diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index a4a1076831..0256552332 100644 --- a/doc/src/Bibliography.rst +++ b/doc/src/Bibliography.rst @@ -191,7 +191,7 @@ Bibliography A.\ Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996). **(Campana)** - C.\ Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) `_ + C.\ Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) `_ **(Cao1)** J.\ Cao and B. Berne, J Chem Phys, 99, 2902 (1993). @@ -767,7 +767,7 @@ Bibliography Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997). **(Moustafa)** - Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , `Phys. Rev. E [92], 043303 (2015) `_ + Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) `_ **(Muller-Plathe1)** Muller-Plathe, J Chem Phys, 106, 6082 (1997). diff --git a/doc/src/Commands_category.rst b/doc/src/Commands_category.rst index da40ada999..4a08d040b7 100644 --- a/doc/src/Commands_category.rst +++ b/doc/src/Commands_category.rst @@ -2,7 +2,7 @@ Commands by category ==================== This page lists most of the LAMMPS commands, grouped by category. The -:doc:`General commands ` doc page lists all general commands +:doc:`General commands ` page lists all general commands alphabetically. Style options for entries like fix, compute, pair etc. have their own pages where they are listed alphabetically. diff --git a/doc/src/Commands_input.rst b/doc/src/Commands_input.rst index 8fc658a215..3313474686 100644 --- a/doc/src/Commands_input.rst +++ b/doc/src/Commands_input.rst @@ -50,6 +50,6 @@ values are not desired, the :doc:`processors ` and tell LAMMPS how to map processors to the simulation box. Many input script errors are detected by LAMMPS and an ERROR or -WARNING message is printed. The :doc:`Errors ` doc page gives +WARNING message is printed. The :doc:`Errors ` page gives more information on what errors mean. The documentation for each command lists restrictions on how the command can be used. diff --git a/doc/src/Commands_parse.rst b/doc/src/Commands_parse.rst index 563b18a4c2..efc3c5030d 100644 --- a/doc/src/Commands_parse.rst +++ b/doc/src/Commands_parse.rst @@ -47,7 +47,7 @@ LAMMPS: named "x" followed by an "x" character. How the variable is converted to a text string depends on what style - of variable it is; see the :doc:`variable ` doc page for + of variable it is; see the :doc:`variable ` page for details. It can be a variable that stores multiple text strings, and return one of them. The returned text string can be multiple "words" (space separated) which will then be interpreted as multiple diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 3bbee1dc36..a26857ebf5 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -570,10 +570,10 @@ Doc page with :doc:`WARNING messages ` See the region prism command for details. *Can only use -plog with multiple partitions* - Self-explanatory. See doc page discussion of command-line switches. + Self-explanatory. See page discussion of command-line switches. *Can only use -pscreen with multiple partitions* - Self-explanatory. See doc page discussion of command-line switches. + Self-explanatory. See page discussion of command-line switches. *Can only use Kokkos supported regions with Kokkos package* Self-explanatory. @@ -1154,7 +1154,7 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Cannot use -reorder after -partition* - Self-explanatory. See doc page discussion of command-line switches. + Self-explanatory. See page discussion of command-line switches. *Cannot use Ewald with 2d simulation* The kspace style ewald cannot be used in 2d simulations. You can use @@ -2347,14 +2347,14 @@ Doc page with :doc:`WARNING messages ` *Compute used in variable between runs is not current* Computes cannot be invoked by a variable in between runs. Thus they must have been evaluated on the last timestep of the previous run in - order for their value(s) to be accessed. See the doc page for the + order for their value(s) to be accessed. See the page for the variable command for more info. *Compute used in variable thermo keyword between runs is not current* Some thermo keywords rely on a compute to calculate their value(s). Computes cannot be invoked by a variable in between runs. Thus they must have been evaluated on the last timestep of the previous run in - order for their value(s) to be accessed. See the doc page for the + order for their value(s) to be accessed. See the page for the variable command for more info. *Compute vcm/chunk does not use chunk/atom compute* @@ -3126,7 +3126,7 @@ Doc page with :doc:`WARNING messages ` *Energy was not tallied on needed timestep* You are using a thermo keyword that requires potentials to have tallied energy, but they did not on this timestep. See the - variable doc page for ideas on how to make this work. + variable page for ideas on how to make this work. *Epsilon or sigma reference not set by pair style in PPPMDisp* Self-explanatory. @@ -4535,10 +4535,10 @@ Doc page with :doc:`WARNING messages ` particles. *Incorrect # of floating-point values in Bodies section of data file* - See doc page for body style. + See page for body style. *Incorrect # of integer values in Bodies section of data file* - See doc page for body style. + See page for body style. *Incorrect %s format in data file* A section of the data file being read by fix property/atom does @@ -4573,7 +4573,7 @@ Doc page with :doc:`WARNING messages ` The number of fields per line is not what expected. *Incorrect bonus data format in data file* - See the read_data doc page for a description of how various kinds of + See the read_data page for a description of how various kinds of bonus data must be formatted for certain atom styles. *Incorrect boundaries with slab Ewald* @@ -4641,7 +4641,7 @@ Doc page with :doc:`WARNING messages ` Incorrect number of words per line in the potential file. *Incorrect integer value in Bodies section of data file* - See doc page for body style. + See page for body style. *Incorrect multiplicity arg for dihedral coefficients* Self-explanatory. Check the input script or data file. @@ -5996,7 +5996,7 @@ Doc page with :doc:`WARNING messages ` Self-explanatory. *Needed bonus data not in data file* - Some atom styles require bonus data. See the read_data doc page for + Some atom styles require bonus data. See the read_data page for details. *Needed molecular topology not in data file* @@ -6198,7 +6198,7 @@ keyword to allow for additional bonds to be formed *One or more atom IDs is too big* The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL - setting in your LAMMPS build. See the :doc:`Build settings ` doc page for more info. + setting in your LAMMPS build. See the :doc:`Build settings ` page for more info. *One or more atom IDs is zero* Either all atoms IDs must be zero or none of them. @@ -6593,7 +6593,7 @@ keyword to allow for additional bonds to be formed *Pair style bop requires comm ghost cutoff at least 3x larger than %g* Use the communicate ghost command to set this. See the pair bop - doc page for more details. + page for more details. *Pair style born/coul/long requires atom attribute q* An atom style that defines this attribute must be used. @@ -6913,7 +6913,7 @@ keyword to allow for additional bonds to be formed *Per-atom energy was not tallied on needed timestep* You are using a thermo keyword that requires potentials to have tallied energy, but they did not on this timestep. See the - variable doc page for ideas on how to make this work. + variable page for ideas on how to make this work. *Per-atom fix in equal-style variable formula* Equal-style variables cannot use per-atom quantities. @@ -6921,7 +6921,7 @@ keyword to allow for additional bonds to be formed *Per-atom virial was not tallied on needed timestep* You are using a thermo keyword that requires potentials to have tallied the virial, but they did not on this timestep. See the - variable doc page for ideas on how to make this work. + variable page for ideas on how to make this work. *Per-processor system is too big* The number of owned atoms plus ghost atoms on a single @@ -8408,7 +8408,7 @@ keyword to allow for additional bonds to be formed *Virial was not tallied on needed timestep* You are using a thermo keyword that requires potentials to have tallied the virial, but they did not on this timestep. See the - variable doc page for ideas on how to make this work. + variable page for ideas on how to make this work. *Voro++ error: narea and neigh have a different size* This error is returned by the Voro++ library. diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index 806dec024b..d7a97c1507 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -213,7 +213,7 @@ Doc page with :doc:`ERROR messages ` in unexpected behavior. *Fix bond/swap will ignore defined angles* - See the doc page for fix bond/swap for more info on this + See the page for fix bond/swap for more info on this restriction. *Fix deposit near setting < possible overlap separation %g* diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 043820c5dd..649be52ab7 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -174,10 +174,10 @@ web site. If you uncomment the :doc:`dump image ` line(s) in the input script a series of JPG images will be produced by the run (assuming you built LAMMPS with JPG support; see the -:doc:`Build_settings ` doc page for details). These can +:doc:`Build_settings ` page for details). These can be viewed individually or turned into a movie or animated by tools like ImageMagick or QuickTime or various Windows-based tools. See the -:doc:`dump image ` doc page for more details. E.g. this +:doc:`dump image ` page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a browser. diff --git a/doc/src/Howto_barostat.rst b/doc/src/Howto_barostat.rst index 87dab8dd95..0c25e2c53c 100644 --- a/doc/src/Howto_barostat.rst +++ b/doc/src/Howto_barostat.rst @@ -50,7 +50,7 @@ a temperature or pressure compute to a barostatting fix. Thermodynamic output, which can be setup via the :doc:`thermo_style ` command, often includes pressure -values. As explained on the doc page for the +values. As explained on the page for the :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 diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index 9bffe5d4c9..172ba3da3a 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -49,7 +49,7 @@ command's documentation for the formula it computes. COMPASS is a general force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers which was developed using ab initio and empirical parameterization techniques. -See the :doc:`Tools ` doc page for the msi2lmp tool for creating +See the :doc:`Tools ` page for the msi2lmp tool for creating LAMMPS template input and data files from BIOVIA's Materials Studio files. Please note that the msi2lmp tool is very old and largely unmaintained, so it does not support all features of Materials Studio diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 0c0a930221..cc02e3d52f 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -10,7 +10,7 @@ deformable objects, etc. Note that other kinds of finite-size spherical and aspherical particles are also supported by LAMMPS, such as spheres, ellipsoids, line segments, and triangles, but they are simpler entities than body particles. See the :doc:`Howto spherical -` doc page for a general overview of all these +` page for a general overview of all these particle types. Body particles are used via the :doc:`atom_style body ` @@ -170,14 +170,14 @@ with this body style to compute body/body and body/non-body interactions. The *rounded/polygon* body style represents body particles as a 2d polygon with a variable number of N vertices. This style can only be used for 2d models; see the :doc:`boundary ` command. See the -"pair_style body/rounded/polygon" doc page for a diagram of two +"pair_style body/rounded/polygon" page for a diagram of two squares with rounded circles at the vertices. Special cases for N = 1 (circle) and N = 2 (rod with rounded ends) can also be specified. One use of this body style is for 2d discrete element models, as described in :ref:`Fraige `. -Similar to body style *nparticle*\ , the atom_style body command for +Similar to body style *nparticle*, the atom_style body command for this body style takes two additional arguments: .. parsed-literal:: @@ -284,7 +284,7 @@ The *rounded/polyhedron* body style represents body particles as a 3d polyhedron with a variable number of N vertices, E edges and F faces. This style can only be used for 3d models; see the :doc:`boundary ` command. See the "pair_style -body/rounded/polygon" doc page for a diagram of a two 2d squares with +body/rounded/polygon" page for a diagram of a two 2d squares with rounded circles at the vertices. A 3d cube with rounded spheres at the 8 vertices and 12 rounded edges would be similar. Special cases for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be @@ -293,7 +293,7 @@ specified. This body style is for 3d discrete element models, as described in :ref:`Wang `. -Similar to body style *rounded/polygon*\ , the atom_style body command +Similar to body style *rounded/polygon*, the atom_style body command for this body style takes two additional arguments: .. parsed-literal:: diff --git a/doc/src/Howto_chunk.rst b/doc/src/Howto_chunk.rst index c0a7792448..858e8241d1 100644 --- a/doc/src/Howto_chunk.rst +++ b/doc/src/Howto_chunk.rst @@ -51,7 +51,7 @@ scales the floating point value to spread it across multiple integers. Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = pencils, 3d bins = boxes, spherical bins, cylindrical bins. -This compute also calculates the number of chunks *Nchunk*\ , which is +This compute also calculates the number of chunks *Nchunk*, which is used by other commands to tally per-chunk data. *Nchunk* can be a static value or change over time (e.g. the number of clusters). The chunk ID for an individual atom can also be static (e.g. a molecule diff --git a/doc/src/Howto_client_server.rst b/doc/src/Howto_client_server.rst index c22e1ca3ab..7e21b78dfd 100644 --- a/doc/src/Howto_client_server.rst +++ b/doc/src/Howto_client_server.rst @@ -119,7 +119,7 @@ server code. Another code could be substituted for either. The examples below show launching both codes from the same window (or batch script), using the "&" character to launch the first code in the -background. For all modes except *mpi/one*\ , you could also launch the +background. For all modes except *mpi/one*, you could also launch the codes in separate windows on your desktop machine. It does not matter whether you launch the client or server first. @@ -132,7 +132,7 @@ mpirun, even if one or both of them runs on a single processor. This is so that MPI can figure out how to connect both MPI processes together to exchange MPI messages between them. -For message exchange in *file*\ , *zmq*\ , or *mpi/two* modes: +For message exchange in *file*, *zmq*, or *mpi/two* modes: .. code-block:: bash diff --git a/doc/src/Howto_coreshell.rst b/doc/src/Howto_coreshell.rst index 0c1fc924ac..bffee0ca01 100644 --- a/doc/src/Howto_coreshell.rst +++ b/doc/src/Howto_coreshell.rst @@ -5,7 +5,7 @@ The adiabatic core-shell model by :ref:`Mitchell and Fincham ` to a system. In order to mimic the electron shell of an ion, a satellite particle is attached to it. This way the ions are split into a core and a shell where the latter is meant to react to the -electrostatic environment inducing polarizability. See the :doc:`Howto polarizable ` doc page for a discussion of all +electrostatic environment inducing polarizability. See the :doc:`Howto polarizable ` page for a discussion of all the polarizable models available in LAMMPS. Technically, shells are attached to the cores by a spring force f = @@ -78,7 +78,7 @@ satellite particle if desired. Since the core/shell model permits distances of r = 0.0 between the 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 are provided in the CORESHELL package. See :doc:`this 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 Ewald solvers can be used. diff --git a/doc/src/Howto_couple.rst b/doc/src/Howto_couple.rst index 36ba2a526e..31cafd1f94 100644 --- a/doc/src/Howto_couple.rst +++ b/doc/src/Howto_couple.rst @@ -42,7 +42,7 @@ context of your application. stand-alone code could communicate with LAMMPS through files that the command writes and reads. - See the :doc:`Modify command ` doc page for info on how + See the :doc:`Modify command ` page for info on how to add a new command to LAMMPS. .. spacer diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index 46d400c9e8..589e9d7b9a 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -91,7 +91,7 @@ DRUDE package) to convert a non-polarizable data file (here This will automatically insert the new atoms and bonds. The masses and charges of DCs and DPs are computed -from *phenol.dff*\ , as well as the DC-DP bond constants. The file +from *phenol.dff*, as well as the DC-DP bond constants. The file *phenol.dff* contains the polarizabilities of the atom types and the mass of the Drude particles, for instance: @@ -106,7 +106,7 @@ and the mass of the Drude particles, for instance: The hydrogen atoms are absent from this file, so they will be treated as non-polarizable atoms. In the non-polarizable data file -*data.102494.lmp*\ , atom names corresponding to the atom type numbers +*data.102494.lmp*, atom names corresponding to the atom type numbers have to be specified as comments at the end of lines of the *Masses* section. You probably need to edit it to add these names. It should look like @@ -125,7 +125,7 @@ look like **Basic input file** -The atom style should be set to (or derive from) *full*\ , so that you +The atom style should be set to (or derive from) *full*, so that you can define atomic charges and molecular bonds, angles, dihedrals... The *polarizer* tool also outputs certain lines related to the input @@ -143,7 +143,7 @@ and N for non-polarizable atoms. Here the atom types 1 to 3 (C and O atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and the atom types 6 to 8 are the newly created DPs. -By recognizing the fix *drude*\ , LAMMPS will find and store matching +By recognizing the fix *drude*, LAMMPS will find and store matching 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 @@ -340,11 +340,11 @@ For the *thole* pair style the coefficients are The special neighbors have charge-charge and charge-dipole interactions screened by the *coul* factors of the *special_bonds* command (0.0, 0.0, and 0.5 in the example above). Without using the -pair_style *thole*\ , dipole-dipole interactions are screened by the -same factor. By using the pair_style *thole*\ , dipole-dipole +pair_style *thole*, dipole-dipole interactions are screened by the +same factor. By using the pair_style *thole*, dipole-dipole interactions are screened by Thole's function, whatever their special relationship (except within each DC-DP pair of course). Consider for -example 1-2 neighbors: using the pair_style *thole*\ , their dipoles +example 1-2 neighbors: using the pair_style *thole*, their dipoles will see each other (despite the *coul* factor being 0.) and the interactions between these dipoles will be damped by Thole's function. @@ -384,7 +384,7 @@ For our phenol example, the groups would be defined as group CORES type 1 2 3 # DCs group DRUDES type 6 7 8 # DPs -Note that with the fixes *drude/transform*\ , it is not required to +Note that with the fixes *drude/transform*, it is not required to specify *comm_modify vel yes* because the fixes do it anyway (several times and for the forces also). diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 311d716f18..0bb931fccd 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -140,8 +140,8 @@ After everything is done, add the files to the branch and commit them: flag) will automatically include **all** modified **and** new files and that is rarely the behavior you want. It can easily lead to accidentally adding unrelated and unwanted changes into the - repository. Instead it is preferable to explicitly use *git add*\ , - *git rm*\ , *git mv* for adding, removing, renaming individual files, + repository. Instead it is preferable to explicitly use *git add*, + *git rm*, *git mv* for adding, removing, renaming individual files, respectively, and then *git commit* to finalize the commit. Carefully check all pending changes with *git status* before committing them. If you find doing this on the command line too diff --git a/doc/src/Howto_kappa.rst b/doc/src/Howto_kappa.rst index 08697ecc84..ca9a418d5e 100644 --- a/doc/src/Howto_kappa.rst +++ b/doc/src/Howto_kappa.rst @@ -4,7 +4,7 @@ Calculate thermal conductivity The thermal conductivity kappa of a material can be measured in at least 4 ways using various options in LAMMPS. See the examples/KAPPA directory for scripts that implement the 4 methods discussed here for -a simple Lennard-Jones fluid model. Also, see the :doc:`Howto viscosity ` doc page for an analogous discussion +a simple Lennard-Jones fluid model. Also, see the :doc:`Howto viscosity ` page for an analogous discussion for viscosity. The thermal conductivity tensor kappa is a measure of the propensity @@ -58,7 +58,7 @@ between hot and cold regions of the simulation box. The :doc:`compute heat/flux ` command can calculate the needed heat flux and describes how to implement the Green_Kubo formalism using additional LAMMPS commands, such as the :doc:`fix ave/correlate ` command to calculate the needed -auto-correlation. See the doc page for the :doc:`compute heat/flux ` command for an example input script +auto-correlation. See the page for the :doc:`compute heat/flux ` command for an example input script that calculates the thermal conductivity of solid Ar via the GK formalism. diff --git a/doc/src/Howto_manifold.rst b/doc/src/Howto_manifold.rst index f09e3017be..8c2cbadc42 100644 --- a/doc/src/Howto_manifold.rst +++ b/doc/src/Howto_manifold.rst @@ -3,7 +3,7 @@ Manifolds (surfaces) **Overview:** -This doc page is not about a LAMMPS input script command, but about +This page is not about a LAMMPS input script command, but about manifolds, which are generalized surfaces, as defined and used by the MANIFOLD package, to track particle motion on the manifolds. See the src/MANIFOLD/README file for more details about the package diff --git a/doc/src/Howto_mdi.rst b/doc/src/Howto_mdi.rst index 7cfcd01a50..12c4cfa527 100644 --- a/doc/src/Howto_mdi.rst +++ b/doc/src/Howto_mdi.rst @@ -3,7 +3,7 @@ Using LAMMPS with the MDI library for code coupling .. note:: - This Howto doc page will eventually replace the + This