@ -185,10 +185,10 @@ Note that some force field styles (pair, bond, angle, etc) do not store their coefficient info in restart files. Typically these are many-body or tabulated potentials which read their parameters from separate files. In these cases you will need to re-specify the -:doc:`pair\_coeff `, :doc:`bond\_coeff `, etc +:doc:`pair_coeff `, :doc:`bond_coeff `, etc commands in your restart input script. The doc pages for individual force field styles mention if this is the case. This is also true of -:doc:`pair\_style hybrid ` (bond hybrid, angle hybrid, etc) +:doc:`pair_style hybrid ` (bond hybrid, angle hybrid, etc) commands; they do not store coefficient info. As indicated in the above list, the :doc:`fixes ` used for a @@ -250,7 +250,7 @@ LAMMPS allows bond interactions (angle, etc) to be turned off or deleted in various ways, which can affect how their info is stored in a restart file. -If bonds (angles, etc) have been turned off by the :doc:`fix shake ` or :doc:`delete\_bonds ` command, +If bonds (angles, etc) have been turned off by the :doc:`fix shake ` or :doc:`delete_bonds ` command, their info will be written to a restart file as if they are turned on. This means they will need to be turned off again in a new run after the restart file is read. @@ -277,8 +277,8 @@ package must be installed. Related commands """""""""""""""" -:doc:`read\_data `, :doc:`read\_dump `, -:doc:`write\_restart `, :doc:`restart ` +:doc:`read_data `, :doc:`read_dump `, +:doc:`write_restart `, :doc:`restart ` **Default:** none diff --git a/doc/src/region.rst b/doc/src/region.rst index 3eaaae30ac..81e247a8e2 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -91,11 +91,11 @@ Description This command defines a geometric region of space. Various other commands use regions. For example, the region can be filled with -atoms via the :doc:`create\_atoms ` command. Or a bounding +atoms via the :doc:`create_atoms ` command. Or a bounding box around the region, can be used to define the simulation box via -the :doc:`create\_box ` command. Or the atoms in the region +the :doc:`create_box ` command. Or the atoms in the region can be identified as a group via the :doc:`group ` command, or -deleted via the :doc:`delete\_atoms ` command. Or the +deleted via the :doc:`delete_atoms ` command. Or the surface of the region can be used as a boundary wall via the :doc:`fix wall/region ` command. Commands which use regions typically test whether an atom's position @@ -127,8 +127,8 @@ box boundary; if the box changes size during a simulation, the region does not. INF means a large negative or positive number (1.0e20), so it should encompass the simulation box even if it changes size. If a region is defined before the simulation box has been created (via -:doc:`create\_box ` or :doc:`read\_data ` or -:doc:`read\_restart ` commands), then an EDGE or INF +:doc:`create_box ` or :doc:`read_data ` or +:doc:`read_restart ` commands), then an EDGE or INF parameter cannot be used. For a *prism* region, a non-zero tilt factor in any pair of dimensions cannot be used if both the lo/hi values in either of those dimensions are INF. E.g. if the xy tilt is @@ -176,7 +176,7 @@ and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped. -A prism region that will be used with the :doc:`create\_box ` +A prism region that will be used with the :doc:`create_box ` command to define a triclinic simulation box must have tilt factors (xy,xz,yz) that do not skew the box more than half the distance of corresponding the parallel box length. For example, if xlo = 2 and @@ -198,7 +198,7 @@ the cylinder axes can be a variable with the same kind of effect and requirements than for the radius. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent radius or have a time dependent position of the sphere or cylinder region. @@ -285,12 +285,12 @@ three variables can be specified as NULL, in which case no displacement is calculated in that dimension. Note that equal-style variables can specify formulas with various -mathematical functions, and include :doc:`thermo\_style ` +mathematical functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a region displacement that change as a function of time or spans consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the -:doc:`run ` command and the *elaplong* keyword of :doc:`thermo\_style custom ` for details. +:doc:`run ` command and the *elaplong* keyword of :doc:`thermo_style custom ` for details. For example, these commands would displace a region from its initial position, in the positive x direction, effectively at a constant @@ -420,8 +420,8 @@ parameters must be 0.0. Related commands """""""""""""""" -:doc:`lattice `, :doc:`create\_atoms `, -:doc:`delete\_atoms `, :doc:`group ` +:doc:`lattice `, :doc:`create_atoms `, +:doc:`delete_atoms `, :doc:`group ` Default """"""" diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index 65d05265c0..6563ef7dd0 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -73,7 +73,7 @@ initial simulation produced the dump file: Conceptually, using the rerun command is like running an input script that has a loop in it (see the :doc:`next ` and :doc:`jump ` commands). Each iteration of the loop reads one snapshot from the -dump file via the :doc:`read\_dump ` command, sets the +dump file via the :doc:`read_dump ` command, sets the timestep to the appropriate value, and then invokes a :doc:`run ` command for zero timesteps to simply compute energy and forces, and any other :doc:`thermodynamic output ` or diagnostic info @@ -81,18 +81,18 @@ you have defined. This computation also invokes any fixes you have defined that apply constraints to the system, such as :doc:`fix shake ` or :doc:`fix indent `. Note that a simulation box must already be defined before using the -rerun command. This can be done by the :doc:`create\_box `, -:doc:`read\_data `, or :doc:`read\_restart ` +rerun command. This can be done by the :doc:`create_box `, +:doc:`read_data `, or :doc:`read_restart ` commands. Also note that reading per-atom information from dump snapshots is limited to the atom coordinates, velocities and image flags as -explained in the :doc:`read\_dump ` command. Other atom +explained in the :doc:`read_dump ` command. Other atom properties, which may be necessary to compute energies and forces, such as atom charge, or bond topology information for a molecular system, are not read from (or even contained in) dump files. Thus this auxiliary information should be defined in the usual way, e.g. in -a data file read in by a :doc:`read\_data ` command, before +a data file read in by a :doc:`read_data ` command, before using the rerun command. Also note that the frequency of thermodynamic or dump output from the @@ -154,10 +154,10 @@ dump file with a timestep value larger than the *stop* setting you have specified. The *dump* keyword is required and must be the last keyword specified. -Its arguments are passed internally to the :doc:`read\_dump ` +Its arguments are passed internally to the :doc:`read_dump ` command. The first argument following the *dump* keyword should be -the *field1* argument of the :doc:`read\_dump ` command. See -the :doc:`read\_dump ` doc page for details on the various +the *field1* argument of the :doc:`read_dump ` command. See +the :doc:`read_dump ` doc page for details on the various options it allows for extracting information from the dump file snapshots, and for using that information to alter the LAMMPS simulation. @@ -181,12 +181,12 @@ in which you are reprocessing the dump snapshots. If you only want the rerun script to perform an analysis that does not involve pair interactions, such as use compute msd to calculated displacements over time, you do not need to define a :doc:`pair style `, which may also mean neighbor lists will not -need to be calculated which saves time. The :doc:`comm\_modify cutoff ` command can also be used to insure ghost +need to be calculated which saves time. The :doc:`comm_modify cutoff ` command can