Howto page will eventually replace the :doc:`Howto client/server ` doc page. Client/server coupling of two codes is where one code is the "client" @@ -120,7 +120,7 @@ input script will continue. After finishing execution of the input script, the instance of LAMMPS will be destroyed. LAMMPS supports the full set of MD-appropriate engine commands defined -by the MDI library. See the :doc:`mdi/engine ` doc page for +by the MDI library. See the :doc:`mdi/engine ` page for a list of these. If those commands are not sufficient for a user-developed driver to use diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index 61afce17ae..d17b865bbd 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -268,7 +268,7 @@ Computes that generate values to output Every :doc:`compute ` in LAMMPS produces either global or per-atom or local values. The values can be scalars or vectors or arrays of data. These values can be output using the other commands -described in this section. The doc page for each compute command +described in this section. The page for each compute command describes what it produces. Computes that produce per-atom or local values have the word "atom" or "local" in their style name. Computes without the word "atom" or "local" produce global values. @@ -281,7 +281,7 @@ Fixes that generate values to output Some :doc:`fixes ` in LAMMPS produces either global or per-atom or local values which can be accessed by other commands. The values can be scalars or vectors or arrays of data. These values can be output -using the other commands described in this section. The doc page for +using the other commands described in this section. The page for each fix command tells whether it produces any output quantities and describes them. diff --git a/doc/src/Howto_replica.rst b/doc/src/Howto_replica.rst index e34f3523f0..d286762e01 100644 --- a/doc/src/Howto_replica.rst +++ b/doc/src/Howto_replica.rst @@ -27,7 +27,7 @@ replicas are coupled together by springs to model a system of ring-polymers whic can represent the quantum nature of atom cores. These commands can only be used if LAMMPS was built with the REPLICA -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. In all these cases, you must run with one or more processors per diff --git a/doc/src/Howto_thermostat.rst b/doc/src/Howto_thermostat.rst index 7bddb1c89d..fbeb1f7785 100644 --- a/doc/src/Howto_thermostat.rst +++ b/doc/src/Howto_thermostat.rst @@ -28,7 +28,7 @@ can be invoked via the *dpd/tstat* pair style: :doc:`Fix nvt ` only thermostats the translational velocity of particles. :doc:`Fix nvt/sllod ` also does this, except that it subtracts out a velocity bias due to a deforming box and -integrates the SLLOD equations of motion. See the :doc:`Howto nemd ` doc page for further details. :doc:`Fix nvt/sphere ` and :doc:`fix nvt/asphere ` thermostat not only translation +integrates the SLLOD equations of motion. See the :doc:`Howto nemd ` page for further details. :doc:`Fix nvt/sphere ` and :doc:`fix nvt/asphere ` thermostat not only translation velocities but also rotational velocities for spherical and aspherical particles. @@ -88,7 +88,7 @@ Below is a list of some custom temperature computes that can be used like that: Thermodynamic output, which can be setup via the :doc:`thermo_style ` command, often includes temperature -values. As explained on the doc page for the +values. As explained on the page for the :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 diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 13383f44df..5e952709c9 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -23,21 +23,21 @@ origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** = 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. In LAMMPS the triclinic -simulation box edge vectors **a**\ , **b**\ , and **c** cannot be arbitrary +simulation box edge vectors **a**, **b**, and **c** cannot be arbitrary vectors. As indicated, **a** must lie on the positive x axis. **b** must lie in the xy plane, with strictly positive y component. **c** may have any orientation with strictly positive z component. The requirement -that **a**\ , **b**\ , and **c** have strictly positive x, y, and z components, -respectively, ensures that **a**\ , **b**\ , and **c** form a complete +that **a**, **b**, and **c** have strictly positive x, y, and z components, +respectively, ensures that **a**, **b**, and **c** form a complete right-handed basis. These restrictions impose no loss of generality, since it is possible to rotate/invert any set of 3 crystal basis vectors so that they conform to the restrictions. -For example, assume that the 3 vectors **A**\ ,\ **B**\ ,\ **C** are the edge +For example, assume that the 3 vectors **A**,\ **B**,\ **C** are the edge vectors of a general parallelepiped, where there is no restriction on -**A**\ ,\ **B**\ ,\ **C** other than they form a complete right-handed basis i.e. -**A** x **B** . **C** > 0. The equivalent LAMMPS **a**\ ,\ **b**\ ,\ **c** are a linear -rotation of **A**\ , **B**\ , and **C** and can be computed as follows: +**A**,\ **B**,\ **C** other than they form a complete right-handed basis i.e. +**A** x **B** . **C** > 0. The equivalent LAMMPS **a**,\ **b**,\ **c** are a linear +rotation of **A**, **B**, and **C** and can be computed as follows: .. math:: @@ -57,9 +57,9 @@ rotation of **A**\ , **B**\ , and **C** and can be computed as follows: where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^) indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles between the vectors described below. Note that by construction, -**a**\ , **b**\ , and **c** have strictly positive x, y, and z components, respectively. +**a**, **b**, and **c** have strictly positive x, y, and z components, respectively. If it should happen that -**A**\ , **B**\ , and **C** form a left-handed basis, then the above equations +**A**, **B**, and **C** form a left-handed basis, then the above equations are not valid for **c**\ . In this case, it is necessary to first apply an inversion. This can be achieved by interchanging two basis vectors or by changing the sign of one of them. @@ -95,7 +95,7 @@ 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 -style *prism*\ , then a triclinic box is setup. See the +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 box, and the header of the data file contains a line with the "xy xz @@ -135,7 +135,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are geometrically all equivalent. If the box tilt exceeds this limit during a dynamics run (e.g. via the :doc:`fix deform ` command), then the box is "flipped" to an equivalent shape with a tilt -factor within the bounds, so the run can continue. See the :doc:`fix deform ` doc page for further details. +factor within the bounds, so the run can continue. See the :doc:`fix deform ` page for further details. One exception to this rule is if the first dimension in the tilt factor (x for xy) is non-periodic. In that case, the limits on the @@ -160,10 +160,10 @@ For extreme values of tilt, LAMMPS may also lose atoms and generate an error. Triclinic crystal structures are often defined using three lattice -constants *a*\ , *b*\ , and *c*\ , and three angles :math:`\alpha`, +constants *a*, *b*, and *c*, and three angles :math:`\alpha`, :math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, the a, b, and c lattice constants are the scalar lengths of the edge -vectors **a**\ , **b**\ , and **c** defined above. The relationship +vectors **a**, **b**, and **c** defined above. The relationship between these 6 quantities (a, b, c, :math:`\alpha`, :math:`\beta`, :math:`\gamma`) and the LAMMPS box sizes (lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: @@ -188,10 +188,10 @@ The inverse relationship can be written as follows: {\rm yz} = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\ {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\ -The values of *a*\ , *b*\ , *c* , :math:`\alpha` , :math:`\beta`, and +The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and :math:`\gamma` can be printed out or accessed by computes using the :doc:`thermo_style custom ` keywords -*cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , *cellbeta*\ , *cellgamma*\ , +*cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*, respectively. As discussed on the :doc:`dump ` command doc page, when the BOX diff --git a/doc/src/Howto_viscosity.rst b/doc/src/Howto_viscosity.rst index cfe9497665..5cabf63de3 100644 --- a/doc/src/Howto_viscosity.rst +++ b/doc/src/Howto_viscosity.rst @@ -42,7 +42,7 @@ command, which determines grad(Vstream) in the equation above. E.g. the derivative in the y-direction of the Vx component of fluid motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of the pressure or stress tensor, as calculated by the :doc:`compute pressure ` command, can also be monitored, which -is the J term in the equation above. See the :doc:`Howto nemd ` doc page for details on NEMD simulations. +is the J term in the equation above. See the :doc:`Howto nemd ` page for details on NEMD simulations. The third method is to perform a reverse non-equilibrium MD simulation using the :doc:`fix viscosity ` command which implements diff --git a/doc/src/Howto_viz.rst b/doc/src/Howto_viz.rst index 2eb009c185..5a313615ef 100644 --- a/doc/src/Howto_viz.rst +++ b/doc/src/Howto_viz.rst @@ -13,7 +13,7 @@ by several popular visualization tools. The :doc:`dump image ` and : output internally rendered images and convert a sequence of them to a movie during the MD run. Several programs included with LAMMPS as auxiliary tools can convert between LAMMPS format files and other -formats. See the :doc:`Tools ` doc page for details. +formats. See the :doc:`Tools ` page for details. A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of diff --git a/doc/src/Howto_walls.rst b/doc/src/Howto_walls.rst index 6e3e22a3f0..a77f116fd4 100644 --- a/doc/src/Howto_walls.rst +++ b/doc/src/Howto_walls.rst @@ -53,7 +53,7 @@ granular particles; all the other commands create smooth walls. * :doc:`fix wall/region ` - use region surface as wall * :doc:`fix wall/gran ` - flat or curved walls with :doc:`pair_style granular ` potential -The *lj93*\ , *lj126*\ , *colloid*\ , *harmonic*\ , and *morse* styles all +The *lj93*, *lj126*, *colloid*, *harmonic*, and *morse* styles all allow the flat walls to move with a constant velocity, or oscillate in time. The :doc:`fix wall/region ` command offers the most generality, since the region surface is treated as a wall, and diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index d034ccb443..84981e1496 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -32,7 +32,7 @@ Here are suggestions on how to perform these tasks: are simple programs that will build simple molecular systems, such as linear bead-spring polymer chains. The moltemplate program is a true molecular builder that will generate complex molecular models. See - the :doc:`Tools ` doc page for details on tools packaged with + the :doc:`Tools ` page for details on tools packaged with LAMMPS. The `Pre/post processing page `_ of the LAMMPS website describes a variety of third party tools for this task. Furthermore, some LAMMPS internal commands allow to reconstruct, or selectively add @@ -49,7 +49,7 @@ Here are suggestions on how to perform these tasks: * **Simulation analysis:** If you want to perform analysis on-the-fly as your simulation runs, see the :doc:`compute ` and :doc:`fix ` doc pages, which list commands that can be used in a - LAMMPS input script. Also see the :doc:`Modify ` doc page for + LAMMPS input script. Also see the :doc:`Modify ` page for info on how to add your own analysis code or algorithms to LAMMPS. For post-processing, LAMMPS output such as :doc:`dump file snapshots ` can be converted into formats used by other MD or post-processing codes. To some degree, that conversion can be done @@ -61,7 +61,7 @@ Here are suggestions on how to perform these tasks: LAMMPS will do these conversions. Scripts provided in the tools/python directory can extract and massage data in dump files to make it easier to import into other programs. See the - :doc:`Tools ` doc page for details on these various options. + :doc:`Tools ` page for details on these various options. * **Visualization:** LAMMPS can produce NETPBM, JPG or PNG snapshot images on-the-fly via its :doc:`dump image ` command and pass them to an external program, `FFmpeg `_ to generate @@ -71,7 +71,7 @@ Here are suggestions on how to perform these tasks: LAMMPS website for visualization packages that can process LAMMPS output data. * **Plotting:** See the next bullet about Pizza.py as well as the - :doc:`Python ` doc page for examples of plotting LAMMPS + :doc:`Python ` page for examples of plotting LAMMPS output. Scripts provided with the *python* tool in the tools directory will extract and massage data in log and dump files to make it easier to analyze and plot. See the :doc:`Tools ` doc page diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst index 8ab85a0d99..930c7a6a16 100644 --- a/doc/src/Intro_overview.rst +++ b/doc/src/Intro_overview.rst @@ -25,7 +25,7 @@ the website for details. All versions can be downloaded from the LAMMPS is designed to be easy to modify or extend with new capabilities, such as new force fields, atom types, boundary -conditions, or diagnostics. See the :doc:`Modify ` doc page for +conditions, or diagnostics. See the :doc:`Modify ` page for more details. In the most general sense, LAMMPS integrates Newton's equations of diff --git a/doc/src/Modify_body.rst b/doc/src/Modify_body.rst index b923416bdc..3435b673e3 100644 --- a/doc/src/Modify_body.rst +++ b/doc/src/Modify_body.rst @@ -6,7 +6,7 @@ Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -See the :doc:`Howto body ` doc page for an overview of using +See the :doc:`Howto body ` page for an overview of using body particles and the various body styles LAMMPS supports. New styles can be created to add new kinds of body particles to LAMMPS. diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index bcd368c3a3..caf31a9196 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -62,7 +62,7 @@ them open-source, i.e. we can release them under the terms of the GPL a LGPL (version 2.1) distribution that we make available to developers on request only and with files that are authorized for that kind of distribution removed (e.g. interface to FFTW). See the -:doc:`LAMMPS license ` doc page for details. +:doc:`LAMMPS license ` page for details. .. note:: @@ -80,7 +80,7 @@ distribution removed (e.g. interface to FFTW). See the .. _lws: https://www.lammps.org -The previous sections of this doc page describe how to add new "style" +The previous sections of this page describe how to add new "style" files of various kinds to LAMMPS. Packages are simply collections of one or more new class files which are invoked as a new style within a LAMMPS input script. If designed correctly, these additions typically @@ -107,7 +107,7 @@ packages in the src directory for examples. If you are uncertain, please ask. your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per - level, **no tabs**\ , no lines over 100 characters. I/O is done via + level, **no tabs**, no lines over 100 characters. I/O is done via the C-style stdio library (mixing of stdio and iostreams is generally discouraged), class header files should not import any system headers outside of , STL containers should be avoided in headers, @@ -203,11 +203,11 @@ packages in the src directory for examples. If you are uncertain, please ask. pdf" in the doc folder. As appropriate, the text files can include inline mathematical expression or figures (see doc/JPG for examples). Additional PDF files with further details (see doc/PDF for examples) - may also be included. The doc page should also include literature + may also be included. The page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. Citation labels must be unique across all .rst files. - The "Restrictions" section of the doc page should indicate if your + The "Restrictions" section of the page should indicate if your command is only available if LAMMPS is built with the appropriate FOO package. See other package doc files for examples of how to do this. Please run at least "make html" and "make spelling" diff --git a/doc/src/Modify_fix.rst b/doc/src/Modify_fix.rst index 556c858735..f065664c6a 100644 --- a/doc/src/Modify_fix.rst +++ b/doc/src/Modify_fix.rst @@ -129,7 +129,7 @@ derived class. See fix.h for details. Typically, only a small fraction of these methods are defined for a particular fix. Setmask is mandatory, as it determines when the fix will be invoked during the timestep. Fixes that perform time -integration (\ *nve*\ , *nvt*\ , *npt*\ ) implement initial_integrate() and +integration (\ *nve*, *nvt*, *npt*\ ) implement initial_integrate() and final_integrate() to perform velocity Verlet updates. Fixes that constrain forces implement post_force(). diff --git a/doc/src/Packages.rst b/doc/src/Packages.rst index 31ac02df3c..933294a9f7 100644 --- a/doc/src/Packages.rst +++ b/doc/src/Packages.rst @@ -7,7 +7,7 @@ specific set of features. For example, force fields for molecular systems or rigid-body constraints are in packages. You can see the list of all packages and "make" commands to manage them by typing "make package" from within the src directory of the LAMMPS -distribution. The :doc:`Build package ` doc page gives +distribution. The :doc:`Build package ` page gives general info on how to install and un-install packages as part of the LAMMPS build process. diff --git a/doc/src/Python_call.rst b/doc/src/Python_call.rst index 3a09678539..796adfe1c0 100644 --- a/doc/src/Python_call.rst +++ b/doc/src/Python_call.rst @@ -43,7 +43,7 @@ complex loop with branching logic, than can be created using the simple looping and branching logic enabled by the :doc:`next ` and :doc:`if ` commands. -See the :doc:`python ` doc page and the :doc:`variable ` +See the :doc:`python ` page and the :doc:`variable ` doc page for its python-style variables for more info, including examples of Python code you can write for both pure Python operations and callbacks to LAMMPS. diff --git a/doc/src/Python_objects.rst b/doc/src/Python_objects.rst index 4c8161b8bd..4a1496632e 100644 --- a/doc/src/Python_objects.rst +++ b/doc/src/Python_objects.rst @@ -20,7 +20,7 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module. global vector or array, a single double value from the vector or array is returned, indexed by I (vector) or I and J (array). I,J are zero-based indices. - See the :doc:`Howto output ` doc page for a discussion of + See the :doc:`Howto output ` page for a discussion of global, per-atom, and local data, and of scalar, vector, and array data types. See the doc pages for individual :doc:`computes ` and :doc:`fixes ` for a description of what they calculate and diff --git a/doc/src/Python_trouble.rst b/doc/src/Python_trouble.rst index b94a043a6a..aae96d6701 100644 --- a/doc/src/Python_trouble.rst +++ b/doc/src/Python_trouble.rst @@ -41,4 +41,4 @@ first importing from the ``lammps`` module: >>> CDLL("liblammps.so") If an error occurs, carefully go through the steps in :ref:`python_install_guides` and on the -:doc:`Build_basics ` doc page about building a shared library. +:doc:`Build_basics ` page about building a shared library. diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index 35d5f829a0..3d57633df2 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -42,7 +42,7 @@ single processor. In theory you should get identical answers on any number of processors and on any machine. In practice, numerical round-off due to using floating-point math can cause slight differences and an eventual divergence of molecular dynamics trajectories. See the -:doc:`Errors common ` doc page for discussion of this. +:doc:`Errors common ` page for discussion of this. LAMMPS can run as large a problem as will fit in the physical memory of one or more processors. If you run out of memory, you must run on more diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index f8c6925dba..c4004c87e0 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -365,7 +365,7 @@ to insure that a specific Kspace processor (in the second partition) is matched up with a specific set of processors in the first partition. See the :doc:`General tips ` page for more details. -If the keyword *nth* is used with a setting *N*\ , then it means every +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 partitions via the -partition command-line switch. The first set of @@ -397,7 +397,7 @@ so that the processors in each partition will be See the "processors" command for how to insure processors from each partition could then be grouped optimally for quad-core nodes. -If the keyword is *custom*\ , then a file that specifies a permutation +If the keyword is *custom*, then a file that specifies a permutation of the processor ranks is also specified. The format of the reorder file is as follows. Any number of initial blank or comment lines (starting with a "#" character) can be present. These should be @@ -464,7 +464,7 @@ The syntax following restartfile (or remap), namely datafile keyword value ... is identical to the arguments of the :doc:`write_data ` -command. See its doc page for details. This includes its +command. See its page for details. This includes its optional keyword/value settings. ---------- @@ -505,11 +505,11 @@ The syntax following restartfile (or remap), namely group-ID dumpstyle dumpfile arg1 arg2 ... is identical to the arguments of the :doc:`write_dump ` -command. See its doc page for details. This includes what per-atom +command. See its 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 ` page for details. ---------- @@ -537,7 +537,7 @@ partition screen files file.N. **-suffix style args** Use variants of various styles if they exist. The specified style can -be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt*\ , or *hybrid*\ . These +be *gpu*, *intel*, *kk*, *omp*, *opt*, or *hybrid*\ . These refer to optional packages that LAMMPS can be built with, as described in :doc:`Accelerate performance `. The "gpu" style corresponds to the GPU package, the "intel" style to the INTEL package, the "kk" diff --git a/doc/src/Run_output.rst b/doc/src/Run_output.rst index d7d92dc5ee..8adfd4b293 100644 --- a/doc/src/Run_output.rst +++ b/doc/src/Run_output.rst @@ -152,7 +152,7 @@ information is provided about the line search and statistics on how many iterations and force-evaluations the minimizer required. Multiple force evaluations are typically done at each iteration to perform a 1d line minimization in the search direction. See the -:doc:`minimize ` doc page for more details. +:doc:`minimize ` page for more details. ---------- diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index 3b6bb8845b..656ce08bbc 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -71,7 +71,7 @@ by AMD. **Building LAMMPS with the GPU package:** -See the :ref:`Build extras ` doc page for +See the :ref:`Build extras ` page for instructions. **Run with the GPU package from the command line:** @@ -118,7 +118,7 @@ automatic selection of the number of GPUs to use. Using the "-pk" switch explicitly allows for setting of the number of GPUs/node to use and additional options. Its syntax is the same as the "package gpu" command. See the :doc:`package ` -command doc page for details, including the default values used for +command page for details, including the default values used for all its options if it is not specified. Note that the default for the :doc:`package gpu ` command is to @@ -182,7 +182,7 @@ deterministic results. calculations can be dynamically balanced across the CPU cores and GPUs. GPU-specific settings can be made which can be optimized for different hardware. See the :doc:`package ` command - doc page for details. + page for details. * As described by the :doc:`package gpu ` command, GPU accelerated pair styles can perform computations asynchronously with CPU computations. The "Pair" time reported by LAMMPS will be the diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index 20371b4256..6526f836b2 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -103,7 +103,7 @@ Quick Start for Experienced Users """"""""""""""""""""""""""""""""" LAMMPS should be built with the INTEL package installed. -Simulations should be run with 1 MPI task per physical *core*\ , +Simulations should be run with 1 MPI task per physical *core*, not *hardware thread*\ . * Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. @@ -205,7 +205,7 @@ this information can normally be obtained with: Building LAMMPS with the INTEL package """"""""""""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for +See the :ref:`Build extras ` page for instructions. Some additional details are covered here. For building with make, several example Makefiles for building with diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index c24c22e926..400db9585c 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -67,7 +67,7 @@ produce an executable compatible with a specific hardware. Building LAMMPS with the KOKKOS package """"""""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for instructions. +See the :ref:`Build extras ` page for instructions. Running LAMMPS with the KOKKOS package """""""""""""""""""""""""""""""""""""" @@ -217,7 +217,7 @@ threads/task as Nt. The product of these two values should be N, i.e. be best for many-body potentials. For simpler pair-wise potentials, it may be faster to use a "full" neighbor list with Newton flag to "off". Use the "-pk kokkos" :doc:`command-line switch ` to change - the default :doc:`package kokkos ` options. See its doc page for + the default :doc:`package kokkos ` options. See its page for details and default settings. Experimenting with its options can provide a speed-up for specific calculations. For example: @@ -279,7 +279,7 @@ one or more nodes, each with two GPUs: setting the neighbor binsize equal to twice the CPU default value will give speedup, which is the default when running on GPUs. Use the "-pk kokkos" :doc:`command-line switch ` to change the default - :doc:`package kokkos ` options. See its doc page for details and + :doc:`package kokkos ` options. See its page for details and default settings. Experimenting with its options can provide a speed-up for specific calculations. For example: diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index 060944e81b..3d9cbe19e0 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -18,7 +18,7 @@ launched by each MPI task on the local node (using shared memory). Building LAMMPS with the OPENMP package """"""""""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for +See the :ref:`Build extras ` page for instructions. Run with the OPENMP package from the command line @@ -50,7 +50,7 @@ threads per MPI task via the OMP_NUM_THREADS environment variable. You can also use the "-pk omp Nt" :doc:`command-line switch `, to explicitly set Nt = # of OpenMP threads per MPI task to use, as well as additional options. Its syntax is the -same as the :doc:`package omp ` command whose doc page gives +same as the :doc:`package omp ` command whose page gives details, including the default values used if it is not specified. It also gives more details on how to set the number of threads via the OMP_NUM_THREADS environment variable. @@ -70,7 +70,7 @@ Use the :doc:`suffix omp ` command, or you can explicitly add an You must also use the :doc:`package omp ` command to enable the OPENMP package. When you do this you also specify how many threads -per MPI task to use. The command doc page explains other options and +per MPI task to use. The command page explains other options and how to set the number of threads via the OMP_NUM_THREADS environment variable. diff --git a/doc/src/Speed_opt.rst b/doc/src/Speed_opt.rst index 338c4f2030..e115393017 100644 --- a/doc/src/Speed_opt.rst +++ b/doc/src/Speed_opt.rst @@ -15,7 +15,7 @@ Any hardware. Any compiler. Building LAMMPS with the OPT package """""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for instructions. +See the :ref:`Build extras ` page for instructions. Run with the OPT package from the command line """""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index e7cd87aa78..1165ff5a82 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -363,7 +363,7 @@ michele.ceriotti at gmail.com, to interface to a variety of molecular dynamics codes. See the tools/i-pi/manual.pdf file for an overview of i-PI, and the -:doc:`fix ipi ` doc page for further details on running PIMD +:doc:`fix ipi ` page for further details on running PIMD calculations with LAMMPS. ---------- diff --git a/doc/src/accel_styles.rst b/doc/src/accel_styles.rst index bd7d88f9d7..27a798d731 100644 --- a/doc/src/accel_styles.rst +++ b/doc/src/accel_styles.rst @@ -1,4 +1,4 @@ -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -7,11 +7,11 @@ produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index d411599eaf..0da31e54e7 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -56,7 +56,7 @@ radian\^2. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -65,13 +65,13 @@ produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See :doc:`Speed packages ` doc page for more +See :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index 280e6ea2c4..b417b7a4a2 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -54,7 +54,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc page +EXTRA-MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index 4983745618..1eb5240011 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -58,7 +58,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc page +EXTRA-MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_hybrid.rst b/doc/src/angle_hybrid.rst index 1a562b0118..cf8ea1a3fb 100644 --- a/doc/src/angle_hybrid.rst +++ b/doc/src/angle_hybrid.rst @@ -58,7 +58,7 @@ specifying additional BondBond (and BondAngle) coefficients either via the input script or in the data file. I.e. *class2* must be added to each line after the angle type. For lines in the BondBond (or BondAngle) section of the data file for angle types that are not -*class2*\ , you must use an angle style of *skip* as a placeholder, e.g. +*class2*, you must use an angle style of *skip* as a placeholder, e.g. .. parsed-literal:: diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index fe0cd3968b..50f4a5b360 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -37,7 +37,7 @@ where :math:`\theta_0` is the equilibrium value of the angle and *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 *lj/sdk*\ , however, the energy is shifted by +pair_style *lj/sdk*, however, the energy is shifted by :math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor is included in :math:`K`. diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index 540d15fee2..0715625d45 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -66,7 +66,7 @@ specified by the associated :doc:`angle_coeff ` command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the :ref:`Commands angle ` doc page are followed by one or more +The individual style names on the :ref:`Commands angle ` page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`none ` - turn off angle interactions @@ -103,7 +103,7 @@ Angle styles can only be set for atom_styles that allow angles to be defined. Most angle styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual bond potentials tell if it is part of a package. Related commands diff --git a/doc/src/atc_control_thermal.rst b/doc/src/atc_control_thermal.rst index d6d6c25405..7a17701c5c 100644 --- a/doc/src/atc_control_thermal.rst +++ b/doc/src/atc_control_thermal.rst @@ -66,7 +66,7 @@ Restrictions Only for be used with the specific controllers *thermal* or *momentum*. They are ignored if a lumped solution is requested. -*control thermal* is only for be used with specific transfers: thermal (*rescale*\ , *hoover*\ , *flux*\ ), *two_temperature* (*flux*\ ). +*control thermal* is only for be used with specific transfers: thermal (*rescale*, *hoover*, *flux*\ ), *two_temperature* (*flux*\ ). *rescale* not valid with time filtering activated *correction_max_iterations* is only for use with *thermal* physics using diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index c142fb6519..2f01877ac7 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -40,7 +40,7 @@ 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 +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 ` commands to initialize atoms. If the value is *no* the IDs for all diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 4d880077d1..bade8c2f79 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -61,7 +61,7 @@ command. Restrictions section. Once a style is assigned, it cannot be changed, so use a style general -enough to encompass all attributes. E.g. with style *bond*\ , angular +enough to encompass all attributes. E.g. with style *bond*, angular terms cannot be used or added later to the model. It is OK to use a style more general than needed, though it may be slightly inefficient. @@ -136,13 +136,13 @@ quantities. It is possible to add some attributes, such as a molecule ID, to atom styles that do not have them via the :doc:`fix property/atom ` command. This command also allows new custom attributes consisting of extra integer or - floating-point values to be added to atoms. See the :doc:`fix property/atom ` doc page for examples of cases + floating-point values to be added to atoms. See the :doc:`fix property/atom ` page for examples of cases where this is useful and details on how to initialize, access, and output the custom values. -All of the above styles define point particles, except the *sphere*\ , -*ellipsoid*\ , *electron*\ , *peri*\ , *wavepacket*\ , *line*\ , *tri*\ , and -*body* styles, which define finite-size particles. See the :doc:`Howto spherical ` doc page for an overview of using +All of the above styles define point particles, except the *sphere*, +*ellipsoid*, *electron*, *peri*, *wavepacket*, *line*, *tri*, and +*body* styles, which define finite-size particles. See the :doc:`Howto spherical ` page for an overview of using finite-size particle models with LAMMPS. All of the point-particle styles assign mass to particles on a @@ -236,7 +236,7 @@ individual physical bodies from penetrating each other. For the *spin* style, a magnetic spin is associated to each atom. Those spins have a norm (their magnetic moment) and a direction. -The *wavepacket* style is similar to *electron*\ , but the electrons may +The *wavepacket* style is similar to *electron*, but the electrons may consist of several Gaussian wave packets, summed up with coefficients cs= (cs_re,cs_im). Each of the wave packets is treated as a separate particle in LAMMPS, wave packets belonging to the same electron must @@ -256,7 +256,7 @@ command. The template stores one or more molecules with a single copy of the topology info (bonds,angles,etc) of each. Individual atoms only store a template index and template atom to identify which molecule and which atom-within-the-molecule they represent. Using the -*template* style instead of the *bond*\ , *angle*\ , *molecular* styles +*template* style instead of the *bond*, *angle*, *molecular* styles can save memory for systems comprised of a large number of small molecules, all of a single type (or small number of types). See the paper by Grime and Voth, in :ref:`(Grime) `, for examples of how this @@ -283,7 +283,7 @@ the *bstyle* argument. Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -The :doc:`Howto body ` doc page describes the body styles +The :doc:`Howto body ` page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent. For all styles, each body particle stores moments of inertia and a quaternion 4-vector, so that its @@ -332,14 +332,14 @@ styles. The accelerated styles are part of the KOKKOS package. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build -package ` doc page for more info. +package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. Restrictions @@ -350,9 +350,9 @@ This command cannot be used after the simulation box is defined by a 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. +` page for more info. -The *angle*\ , *bond*\ , *full*\ , *molecular*\ , and *template* styles are +The *angle*, *bond*, *full*, *molecular*, and *template* styles are part of the MOLECULE package. The *line* and *tri* styles are part of the ASPHERE package. @@ -370,7 +370,7 @@ The *electron* style is part of the EFF package for :doc:`electronic force field The *dpd* style is part of the DPD-REACT package for dissipative particle dynamics (DPD). -The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the DPD-MESO package +The *edpd*, *mdpd*, and *tdpd* styles are part of the DPD-MESO package for energy-conserving dissipative particle dynamics (eDPD), many-body dissipative particle dynamics (mDPD), and transport dissipative particle dynamics (tDPD), respectively. diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 5d42fabb21..b3ac360ca2 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -11,7 +11,7 @@ Syntax balance thresh style args ... keyword args ... * thresh = imbalance threshold that must be exceeded to perform a re-balance -* one style/arg pair can be used (or multiple for *x*\ ,\ *y*\ ,\ *z*\ ) +* one style/arg pair can be used (or multiple for *x*,\ *y*,\ *z*\ ) * style = *x* or *y* or *z* or *shift* or *rcb* .. parsed-literal:: @@ -170,10 +170,10 @@ fractions of the box length) are also printed. ---------- The method used to perform a load balance is specified by one of the -listed styles (or more in the case of *x*\ ,\ *y*\ ,\ *z*\ ), which are +listed styles (or more in the case of *x*,\ *y*,\ *z*\ ), which are described in detail below. There are 2 kinds of styles. -The *x*\ , *y*\ , *z*\ , and *shift* styles are "grid" methods which +The *x*, *y*, *z*, and *shift* styles are "grid" methods which produce a logical 3d grid of processors. They operate by changing the cutting planes (or lines) between processors in 3d (or 2d), to adjust the volume (area in 2d) assigned to each processor, as in the @@ -222,7 +222,7 @@ from scratch. ---------- -The *x*\ , *y*\ , and *z* styles invoke a "grid" method for balancing, as +The *x*, *y*, and *z* styles invoke a "grid" method for balancing, as described above. Note that any or all of these 3 styles can be specified together, one after the other, but they cannot be used with any other style. This style adjusts the position of cutting planes @@ -263,7 +263,7 @@ once. You should normally only list dimensions where you expect there to be a density variation in the particles. Balancing proceeds by adjusting the cutting planes in each of the -dimensions listed in *dimstr*\ , one dimension at a time. For a single +dimensions listed in *dimstr*, one dimension at a time. For a single dimension, the balancing operation (described below) is iterated on up to *Niter* times. After each dimension finishes, the imbalance factor is re-computed, and the balancing operation halts if the *stopthresh* @@ -428,8 +428,8 @@ weights. It assigns the same weight to each particle owned by a processor based on the total computational time spent by that processor. See details below on what time window is used. It uses the same timing information as is used for the :doc:`MPI task timing -breakdown `, namely, for sections *Pair*\ , *Bond*\ , -*Kspace*\ , and *Neigh*\ . The time spent in those portions of the +breakdown `, namely, for sections *Pair*, *Bond*, +*Kspace*, and *Neigh*\ . The time spent in those portions of the timestep are measured for each MPI rank, summed, then divided by the number of particles owned by that processor. I.e. the weight is an effective CPU time/particle averaged over the particles on that @@ -455,7 +455,7 @@ are for the entire previous run. For the *fix balance* command the timing data is for only the timesteps since the last balancing operation was performed. If timing information for the required sections is not available, e.g. at the beginning of a run, or when the -:doc:`timer ` command is set to either *loop* or *off*\ , a warning +:doc:`timer ` command is set to either *loop* or *off*, a warning is issued. In this case no weights are computed. .. note:: diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index aea503738f..559e031229 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -55,7 +55,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the CLASS2 -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index 0c6a37ca62..108f538628 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -58,7 +58,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. You typically should specify :doc:`special_bonds fene ` diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index 1be06561e9..8e04da6146 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -60,7 +60,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. You typically should specify :doc:`special_bonds fene ` diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index d4eb958ebe..16b5cb0f36 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -51,7 +51,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index e3320f2e19..a76cc54746 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -53,7 +53,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_hybrid.rst b/doc/src/bond_hybrid.rst index 0da93ccade..1ffd4a1c98 100644 --- a/doc/src/bond_hybrid.rst +++ b/doc/src/bond_hybrid.rst @@ -64,7 +64,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Unlike other bond styles, the hybrid bond style does not store bond diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index f096624ba0..4aa76a6712 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -52,7 +52,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index 77271502ea..91bd03421a 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -51,8 +51,8 @@ or :doc:`read_restart ` commands: Restrictions """""""""""" -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +This bond style can only be used if LAMMPS was built with the EXTRA-MOLECULE +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 3b35f92d89..f863c0e98f 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -39,7 +39,7 @@ Examples Description """"""""""" -The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential +The *oxdna/fene*, *oxdna2/fene*, and *oxrna2/fene* bond styles use the potential .. math:: @@ -118,7 +118,7 @@ Restrictions This bond style can only be used if LAMMPS was built with the CG-DNA package and the MOLECULE and ASPHERE package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index 8c5b363e54..89c33607ac 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -96,7 +96,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. The *quartic* style requires that :doc:`special_bonds ` diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index e302ea792d..177dc8cc05 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -111,7 +111,7 @@ Bond styles can only be set for atom styles that allow bonds to be defined. Most bond styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual bond potentials tell if it is part of a package. Related commands diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index fedb50355d..898503b951 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -143,7 +143,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index aa68357e1d..d6458e7c39 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -10,7 +10,7 @@ Syntax boundary x y z -* x,y,z = *p* or *s* or *f* or *m*\ , one or two letters +* x,y,z = *p* or *s* or *f* or *m*, one or two letters .. parsed-literal:: @@ -45,17 +45,17 @@ the other end. A periodic dimension can change in size due to constant pressure boundary conditions or box deformation (see the :doc:`fix npt ` and :doc:`fix deform ` commands). The *p* style must be applied to both faces of a dimension. -The styles *f*\ , *s*\ , and *m* mean the box is non-periodic, so that +The styles *f*, *s*, and *m* mean the box is non-periodic, so that particles do not interact across the boundary and do not move from one side of the box to the other. -For style *f*\ , the position of the face is fixed. If an atom moves +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 allow for lost atoms. -For style *s*\ , the position of the face is set so as to encompass the +For style *s*, the position of the face is set so as to encompass the atoms in that dimension (shrink-wrapping), no matter how far they move. Note that when the difference between the current box dimensions and the shrink-wrap box dimensions is large, this can lead to lost @@ -67,7 +67,7 @@ This is best addressed by setting initial box dimensions to match the shrink-wrapped dimensions more closely, by using *m* style boundaries (see below). -For style *m*\ , shrink-wrapping occurs, but is bounded by the value +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 face has a value of 50.0 in the data file, the face will always be @@ -85,7 +85,7 @@ and xhi faces of the box are planes tilting in the +y direction as