also be used to insure ghost atoms are acquired from far enough away for operations like bond and angle evaluations, if no pair style is being used. Every time a snapshot is read, the timestep for the simulation is -reset, as if the :doc:`reset\_timestep ` command were +reset, as if the :doc:`reset_timestep ` command were used. This command has some restrictions as to what fixes can be defined. See its doc page for details. For example, the :doc:`fix deposit ` and :doc:`fix dt/reset ` fixes are in this category. They also make no sense to use with a rerun @@ -201,7 +201,7 @@ are read from the dump file(s). If an averaging fix is not invoked on a timestep it expects to be, LAMMPS will flag an error. The various forms of LAMMPS output, as defined by the -:doc:`thermo\_style `, :doc:`thermo `, +:doc:`thermo_style `, :doc:`thermo `, :doc:`dump `, and :doc:`restart ` commands occur with specified frequency, e.g. every N steps. If the timestep for a dump snapshot is not a multiple of N, then it will be read and processed, @@ -224,7 +224,7 @@ doc page for details. Related commands """""""""""""""" -:doc:`read\_dump ` +:doc:`read_dump ` Default """"""" diff --git a/doc/src/reset_ids.rst b/doc/src/reset_ids.rst index 774b9d4628..e41745fa52 100644 --- a/doc/src/reset_ids.rst +++ b/doc/src/reset_ids.rst @@ -39,7 +39,7 @@ Note that the resetting of IDs is not really a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. Instead the IDs for all atoms are erased, and new IDs are assigned so that the atoms owned by an individual processor have consecutive IDs, -as the :doc:`create\_atoms ` command explains. +as the :doc:`create_atoms ` command explains. .. note:: @@ -47,7 +47,7 @@ as the :doc:`create\_atoms ` command explains. defined, an error about bond topology atom IDs not being found may result. This is because the cutoff distance for ghost atom communication was not sufficient to find atoms in bonds, angles, etc - that are owned by other processors. The :doc:`comm\_modify cutoff ` command can be used to correct this issue. + that are owned by other processors. The :doc:`comm_modify cutoff ` command can be used to correct this issue. Or you can define a pair style before using this command. If you do the former, you should unset the comm\_modify cutoff after using reset\_ids so that subsequent communication is not inefficient. @@ -59,7 +59,7 @@ Restrictions Related commands """""""""""""""" -:doc:`delete\_atoms ` +:doc:`delete_atoms ` **Default:** none diff --git a/doc/src/reset_timestep.rst b/doc/src/reset_timestep.rst index f898bf2453..e9f8818653 100644 --- a/doc/src/reset_timestep.rst +++ b/doc/src/reset_timestep.rst @@ -27,11 +27,11 @@ Description Set the timestep counter to the specified value. This command normally comes after the timestep has been set by reading a restart -file via the :doc:`read\_restart ` command, or a previous +file via the :doc:`read_restart ` command, or a previous simulation advanced the timestep. -The :doc:`read\_data ` and :doc:`create\_box ` -commands set the timestep to 0; the :doc:`read\_restart ` +The :doc:`read_data ` and :doc:`create_box ` +commands set the timestep to 0; the :doc:`read_restart ` command sets the timestep to the value it had when the restart file was written. diff --git a/doc/src/restart.rst b/doc/src/restart.rst index e061adece3..6cfbdec475 100644 --- a/doc/src/restart.rst +++ b/doc/src/restart.rst @@ -102,7 +102,7 @@ written and read using MPI-IO. Restart files are written on timesteps that are a multiple of N but not on the first timestep of a run or minimization. You can use the -:doc:`write\_restart ` command to write a restart file +:doc:`write_restart ` command to write a restart file before a run begins. A restart file is not written on the last timestep of a run unless it is a multiple of N. A restart file is written on the last timestep of a minimization if N > 0 and the @@ -132,10 +132,10 @@ a simulation where something goes wrong at step 1163: ---------- -See the :doc:`read\_restart ` command for information about +See the :doc:`read_restart ` command for information about what is stored in a restart file. -Restart files can be read by a :doc:`read\_restart ` +Restart files can be read by a :doc:`read_restart ` command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on another machine. In this case, you can use the :doc:`-r command-line switch ` to convert a restart file to a data file. @@ -149,7 +149,7 @@ another machine. In this case, you can use the :doc:`-r command-line switch ` + to re-use that information. See the :doc:`read_restart ` command for information about what is stored in a restart file. @@ -188,7 +188,7 @@ package must be installed. Related commands """""""""""""""" -:doc:`write\_restart `, :doc:`read\_restart ` +:doc:`write_restart `, :doc:`read_restart ` Default """"""" diff --git a/doc/src/run.rst b/doc/src/run.rst index 1399c6a963..0cf9f3de1d 100644 --- a/doc/src/run.rst +++ b/doc/src/run.rst @@ -226,7 +226,7 @@ successive runs to run a simulation for any number of steps (ok, up to Related commands """""""""""""""" -:doc:`minimize `, :doc:`run\_style `, +:doc:`minimize `, :doc:`run_style `, :doc:`temper `, :doc:`fix halt ` Default diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index 5dd51f7f1a..b320c57ea8 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -83,10 +83,10 @@ processors. See the :doc:`-partition command-line switch ` for info on how to run LAMMPS with multiple partitions. Specifically, this style performs all computation except the -:doc:`kspace\_style ` portion of the force field on the 1st +:doc:`kspace_style ` portion of the force field on the 1st partition. This include the :doc:`pair style `, :doc:`bond style `, :doc:`neighbor list building `, :doc:`fixes ` including time integration, and output. The -:doc:`kspace\_style ` portion of the calculation is +:doc:`kspace_style ` portion of the calculation is performed on the 2nd partition. This is most useful for the PPPM kspace\_style when its performance on @@ -163,7 +163,7 @@ outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for 4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the inner timestep would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that specify number of timesteps (e.g. :doc:`thermo ` -for thermo output every N steps, :doc:`neigh\_modify delay/every ` parameters, :doc:`dump ` every N +for thermo output every N steps, :doc:`neigh_modify delay/every ` parameters, :doc:`dump ` every N steps, etc) refer to the outermost timesteps. The rRESPA keywords enable you to specify at what level of the @@ -176,7 +176,7 @@ outermost level, and kspace forces are computed where pair forces are. The inner, middle, outer forces have no defaults. For fixes that support it, the rRESPA level at which a given fix is -active, can be selected through the :doc:`fix\_modify ` command. +active, can be selected through the :doc:`fix_modify ` command. The *inner* and *middle* keywords take additional arguments for cutoffs that are used by the pairwise force computations. If the 2 @@ -200,7 +200,7 @@ are computed at the same rRESPA level. See the doc pages for individual pair styles for details. Another option for using pair potentials with rRESPA is with the -*hybrid* keyword, which requires the use of the :doc:`pair\_style hybrid or hybrid/overlay ` command. In this scenario, different +*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid or hybrid/overlay ` command. In this scenario, different sub-styles of the hybrid pair style are evaluated at different rRESPA levels. This can be useful, for example, to set different timesteps for hybrid coarse-grained/all-atom models. The *hybrid* keyword diff --git a/doc/src/set.rst b/doc/src/set.rst index 087c3487e5..613c19bcca 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -141,11 +141,11 @@ Description """"""""""" Set one or more properties of one or more atoms. Since atom -properties are initially assigned by the :doc:`read\_data `, -:doc:`read\_restart ` or :doc:`create\_atoms ` +properties are initially assigned by the :doc:`read_data `, +:doc:`read_restart ` or :doc:`create_atoms ` commands, this command changes those assignments. This can be useful for overriding the default values assigned by the -:doc:`create\_atoms ` command (e.g. charge = 0.0). It can +:doc:`create_atoms ` command (e.g. charge = 0.0). It can be useful for altering pairwise and molecular force interactions, since force-field coefficients are defined in terms of types. It can be used to change the labeling of atoms by atom type or molecule ID @@ -204,7 +204,7 @@ the variable to reset a property for all atoms is to use style *atom* with *ID* = "\*"; this selects all atom IDs. Atom-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. They can also include per-atom values, such as atom coordinates. Thus it is easy to specify a time-dependent or @@ -223,8 +223,8 @@ from a file. Keyword *type* sets the atom type for all selected atoms. The specified value must be from 1 to ntypes, where ntypes was set by the -:doc:`create\_box ` command or the *atom types* field in the -header of the data file read by the :doc:`read\_data ` +:doc:`create_box ` command or the *atom types* field in the +header of the data file read by the :doc:`read_data ` command. Keyword *type/fraction* sets the atom type for a fraction of the @@ -281,8 +281,8 @@ Keyword *quat* uses the specified values to create a quaternion (4-vector) that represents the orientation of the selected atoms. The particles must define a quaternion for their orientation (e.g. ellipsoids, triangles, body particles) as defined by the -:doc:`atom\_style ` command. Note that particles defined by -:doc:`atom\_style ellipsoid ` have 3 shape parameters. The 3 +:doc:`atom_style ` command. Note that particles defined by +:doc:`atom_style ellipsoid ` have 3 shape parameters. The 3 values must be non-zero for each particle set by this command. They are used to specify the aspect ratios of an ellipsoidal particle, which is oriented by default with its x-axis along the simulation @@ -298,7 +298,7 @@ ignored, since a rotation vector of (0,0,1) is the only valid choice. Keyword *quat/random* randomizes the orientation of the quaternion for the selected atoms. The particles must define a quaternion for their orientation (e.g. ellipsoids, triangles, body particles) as defined by -the :doc:`atom\_style ` command. Random numbers are used in +the :doc:`atom_style ` command. Random numbers are used in such a way that the orientation of a particular atom is the same, regardless of how many processors are being used. For 2d systems, only orientations in the xy plane are generated. As with keyword @@ -307,32 +307,32 @@ for each particle set by this command. This keyword does not allow use of an atom-style variable. Keyword *diameter* sets the size of the selected atoms. The particles -must be finite-size spheres as defined by the :doc:`atom\_style sphere ` command. The diameter of a particle can be +must be finite-size spheres as defined by the :doc:`atom_style sphere ` command. The diameter of a particle can be set to 0.0, which means they will be treated as point particles. Note that this command does not adjust the particle mass, even if it was -defined with a density, e.g. via the :doc:`read\_data ` +defined with a density, e.g. via the :doc:`read_data ` command. Keyword *shape* sets the size and shape of the selected atoms. The -particles must be ellipsoids as defined by the :doc:`atom\_style ellipsoid ` command. The *Sx*\ , *Sy*\ , *Sz* settings are +particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid ` command. The *Sx*\ , *Sy*\ , *Sz* settings are the 3 diameters of the ellipsoid in each direction. All 3 can be set to the same value, which means the ellipsoid is effectively a sphere. They can also all be set to 0.0 which means the particle will be treated as a point particle. Note that this command does not adjust the particle mass, even if it was defined with a density, e.g. via the -:doc:`read\_data ` command. +:doc:`read_data ` command. Keyword *length* sets the length of selected atoms. The particles -must be line segments as defined by the :doc:`atom\_style line ` command. If the specified value is non-zero the +must be line segments as defined by the :doc:`atom_style line ` command. If the specified value is non-zero the line segment is (re)set to a length = the specified value, centered around the particle position, with an orientation along the x-axis. If the specified value is 0.0, the particle will become a point particle. Note that this command does not adjust the particle mass, even if it was defined with a density, e.g. via the -:doc:`read\_data ` command. +:doc:`read_data ` command. Keyword *tri* sets the size of selected atoms. The particles must be -triangles as defined by the :doc:`atom\_style tri ` command. +triangles as defined by the :doc:`atom_style tri ` command. If the specified value is non-zero the triangle is (re)set to be an equilateral triangle in the xy plane with side length = the specified value, with a centroid at the particle position, with its base @@ -340,22 +340,22 @@ parallel to the x axis, and the y-axis running from the center of the base to the top point of the triangle. If the specified value is 0.0, the particle will become a point particle. Note that this command does not adjust the particle mass, even if it was defined with a -density, e.g. via the :doc:`read\_data ` command. +density, e.g. via the :doc:`read_data ` command. Keyword *theta* sets the orientation of selected atoms. The particles -must be line segments as defined by the :doc:`atom\_style line ` command. The specified value is used to set the +must be line segments as defined by the :doc:`atom_style line ` command. The specified value is used to set the orientation angle of the line segments with respect to the x axis. Keyword *theta/random* randomizes the orientation of theta for the selected atoms. The particles must be line segments as defined by the -:doc:`atom\_style line ` command. Random numbers are used in +:doc:`atom_style line ` command. Random numbers are used in such a way that the orientation of a particular atom is the same, regardless of how many processors are being used. This keyword does not allow use of an atom-style variable. Keyword *angmom* sets the angular momentum of selected atoms. The -particles must be ellipsoids as defined by the :doc:`atom\_style ellipsoid ` command or triangles as defined by the -:doc:`atom\_style tri ` command. The angular momentum vector +particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid ` command or triangles as defined by the +:doc:`atom_style tri ` command. The angular momentum vector of the particles is set to the 3 specified components. Keyword *omega* sets the angular velocity of selected atoms. The @@ -365,13 +365,13 @@ is set to the 3 specified components. Keyword *mass* sets the mass of all selected particles. The particles must have a per-atom mass attribute, as defined by the -:doc:`atom\_style ` command. See the "mass" command for how +:doc:`atom_style ` command. See the "mass" command for how to set mass values on a per-type basis. Keyword *density* or *density/disc* also sets the mass of all selected particles, but in a different way. The particles must have a per-atom -mass attribute, as defined by the :doc:`atom\_style ` -command. If the atom has a radius attribute (see :doc:`atom\_style sphere `) and its radius is non-zero, its mass is set +mass attribute, as defined by the :doc:`atom_style ` +command. If the atom has a radius attribute (see :doc:`atom_style sphere `) and its radius is non-zero, its mass is set from the density and particle volume for 3d systems (the input density is assumed to be in mass/distance\^3 units). For 2d, the default is for LAMMPS to model particles with a radius attribute as spheres. @@ -380,16 +380,16 @@ modeled as 2d discs (circles). Their mass is set from the density and particle area (the input density is assumed to be in mass/distance\^2 units). -If the atom has a shape attribute (see :doc:`atom\_style ellipsoid `) and its 3 shape parameters are non-zero, +If the atom has a shape attribute (see :doc:`atom_style ellipsoid `) and its 3 shape parameters are non-zero, then its mass is set from the density and particle volume (the input density is assumed to be in mass/distance\^3 units). The *density/disc* keyword has no effect; it does not (yet) treat 3d ellipsoids as 2d ellipses. -If the atom has a length attribute (see :doc:`atom\_style line `) and its length is non-zero, then its mass is +If the atom has a length attribute (see :doc:`atom_style line `) and its length is non-zero, then its mass is set from the density and line segment length (the input density is assumed to be in mass/distance units). If the atom has an area -attribute (see :doc:`atom\_style tri `) and its area is +attribute (see :doc:`atom_style tri `) and its area is non-zero, then its mass is set from the density and triangle area (the input density is assumed to be in mass/distance\^2 units). @@ -397,7 +397,7 @@ If none of these cases are valid, then the mass is set to the density value directly (the input density is assumed to be in mass units). Keyword *volume* sets the volume of all selected particles. -Currently, only the :doc:`atom\_style peri ` command defines +Currently, only the :doc:`atom_style peri ` command defines particles with a volume attribute. Note that this command does not adjust the particle mass. @@ -428,7 +428,7 @@ the specified value from 1 to nbondtypes (nangletypes, etc). All atoms in a particular bond (angle, etc) must be selected atoms in order for the change to be made. The value of nbondtype (nangletypes, etc) was set by the *bond types* (\ *angle types*\ , etc) field in the -header of the data file read by the :doc:`read\_data ` +header of the data file read by the :doc:`read_data ` command. These keywords do not allow use of an atom-style variable. Keywords *meso/e*\ , *meso/cv*\ , and *meso/rho* set the energy, heat @@ -463,13 +463,13 @@ temperature is set to that value. Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric heat capacity of an eDPD particle as defined by the USER-MESO package. -Currently, only :doc:`atom\_style edpd ` defines particles +Currently, only :doc:`atom_style edpd ` defines particles with these attributes. The values for the temperature and heat capacity must be positive. Keyword *cc* sets the chemical concentration of a tDPD particle for a specified species as defined by the USER-MESO package. Currently, only -:doc:`atom\_style tdpd ` defines particles with this +:doc:`atom_style tdpd ` defines particles with this attribute. An integer for "index" selects a chemical species (1 to Nspecies) where Nspecies is set by the atom\_style command. The value for the chemical concentration must be >= 0.0. @@ -485,7 +485,7 @@ Restrictions You cannot set an atom attribute (e.g. *mol* or *q* or *volume*\ ) if -the :doc:`atom\_style ` does not have that attribute. +the :doc:`atom_style ` does not have that attribute. This command requires inter-processor communication to coordinate the setting of bond types (angle types, etc). This means that your system @@ -502,8 +502,8 @@ coordinates outside the simulation box if they are ghost atoms. Related commands """""""""""""""" -:doc:`create\_box `, :doc:`create\_atoms `, -:doc:`read\_data ` +:doc:`create_box `, :doc:`create_atoms `, +:doc:`read_data ` **Default:** none diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index 1e30dc2761..824ed5ead0 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -51,8 +51,8 @@ either directly or via one or two intermediate bonds. These weighting factors are used by nearly all :doc:`pair styles ` in LAMMPS that compute simple pairwise interactions. Permanent bonds between atoms are specified by defining the bond topology in the data file -read by the :doc:`read\_data ` command. Typically a -:doc:`bond\_style ` command is also used to define a bond +read by the :doc:`read_data ` command. Typically a +:doc:`bond_style ` command is also used to define a bond potential. The rationale for using these weighting factors is that the interaction between a pair of bonded atoms is all (or mostly) specified by the bond, angle, dihedral potentials, and thus the @@ -68,7 +68,7 @@ atoms should be excluded (or reduced by a weighting factor). Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no sense to define permanent bonds between atoms that interact via these potentials, though such bonds may exist elsewhere in your system, - e.g. when using the :doc:`pair\_style hybrid ` command. + e.g. when using the :doc:`pair_style hybrid ` command. Thus LAMMPS ignores special\_bonds settings when many-body potentials are calculated. Please note, that the existence of explicit bonds for atoms that are described by a many-body potential will alter the @@ -112,8 +112,8 @@ that interaction will be at full strength. and 1-4 interactions are not defined from the list of angles or dihedrals used by the simulation. Rather, they are inferred topologically from the set of bonds specified when the simulation is - defined from a data or restart file (see :doc:`read\_data ` or - :doc:`read\_restart ` commands). Thus the set of + defined from a data or restart file (see :doc:`read_data ` or + :doc:`read_restart ` commands). Thus the set of 1-2,1-3,1-4 interactions that the weights apply to is the same whether angle and dihedral potentials are computed or not, and remains the same even if bonds are constrained, or turned off, or removed during a @@ -121,9 +121,9 @@ that interaction will be at full strength. The two exceptions to this rule are (a) if the *angle* or *dihedral* keywords are set to *yes* (see below), or (b) if the -:doc:`delete\_bonds ` command is used with the *special* +:doc:`delete_bonds ` command is used with the *special* option that re-computes the 1-2,1-3,1-4 topologies after bonds are -deleted; see the :doc:`delete\_bonds ` command for more +deleted; see the :doc:`delete_bonds ` command for more details. The *amber* keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ @@ -138,7 +138,7 @@ used version of the CHARMM force field. Note that in pair styles *lj/charmm/coul/charmm* and *lj/charmm/coul/long* the 1-4 coefficients are defined explicitly, and these pairwise contributions are computed as part of the charmm dihedral style - see the -:doc:`pair\_coeff ` and :doc:`dihedral\_style ` +:doc:`pair_coeff ` and :doc:`dihedral_style ` commands for more information. See :ref:`(MacKerell) ` for a description of the CHARMM force field. @@ -200,7 +200,7 @@ default, then the 2,5 interaction will also be weighted by 0.5. grow. Note that adding a single bond always adds a new 1st neighbor but may also induce \*many\* new 2nd and 3rd neighbors, depending on the molecular topology of your system. Using the *extra/special/per/atom* - keyword to either :doc:`read\_data ` or :doc:`create\_box ` + keyword to either :doc:`read_data ` or :doc:`create_box ` reserves empty space in the list for this N additional 1st, 2nd, or 3rd neighbors to be added. If you do not do this, you may get an error when bonds (or molecules) are added. @@ -255,7 +255,7 @@ Restrictions Related commands """""""""""""""" -:doc:`delete\_bonds `, :doc:`fix bond/create ` +:doc:`delete_bonds `, :doc:`fix bond/create ` Default """"""" diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst index 263b83187c..f7737b00d9 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -60,7 +60,7 @@ These are the variants these packages provide: * HYBRID = a combination of two packages can be specified (see below) -As an example, all of the packages provide a :doc:`pair\_style lj/cut ` variant, with style names lj/cut/opt, lj/cut/omp, +As an example, all of the packages provide a :doc:`pair_style lj/cut ` variant, with style names lj/cut/opt, lj/cut/omp, lj/cut/gpu, lj/cut/intel, or lj/cut/kk. A variant styles can be specified explicitly in your input script, e.g. pair\_style lj/cut/gpu. If the suffix command is used with the appropriate style, @@ -93,7 +93,7 @@ commands in your input script. .. note:: - The default :doc:`run\_style ` verlet is invoked prior to + The default :doc:`run_style ` verlet is invoked prior to reading the input script and is therefore not affected by a suffix command in the input script. The KOKKOS package requires "run\_style verlet/kk", so when using the KOKKOS package it is necessary to either use the command diff --git a/doc/src/tad.rst b/doc/src/tad.rst index 5322251ed5..d74fb2e8fb 100644 --- a/doc/src/tad.rst +++ b/doc/src/tad.rst @@ -129,7 +129,7 @@ check is performed by quenching the system and comparing the resulting atom coordinates to the coordinates from the previous basin. A quench is an energy minimization and is performed by whichever -algorithm has been defined by the :doc:`min\_style ` command; +algorithm has been defined by the :doc:`min_style ` command; its default is the CG minimizer. The tolerances and limits for each quench can be set by the *min* keyword. Note that typically, you do not need to perform a highly-converged minimization to detect a @@ -304,8 +304,8 @@ Related commands """""""""""""""" :doc:`compute event/displace `, -:doc:`min\_modify `, :doc:`min\_style `, -:doc:`run\_style `, :doc:`minimize `, +:doc:`min_modify `, :doc:`min_style `, +:doc:`run_style `, :doc:`minimize `, :doc:`temper `, :doc:`neb `, :doc:`prd ` diff --git a/doc/src/temper_npt.rst b/doc/src/temper_npt.rst index 8140989189..847d91fb1b 100644 --- a/doc/src/temper_npt.rst +++ b/doc/src/temper_npt.rst @@ -66,7 +66,7 @@ isothermal-isobaric (NPT) ensemble. Related commands """""""""""""""" -:doc:`temper `, :doc:`variable `, :doc:`fix\_npt ` +:doc:`temper `, :doc:`variable `, :doc:`fix_npt ` **Default:** none diff --git a/doc/src/thermo.rst b/doc/src/thermo.rst index 8b11ff9078..503ef84f6d 100644 --- a/doc/src/thermo.rst +++ b/doc/src/thermo.rst @@ -31,8 +31,8 @@ and end of a simulation. A value of 0 will only print thermodynamics at the beginning and end. The content and format of what is printed is controlled by the -:doc:`thermo\_style ` and -:doc:`thermo\_modify ` commands. +:doc:`thermo_style ` and +:doc:`thermo_modify ` commands. Instead of a numeric value, N can be specified as an :doc:`equal-style variable `, which should be specified as v\_name, where name is the variable name. In this case, the variable is evaluated at @@ -60,7 +60,7 @@ Restrictions Related commands """""""""""""""" -:doc:`thermo\_style `, :doc:`thermo\_modify ` +:doc:`thermo_style `, :doc:`thermo_modify ` Default """"""" diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index f0b27d2bc6..c0ec18b465 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -49,7 +49,7 @@ by LAMMPS. .. note:: These options apply to the currently defined thermo style. When - you specify a :doc:`thermo\_style ` command, all + you specify a :doc:`thermo_style ` command, all thermodynamic settings are restored to their default values, including those previously reset by a thermo\_modify command. Thus if your input script specifies a thermo\_style command, you should use the @@ -86,12 +86,12 @@ different defaults for this setting (see below). Even if *norm* is set to *yes*\ , a value is only normalized if it is an "extensive" quantity, meaning that it scales with the number of atoms in the system. For the thermo keywords described by the doc page for the -:doc:`thermo\_style ` command, all energy-related keywords +:doc:`thermo_style ` command, all energy-related keywords are extensive, such as *pe* or *ebond* or *enthalpy*\ . Other keywords such as *temp* or *press* are "intensive" meaning their value is independent (in a statistical sense) of the number of atoms in the system and thus are never normalized. For thermodynamic output values -extracted from fixes and computes in a :doc:`thermo\_style custom ` command, the doc page for the individual +extracted from fixes and computes in a :doc:`thermo_style custom ` command, the doc page for the individual :doc:`fix ` or :doc:`compute ` lists whether the value is "extensive" or "intensive" and thus whether it is normalized. Thermodynamic output values calculated by a variable formula are @@ -111,7 +111,7 @@ containing the timestep and CPU time. This modify option overrides the *one* and *multi* thermo\_style settings. The *format* keyword can be used to change the default numeric format -of any of quantities the :doc:`thermo\_style ` command +of any of quantities the :doc:`thermo_style ` command outputs. All the specified format strings are C-style formats, e.g. as used by the C/C++ printf() command. The *line* keyword takes a single argument which is the format string for the entire line of @@ -147,7 +147,7 @@ temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc). The specified compute ID must have been previously defined by the user via the :doc:`compute ` command and it must be a style of compute that calculates a temperature. As described in the -:doc:`thermo\_style ` command, thermo output uses a default +:doc:`thermo_style ` command, thermo output uses a default compute for temperature with ID = *thermo\_temp*. This option allows the user to override the default. @@ -157,7 +157,7 @@ pressure ("press", "enthalpy", "pxx", etc). The specified compute ID must have been previously defined by the user via the :doc:`compute ` command and it must be a style of compute that calculates a pressure. As described in the -:doc:`thermo\_style ` command, thermo output uses a default +:doc:`thermo_style ` command, thermo output uses a default compute for pressure with ID = *thermo\_press*. This option allows the user to override the default. @@ -180,7 +180,7 @@ Restrictions Related commands """""""""""""""" -:doc:`thermo `, :doc:`thermo\_style ` +:doc:`thermo `, :doc:`thermo_style ` Default """"""" diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 480b14ae63..0aa401dd96 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -131,7 +131,7 @@ include values from previous timesteps, can be output by using the f\_ID keyword and accessing a fix that does time-averaging such as the :doc:`fix ave/time ` command. -Options invoked by the :doc:`thermo\_modify ` command can +Options invoked by the :doc:`thermo_modify ` command can be used to set the one- or multi-line format of the print-out, the normalization of thermodynamic output (total values versus per-atom values for extensive quantities (ones which scale with the number of @@ -141,7 +141,7 @@ atoms in the system), and the numeric precision of each printed value. When you use a "thermo\_style" command, all thermodynamic settings are restored to their default values, including those - previously set by a :doc:`thermo\_modify ` command. Thus + previously set by a :doc:`thermo_modify ` command. Thus if your input script specifies a thermo\_style command, you should use the thermo\_modify command after it. @@ -162,11 +162,11 @@ when LAMMPS starts up, as if this command had been issued: See the :doc:`compute temp ` command for details. Note that the ID of this compute is *thermo\_temp* and the group is *all*\ . You can change the attributes of this temperature (e.g. its -degrees-of-freedom) via the :doc:`compute\_modify ` +degrees-of-freedom) via the :doc:`compute_modify ` command. Alternatively, you can directly assign a new compute (that calculates temperature) which you have defined, to be used for calculating any thermodynamic quantity that requires a temperature. -This is done via the :doc:`thermo\_modify ` command. +This is done via the :doc:`thermo_modify ` command. Several of the thermodynamic quantities require a pressure to be computed: "press", "enthalpy", "pxx", etc. By default this is done by @@ -181,11 +181,11 @@ if this command had been issued: See the :doc:`compute pressure ` command for details. Note that the ID of this compute is *thermo\_press* and the group is *all*\ . You can change the attributes