y increases. These tilted planes are shrink-wrapped around the atoms to determine the x extent of the box. -See the :doc:`Howto triclinic ` doc page for a +See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. diff --git a/doc/src/box.rst b/doc/src/box.rst index c5937df75c..b9c586b6f7 100644 --- a/doc/src/box.rst +++ b/doc/src/box.rst @@ -34,15 +34,15 @@ 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 -skewed the triclinic box is; see the :doc:`Howto triclinic ` doc page for a discussion of triclinic +skewed the triclinic box is; see the :doc:`Howto triclinic ` page for a discussion of triclinic boxes in LAMMPS. LAMMPS normally requires that no tilt factor can skew the box more than half the distance of the parallel box length, which is the first dimension in the tilt factor (x for xz). If *tilt* is set to -*small*\ , which is the default, then an error will be +*small*, which is the default, then an error will be generated if a box is created which exceeds this limit. If *tilt* -is set to *large*\ , then no limit is enforced. You can create +is set to *large*, then no limit is enforced. You can create a box with any tilt factors you wish. Note that if a simulation box has a large tilt factor, LAMMPS will run diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst index 328326a83a..f63949bcd8 100644 --- a/doc/src/change_box.rst +++ b/doc/src/change_box.rst @@ -16,7 +16,7 @@ Syntax .. parsed-literal:: parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *boundary* or *ortho* or *triclinic* or *set* or *remap* - *x*\ , *y*\ , *z* args = style value(s) + *x*, *y*, *z* args = style value(s) style = *final* or *delta* or *scale* or *volume* *final* values = lo hi lo hi = box boundaries after displacement (distance units) @@ -25,14 +25,14 @@ Syntax *scale* values = factor factor = multiplicative factor for change in box length after displacement *volume* value = none = adjust this dim to preserve volume of system - *xy*\ , *xz*\ , *yz* args = style value + *xy*, *xz*, *yz* args = style value style = *final* or *delta* *final* value = tilt tilt = tilt factor after displacement (distance units) *delta* value = dtilt dtilt = change in tilt factor after displacement (distance units) *boundary* args = x y z - x,y,z = *p* or *s* or *f* or *m*\ , one or two letters + x,y,z = *p* or *s* or *f* or *m*, one or two letters *p* is periodic *f* is non-periodic and fixed *s* is non-periodic and shrink-wrapped @@ -82,7 +82,7 @@ The :doc:`create_box `, :doc:`read data `, and simulation box is orthogonal or triclinic and their doc pages explain the meaning of the xy,xz,yz tilt factors. -See the :doc:`Howto triclinic ` doc page for a +See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. @@ -179,18 +179,18 @@ new owning processors. ---------- -For the *x*\ , *y*\ , and *z* parameters, this is the meaning of their +For the *x*, *y*, and *z* parameters, this is the meaning of their styles and values. -For style *final*\ , the final lo and hi box boundaries of a dimension +For style *final*, the final lo and hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. See the discussion of the units keyword below. -For style *delta*\ , plus or minus changes in the lo/hi box boundaries +For style *delta*, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. See the discussion of the units keyword below. -For style *scale*\ , a multiplicative factor to apply to the box length +For style *scale*, a multiplicative factor to apply to the box length of a dimension is specified. For example, if the initial box length is 10, and the factor is 1.1, then the final box length will be 11. A factor less than 1.0 means compression. @@ -199,7 +199,7 @@ The *volume* style changes the specified dimension in such a way that the overall box volume remains constant with respect to the operation performed by the preceding keyword. The *volume* style can only be used following a keyword that changed the volume, which is any of the -*x*\ , *y*\ , *z* keywords. If the preceding keyword "key" had a *volume* +*x*, *y*, *z* keywords. If the preceding keyword "key" had a *volume* style, then both it and the current keyword apply to the keyword preceding "key". I.e. this sequence of keywords is allowed: @@ -249,15 +249,15 @@ compressed around its mid point. ---------- -For the *xy*\ , *xz*\ , and *yz* parameters, this is the meaning of their +For the *xy*, *xz*, and *yz* parameters, this is the meaning of their styles and values. Note that changing the tilt factors of a triclinic box does not change its volume. -For style *final*\ , the final tilt factor is specified. The value +For style *final*, the final tilt factor is specified. The value can be in lattice or box distance units. See the discussion of the units keyword below. -For style *delta*\ , a plus or minus change in the tilt factor is +For style *delta*, a plus or minus change in the tilt factor is specified. The value can be in lattice or box distance units. See the discussion of the units keyword below. @@ -281,10 +281,10 @@ 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 style *p* means the box is periodic; the other styles mean -non-periodic. For style *f*\ , the position of the face is fixed. For -style *s*\ , the position of the face is set so as to encompass the +non-periodic. For style *f*, the position of the face is fixed. For +style *s*, the position of the face is set so as to encompass the atoms in that dimension (shrink-wrapping), no matter how far they -move. For style *m*\ , shrink-wrapping occurs, but is bounded by the +move. For style *m*, shrink-wrapping occurs, but is bounded by the current box edge in that dimension, so that the box will become no smaller. See the :doc:`boundary ` command for more explanation of these style options. diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 27b370c941..914509b14d 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -80,7 +80,7 @@ with the *multi* neighbor style. The *multi/old* communication mode is comparabl with both the *multi* and *multi/old* neighbor styles. The *cutoff* keyword allows you to extend the ghost cutoff distance -for communication mode *single*\ , which is the distance from the borders +for communication mode *single*, which is the distance from the borders of a processor's sub-domain at which ghost atoms are acquired from other processors. By default the ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See the :doc:`neighbor ` command @@ -96,7 +96,7 @@ style present and no *comm_modify cutoff* command used. Otherwise a warning is printed, if this bond based estimate is larger than the communication cutoff used. -The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to +The *cutoff/multi* option is equivalent to *cutoff*, but applies to communication mode *multi* instead. Since the communication cutoffs are determined per atom collections, a collection specifier is needed and cutoff for one or multiple collections can be extended. Also ranges of @@ -132,9 +132,9 @@ different processors, or when the interaction straddles a periodic boundary. The appropriate ghost cutoff depends on the :doc:`newton bond ` -setting. For newton bond *off*\ , the distance needs to be the furthest +setting. For newton bond *off*, the distance needs to be the furthest distance between any two atoms in the bond, angle, etc. E.g. the -distance between 1-4 atoms in a dihedral. For newton bond *on*\ , the +distance between 1-4 atoms in a dihedral. For newton bond *on*, the distance between the central atom in the bond, angle, etc and any other atom is sufficient. E.g. the distance between 2-4 atoms in a dihedral. @@ -173,7 +173,7 @@ The *vel* keyword enables velocity information to be communicated with 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 +*yes*, then ghost atoms store these quantities; if *no* then they do not. The *yes* setting is needed by some pair styles which require the velocity state of both the I and J particles to compute a pairwise I,J interaction, as well as by some compute and fix commands. diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 7a89c6cc87..71d3bada76 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -35,7 +35,7 @@ information about a previous state of the system. Defining a compute does not perform a computation. Instead computes are invoked by other LAMMPS commands as needed, e.g. to calculate a temperature needed for a thermostat fix or to generate thermodynamic or dump file output. -See the :doc:`Howto output ` doc page for a summary of +See the :doc:`Howto output ` page for a summary of various LAMMPS output options, many of which involve computes. The ID of a compute can only contain alphanumeric characters and @@ -59,7 +59,7 @@ style produce global quantities. Note that a single compute can produce either global or per-atom or local quantities, but not both global and per-atom. It can produce local quantities in tandem with global or per-atom quantities. The -compute doc page will explain. +compute page will explain. Global, per-atom, and local quantities each come in three kinds: a single scalar value, a vector of values, or a 2d array of values. The @@ -119,7 +119,7 @@ values by the number of atoms in the system, depending on the "thermo_modify norm" setting. It will not normalize intensive values. If a compute value is accessed in another way, e.g. by a :doc:`variable `, you may want to know whether it is an -intensive or extensive value. See the doc page for individual +intensive or extensive value. See the page for individual computes for further info. ---------- @@ -153,19 +153,19 @@ via the :doc:`compute_modify ` command. Computes can be deleted with the :doc:`uncompute ` command. Code for new computes can be added to LAMMPS; see the -:doc:`Modify ` doc page for details. The results of their +:doc:`Modify ` page for details. The results of their calculations accessed in the various ways described above. ---------- -Each compute style has its own doc page which describes its arguments +Each compute style has its own page which describes its arguments and what it does. Here is an alphabetic list of compute styles available in LAMMPS. They are also listed in more compact form on the :doc:`Commands compute ` doc page. There are also additional accelerated compute styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the :doc:`Commands compute ` doc page are followed by one or more of +The individual style names on the :doc:`Commands compute ` page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`ackland/atom ` - determines the local lattice structure based on the Ackland formulation diff --git a/doc/src/compute_ackland_atom.rst b/doc/src/compute_ackland_atom.rst index b4d4268244..0dc6630980 100644 --- a/doc/src/compute_ackland_atom.rst +++ b/doc/src/compute_ackland_atom.rst @@ -63,14 +63,14 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. Restrictions """""""""""" This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The per-atom vector values will be unitless since they are the integers defined above. diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index 6ec5c5bc10..31351a547c 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -62,7 +62,7 @@ neighbor atom in each requested ADF. 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 - using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ , + using long-range coulomb interactions (\ *coul/long*, *coul/msm*, *coul/wolf* or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and @@ -81,7 +81,7 @@ neighbor atom in each requested ADF. cannot be performed, and LAMMPS will give an error message. The *skin* value is what is specified with the :doc:`neighbor ` command. -The *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN* settings can be specified in one of two +The *itypeN*,\ *jtypeN*,\ *ktypeN* settings can be specified in one of two ways. An explicit numeric value can be used, as in the first example above. Or a wild-card asterisk can be used to specify a range of atom types as in the second example above. @@ -92,10 +92,10 @@ all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A middle asterisk means all types from m to n (inclusive). -If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the first example +If *itypeN*, *jtypeN*, and *ktypeN* are single values, as in the first example above, this means that the ADF is computed where atoms of type *itypeN* are the central atom, and neighbor atoms of type *jtypeN* and *ktypeN* -are forming the angle. If any of *itypeN*\ , *jtypeN*\ , or *ktypeN* +are forming the angle. If any of *itypeN*, *jtypeN*, or *ktypeN* represent a range of values via the wild-card asterisk, as in the second example above, this means that the ADF is computed where atoms of any of the range of types represented @@ -103,7 +103,7 @@ by *itypeN* are the central atom, and the angle is formed by two neighbors, one neighbor in the range of types represented by *jtypeN* and another neighbor in the range of types represented by *ktypeN*\ . -If no *itypeN*\ , *jtypeN*\ , *ktypeN* settings are specified, then +If no *itypeN*, *jtypeN*, *ktypeN* settings are specified, then LAMMPS will generate a single ADF for all atoms in the group. The inner cutoff is set to zero and the outer cutoff is set to the force cutoff. If no pair_style is specified, there is no @@ -135,7 +135,7 @@ Each unique angle satisfying the above criteria is counted only once, regardless of whether either or both of the neighbor atoms making up the angle appear in both the J and K lists. It is OK if a particular angle is included in more than -one individual histogram, due to the way the *itypeN*\ , *jtypeN*\ , *ktypeN* +one individual histogram, due to the way the *itypeN*, *jtypeN*, *ktypeN* arguments are specified. The first ADF value for a bin is calculated from the histogram count by @@ -177,13 +177,13 @@ Output info """"""""""" This compute calculates a global array with the number of rows = -*Nbins*\ , and the number of columns = 1 + 2\*Ntriples, where Ntriples is the +*Nbins*, and the number of columns = 1 + 2\*Ntriples, where Ntriples is the number of I,J,K triples specified. The first column has the bin coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has -the two ADF values for a specific set of (\ *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN*\ ) +the two ADF values for a specific set of (\ *itypeN*,\ *jtypeN*,\ *ktypeN*\ ) interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values calculated by this compute are all "intensive". @@ -191,7 +191,7 @@ The array values calculated by this compute are all "intensive". The first column of array values is the angle-related ordinate, either the angle in degrees or radians, or the cosine of the angle. Each subsequent pair of columns gives the first and second kinds of ADF -for a specific set of (\ *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN*\ ). The values +for a specific set of (\ *itypeN*,\ *jtypeN*,\ *ktypeN*\ ). The values in the first ADF column are normalized numbers >= 0.0, whose integral w.r.t. the ordinate is 1, i.e. the first ADF is a normalized probability distribution. @@ -204,6 +204,9 @@ angles per atom satisfying the ADF criteria. Restrictions """""""""""" +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. + The ADF is not computed for neighbors outside the force cutoff, since processors (in parallel) don't know about atom coordinates for atoms further away than that distance. If you want an ADF for larger diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst index f3e5ee93c0..93677b4953 100644 --- a/doc/src/compute_angle.rst +++ b/doc/src/compute_angle.rst @@ -38,7 +38,7 @@ 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 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 +or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index 169ef4f238..688bfbeecb 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -128,7 +128,7 @@ array is the number of angles. If a single value is specified, a local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of values. The vector or array can be accessed by any command that uses -local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *theta* will be in degrees. The output for *eng* will diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index da27cb3d19..10678c4e47 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -75,7 +75,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 3 for the 3 xyz components of the angular momentum for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_basal_atom.rst b/doc/src/compute_basal_atom.rst index e1b04d48c4..3a74379acb 100644 --- a/doc/src/compute_basal_atom.rst +++ b/doc/src/compute_basal_atom.rst @@ -59,7 +59,7 @@ Restrictions """""""""""" This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The output of this compute will be meaningless unless the atoms are on (or near) hcp lattice sites, since the calculation assumes a diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index e0369049cb..662838b08f 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -36,7 +36,7 @@ Define a computation that calculates properties of individual body sub-particles. The number of datums generated, aggregated across all processors, equals the number of body sub-particles plus the number of non-body particles in the system, modified by the group parameter as -explained below. See the :doc:`Howto body ` doc page for +explained below. See the :doc:`Howto body ` page for more details on using body particles. The local data stored by this command is generated by looping over all @@ -52,7 +52,7 @@ For both body particles and non-body particles, the *type* keyword will store the type of the particle. The *integer* keywords mean different things for body and non-body -particles. If the atom is not a body particle, only its *x*\ , *y*\ , *z* +particles. If the atom is not a body particle, only its *x*, *y*, *z* coordinates can be referenced, using the *integer* keywords 1,2,3. Note that this means that if you want to access more fields than this for body particles, then you cannot include non-body particles in the @@ -84,7 +84,7 @@ is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The :doc:`units ` for output values depend on the body style. diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst index 00b99d1f9f..ddca97420d 100644 --- a/doc/src/compute_bond.rst +++ b/doc/src/compute_bond.rst @@ -38,7 +38,7 @@ 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. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index 5264a86634..8bdde70dd9 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -21,7 +21,7 @@ Syntax *engpot* = bond potential energy *force* = bond force - *fx*\ ,\ *fy*\ ,\ *fz* = components of bond force + *fx*,\ *fy*,\ *fz* = components of bond force *engvib* = bond kinetic energy of vibration *engrot* = bond kinetic energy of rotation *engtrans* = bond kinetic energy of translation @@ -70,7 +70,7 @@ based on the current separation of the pair of atoms in the bond. The value *force* is the magnitude of the force acting between the pair of atoms in the bond. -The values *fx*\ , *fy*\ , and *fz* are the xyz components of +The values *fx*, *fy*, and *fz* are the xyz components of *force* between the pair of atoms in the bond. The remaining properties are all computed for motion of the two atoms @@ -178,13 +178,13 @@ array is the number of bonds. If a single value is specified, a local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of values. The vector or array can be accessed by any command that uses local -values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *dist* will be in distance :doc:`units `. The output for *velvib* will be in velocity :doc:`units `. The output for *omega* will be in velocity/distance :doc:`units `. The -output for *engtrans*\ , *engvib*\ , *engrot*\ , and *engpot* will be in +output for *engtrans*, *engvib*, *engrot*, and *engpot* will be in energy :doc:`units `. The output for *force* will be in force :doc:`units `. diff --git a/doc/src/compute_centro_atom.rst b/doc/src/compute_centro_atom.rst index b250634b5c..3d32b75459 100644 --- a/doc/src/compute_centro_atom.rst +++ b/doc/src/compute_centro_atom.rst @@ -76,7 +76,7 @@ positive parameter. If the atom does not have :math:`N` neighbors (within the potential cutoff), then its centro-symmetry parameter is set to 0.0. -If the keyword *axes* has the setting *yes*\ , then this compute also +If the keyword *axes* has the setting *yes*, then this compute also estimates three symmetry axes for each atom's local neighborhood. The first two of these are the vectors joining the two pairs of neighbor atoms with smallest contributions to the centrosymmetry parameter, @@ -106,10 +106,10 @@ Output info By default, this compute calculates the centrosymmetry value for each atom as a per-atom vector, which can be accessed by any command that -uses per-atom values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -If the *axes* keyword setting is *yes*\ , then a per-atom array is +If the *axes* keyword setting is *yes*, then a per-atom array is calculated. The first column is the centrosymmetry parameter. The next three columns are the x, y, and z components of the first symmetry axis, followed by the second, and third symmetry axes in diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index a650c8fb0a..42a5ca9301 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -108,7 +108,7 @@ can simply be accessed by any command that uses per-atom values from a compute as input, as discussed on the :doc:`Howto output ` doc page. -See the :doc:`Howto chunk ` doc page for an overview of how +See the :doc:`Howto chunk ` page for an overview of how this compute can be used with a variety of other commands to tabulate properties of a simulation. The page gives several examples of input script commands that can be used to calculate interesting properties. @@ -130,7 +130,7 @@ those chunks, or not assigned to any chunk. There are many options for specifying for how and when *Nchunk* is calculated, and how and when chunk IDs are assigned to atoms. The -details depend on the chunk *style* and its *args*\ , as well as +details depend on the chunk *style* and its *args*, as well as optional keyword settings. They can also depend on whether a :doc:`fix ave/chunk ` command is using this compute, since that command requires *Nchunk* to remain static across windows of timesteps it specifies, while it accumulates per-chunk averages. @@ -153,13 +153,13 @@ size changes. This also depends on the setting of the *units* keyword; e.g. for *reduced* units the number of chunks may not change even if the box size does. -The *bin/1d*\ , *bin/2d*\ , and *bin/3d* styles define bins as 1d layers -(slabs), 2d pencils, or 3d boxes. The *dim*\ , *origin*\ , and *delta* +The *bin/1d*, *bin/2d*, and *bin/3d* styles define bins as 1d layers +(slabs), 2d pencils, or 3d boxes. The *dim*, *origin*, and *delta* settings are specified 1, 2, or 3 times. For 2d or 3d bins, there is no restriction on specifying dim = x before dim = y or z, or dim = y before dim = z. Bins in a particular *dim* have a bin size in that dimension given by *delta*\ . In each dimension, bins are defined -relative to a specified *origin*\ , which may be the lower/upper edge of +relative to a specified *origin*, which may be the lower/upper edge of the simulation box (in that dimension), or its center point, or a specified coordinate value. Starting at the origin, sufficient bins are created in both directions to completely span the simulation box @@ -168,7 +168,7 @@ or the bounds specified by the optional *bounds* keyword. For orthogonal simulation boxes, the bins are layers, pencils, or boxes aligned with the xyz coordinate axes. For triclinic (non-orthogonal) simulation boxes, the bin faces are parallel to the -tilted faces of the simulation box. See the :doc:`Howto triclinic ` doc page for a discussion of the +tilted faces of the simulation box. See the :doc:`Howto triclinic ` page for a discussion of the geometry of triclinic boxes in LAMMPS. As described there, a tilted simulation box has edge vectors a,b,c. In that nomenclature, bins in the x dimension have faces with normals in the "b" cross "c" @@ -188,7 +188,7 @@ means there will be 10 layers from 0.0 to 1.0, regardless of the current size or shape of the simulation box. The *bin/sphere* style defines a set of spherical shell bins around -the origin (\ *xorig*\ ,\ *yorig*\ ,\ *zorig*\ ), using *nsbin* bins with radii +the origin (\ *xorig*,\ *yorig*,\ *zorig*\ ), using *nsbin* bins with radii equally spaced between *srmin* and *srmax*\ . This is effectively a 1d vector of bins. For example, if *srmin* = 1.0 and *srmax* = 10.0 and *nsbin* = 9, then the first bin spans 1.0 < r < 2.0, and the last bin @@ -199,12 +199,12 @@ transform them into ellipsoidal shells. The *bin/cylinder* style defines bins for a cylinder oriented along the axis *dim* with the axis coordinates in the other two radial -dimensions at (\ *c1*\ ,\ *c2*\ ). For dim = x, c1/c2 = y/z; for dim = y, +dimensions at (\ *c1*,\ *c2*\ ). For dim = x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array of bins. The first dimension is along the cylinder axis, the second dimension is radially outward from the cylinder axis. The bin size and positions along the cylinder axis are specified by the *origin* -and *delta* values, the same as for the *bin/1d*\ , *bin/2d*\ , and +and *delta* values, the same as for the *bin/1d*, *bin/2d*, and *bin/3d* styles. There are *ncbin* concentric circle bins in the radial direction from the cylinder axis with radii equally spaced between *crmin* and *crmax*\ . For example, if *crmin* = 1.0 and @@ -216,12 +216,12 @@ scaled differently in the two different dimensions to transform them into ellipses. The created bins (and hence the chunk IDs) are numbered consecutively -from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*\ , the +from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*, the numbering varies most rapidly in the first dimension (which could be x, y, or z), next rapidly in the second dimension, and most slowly in the -third dimension. For *bin/sphere*\ , the bin with smallest radii is chunk +third dimension. For *bin/sphere*, the bin with smallest radii is chunk 1 and the bni with largest radii is chunk Nchunk = *ncbin*\ . For -*bin/cylinder*\ , the numbering varies most rapidly in the dimension +*bin/cylinder*, the numbering varies most rapidly in the dimension along the cylinder axis and most slowly in the radial direction. Each time this compute is invoked, each atom is mapped to a bin based @@ -254,7 +254,7 @@ only the first time that *Nchunk* is calculated. Note that atoms with a molecule ID = 0, which may be non-molecular solvent atoms, have an out-of-range chunk ID. These atoms are -discarded (not assigned to any chunk) or assigned to *Nchunk*\ , +discarded (not assigned to any chunk) or assigned to *Nchunk*, depending on the value of the *discard* keyword. ---------- @@ -304,14 +304,14 @@ explained below, the *nchunk* keyword can be set to *once* which means If a :doc:`fix ave/chunk ` command uses this compute, it can also turn off the re-calculation of *Nchunk* for one or more windows of timesteps. The extent of the windows, during which Nchunk -is held constant, are determined by the *Nevery*\ , *Nrepeat*\ , *Nfreq* +is held constant, are determined by the *Nevery*, *Nrepeat*, *Nfreq* values and the *ave* keyword setting that are used by the :doc:`fix ave/chunk ` command. -Specifically, if *ave* = *one*\ , then for each span of *Nfreq* +Specifically, if *ave* = *one*, then for each span of *Nfreq* timesteps, *Nchunk* is held constant between the first timestep when averaging is done (within the Nfreq-length window), and the last timestep when averaging is done (multiple of Nfreq). If *ave* = -*running* or *window*\ , then *Nchunk* is held constant forever, +*running* or *window*, then *Nchunk* is held constant forever, starting on the first timestep when the :doc:`fix ave/chunk ` command invokes this compute. Note that multiple :doc:`fix ave/chunk ` commands can use @@ -336,9 +336,9 @@ The *nchunk* keyword applies to all chunk styles. It specifies how often *Nchunk* is recalculated, which in turn can affect the chunk IDs assigned to individual atoms. -If *nchunk* is set to *once*\ , then *Nchunk* is only calculated once, +If *nchunk* is set to *once*, then *Nchunk* is only calculated once, the first time this compute is invoked. If *nchunk* is set to -*every*\ , then *Nchunk* is re-calculated every time the compute is +*every*, then *Nchunk* is re-calculated every time the compute is invoked. Note that, as described above, the use of this compute by the :doc:`fix ave/chunk ` command can override the *every* setting. @@ -358,12 +358,12 @@ any atom. The *limit* keyword is used by all chunk styles except the can be tailored using the *bound* keyword (described below) which effectively limits the size of *Nchunk*\ . -If *limit* is set to *Nc* = 0, then no limit is imposed on *Nchunk*\ , -though the *compress* keyword can still be used to reduce *Nchunk*\ , as +If *limit* is set to *Nc* = 0, then no limit is imposed on *Nchunk*, +though the *compress* keyword can still be used to reduce *Nchunk*, as described below. If *Nc* > 0, then the effect of the *limit* keyword depends on whether -the *compress* keyword is also used with a setting of *yes*\ , and +the *compress* keyword is also used with a setting of *yes*, and whether the *compress* keyword is specified before the *limit* keyword or after. @@ -371,11 +371,11 @@ In all cases, *Nchunk* is first calculated in the usual way for each chunk style, as described above. First, here is what occurs if *compress yes* is not set. If *limit* -is set to *Nc max*\ , then *Nchunk* is reset to the smaller of *Nchunk* -and *Nc*\ . If *limit* is set to *Nc exact*\ , then *Nchunk* is reset to -*Nc*\ , whether the original *Nchunk* was larger or smaller than *Nc*\ . +is set to *Nc max*, then *Nchunk* is reset to the smaller of *Nchunk* +and *Nc*\ . If *limit* is set to *Nc exact*, then *Nchunk* is reset to +*Nc*, whether the original *Nchunk* was larger or smaller than *Nc*\ . If *Nchunk* shrank due to the *limit* setting, then atom chunk IDs > -*Nchunk* will be reset to 0 or *Nchunk*\ , depending on the setting of +*Nchunk* will be reset to 0 or *Nchunk*, depending on the setting of the *discard* keyword. If *Nchunk* grew, there will simply be some chunks with no atoms assigned to them. @@ -384,21 +384,21 @@ If *compress yes* is set, and the *compress* keyword comes before the described below, which resets *Nchunk*\ . The *limit* keyword is then applied to the new *Nchunk* value, exactly as described in the preceding paragraph. Note that in this case, all atoms will end up -with chunk IDs <= *Nc*\ , but their original values (e.g. molecule ID or -compute/fix/variable) may have been > *Nc*\ , because of the compression +with chunk IDs <= *Nc*, but their original values (e.g. molecule ID or +compute/fix/variable) may have been > *Nc*, because of the compression operation. If *compress yes* is set, and the *compress* keyword comes after the *limit* keyword, then the *limit* value of *Nc* is applied first to -the uncompressed value of *Nchunk*\ , but only if *Nc* < *Nchunk* +the uncompressed value of *Nchunk*, but only if *Nc* < *Nchunk* (whether *Nc max* or *Nc exact* is used). This effectively means all -atoms with chunk IDs > *Nc* have their chunk IDs reset to 0 or *Nc*\ , +atoms with chunk IDs > *Nc* have their chunk IDs reset to 0 or *Nc*, depending on the setting of the *discard* keyword. The compression operation is then performed, which may shrink *Nchunk* further. If the new *Nchunk* < *Nc* and *limit* = *Nc exact* is specified, then -*Nchunk* is reset to *Nc*\ , which results in extra chunks with no atoms +*Nchunk* is reset to *Nc*, which results in extra chunks with no atoms assigned to them. Note that in this case, all atoms will end up with -chunk IDs <= *Nc*\ , and their original values (e.g. molecule ID or +chunk IDs <= *Nc*, and their original values (e.g. molecule ID or compute/fix/variable value) will also have been <= *Nc*\ . ---------- @@ -413,7 +413,7 @@ time windows (discussed above), the chunk ID's assigned to atoms on the first step of the time window will persist until the end of the time window. -If the setting is *every*\ , which is the default, then chunk IDs are +If the setting is *every*, which is the default, then chunk IDs are re-calculated on any timestep this compute is invoked. .. note:: @@ -435,18 +435,18 @@ set of IDs, where every chunk has one or more atoms assigned to it. Two possible use cases are as follows. If a large simulation box is mostly empty space, then the *binning* style may produce many bins -with no atoms. If *compress* is set to *yes*\ , only bins with atoms +with no atoms. If *compress* is set to *yes*, only bins with atoms will be contribute to *Nchunk*\ . Likewise, the *molecule* or *compute/fix/variable* styles may produce large *Nchunk* values. For example, the :doc:`compute cluster/atom ` command assigns every atom an atom ID for one of the atoms it is clustered with. For a million-atom system with 5 clusters, there would only be 5 unique chunk IDs, but the largest chunk ID might be 1 million, -resulting in *Nchunk* = 1 million. If *compress* is set to *yes*\ , +resulting in *Nchunk* = 1 million. If *compress* is set to *yes*, *Nchunk* will be reset to 5. -If *compress* is set to *no*\ , which is the default, no compression is -done. If it is set to *yes*\ , all chunk IDs with no atoms are removed +If *compress* is set to *no*, which is the default, no compression is +done. If it is set to *yes*, all chunk IDs with no atoms are removed from the list of chunk IDs, and the list is sorted. The remaining chunk IDs are renumbered from 1 to *Nchunk* where *Nchunk* is the new length of the list. The chunk IDs assigned to each atom reflect @@ -498,23 +498,23 @@ return chunk IDs that are invalid for the previously calculated *Nchunk*\ . All the chunk styles except the *binning* styles, must use *discard* -set to either *yes* or *no*\ . If *discard* is set to *yes*\ , which is +set to either *yes* or *no*\ . If *discard* is set to *yes*, which is the default, then every "discard" atom has its chunk ID set to 0. If -*discard* is set to *no*\ , every "discard" atom has its chunk ID set to +*discard* is set to *no*, every "discard" atom has its chunk ID set to *Nchunk*\ . I.e. it becomes part of the last chunk. The *binning* styles use the *discard* keyword to decide whether to discard atoms outside the spatial domain covered by bins, or to assign them to the bin they are nearest to. -For the *bin/1d*\ , *bin/2d*\ , *bin/3d* styles the details are as -follows. If *discard* is set to *yes*\ , an out-of-domain atom will -have its chunk ID set to 0. If *discard* is set to *no*\ , the atom +For the *bin/1d*, *bin/2d*, *bin/3d* styles the details are as +follows. If *discard* is set to *yes*, an out-of-domain atom will +have its chunk ID set to 0. If *discard* is set to *no*, the atom will have its chunk ID set to the first or last bin in that dimension. -If *discard* is set to *mixed*\ , which is the default, it will only +If *discard* is set to *mixed*, which is the default, it will only have its chunk ID set to the first or last bin if bins extend to the simulation box boundary in that dimension. This is the case if the -*bound* keyword settings are *lower* and *upper*\ , which is the +*bound* keyword settings are *lower* and *upper*, which is the default. If the *bound* keyword settings are numeric values, then the atom will have its chunk ID set to 0 if it is outside the bounds of any bin. Note that in this case, it is possible that the first or @@ -524,24 +524,24 @@ is only set to 0 if it is outside the first or last bin, not if it is simply outside the numeric *bounds* setting. For the *bin/sphere* style the details are as follows. If *discard* -is set to *yes*\ , an out-of-domain atom will have its chunk ID set to -0. If *discard* is set to *no* or *mixed*\ , the atom will have its +is set to *yes*, an out-of-domain atom will have its chunk ID set to +0. If *discard* is set to *no* or *mixed*, the atom will have its chunk ID set to the first or last bin, i.e. the innermost or outermost spherical shell. If the distance of the atom from the origin is less -than *rmin*\ , it will be assigned to the first bin. If the distance of -the atom from the origin is greater than *rmax*\ , it will be assigned +than *rmin*, it will be assigned to the first bin. If the distance of +the atom from the origin is greater than *rmax*, it will be assigned to the last bin. For the *bin/cylinder* style the details are as follows. If *discard* -is set to *yes*\ , an out-of-domain atom will have its chunk ID set to -0. If *discard* is set to *no*\ , the atom will have its chunk ID set +is set to *yes*, an out-of-domain atom will have its chunk ID set to +0. If *discard* is set to *no*, the atom will have its chunk ID set to the first or last bin in both the radial and axis dimensions. If -*discard* is set to *mixed*\ , which is the default, the radial +*discard* is set to *mixed*, which is the default, the radial dimension is treated the same as for *discard* = no. But for the axis dimension, it will only have its chunk ID set to the first or last bin if bins extend to the simulation box boundary in the axis dimension. This is the case if the *bound* keyword settings are -*lower* and *upper*\ , which is the default. If the *bound* keyword +*lower* and *upper*, which is the default. If the *bound* keyword settings are numeric values, then the atom will have its chunk ID set to 0 if it is outside the bounds of any bin. Note that in this case, it is possible that the first or last bin extends beyond the numeric @@ -550,22 +550,22 @@ the case, the chunk ID of the atom is only set to 0 if it is outside the first or last bin, not if it is simply outside the numeric *bounds* setting. -If *discard* is set to *no* or *mixed*\ , the atom will have its +If *discard* is set to *no* or *mixed*, the atom will have its chunk ID set to the first or last bin, i.e. the innermost or outermost spherical shell. If the distance of the atom from the origin is less -than *rmin*\ , it will be assigned to the first bin. If the distance of -the atom from the origin is greater than *rmax*\ , it will be assigned +than *rmin*, it will be assigned to the first bin. If the distance of +the atom from the origin is greater than *rmax*, it will be assigned to the last bin. ---------- -The *bound* keyword only applies to the *bin/1d*\ , *bin/2d*\ , *bin/3d* +The *bound* keyword only applies to the *bin/1d*, *bin/2d*, *bin/3d* styles and to the axis dimension of the *bin/cylinder* style; otherwise it is ignored. It can be used one or more times to limit the extent of bin coverage in a specified dimension, i.e. to only bin a portion of the box. If the *lo* setting is *lower* or the *hi* -setting is *upper*\ , the bin extent in that direction extends to the -box boundary. If a numeric value is used for *lo* and/or *hi*\ , then +setting is *upper*, the bin extent in that direction extends to the +box boundary. If a numeric value is used for *lo* and/or *hi*, then the bin extent in the *lo* or *hi* direction extends only to that value, which is assumed to be inside (or at least near) the simulation box boundaries, though LAMMPS does not check for this. Note that @@ -573,7 +573,7 @@ using the *bound* keyword typically reduces the total number of bins and thus the number of chunks *Nchunk*\ . The *pbc* keyword only applies to the *bin/sphere* and *bin/cylinder* -styles. If set to *yes*\ , the distance an atom is from the sphere +styles. If set to *yes*, the distance an atom is from the sphere origin or cylinder axis is calculated in a minimum image sense with respect to periodic dimensions, when determining which bin the atom is in. I.e. if x is a periodic dimension and the distance between the @@ -582,18 +582,18 @@ simulation box length in x, then a box length is subtracted to give a distance < 0.5 \* simulation box length. This allosws the sphere or cylinder center to be near a box edge, and atoms on the other side of the periodic box will still be close to the center point/axis. Note -that with a setting of *yes*\ , the outer sphere or cylinder radius must +that with a setting of *yes*, the outer sphere or cylinder radius must also be <= 0.5 \* simulation box length in any periodic dimension except for the cylinder axis dimension, or an error is generated. The *units* keyword only applies to the *binning* styles; otherwise it -is ignored. For the *bin/1d*\ , *bin/2d*\ , *bin/3d* styles, it +is ignored. For the *bin/1d*, *bin/2d*, *bin/3d* styles, it determines the meaning of the distance units used for the bin sizes *delta* and for *origin* and *bounds* values if they are coordinate values. For the *bin/sphere* style it determines the meaning of the -distance units used for *xorig*\ ,\ *yorig*\ ,\ *zorig* and the radii *srmin* +distance units used for *xorig*,\ *yorig*,\ *zorig* and the radii *srmin* and *srmax*\ . For the *bin/cylinder* style it determines the meaning -of the distance units used for *delta*\ ,\ *c1*\ ,\ *c2* and the radii *crmin* +of the distance units used for *delta*,\ *c1*,\ *c2* and the radii *crmin* and *crmax*\ . For orthogonal simulation boxes, any of the 3 options may @@ -627,7 +627,7 @@ This compute calculates a per-atom vector (the chunk ID), which can be accessed by any command that uses per-atom values from a compute as input. It also calculates a global scalar (the number of chunks), which can be similarly accessed everywhere outside of a per-atom context. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values are unitless chunk IDs, ranging from 1 to @@ -637,7 +637,7 @@ belonging to a chunk. The scalar contains the value of *Nchunk*. Restrictions """""""""""" -Even if the *nchunk* keyword is set to *once*\ , the chunk IDs assigned +Even if the *nchunk* keyword is set to *once*, the chunk IDs assigned to each atom are not stored in a restart files. This means you cannot expect those assignments to persist in a restarted simulation. Instead you must re-specify this command and assign atoms to chunks when diff --git a/doc/src/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst index 9e6489f828..1fd260ab2c 100644 --- a/doc/src/compute_chunk_spread_atom.rst +++ b/doc/src/compute_chunk_spread_atom.rst @@ -193,7 +193,7 @@ Output info This compute calculates a per-atom vector or array, which can be accessed by any command that uses per-atom values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output is a per-atom vector if a single input value is specified, diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index ab47aed9b3..f82b2affa5 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -89,7 +89,7 @@ style computes. 