of this pressure via the -:doc:`compute\_modify ` command. Alternatively, you can +:doc:`compute_modify ` command. Alternatively, you can directly assign a new compute (that calculates pressure) which you have defined, to be used for calculating any thermodynamic quantity that requires a pressure. This is done via the -:doc:`thermo\_modify ` command. +:doc:`thermo_modify ` command. Several of the thermodynamic quantities require a potential energy to be computed: "pe", "etotal", "ebond", etc. This is done by using a @@ -200,7 +200,7 @@ command had been issued: See the :doc:`compute pe ` command for details. Note that the ID of this compute is *thermo\_pe* and the group is *all*\ . You can change the attributes of this potential energy via the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. ---------- @@ -209,20 +209,20 @@ change the attributes of this potential energy via the The kinetic energy of the system *ke* is inferred from the temperature of the system with 1/2 Kb T of energy for each degree of freedom. Thus, using different :doc:`compute commands ` for calculating -temperature, via the :doc:`thermo\_modify temp ` command, +temperature, via the :doc:`thermo_modify temp ` command, may yield different kinetic energies, since different computes that calculate temperature can subtract out different non-thermal components of velocity and/or include different degrees of freedom (translational, rotational, etc). The potential energy of the system *pe* will include contributions -from fixes if the :doc:`fix\_modify thermo ` option is set +from fixes if the :doc:`fix_modify thermo ` option is set for a fix that calculates such a contribution. For example, the :doc:`fix wall/lj93 ` fix calculates the energy of atoms interacting with the wall. See the doc pages for "individual fixes" to see which ones contribute. A long-range tail correction *etail* for the VanderWaal pairwise -energy will be non-zero only if the :doc:`pair\_modify tail ` option is turned on. The *etail* contribution +energy will be non-zero only if the :doc:`pair_modify tail ` option is turned on. The *etail* contribution is included in *evdwl*\ , *epair*\ , *pe*\ , and *etotal*\ , and the corresponding tail correction to the pressure is included in *press* and *pxx*\ , *pyy*\ , etc. @@ -302,7 +302,7 @@ printed with the end-of-run statistics. The *nbuild* keyword is the number of re-builds during the current run. The *ndanger* keyword is the number of re-builds that LAMMPS considered potentially "dangerous". If atom movement triggered neighbor list rebuilding (see -the :doc:`neigh\_modify ` command), then dangerous +the :doc:`neigh_modify ` command), then dangerous reneighborings are those that were triggered on the first timestep atom movement was checked for. If this count is non-zero you may wish to reduce the delay factor to insure no force interactions are missed @@ -372,7 +372,7 @@ kinetic energy that are summed over all atoms in the compute group. Intensive quantities are printed directly without normalization by thermo\_style custom. Extensive quantities may be normalized by the total number of atoms in the simulation (NOT the number of atoms in -the compute group) when output, depending on the :doc:`thermo\_modify norm ` option being used. +the compute group) when output, depending on the :doc:`thermo_modify norm ` option being used. The *f\_ID* and *f\_ID[I]* and *f\_ID[I][J]* keywords allow global values calculated by a fix to be output. As discussed on the @@ -396,7 +396,7 @@ energy that are summed over all atoms in the fix group. Intensive quantities are printed directly without normalization by thermo\_style custom. Extensive quantities may be normalized by the total number of atoms in the simulation (NOT the number of atoms in the fix group) -when output, depending on the :doc:`thermo\_modify norm ` +when output, depending on the :doc:`thermo_modify norm ` option being used. The *v\_name* keyword allow the current value of a variable to be @@ -427,14 +427,14 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. Related commands """""""""""""""" -:doc:`thermo `, :doc:`thermo\_modify `, -:doc:`fix\_modify `, :doc:`compute temp `, +:doc:`thermo `, :doc:`thermo_modify `, +:doc:`fix_modify `, :doc:`compute temp `, :doc:`compute pressure ` Default diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index 13a230d511..d49f790812 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -66,7 +66,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix phonon ` :doc:`dynamical\_matrix ` +:doc:`fix phonon ` :doc:`dynamical_matrix ` Default """"""" diff --git a/doc/src/timer.rst b/doc/src/timer.rst index c36b436b06..a5ef8ca137 100644 --- a/doc/src/timer.rst +++ b/doc/src/timer.rst @@ -122,7 +122,7 @@ Restrictions Related commands """""""""""""""" -:doc:`run post no `, :doc:`kspace\_modify fftbench ` +:doc:`run post no `, :doc:`kspace_modify fftbench ` Default """"""" diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst index da1a132a32..ddbe33a9d2 100644 --- a/doc/src/timestep.rst +++ b/doc/src/timestep.rst @@ -43,7 +43,7 @@ Related commands """""""""""""""" :doc:`fix dt/reset `, :doc:`run `, -:doc:`run\_style ` respa, :doc:`units ` +:doc:`run_style ` respa, :doc:`units ` Default """"""" diff --git a/doc/src/uncompute.rst b/doc/src/uncompute.rst index e27a5fcc34..941a7b7b38 100644 --- a/doc/src/uncompute.rst +++ b/doc/src/uncompute.rst @@ -27,7 +27,7 @@ Description Delete a compute that was previously defined with a :doc:`compute ` command. This also wipes out any additional changes made to the compute -via the :doc:`compute\_modify ` command. +via the :doc:`compute_modify ` command. Restrictions """""""""""" diff --git a/doc/src/unfix.rst b/doc/src/unfix.rst index dcd4e58c3d..016ac211aa 100644 --- a/doc/src/unfix.rst +++ b/doc/src/unfix.rst @@ -27,7 +27,7 @@ Description Delete a fix that was previously defined with a :doc:`fix ` command. This also wipes out any additional changes made to the fix -via the :doc:`fix\_modify ` command. +via the :doc:`fix_modify ` command. Restrictions """""""""""" diff --git a/doc/src/units.rst b/doc/src/units.rst index 6c0815f302..57558a4f53 100644 --- a/doc/src/units.rst +++ b/doc/src/units.rst @@ -80,12 +80,12 @@ results from a unitless LJ simulation into physical quantities. * density = mass/volume, where rho\* = rho sigma\^dim Note that for LJ units, the default mode of thermodynamic output via -the :doc:`thermo\_style ` command is to normalize all +the :doc:`thermo_style ` command is to normalize all extensive quantities by the number of atoms. E.g. potential energy is extensive because it is summed over atoms, so it is output as energy/atom. Temperature is intensive since it is already normalized by the number of atoms, so it is output as-is. This behavior can be -changed via the :doc:`thermo\_modify norm ` command. +changed via the :doc:`thermo_modify norm ` command. For style *real*\ , these are the units: @@ -220,7 +220,7 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. **Related commands:** none diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 99413ce96c..3e44b56f37 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -113,7 +113,7 @@ strings, the :doc:`next ` command can be used to increment which string is assigned to the variable. Variables of style *equal* store a formula which when evaluated produces a single numeric value which can be output either directly (see the :doc:`print `, :doc:`fix print `, and :doc:`run every ` commands) or as part -of thermodynamic output (see the :doc:`thermo\_style ` +of thermodynamic output (see the :doc:`thermo_style ` command), or used as input to an averaging fix (see the :doc:`fix ave/time ` command). Variables of style *vector* store a formula which produces a vector of such values which can be used as input to various averaging fixes, or elements of which can be @@ -425,7 +425,7 @@ For the *internal* style a numeric value is provided. This value will be assigned to the variable until a LAMMPS command sets it to a new value. There are currently only two LAMMPS commands that require *internal* variables as inputs, because they reset them: -:doc:`create\_atoms ` and :doc:`fix controller `. As mentioned above, an +:doc:`create_atoms ` and :doc:`fix controller `. As mentioned above, an internal-style variable can be used in place of an equal-style variable anywhere else in an input script, e.g. as an argument to another command that allows for equal-style variables. @@ -557,10 +557,10 @@ will not work, since the *version* has been introduced more recently): if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes" The thermo keywords allowed in a formula are those defined by the -:doc:`thermo\_style custom ` command. Thermo keywords that +:doc:`thermo_style custom ` command. Thermo keywords that require a :doc:`compute ` to calculate their values such as "temp" or "press", use computes stored and invoked by the -:doc:`thermo\_style ` command. This means that you can +:doc:`thermo_style ` command. This means that you can only use those keywords in a variable if the style you are using with the thermo\_style command (and the thermo keywords associated with that style) also define and use the needed compute. Note that some thermo @@ -688,7 +688,7 @@ timestep. X,y > 0 and x > y are required. The generated timesteps increase in a staggered fashion, as the sequence x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next timestep in the sequence is returned. Thus if stagger(1000,100) is -used in a variable by the :doc:`dump\_modify every ` +used in a variable by the :doc:`dump_modify every ` command, it will generate the sequence of output timesteps: @@ -703,7 +703,7 @@ y value is how many of the z-1 possible timesteps within one logarithmic interval are generated. I.e. the timesteps follow the sequence x,2x,3x,...y\*x,x\*z,2x\*z,3x\*z,...y\*x\*z,x\*z\^2,2x\*z\^2,etc. For any current timestep, the next timestep in the sequence is returned. -Thus if logfreq(100,4,10) is used in a variable by the :doc:`dump\_modify every ` command, it will generate this sequence of +Thus if logfreq(100,4,10) is used in a variable by the :doc:`dump_modify every ` command, it will generate this sequence of output timesteps: @@ -714,7 +714,7 @@ output timesteps: The logfreq2(x,y,z) function is similar to logfreq, except a single logarithmic interval is divided into y equally-spaced timesteps and all of them are output. Y < z is not required. Thus, if -logfreq2(100,18,10) is used in a variable by the :doc:`dump\_modify every ` command, then the interval between 100 and +logfreq2(100,18,10) is used in a variable by the :doc:`dump_modify every ` command, then the interval between 100 and 1000 is divided as 900/18 = 50 steps, and it will generate the sequence of output timesteps: @@ -743,7 +743,7 @@ the sequence x,x+z,x+2z,...,y. If y-x is not a multiple of z, then similar to the way a for loop operates, the last value will be one that does not exceed y. For any current timestep, the next timestep in the sequence is returned. Thus if stride(1000,2000,100) is used -in a variable by the :doc:`dump\_modify every ` command, it +in a variable by the :doc:`dump_modify every ` command, it will generate the sequence of output timesteps: @@ -763,7 +763,7 @@ that point the timestep increases in increments of c, from a to b, then after b, increments by z are resumed until y is reached. For any current timestep, the next timestep in the sequence is returned. Thus if stride2(1000,2000,100,1350,1360,1) is used in a variable by the -:doc:`dump\_modify every ` command, it will generate the +:doc:`dump_modify every ` command, it will generate the sequence of output timesteps: @@ -786,7 +786,7 @@ where dt = the timestep size. The run begins on startstep. Startstep can span multiple runs, using the *start* keyword of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. Note that the -:doc:`thermo\_style ` keyword elaplong = +:doc:`thermo_style ` keyword elaplong = timestep-startstep. The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments: @@ -805,7 +805,7 @@ where dt = the timestep size. The run begins on startstep. Startstep can span multiple runs, using the *start* keyword of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. Note that the -:doc:`thermo\_style ` keyword elaplong = +:doc:`thermo_style ` keyword elaplong = timestep-startstep. @@ -1045,7 +1045,7 @@ evaluating the variable. The meaning of the different atom values and vectors is mostly self-explanatory. *Mol* refers to the molecule ID of an atom, and is -only defined if an :doc:`atom\_style ` is being used that +only defined if an :doc:`atom_style ` is being used that defines molecule IDs. Note that many other atom attributes can be used as inputs to a @@ -1260,7 +1260,7 @@ the string between the parenthesis as an equal-style variable formula. Referencing a variable with a leading "v\_" is an optional or required kind of argument for some commands (e.g. the :doc:`fix ave/chunk ` or :doc:`dump custom ` or -:doc:`thermo\_style ` commands) if you wish it to evaluate +:doc:`thermo_style ` commands) if you wish it to evaluate a variable periodically during a run. It can also be used in a variable formula if you wish to reference a second variable. The second variable will be evaluated whenever the first variable is @@ -1333,7 +1333,7 @@ bond, etc) on timesteps that the variable will need the values. LAMMPS keeps track of all of this during a :doc:`run ` or :doc:`energy minimization `. An error will be generated if you attempt to evaluate a variable on timesteps when it cannot produce -accurate values. For example, if a :doc:`thermo\_style custom ` command prints a variable which accesses +accurate values. For example, if a :doc:`thermo_style custom ` command prints a variable which accesses values stored by a :doc:`fix ave/time ` command and the timesteps on which thermo output is generated are not multiples of the averaging frequency used in the fix command, then an error will occur. @@ -1423,10 +1423,10 @@ commands: print "Final potential energy = $e" The first run is performed using one setting for the pairwise -potential defined by the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands. The potential energy is +potential defined by the :doc:`pair_style ` and +:doc:`pair_coeff ` commands. The potential energy is evaluated on the final timestep and stored by the :doc:`compute pe ` compute (this is done by the -:doc:`thermo\_style ` command). Then a pair coefficient is +:doc:`thermo_style ` command). Then a pair coefficient is changed, altering the potential energy of the system. When the potential energy is printed via the "e" variable, LAMMPS will use the potential energy value stored by the :doc:`compute pe ` @@ -1461,7 +1461,7 @@ Restrictions Indexing any formula element by global atom ID, such as an atom value, requires the :doc:`atom style ` to use a global mapping in order to look up the vector indices. By default, only atom styles -with molecular information create global maps. The :doc:`atom\_modify map ` command can override the default, e.g. for +with molecular information create global maps. The :doc:`atom_modify map ` command can override the default, e.g. for atomic-style atom styles. All *universe*\ - and *uloop*\ -style variables defined in an input script diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index 5a4bb33d0c..314a5681e5 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -85,7 +85,7 @@ variable is used, the velocity it calculates must be in box units, not lattice units; see the discussion of the *units* keyword below. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters or other parameters. Atom-style variables can specify the same formulas as equal-style @@ -202,7 +202,7 @@ it owns. This can be a slow loop for a large simulation. If atoms were read from a data file, the velocity assigned to a particular atom will be the same, independent of how many processors are being used. This will not be the case if atoms were created using the -:doc:`create\_atoms ` command, since atom IDs will likely +:doc:`create_atoms ` command, since atom IDs will likely be assigned to atoms differently. If loop = local, then each processor loops over only its atoms to diff --git a/doc/src/write_coeff.rst b/doc/src/write_coeff.rst index 4b452d7928..4a293f7e3f 100644 --- a/doc/src/write_coeff.rst +++ b/doc/src/write_coeff.rst @@ -27,7 +27,7 @@ Description Write a text format file with the currently defined force field coefficients in a way, that it can be read by LAMMPS with the :doc:`include ` command. In combination with the nocoeff -option of :doc:`write\_data ` this can be used to move +option of :doc:`write_data ` this can be used to move the Coeffs sections from a data file into a separate file. .. note:: @@ -49,8 +49,8 @@ none Related commands """""""""""""""" -:doc:`read\_data `, :doc:`write\_restart `, -:doc:`write\_data ` +:doc:`read_data `, :doc:`write_restart `, +:doc:`write_data ` .. _lws: http://lammps.sandia.gov diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index 63e15c45f3..3ff9f155b0 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -39,7 +39,7 @@ Description Write a data file in text format of the current state of the simulation. Data files can be read by the :doc:`read data ` -command to begin a simulation. The :doc:`read\_data ` command +command to begin a simulation. The :doc:`read_data ` command also describes their format. Similar to :doc:`dump ` files, the data filename can contain a "\*" @@ -52,7 +52,7 @@ value. respects. First, most pair styles do not yet write their coefficient information into the data file. This means you will need to specify that information in your input script that reads the data file, via - the :doc:`pair\_coeff ` command. Second, a few of the :doc:`atom styles ` (body, ellipsoid, line, tri) that store + the :doc:`pair_coeff ` command. Second, a few of the :doc:`atom styles ` (body, ellipsoid, line, tri) that store auxiliary "bonus" information about aspherical particles, do not yet write the bonus info into the data file. Both these functionalities will be added to the write\_data command later. @@ -66,8 +66,8 @@ thus typically diverge from a simulation that continued in the original input script. If you want to do more exact restarts, using binary files, see the -:doc:`restart `, :doc:`write\_restart `, and -:doc:`read\_restart ` commands. You can also convert +:doc:`restart `, :doc:`write_restart `, and +:doc:`read_restart ` commands. You can also convert binary restart files to text data files, after a simulation has run, using the :doc:`-r command-line switch `. @@ -78,7 +78,7 @@ using the :doc:`-r command-line switch `. :doc:`fixes ` are stored. :doc:`Binary restart files ` store more information. -Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake ` or :doc:`delete\_bonds ` command will +Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake ` or :doc:`delete_bonds ` command will be written to a data file as if they are turned on. This means they will need to be turned off again in a new run after the data file is read. @@ -98,7 +98,7 @@ are read in separately anyway, e.g. from an include file. The *nofix* keyword requests that no extra sections read by fixes should be written to the data file (see the *fix* option of the -:doc:`read\_data ` command for details). For example, this +:doc:`read_data ` command for details). For example, this option excludes sections for user-created per-atom properties from :doc:`fix property/atom `. @@ -108,9 +108,9 @@ is specified as *ii*\ , then one line per atom type is written, to specify the coefficients for each of the I=J interactions. This means that no cross-interactions for I != J will be specified in the data file and the pair style will apply its mixing rule, as documented on -individual :doc:`pair\_style ` doc pages. Of course this +individual :doc:`pair_style ` doc pages. Of course this behavior can be overridden in the input script after reading the data -file, by specifying additional :doc:`pair\_coeff ` commands +file, by specifying additional :doc:`pair_coeff ` commands for any desired I,J pairs. If the value is specified as *ij*\ , then one line of coefficients is @@ -120,7 +120,7 @@ point. The presence of these I != J coefficients in the data file will effectively turn off the default mixing rule for the pair style. Again, the coefficient values in the data file can be overridden in the input script after reading the data file, by specifying -additional :doc:`pair\_coeff ` commands for any desired I,J +additional :doc:`pair_coeff ` commands for any desired I,J pairs. @@ -139,7 +139,7 @@ setup, atom masses initialized, etc). Related commands """""""""""""""" -:doc:`read\_data `, :doc:`write\_restart ` +:doc:`read_data `, :doc:`write_restart ` Default """"""" diff --git a/doc/src/write_dump.rst b/doc/src/write_dump.rst index e894406a22..afd7470ce8 100644 --- a/doc/src/write_dump.rst +++ b/doc/src/write_dump.rst @@ -15,8 +15,8 @@ Syntax * style = any of the supported :doc:`dump styles ` * file = name of file to write dump info to * dump-args = any additional args needed for a particular :doc:`dump style ` -* modify = all args after this keyword are passed to :doc:`dump\_modify ` (optional) -* dump-modify-args = args for :doc:`dump\_modify ` (optional) +* modify = all args after this keyword are passed to :doc:`dump_modify ` (optional) +* dump-modify-args = args for :doc:`dump_modify ` (optional) Examples @@ -45,11 +45,11 @@ dump style to write out snapshots periodically during a running simulation. The syntax for this command is mostly identical to that of the -:doc:`dump ` and :doc:`dump\_modify ` commands as if +:doc:`dump ` and :doc:`dump_modify ` commands as if they were concatenated together, with the following exceptions: There is no need for a dump ID or dump frequency and the keyword *modify* is added. The latter is so that the full range of -:doc:`dump\_modify ` options can be specified for the single +:doc:`dump_modify ` options can be specified for the single snapshot, just as they can be for multiple snapshots. The *modify* keyword separates the arguments that would normally be passed to the *dump* command from those that would be given the *dump\_modify*. Both @@ -71,7 +71,7 @@ Restrictions All restrictions for the :doc:`dump ` and -:doc:`dump\_modify ` commands apply to this command as well, +:doc:`dump_modify ` commands apply to this command as well, with the exception of the :doc:`dump image ` filename not requiring a wildcard "\*" character, as noted above. @@ -90,13 +90,13 @@ Related commands """""""""""""""" :doc:`dump `, :doc:`dump image `, -:doc:`dump\_modify ` +:doc:`dump_modify ` Default """"""" The defaults are listed on the doc pages for the :doc:`dump ` and -:doc:`dump image ` and :doc:`dump\_modify ` +:doc:`dump image ` and :doc:`dump_modify ` commands. diff --git a/doc/src/write_restart.rst b/doc/src/write_restart.rst index 853a046ed9..734bbb3a44 100644 --- a/doc/src/write_restart.rst +++ b/doc/src/write_restart.rst @@ -73,7 +73,7 @@ does not have to end in ".mpiio", just contain those characters. Unlike MPI-IO dump files, a particular restart file must be both written and read using MPI-IO. -Restart files can be read by a :doc:`read\_restart ` +Restart files can be read by a :doc:`read_restart ` command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on another machine. In this case, you can use the :doc:`-r command-line switch ` to convert a restart file to a data file. @@ -89,7 +89,7 @@ another machine. In this case, you can use the :doc:`-r command-line switch ` command for general information about + :doc:`read_restart ` command for general information about what is stored in a restart file. @@ -133,8 +133,8 @@ package must be installed. Related commands """""""""""""""" -:doc:`restart `, :doc:`read\_restart `, -:doc:`write\_data ` +:doc:`restart `, :doc:`read_restart `, +:doc:`write_data ` **Default:** none