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 - does not apply when using long-range coulomb (\ *coul/long*\ , *coul/msm*\ , + does not apply when using long-range coulomb (\ *coul/long*, *coul/msm*, *coul/wolf* or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and @@ -111,14 +111,16 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be an ID > 0, as explained above. Restrictions """""""""""" - none + +These computes are part of the EXTRA-COMPUTE package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" @@ -128,6 +130,5 @@ Related commands Default """"""" - The default for fragment/atom is single no. diff --git a/doc/src/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst index 41d7113b60..756a9d932c 100644 --- a/doc/src/compute_cna_atom.rst +++ b/doc/src/compute_cna_atom.rst @@ -84,7 +84,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be a number from 0 to 5, as explained diff --git a/doc/src/compute_cnp_atom.rst b/doc/src/compute_cnp_atom.rst index 30f045a67b..59c45107b3 100644 --- a/doc/src/compute_cnp_atom.rst +++ b/doc/src/compute_cnp_atom.rst @@ -43,7 +43,7 @@ This parameter is computed using the following formula from Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} \left | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} \right | ^{2} where the index *j* goes over the :math:`n_i` nearest neighbors of atom -*i*\ , and the index *k* goes over the :math:`n_{ij}` common nearest neighbors +*i*, and the index *k* goes over the :math:`n_{ij}` common nearest neighbors between atom *i* and atom *j*\ . :math:`\vec{R}_{ik}` and :math:`\vec{R}_{jk}` are the vectors connecting atom *k* to atoms *i* and *j*\ . The quantity in the double sum is computed @@ -91,7 +91,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be real positive numbers. Some typical CNP @@ -111,7 +111,7 @@ Restrictions """""""""""" This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst index f22a78c63c..20dcbfae29 100644 --- a/doc/src/compute_contact_atom.rst +++ b/doc/src/compute_contact_atom.rst @@ -39,7 +39,7 @@ Output info This compute calculates a per-atom vector, whose values can be accessed by any command that uses per-atom values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be a number >= 0.0, as explained @@ -48,6 +48,10 @@ above. Restrictions """""""""""" +This compute is part of the GRANULAR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. + This compute requires that atoms store a radius as defined by the :doc:`atom_style sphere ` command. diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index f3c6f818af..bff2a8a8af 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -73,7 +73,7 @@ from 1 to N. A leading asterisk means all types from 1 to n (inclusive). The *orientorder* cstyle calculates the number of "connected" neighbor -atoms J around each central atom I. For this *cstyle*\ , connected is +atoms J around each central atom I. For this *cstyle*, connected is defined by the orientational order parameter calculated by the :doc:`compute orientorder/atom ` command. This *cstyle* thus allows one to apply the ten Wolde's criterion to @@ -85,7 +85,7 @@ calculate components of the *Ybar_lm* vector for each atoms, as described in its documentation. Note that orientorder/atom compute defines its own criteria for identifying neighboring atoms. If the scalar product (*Ybar_lm(i)*,*Ybar_lm(j)*), calculated by the -orientorder/atom compute is larger than the specified *threshold*\ , +orientorder/atom compute is larger than the specified *threshold*, then I and J are connected, and the coordination value of I is incremented by one. diff --git a/doc/src/compute_damage_atom.rst b/doc/src/compute_damage_atom.rst index 2439bd5a1b..3847a4de66 100644 --- a/doc/src/compute_damage_atom.rst +++ b/doc/src/compute_damage_atom.rst @@ -45,7 +45,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values are unitless numbers (damage) >= 0.0. @@ -54,7 +54,7 @@ Restrictions """""""""""" This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst index 0bbcb370b5..d4198dde3c 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -37,7 +37,7 @@ 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 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 +or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 75c0e69790..82d3c3ab72 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -122,7 +122,7 @@ array is the number of dihedrals. If a single value is specified, a local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of values. The vector or array can be accessed by any command that uses -local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *phi* will be in degrees. diff --git a/doc/src/compute_dilatation_atom.rst b/doc/src/compute_dilatation_atom.rst index 85b5770c64..0e3159ffe7 100644 --- a/doc/src/compute_dilatation_atom.rst +++ b/doc/src/compute_dilatation_atom.rst @@ -48,7 +48,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values are unitless numbers (theta) >= 0.0. @@ -57,7 +57,7 @@ Restrictions """""""""""" This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_dipole.rst b/doc/src/compute_dipole.rst index c0e17f27d3..243efc0576 100644 --- a/doc/src/compute_dipole.rst +++ b/doc/src/compute_dipole.rst @@ -12,7 +12,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * dipole = style name of this compute command -* charge-correction = *mass* or *geometry*\ , use COM or geometric center for charged chunk correction (optional) +* charge-correction = *mass* or *geometry*, use COM or geometric center for charged chunk correction (optional) Examples """""""" @@ -51,7 +51,7 @@ Output info This compute calculations a global scalar containing the magnitude of the computed dipole moment and a global vector of length 3 with the -dipole vector. See the :doc:`Howto output ` doc page for +dipole vector. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The computed values are "intensive". The array values will be in diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index 4207d3d180..fc1e8d7709 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * dipole/chunk = style name of this compute command * chunkID = ID of :doc:`compute chunk/atom ` command -* charge-correction = *mass* or *geometry*\ , use COM or geometric center for charged chunk correction (optional) +* charge-correction = *mass* or *geometry*, use COM or geometric center for charged chunk correction (optional) Examples """""""" @@ -84,7 +84,7 @@ chunk/atom ` command. The number of columns = 4 for the x,y,z dipole vector components and the total dipole of each chunk. These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output -` doc page for an overview of LAMMPS output options. +` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in dipole units, i.e. charge units times distance :doc:`units `. diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index 72cae28c22..bc6e1d2321 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -52,7 +52,7 @@ Output info This compute calculates a global vector of length 5 (:math:`U^{cond}`, :math:`U^{mech}`, :math:`U^{chem}`, :math:`\theta_{avg}`, :math:`N`), which can be accessed by indices 1-5. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values will be in energy and temperature :doc:`units `. @@ -61,7 +61,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst index 6abbce10f0..6104c4a273 100644 --- a/doc/src/compute_dpd_atom.rst +++ b/doc/src/compute_dpd_atom.rst @@ -40,7 +40,7 @@ This compute calculates a per-particle array with 4 columns (:math:`u^{cond}`, :math:`u^{mech}`, :math:`u^{chem}`, :math:`\theta`), which can be accessed by indices 1-4 by any command that uses per-particle values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle array values will be in energy (:math:`u^{cond}`, @@ -51,7 +51,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index 920bda1a87..3568a6364f 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -36,7 +36,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in temperature :doc:`units `. @@ -45,7 +45,7 @@ Restrictions """""""""""" This compute is part of the DPD-MESO package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_efield_atom.rst b/doc/src/compute_efield_atom.rst index 04f3e4dc37..a3d2cb888d 100644 --- a/doc/src/compute_efield_atom.rst +++ b/doc/src/compute_efield_atom.rst @@ -52,7 +52,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in electric field :doc:`units `. diff --git a/doc/src/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst index 0ca07815d3..e3d585dfde 100644 --- a/doc/src/compute_entropy_atom.rst +++ b/doc/src/compute_entropy_atom.rst @@ -67,7 +67,7 @@ is a parameter to control the smoothing. The input parameters are *sigma* the smoothing parameter :math:`\sigma`, and the *cutoff* for the calculation of g(r). -If the keyword *avg* has the setting *yes*\ , then this compute also +If the keyword *avg* has the setting *yes*, then this compute also averages the parameter over the neighbors of atom i according to: .. math:: @@ -114,7 +114,7 @@ Output info By default, this compute calculates the pair entropy value for each atom as a per-atom vector, which can be accessed by any command that -uses per-atom values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The pair entropy values have units of the Boltzmann constant. They are @@ -125,7 +125,7 @@ Restrictions """""""""""" This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index 0210279560..2b4edc8017 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -45,7 +45,7 @@ Output info This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst index b5b594f781..acbcf5cb0c 100644 --- a/doc/src/compute_erotate_rigid.rst +++ b/doc/src/compute_erotate_rigid.rst @@ -43,7 +43,7 @@ Output info This compute calculates a global scalar (the summed rotational energy of all the rigid bodies). This value can be used by any command that -uses a global scalar value from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The @@ -53,7 +53,7 @@ Restrictions """""""""""" This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index c10d13c318..6890f18212 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -40,7 +40,7 @@ Output info This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst index b12669ed0c..76025b36f7 100644 --- a/doc/src/compute_erotate_sphere_atom.rst +++ b/doc/src/compute_erotate_sphere_atom.rst @@ -44,7 +44,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst index a147ca0d7d..6cf04e83ba 100644 --- a/doc/src/compute_event_displace.rst +++ b/doc/src/compute_event_displace.rst @@ -48,7 +48,7 @@ Output info This compute calculates a global scalar (the flag). This value can be used by any command that uses a global scalar value from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index 5427538a73..5275716c45 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -269,7 +269,7 @@ 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. -If the keyword *volume* = *yes*\ , then the Boltzmann term is multiplied +If the keyword *volume* = *yes*, then the Boltzmann term is multiplied by the volume so that correct ensemble averaging can be performed over trajectories during which the volume fluctuates or changes :ref:`(Allen and Tildesley) `: @@ -295,7 +295,7 @@ unperturbed parameters. The energies include kspace terms if these are used in the simulation. These output results can be used by any command that uses a global -scalar or vector from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +scalar or vector from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. For example, the computed values can be averaged using :doc:`fix ave/time `. The values calculated by this compute are "extensive". @@ -304,7 +304,7 @@ Restrictions """""""""""" This compute is distributed as the FEP package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" @@ -315,7 +315,7 @@ Related commands Default """"""" -The option defaults are *tail* = *no*\ , *volume* = *no*\ . +The option defaults are *tail* = *no*, *volume* = *no*\ . ---------- diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index 1c8ff6c85e..1ee4abdde0 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -146,7 +146,7 @@ to effectively specify multiple values. If *index* begins with "f\_", a fix ID must follow which has been previously defined in the input script. The Fix must generate -per-atom quantities. See the individual :doc:`fix ` doc page for +per-atom quantities. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute global/atom references the values, else an error results. If no bracketed integer @@ -213,7 +213,7 @@ vector. If multiple inputs are specified, this compute produces a per-atom array values, where the number of columns is equal to the number of inputs specified. These values can be used by any command that uses per-atom vector or array values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector or array values will be in whatever units the diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index b22689d4b3..d361bc806d 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -39,7 +39,7 @@ Define a computation that calculates the total energy and force interaction between two groups of atoms: the compute group and the specified group2. The two groups can be the same. -If the *pair* keyword is set to *yes*\ , which is the default, then the +If the *pair* keyword is set to *yes*, which is the default, then the the interaction energy will include a pair component which is defined as the pairwise energy between all pairs of atoms where one atom in the pair is in the first group and the other is in the second group. @@ -60,7 +60,7 @@ force. For the *inter* setting, the two atoms must be in different 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 the *kspace* keyword is set to *yes*, which is not the default, and 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 @@ -73,7 +73,7 @@ charge of the unit cell is zero. However, one can assume the net charge of the system is neutralized by a uniform background plasma, and a correction to the system energy can be applied to reduce artifacts. For more information see :ref:`(Bogusz) `. If the -*boundary* keyword is set to *yes*\ , which is the default, and *kspace* +*boundary* keyword is set to *yes*, which is the default, and *kspace* contributions are included, then this energy correction term will be added to the total group-group energy. This correction term does not affect the force calculation and will be zero if one or both of the @@ -108,7 +108,7 @@ frequently. neighbor list. Because this compute uses a neighbor list, it also means those pairs will not be included in the group/group interaction. This does not apply when using long-range coulomb interactions - (\ *coul/long*\ , *coul/msm*\ , *coul/wolf* or similar. One way to get + (\ *coul/long*, *coul/msm*, *coul/wolf* or similar. One way to get around this would be to set special_bond scaling factors to very tiny 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 @@ -134,7 +134,7 @@ Output info This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. Both the scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index da0b14abe8..18c46f4772 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -62,7 +62,7 @@ Output info This compute calculates a global scalar (:math:`R_g`) and a global vector of length 6 (:math:`{R_g}^2` tensor), which can be accessed by indices 1-6. These values can be used by any command that uses a global scalar value or -vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index eaa048c111..0255d4f95a 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -101,7 +101,7 @@ number of rows in the array = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. If the *tensor* keyword is specified, the global array has 6 columns. The vector or array can be accessed by any command that uses global values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. All the vector or array values calculated by this compute are diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index b2b22df9ef..8eee14e787 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -70,7 +70,7 @@ This compute calculates a global vector of length 6, which can be accessed by indices 1-6. The first three values are the eigenvalues of the gyration tensor followed by the asphericity, the acylindricity and the relative shape anisotropy. The computed values can be used by any command -that uses global vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +that uses global vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values calculated by this compute are @@ -81,7 +81,7 @@ Restrictions """""""""""" This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index fd0b08cae6..f9d9df8db0 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -71,7 +71,7 @@ This compute calculates a global array with six columns, which can be accessed by indices 1-6. The first three columns are the eigenvalues of the gyration tensor followed by the asphericity, the acylindricity and the relative shape anisotropy. The computed values can be used by any command -that uses global array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +that uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array calculated by this compute is @@ -82,7 +82,7 @@ Restrictions """""""""""" This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index 3e8469617f..94d6f09700 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -41,7 +41,7 @@ which can add or subtract heat from groups of atoms. The compute takes three arguments which are IDs of other :doc:`computes `. One calculates per-atom kinetic energy -(\ *ke-ID*\ ), one calculates per-atom potential energy (\ *pe-ID)*\ , and the +(\ *ke-ID*\ ), one calculates per-atom potential energy (\ *pe-ID)*, and the third calculates per-atom stress (\ *stress-ID*\ ). .. note:: @@ -131,7 +131,7 @@ of just the convective portion of the flux, i.e. the first term in the equation for :math:`\mathbf{J}`. Each component can be accessed by indices 1-6. These values can be used by any command that -uses global vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses global vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values calculated by this compute are "extensive", meaning diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index a8e70245df..8b8bc3f4d0 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -48,7 +48,7 @@ is formed by the bond vector :math:`r_{ij}` and the *x* axis. :math:`\theta` is calculated only using the *x* and *y* components, whereas the distance from the central atom is calculated using all three -*x*\ , *y*\ , and *z* components of the bond vector. +*x*, *y*, and *z* components of the bond vector. Neighbor atoms not in the group are included in the order parameter of atoms in the group. @@ -110,7 +110,9 @@ page for an overview of LAMMPS output options. Restrictions """""""""""" - none + +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index 575740a2d5..e9c3133ebb 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -161,7 +161,7 @@ Output info This compute calculates a global vector that includes the n properties requested as arguments to the command (the potential energy, pressure and/or heat capacity). The elements of the vector can be accessed by indices 1-n by any -command that uses global vector values as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. +command that uses global vector values as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values calculated by this compute are "extensive". The scalar value will be in energy :doc:`units `. @@ -170,7 +170,7 @@ Restrictions """""""""""" This compute is part of the EXTRA-COMPUTE package. It is enabled only -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Usage restricted to canonical (NVT) ensemble simulation only. @@ -192,5 +192,5 @@ none .. _hma-Moustafa: -**(Moustafa)** Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , +**(Moustafa)** Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) `_ diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index 3eb008c3b2..2d6684b240 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -37,7 +37,7 @@ 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 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 +or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index 4c4af36149..3a849bf20c 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -69,7 +69,7 @@ array is the number of impropers. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *chi* will be in degrees. diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index 638a0baec8..42f5725d92 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -74,7 +74,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 6 for the 6 components of the inertia tensor for each chunk, ordered as listed above. These values can be accessed by any command that -uses global array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_ke_atom.rst b/doc/src/compute_ke_atom.rst index 8828ee4e3f..277b6ea6d6 100644 --- a/doc/src/compute_ke_atom.rst +++ b/doc/src/compute_ke_atom.rst @@ -37,7 +37,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst index e364b20f31..4587632818 100644 --- a/doc/src/compute_ke_atom_eff.rst +++ b/doc/src/compute_ke_atom_eff.rst @@ -65,7 +65,7 @@ Output info This compute calculates a scalar quantity for each atom, which can be accessed by any command that uses per-atom computes as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. @@ -74,7 +74,7 @@ Restrictions """""""""""" This compute is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst index 6028099d07..233352ba7a 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -69,7 +69,7 @@ Output info This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The @@ -79,7 +79,7 @@ Restrictions """""""""""" This compute is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_ke_rigid.rst b/doc/src/compute_ke_rigid.rst index c8bd663da7..680b1a60fc 100644 --- a/doc/src/compute_ke_rigid.rst +++ b/doc/src/compute_ke_rigid.rst @@ -42,7 +42,7 @@ Output info This compute calculates a global scalar (the summed KE of all the rigid bodies). This value can be used by any command that uses a -global scalar value from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The @@ -52,7 +52,7 @@ Restrictions """""""""""" This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_mesont.rst b/doc/src/compute_mesont.rst index c449a0a175..c396a33dbc 100644 --- a/doc/src/compute_mesont.rst +++ b/doc/src/compute_mesont.rst @@ -36,7 +36,7 @@ Output info These computes calculate per-node (per-atom) vectors, which can be accessed by any command that uses per-atom values from a compute as input, and global -scalars. See the :doc:`Howto output ` doc page for an overview of +scalars. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The computed values are provided in energy :doc:`units `. diff --git a/doc/src/compute_mliap.rst b/doc/src/compute_mliap.rst index 86dfe5a856..350f4c800c 100644 --- a/doc/src/compute_mliap.rst +++ b/doc/src/compute_mliap.rst @@ -169,7 +169,7 @@ This compute is part of the ML-IAP package. It is only enabled if LAMMPS was built with that package. In addition, building LAMMPS with the ML-IAP package requires building LAMMPS with the ML-SNAP package. The *mliappy* model also requires building LAMMPS with the PYTHON -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/compute_modify.rst b/doc/src/compute_modify.rst index 3b8f613744..a68f3c14e1 100644 --- a/doc/src/compute_modify.rst +++ b/doc/src/compute_modify.rst @@ -18,10 +18,10 @@ Syntax *extra/dof* value = N N = # of extra degrees of freedom to subtract - *extra* syntax is identical to *extra/dof*\ , will be disabled at some point + *extra* syntax is identical to *extra/dof*, will be disabled at some point *dynamic/dof* value = *yes* or *no* yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature - *dynamic* syntax is identical to *dynamic/dof*\ , will be disabled at some point + *dynamic* syntax is identical to *dynamic/dof*, will be disabled at some point Examples """""""" diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst index 266e4b5e18..c86901933b 100644 --- a/doc/src/compute_momentum.rst +++ b/doc/src/compute_momentum.rst @@ -34,7 +34,7 @@ Output info This compute calculates a global vector (the summed momentum) of length 3. This value can be used by any command that uses a global -vector value from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector value calculated by this compute is "extensive". The vector @@ -44,7 +44,7 @@ Restrictions """""""""""" This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index ee2c4612d7..ed13a32b7c 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -112,7 +112,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 4 for dx,dy,dz and the total displacement. These values can be accessed by any command that uses global array values from a compute -as input. See the :doc:`Howto output ` doc page for an +as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst index 63d8deb2cd..70f4505d7f 100644 --- a/doc/src/compute_msd_nongauss.rst +++ b/doc/src/compute_msd_nongauss.rst @@ -56,7 +56,7 @@ If the *com* option is set to *yes* then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacement of each atom is calculated. -See the :doc:`compute msd ` doc page for further important +See the :doc:`compute msd ` page for further important NOTEs, which also apply to this compute. Output info @@ -74,8 +74,8 @@ the third is dimensionless. Restrictions """""""""""" -This compute is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index d0af88b1a4..90baf9e2b3 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -75,7 +75,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 3 for the 3 xyz components of the angular velocity for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index af4e6a21e8..2efea311a0 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -181,7 +181,9 @@ page for an overview of LAMMPS output options. Restrictions """""""""""" - none + +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst index abfd1ebed4..b43c4bd6d7 100644 --- a/doc/src/compute_pair.rst +++ b/doc/src/compute_pair.rst @@ -50,11 +50,11 @@ two parts: *evdwl* and *ecoul* such that *epair* = *evdwl* + *ecoul*\ . If the pair style calculates Coulombic interactions, their energy will 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 +*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 of the total energy contributed by one sub-style. If *evalue* is -specified as *evdwl* or *ecoul*\ , then just that portion of the energy +specified as *evdwl* or *ecoul*, then just that portion of the energy is stored as a global scalar. .. note:: @@ -66,7 +66,7 @@ is stored as a global scalar. Some pair styles tally additional quantities, e.g. a breakdown of potential energy into 14 components is tallied by the :doc:`pair_style reaxff ` command. These values (1 or more) -are stored as a global vector by this compute. See the doc page for +are stored as a global vector by this compute. See the page for :doc:`individual pair styles ` for info on these values. Output info @@ -84,7 +84,7 @@ The scalar and vector values calculated by this compute are The scalar value will be in energy :doc:`units `. The vector values will typically also be in energy :doc:`units `, but see -the doc page for the pair style for details. +the page for the pair style for details. Restrictions """""""""""" @@ -98,4 +98,4 @@ Related commands Default """"""" -The keyword defaults are *evalue* = *epair*\ , nsub = 0. +The keyword defaults are *evalue* = *epair*, nsub = 0. diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index e269aaadfe..f464c7cec6 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -20,7 +20,7 @@ Syntax *dist* = pairwise distance *eng* = pairwise energy *force* = pairwise force - *fx*\ ,\ *fy*\ ,\ *fz* = components of pairwise force + *fx*,\ *fy*,\ *fz* = components of pairwise force *pN* = pair style specific quantities for allowed N values * zero or more keyword/arg pairs may be appended @@ -61,20 +61,20 @@ The value *eng* is the interaction energy for the pair of atoms. The value *force* is the force acting between the pair of atoms, which is positive for a repulsive force and negative for an attractive -force. The values *fx*\ , *fy*\ , and *fz* are the xyz components of +force. The values *fx*, *fy*, and *fz* are the xyz components of *force* on atom I. A pair style may define additional pairwise quantities which can be -accessed as *p1* to *pN*\ , where N is defined by the pair style. Most +accessed as *p1* to *pN*, where N is defined by the pair style. Most pair styles do not define any additional quantities, so N = 0. An example of ones that do are the :doc:`granular pair styles ` which calculate the tangential force between two particles and return its components and magnitude acting on atom I for N = 1,2,3,4. See individual pair styles for details. -When using *pN* with pair style *hybrid*\ , the output will be the Nth +When using *pN* with pair style *hybrid*, the output will be the Nth quantity from the sub-style that computes the pairwise interaction -(based on atom types). If that sub-style does not define a *pN*\ , +(based on atom types). If that sub-style does not define a *pN*, the output will be 0.0. The maximum allowed N is the maximum number of quantities provided by any sub-style. @@ -90,12 +90,12 @@ is not computed for the specific pairwise interaction (based on atom types), then the output will be 0.0. The value *dist* will be in distance :doc:`units `. The value -*eng* will be in energy :doc:`units `. The values *force*\ , *fx*\ , -*fy*\ , and *fz* will be in force :doc:`units `. The values *pN* +*eng* will be in energy :doc:`units `. The values *force*, *fx*, +*fy*, and *fz* will be in force :doc:`units `. The values *pN* 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*\ , +for an interaction is determined. For the default setting of *type*, 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 @@ -147,12 +147,12 @@ array is the number of pairs. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +uses local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The output for *dist* will be in distance :doc:`units `. The output for *eng* will be in energy :doc:`units `. The output for -*force*\ , *fx*\ , *fy*\ , and *fz* will be in force :doc:`units `. +*force*, *fx*, *fy*, and *fz* will be in force :doc:`units `. The output for *pN* will be in whatever units the pair style defines. Restrictions diff --git a/doc/src/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst index 91aaaf867c..ab6db9c786 100644 --- a/doc/src/compute_pe_atom.rst +++ b/doc/src/compute_pe_atom.rst @@ -89,7 +89,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst index b78f706afd..6861dd7cfc 100644 --- a/doc/src/compute_plasticity_atom.rst +++ b/doc/src/compute_plasticity_atom.rst @@ -43,7 +43,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values are unitless numbers (lambda) >= 0.0. @@ -52,7 +52,7 @@ Restrictions """""""""""" This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 3c98208261..6d76713b41 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -124,7 +124,7 @@ This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1-6. 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. +` page for an overview of LAMMPS output options. The ordering of values in the symmetric pressure tensor is as follows: pxx, pyy, pzz, pxy, pxz, pyz. diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst index cc94c339c8..a008254540 100644 --- a/doc/src/compute_pressure_cylinder.rst +++ b/doc/src/compute_pressure_cylinder.rst @@ -68,7 +68,7 @@ the configurational terms only; the kinetic contribution is not included and may be calculated from the number density output by P_kin=density\*k\*T. This compute is part of the EXTRA-COMPUTE package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst index 1e32c4d9b4..2e53961d00 100644 --- a/doc/src/compute_pressure_uef.rst +++ b/doc/src/compute_pressure_uef.rst @@ -42,7 +42,7 @@ Restrictions """""""""""" This fix is part of the UEF package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This command can only be used when :doc:`fix nvt/uef ` or :doc:`fix npt/uef ` is active. diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index 32cda56659..333f31d013 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -130,25 +130,25 @@ quantities that are not defined for a particular particle in the group The additional quantities only accessible via this command, and not directly via the :doc:`dump custom ` command, are as follows. -*Shapex*\ , *shapey*\ , and *shapez* are defined for ellipsoidal particles +*Shapex*, *shapey*, and *shapez* are defined for ellipsoidal particles and define the 3d shape of each particle. -*Quatw*\ , *quati*\ , *quatj*\ , and *quatk* are defined for ellipsoidal +*Quatw*, *quati*, *quatj*, and *quatk* are defined for ellipsoidal particles and body particles and store the 4-vector quaternion representing the orientation of each particle. See the :doc:`set ` command for an explanation of the quaternion vector. -*End1x*\ , *end1y*\ , *end1z*\ , *end2x*\ , *end2y*\ , *end2z*\ , are +*End1x*, *end1y*, *end1z*, *end2x*, *end2y*, *end2z*, are defined for line segment particles and define the end points of each line segment. -*Corner1x*\ , *corner1y*\ , *corner1z*\ , *corner2x*\ , *corner2y*\ , -*corner2z*\ , *corner3x*\ , *corner3y*\ , *corner3z*\ , are defined for +*Corner1x*, *corner1y*, *corner1z*, *corner2x*, *corner2y*, +*corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for triangular particles and define the corner points of each triangle. *Nbonds* is available for all molecular atom styles and refers to the number of explicit bonds assigned to an atom. Note that if the -:doc:`newton bond ` command is set to *on*\ , which is the +:doc:`newton bond ` command is set to *on*, which is the default, then every bond in the system is assigned to only one of the two atoms in the bond. Thus a bond between atoms I,J may be tallied for either atom I or atom J. If :doc:`newton bond off ` is @@ -169,7 +169,7 @@ per-atom vector is produced. If two or more inputs are specified, a per-atom array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses per-atom values from a compute as input. See the :doc:`Howto output -` doc page for an overview of LAMMPS output options. +` page for an overview of LAMMPS output options. The vector or array values will be in whatever :doc:`units ` the corresponding attribute is in, e.g. velocity units for vx, charge diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index 246ab09120..48b3641e84 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -67,14 +67,14 @@ then be 415 for the third chunk. The *coordN* attributes can only be used if a *binning* style was used in the :doc:`compute chunk/atom ` command referenced -by chunkID. For *bin/1d*\ , *bin/2d*\ , and *bin/3d* styles the attribute +by chunkID. For *bin/1d*, *bin/2d*, and *bin/3d* styles the attribute is the center point of the bin in the corresponding dimension. Style *bin/1d* only defines a *coord1* attribute. Style *bin/2d* adds a *coord2* attribute. Style *bin/3d* adds a *coord3* attribute. -Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*\ , the +Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*, the *coordN* attributes will be in distance :doc:`units `. If the -value of the *units* keyword is *reduced*\ , the *coordN* attributes +value of the *units* keyword is *reduced*, the *coordN* attributes will be in unitless reduced units (0-1). The simplest way to output the results of the compute property/chunk @@ -102,7 +102,7 @@ single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector or array values are "intensive". The values will be diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index dd92334266..357f46b70d 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -72,17 +72,17 @@ property/local command. If the inputs are pair attributes, the local data is generated by looping over the 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. For *natom1* and *natom2*\ , all +are in the specified compute group. For *natom1* and *natom2*, all 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 +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 ` 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 +attributes. For the default setting of *type*, 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 @@ -113,10 +113,10 @@ same for local vectors or arrays generated by other compute commands. For example, output from the :doc:`compute bond/local ` command can be combined with bond atom indices from this command and output by the :doc:`dump local ` command in a consistent way. -The *natom1* and *natom2*\ , or *patom1* and *patom2* attributes refer +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 -*ntype2*\ , or *ptype1* and *ptype2* attributes refer to the atom types +*ntype2*, or *ptype1* and *ptype2* attributes refer to the atom types of the 2 atoms in each pairwise interaction. .. note:: @@ -149,7 +149,7 @@ the array is the number of bonds, angles, etc. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +that uses local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector or array values will be integers that correspond to the diff --git a/doc/src/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst index e271131987..3e209d1dc5 100644 --- a/doc/src/compute_ptm_atom.rst +++ b/doc/src/compute_ptm_atom.rst @@ -89,7 +89,7 @@ Output info This compute calculates a per-atom array, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. Results are stored in the per-atom array in the following order: @@ -113,7 +113,7 @@ Restrictions """""""""""" This fix is part of the PTM package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index a9e6674816..85366eab2a 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -55,7 +55,7 @@ shell of distances in 3d and a thin ring of distances in 2d. 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 - using long-range coulomb interactions (\ *coul/long*\ , *coul/msm*\ , + using long-range coulomb interactions (\ *coul/long*, *coul/msm*, *coul/wolf* or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and @@ -94,7 +94,7 @@ The *itypeN* and *jtypeN* arguments are optional. These arguments must come in pairs. If no pairs are listed, then a single histogram is computed for g(r) between all atom types. If one or more pairs are listed, then a separate histogram is generated for each -*itype*\ ,\ *jtype* pair. +*itype*,\ *jtype* pair. The *itypeN* and *jtypeN* settings can be specified in one of two ways. An explicit numeric value can be used, as in the fourth example @@ -156,13 +156,13 @@ Output info """"""""""" This compute calculates a global array with the number of rows = -*Nbins*\ , and the number of columns = 1 + 2\*Npairs, where Npairs is the +*Nbins*, and the number of columns = 1 + 2\*Npairs, where Npairs is the number of I,J pairings specified. The first column has the bin coordinate (center of the bin), Each successive set of 2 columns has the g(r) and coord(r) values for a specific set of *itypeN* versus *jtypeN* interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values calculated by this compute are all "intensive". @@ -186,7 +186,7 @@ your model. The definition of g(r) used by LAMMPS is only appropriate for characterizing atoms that are uniformly distributed throughout the simulation cell. In such cases, the coordination number is still correct and meaningful. As an example, if a large simulation cell -contains only one atom of type *itypeN* and one of *jtypeN*\ , then g(r) +contains only one atom of type *itypeN* and one of *jtypeN*, then g(r) will register an arbitrarily large spike at whatever distance they happen to be at, and zero everywhere else. Coord(r) will show a step change from zero to one at the location of the spike in g(r). diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index 660ef87042..1793830e0a 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -74,7 +74,7 @@ or *max* options find the minimum or maximum value across all vector values. The *ave* setting adds the vector values into a global total, then divides by the number of values in the vector. The *sumsq* option sums the square of the values in the vector into a global -total. The *avesq* setting does the same as *sumsq*\ , then divides the +total. The *avesq* setting does the same as *sumsq*, then divides the sum of squares by the number of values. The last two options can be useful for calculating the variance of some quantity, e.g. variance = sumsq - ave\^2. @@ -126,7 +126,7 @@ an input value from that compute. If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. Computes can generate per-atom or local quantities. See the individual -:doc:`compute ` doc page for details. If no bracketed integer +:doc:`compute ` page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own @@ -136,7 +136,7 @@ to effectively specify multiple values. If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom -or local quantities. See the individual :doc:`fix ` doc page for +or local quantities. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute reduce references the values, else an error results. If no bracketed integer diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index 342c6ceb05..256ff15920 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -169,7 +169,7 @@ in the array is the number of inputs provided. The length of the vector or the number of vector elements or array rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The vector or array can be accessed by any command that uses global values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom values for the vector or each column of the array will be diff --git a/doc/src/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst index f7bb6d6166..574f3343be 100644 --- a/doc/src/compute_rigid_local.rst +++ b/doc/src/compute_rigid_local.rst @@ -61,7 +61,7 @@ command and its variants. The ID of the :doc:`fix rigid/small ` comm be specified as *rigidID*\ . The :doc:`fix rigid ` command is typically used to define a handful of (potentially very large) rigid bodies. It outputs similar per-body information as this command -directly from the fix as global data; see the :doc:`fix rigid ` doc page for details +directly from the fix as global data; see the :doc:`fix rigid ` page for details The local data stored by this command is generated by looping over all the atoms owned on a processor. If the atom is not in the specified @@ -107,43 +107,43 @@ rigid bodies. The *mass* attribute is the total mass of the rigid body. There are two options for outputting the coordinates of the center of -mass (COM) of the body. The *x*\ , *y*\ , *z* attributes write the COM +mass (COM) of the body. The *x*, *y*, *z* attributes write the COM "unscaled", in the appropriate distance :doc:`units ` (Angstroms, -sigma, etc). Use *xu*\ , *yu*\ , *zu* if you want the COM "unwrapped" by +sigma, etc). Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by the image flags for each body. Unwrapped means that if the body COM has passed through a periodic boundary one or more times, the value is generated what the COM coordinate would be if it had not been wrapped back into the periodic box. -The image flags for the body can be generated directly using the *ix*\ , -*iy*\ , *iz* attributes. For periodic dimensions, they specify which +The image flags for the body can be generated directly using the *ix*, +*iy*, *iz* attributes. For periodic dimensions, they specify which image of the simulation box the COM is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths to get the true value. A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as the rigid body COMs cross periodic boundaries during the simulation. -The *vx*\ , *vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz* attributes are components of +The *vx*, *vy*, *vz*, *fx*, *fy*, *fz* attributes are components of the COM velocity and force on the COM of the body. -The *omegax*\ , *omegay*\ , and *omegaz* attributes are the angular +The *omegax*, *omegay*, and *omegaz* attributes are the angular velocity components of the body around its COM. -The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are the angular +The *angmomx*, *angmomy*, and *angmomz* attributes are the angular momentum components of the body around its COM. -The *quatw*\ , *quati*\ , *quatj*\ , and *quatk* attributes are the +The *quatw*, *quati*, *quatj*, and *quatk* attributes are the components of the 4-vector quaternion representing the orientation of the rigid body. See the :doc:`set ` command for an explanation of the quaternion vector. -The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are the angular +The *angmomx*, *angmomy*, and *angmomz* attributes are the angular momentum components of the body around its COM. -The *tqx*\ , *tqy*\ , *tqz* attributes are components of the torque acting +The *tqx*, *tqy*, *tqz* attributes are components of the torque acting on the body around its COM. -The *inertiax*\ , *inertiay*\ , *inertiaz* attributes are components of +The *inertiax*, *inertiay*, *inertiaz* attributes are components of diagonalized inertia tensor for the body, i.e the 3 moments of inertia for the body around its principal axes, as computed internally by LAMMPS. @@ -160,7 +160,7 @@ specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The vector or array values will be in whatever :doc:`units ` the @@ -181,7 +181,7 @@ Restrictions """""""""""" This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index 989fe63d3d..37ee302f8f 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -90,7 +90,7 @@ unless small spacing parameters <0.05 Angstrom\^(-1) are implemented. Meshes with manual spacing do not require a periodic boundary. The limits of the reciprocal lattice mesh are determined by the use of -the *Kmax*\ , *Zone*\ , and *dR_Ewald* parameters. The rectilinear mesh +the *Kmax*, *Zone*, and *dR_Ewald* parameters. The rectilinear mesh created about the origin of reciprocal space is terminated at the boundary of a sphere of radius *Kmax* centered at the origin. If *Zone* parameters z1=z2=z3=0 are used, diffraction intensities are @@ -246,7 +246,7 @@ Restrictions """""""""""" This compute is part of the DIFFRACTION package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The compute_saed command does not work for triclinic cells. diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index 2d558b871f..9b4e7df626 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -44,9 +44,9 @@ quantities; they cannot be per-atom or local quantities. group specified with this command is ignored. The values extracted from the input vector(s) are determined by the -*Nstart*\ , *Nstop*\ , and *Nskip* parameters. The elements of an input +*Nstart*, *Nstop*, and *Nskip* parameters. The elements of an input vector of length N are indexed from 1 to N. Starting at element -*Nstart*\ , every Mth element is extracted, where M = *Nskip*\ , until +*Nstart*, every Mth element is extracted, where M = *Nskip*, until element *Nstop* is reached. The extracted quantities are stored as a vector, which is typically shorter than the input vector. @@ -65,7 +65,7 @@ used. Users can also write code for their own compute styles and :doc:`add them If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script and which generates a global -vector or array. See the individual :doc:`fix ` doc page for +vector or array. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute slice references the values, else an error results. If no bracketed integer is @@ -97,7 +97,7 @@ specified or a global array with N columns where N is the number of inputs. The length of the vector or the number of rows in the array is equal to the number of values extracted from each input vector. These values can be used by any command that uses global vector or -array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector or array values calculated by this compute are simply diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst index d310de826a..25f346625c 100644 --- a/doc/src/compute_smd_contact_radius.rst +++ b/doc/src/compute_smd_contact_radius.rst @@ -40,7 +40,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector values will be in distance :doc:`units `. @@ -49,7 +49,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst index e11fce1e9e..10070eaf0e 100644 --- a/doc/src/compute_smd_damage.rst +++ b/doc/src/compute_smd_damage.rst @@ -32,7 +32,7 @@ See `this PDF guide `_ to use Smooth Mach Dynamics This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values are dimensionless an in the range of zero to one. diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst index c3664997f9..aee87592aa 100644 --- a/doc/src/compute_smd_hourglass_error.rst +++ b/doc/src/compute_smd_hourglass_error.rst @@ -41,7 +41,7 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector values will are dimensionless. See @@ -51,7 +51,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with tlsph pair style. diff --git a/doc/src/compute_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst index f596b0ce54..535384e38b 100644 --- a/doc/src/compute_smd_internal_energy.rst +++ b/doc/src/compute_smd_internal_energy.rst @@ -34,7 +34,7 @@ Output Info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector values will be given in :doc:`units ` of energy. @@ -43,7 +43,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. diff --git a/doc/src/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst index 018b999716..17614df548 100644 --- a/doc/src/compute_smd_plastic_strain.rst +++ b/doc/src/compute_smd_plastic_strain.rst @@ -34,7 +34,7 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be given dimensionless. See :doc:`units `. @@ -43,7 +43,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. diff --git a/doc/src/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst index 4edb7c2ae5..dc78b627ef 100644 --- a/doc/src/compute_smd_plastic_strain_rate.rst +++ b/doc/src/compute_smd_plastic_strain_rate.rst @@ -34,7 +34,7 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be given in :doc:`units ` of one over time. @@ -43,7 +43,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. diff --git a/doc/src/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst index 672fe225f0..0adbc9db34 100644 --- a/doc/src/compute_smd_rho.rst +++ b/doc/src/compute_smd_rho.rst @@ -36,7 +36,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be in :doc:`units ` of mass over volume. @@ -45,7 +45,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst index a8c2e80a12..813bd32507 100644 --- a/doc/src/compute_smd_tlsph_defgrad.rst +++ b/doc/src/compute_smd_tlsph_defgrad.rst @@ -48,7 +48,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. TThis compute can +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. TThis compute can only be used for particles which interact via the total Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst index 6c6ad54187..44b2311898 100644 --- a/doc/src/compute_smd_tlsph_dt.rst +++ b/doc/src/compute_smd_tlsph_dt.rst @@ -40,7 +40,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be given in :doc:`units ` of time. @@ -49,7 +49,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst index 1a42373717..bc76ec260f 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.rst +++ b/doc/src/compute_smd_tlsph_num_neighs.rst @@ -35,7 +35,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values are dimensionless. See :doc:`units `. @@ -44,7 +44,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian pair style. diff --git a/doc/src/compute_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst index 33bd02d894..aefedb64eb 100644 --- a/doc/src/compute_smd_tlsph_shape.rst +++ b/doc/src/compute_smd_tlsph_shape.rst @@ -36,7 +36,7 @@ Output info This compute calculates a per-particle vector of vectors, which can be accessed by any command that uses per-particle values from a compute -as input. See the :doc:`Howto output ` doc page for an +as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector has 7 entries. The first three entries @@ -51,7 +51,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst index a05dbab8d7..3ecb509e9f 100644 --- a/doc/src/compute_smd_tlsph_strain.rst +++ b/doc/src/compute_smd_tlsph_strain.rst @@ -47,7 +47,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst index f75db80d94..41251d7095 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.rst +++ b/doc/src/compute_smd_tlsph_strain_rate.rst @@ -46,7 +46,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst index 0a194bea3d..11cec3bda8 100644 --- a/doc/src/compute_smd_tlsph_stress.rst +++ b/doc/src/compute_smd_tlsph_stress.rst @@ -48,7 +48,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst index 0f2f1cdd45..9f478b7262 100644 --- a/doc/src/compute_smd_triangle_vertices.rst +++ b/doc/src/compute_smd_triangle_vertices.rst @@ -34,7 +34,7 @@ Output info This compute returns a per-particle vector of vectors, which can be accessed by any command that uses per-particle values from a compute -as input. See the :doc:`Howto output ` doc page for an +as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and @@ -54,7 +54,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_smd_ulsph_effm.rst b/doc/src/compute_smd_ulsph_effm.rst index 388969f4ae..4b4959fbe1 100644 --- a/doc/src/compute_smd_ulsph_effm.rst +++ b/doc/src/compute_smd_ulsph_effm.rst @@ -34,7 +34,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector contains the current effective per atom shear @@ -45,7 +45,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_num_neighs.rst b/doc/src/compute_smd_ulsph_num_neighs.rst index b356b8adaa..c446c477c0 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.rst +++ b/doc/src/compute_smd_ulsph_num_neighs.rst @@ -35,7 +35,7 @@ Output info This compute returns a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle values will be given dimensionless, see :doc:`units `. @@ -44,7 +44,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_strain.rst b/doc/src/compute_smd_ulsph_strain.rst index 5a3617fd24..31defe4b32 100644 --- a/doc/src/compute_smd_ulsph_strain.rst +++ b/doc/src/compute_smd_ulsph_strain.rst @@ -34,7 +34,7 @@ Output info This compute calculates a per-particle tensor, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector has 6 entries, corresponding to the xx, yy, @@ -47,7 +47,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_strain_rate.rst b/doc/src/compute_smd_ulsph_strain_rate.rst index 4fe5d53936..0a2ca91081 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.rst +++ b/doc/src/compute_smd_ulsph_strain_rate.rst @@ -47,7 +47,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_stress.rst b/doc/src/compute_smd_ulsph_stress.rst index 392b72e0fd..a993a08c06 100644 --- a/doc/src/compute_smd_ulsph_stress.rst +++ b/doc/src/compute_smd_ulsph_stress.rst @@ -47,7 +47,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst index 862ed15a3e..f09c48e0ed 100644 --- a/doc/src/compute_smd_vol.rst +++ b/doc/src/compute_smd_vol.rst @@ -34,7 +34,7 @@ Output info This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See the :doc:`Howto output ` doc page for an overview of +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-particle vector values will be given in :doc:`units ` of @@ -47,7 +47,7 @@ Restrictions """""""""""" This compute is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 4165c4e47a..f156133521 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -161,7 +161,7 @@ components summed separately for each LAMMPS atom type: -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial {\bf r}_i} -The sum is over all atoms *i'* of atom type *I*\ . For each atom *i*\ , +The sum is over all atoms *i'* of atom type *I*\ . For each atom *i*, this compute evaluates the above expression for each direction, each atom type, and each bispectrum component. See section below on output for a detailed explanation. @@ -174,12 +174,12 @@ derivatives: -{\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i} Again, the sum is over all atoms *i'* of atom type *I*\ . For each atom -*i*\ , this compute evaluates the above expression for each of the six +*i*, this compute evaluates the above expression for each of the six virial components, each atom type, and each bispectrum component. See section below on output for a detailed explanation. Compute *snap* calculates a global array containing information related -to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ , +to all three of the above per-atom computes *sna/atom*, *snad/atom*, and *snav/atom*\ . The first row of the array contains the summation of *sna/atom* over all atoms, but broken out by type. The last six rows of the array contain the summation of *snav/atom* over all atoms, broken @@ -225,7 +225,7 @@ ordered in which they are listed. The keyword *switchflag* can be used to turn off the switching function :math:`f_c(r)`. -The keyword *bzeroflag* determines whether or not *B0*\ , the bispectrum +The keyword *bzeroflag* determines whether or not *B0*, the bispectrum components of an atom with no neighbors, are subtracted from the calculated bispectrum components. This optional keyword normally only affects compute *sna/atom*\ . However, when *quadraticflag* is on, it @@ -318,7 +318,7 @@ Output info Compute *sna/atom* calculates a per-atom array, each column corresponding to a particular bispectrum component. The total number of columns and the identity of the bispectrum component contained in each -column depend of the value of *twojmax*\ , as described by the following +column depend of the value of *twojmax*, as described by the following piece of python code: .. parsed-literal:: @@ -339,15 +339,15 @@ For even twojmax = 2(*m*\ -1), :math:`K = m(m+1)(2m+1)/6`, the *m*\ -th pyramida Compute *snad/atom* evaluates a per-atom array. The columns are arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each block -contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z* +contains three sub-blocks corresponding to the *x*, *y*, and *z* components of the atom position. Each of these sub-blocks contains *K* columns for the *K* bispectrum components, the same as for compute *sna/atom* Compute *snav/atom* evaluates a per-atom array. The columns are arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each block -contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ , -*yz*\ , *xz*\ , and *xy* components of the virial tensor in Voigt +contains six sub-blocks corresponding to the *xx*, *yy*, *zz*, +*yz*, *xz*, and *xy* components of the virial tensor in Voigt notation. Each of these sub-blocks contains *K* columns for the *K* bispectrum components, the same as for compute *sna/atom* @@ -363,7 +363,7 @@ appear in the following order: * 6 rows: *snav/atom* quantities summed for all atoms of type *I* For example, if *K* =30 and ntypes=1, the number of columns in the -per-atom arrays generated by *sna/atom*\ , *snad/atom*\ , and +per-atom arrays generated by *sna/atom*, *snad/atom*, and *snav/atom* are 30, 90, and 180, respectively. With *quadratic* value=1, the numbers of columns are 930, 2790, and 5580, respectively. The number of columns in the global array generated by *snap* are 31, and @@ -372,11 +372,11 @@ is the total number of atoms. If the *quadratic* keyword value is set to 1, then additional columns are generated, corresponding to the products of all distinct pairs of -bispectrum components. If the number of bispectrum components is *K*\ , +bispectrum components. If the number of bispectrum components is *K*, then the number of distinct pairs is *K*\ (\ *K*\ +1)/2. For compute *sna/atom* these columns are appended to existing *K* columns. The ordering of quadratic terms is upper-triangular, (1,1),(1,2)...(1,\ *K*\ -),(2,1)...(\ *K*\ -1,\ *K*\ -1),(\ *K*\ -1,\ *K*\ ),(\ *K*\ ,\ *K*\ ). +),(2,1)...(\ *K*\ -1,\ *K*\ -1),(\ *K*\ -1,\ *K*\ ),(\ *K*,\ *K*\ ). For computes *snad/atom* and *snav/atom* each set of *K*\ (\ *K*\ +1)/2 additional columns is inserted directly after each of sub-block of linear terms i.e. linear and quadratic terms are contiguous. So the @@ -402,7 +402,7 @@ Restrictions These computes are part of the ML-SNAP package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_sph_e_atom.rst b/doc/src/compute_sph_e_atom.rst index a0410825aa..5e6706fa27 100644 --- a/doc/src/compute_sph_e_atom.rst +++ b/doc/src/compute_sph_e_atom.rst @@ -41,7 +41,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in energy :doc:`units `. @@ -50,7 +50,7 @@ Restrictions """""""""""" This compute is part of the SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_sph_rho_atom.rst b/doc/src/compute_sph_rho_atom.rst index a7aad3c6fa..7fcec0c9da 100644 --- a/doc/src/compute_sph_rho_atom.rst +++ b/doc/src/compute_sph_rho_atom.rst @@ -40,7 +40,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in mass/volume :doc:`units `. @@ -49,7 +49,7 @@ Restrictions """""""""""" This compute is part of the SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_sph_t_atom.rst b/doc/src/compute_sph_t_atom.rst index d09a20c963..702d81027d 100644 --- a/doc/src/compute_sph_t_atom.rst +++ b/doc/src/compute_sph_t_atom.rst @@ -45,7 +45,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -the :doc:`Howto output ` doc page for an overview of +the :doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in temperature :doc:`units `. @@ -54,7 +54,7 @@ Restrictions """""""""""" This compute is part of the SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_spin.rst b/doc/src/compute_spin.rst index aaf9d8cc74..6694da000b 100644 --- a/doc/src/compute_spin.rst +++ b/doc/src/compute_spin.rst @@ -65,7 +65,7 @@ Restrictions """""""""""" The *spin* compute is part of the SPIN package. This compute is only -enabled if LAMMPS was built with this package. See the :doc:`Build package ` doc page for more info. The atom_style +enabled if LAMMPS was built with this package. See the :doc:`Build package ` page for more info. The atom_style has to be "spin" for this compute to be valid. **Related commands:** diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index 0f90f9bafe..cdb464a9d0 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -213,7 +213,7 @@ which can be accessed by indices 1-6 by any command that uses per-atom values from a compute as input. Compute *centroid/stress/atom* produces a per-atom array with 9 columns, but otherwise can be used in an identical manner to compute *stress/atom*. See the :doc:`Howto -output ` doc page for an overview of LAMMPS output +output ` page for an overview of LAMMPS output options. The ordering of the 6 columns for *stress/atom* is as follows: xx, yy, diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index f02d279414..bcc1a87e5f 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -45,8 +45,8 @@ Description Compute *stress/mop* and compute *stress/mop/profile* define computations that calculate components of the local stress tensor using the method of planes :ref:`(Todd) `. Specifically in compute *stress/mop* calculates 3 -components are computed in directions *dir*\ ,\ *x*\ ; *dir*\ ,\ *y*\ ; and -*dir*\ ,\ *z*\ ; where *dir* is the direction normal to the plane, while +components are computed in directions *dir*,\ *x*\ ; *dir*,\ *y*\ ; and +*dir*,\ *z*\ ; where *dir* is the direction normal to the plane, while in compute *stress/mop/profile* the profile of the stress is computed. Contrary to methods based on histograms of atomic stress (i.e. using diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index 8aca53bb3c..313b54645c 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -54,7 +54,7 @@ Except for *heat/flux/virial/tally*, the two groups can be the same. This is similar to :doc:`compute group/group ` only that the data is accumulated directly during the non-bonded force computation. The -computes *force/tally*\ , *pe/tally*\ , *stress/tally*\ , and +computes *force/tally*, *pe/tally*, *stress/tally*, and *heat/flux/tally* are primarily provided as example how to program additional, more sophisticated computes using the tally callback mechanism. Compute *pe/mol/tally* is one such style, that can @@ -180,7 +180,7 @@ Restrictions """""""""""" This compute is part of the TALLY package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Not all pair styles can be evaluated in a pairwise mode as required by this compute. For example, 3-body and other many-body potentials, diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index 4c32fc448c..d12cca7591 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -37,7 +37,7 @@ Output info This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See the -:doc:`Howto output ` doc page for an overview of LAMMPS +:doc:`Howto output ` page for an overview of LAMMPS output options. The per-atom vector values will be in the units of chemical species @@ -47,7 +47,7 @@ Restrictions """""""""""" This compute is part of the DPD-MESO package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index a82046367e..3163de2272 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -63,7 +63,7 @@ LAMMPS starts up, as if this command were in the input script: See the "thermo_style" command for more details. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -79,7 +79,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index ef04cad327..815a42f76c 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -99,7 +99,7 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -129,7 +129,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -142,7 +142,7 @@ Restrictions """""""""""" 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. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute requires that atoms store angular momentum and a quaternion as defined by the :doc:`atom_style ellipsoid ` diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index f334c1e11b..72d74d0c4a 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -79,7 +79,7 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -109,7 +109,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -122,7 +122,7 @@ Restrictions """""""""""" 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. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This compute requires that atoms store angular momentum and a quaternion as defined by the :doc:`atom_style body ` diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index f1c34b42fa..1bd5ecbb40 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -172,7 +172,7 @@ allows calculation of the global or per-chunk temperature using only the thermal temperature of atoms in each chunk after the translational kinetic energy components have been altered in a prescribed way, e.g. to remove a velocity profile. It also applies to the calculation -of the other per-chunk values, such as *kecom* or *internal*\ , which +of the other per-chunk values, such as *kecom* or *internal*, which involve the center-of-mass velocity of each chunk, which is calculated after the velocity bias is removed from each atom. Note that the temperature compute will apply its bias globally to the entire system, @@ -207,7 +207,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. This compute also optionally calculates a global array, if one or more diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index 07ae9ad648..d233029ea0 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -63,7 +63,7 @@ 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. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -73,7 +73,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 6b9f0a7e83..8a7fd0a3a5 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -30,7 +30,7 @@ Define a computation that calculates the temperature of a system based on the center-of-mass velocity of atom pairs that are bonded to each other. This compute is designed to be used with the adiabatic core/shell model of :ref:`(Mitchell and Finchham) `. See -the :doc:`Howto coreshell ` doc page for an overview of +the :doc:`Howto coreshell ` page for an overview of the model as implemented in LAMMPS. Specifically, this compute enables correct temperature calculation and thermostatting of core/shell pairs where it is desirable for the internal degrees of @@ -81,7 +81,7 @@ Thermostatting fixes that work in this way include :doc:`fix nvt `, :doc The internal energy of core/shell pairs can be calculated by the :doc:`compute temp/chunk ` command, if chunks are -defined as core/shell pairs. See the :doc:`Howto coreshell ` doc page doc page for more discussion +defined as core/shell pairs. See the :doc:`Howto coreshell ` page doc page for more discussion on how to do this. Output info diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index 026064000c..bc4d1ae3f3 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -104,7 +104,7 @@ 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. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -114,7 +114,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index bff5fb3bfb..b03aa00702 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -49,7 +49,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -62,7 +62,7 @@ Restrictions """""""""""" This compute is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index 7b92198cb9..c2a0479cae 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -60,7 +60,7 @@ are 6. kinetic energy of the dipoles (energy units) 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. Both the scalar value and the first two values of the vector diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index 7bd0559090..ba139dd547 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -74,7 +74,7 @@ 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. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -90,7 +90,7 @@ Restrictions """""""""""" This compute is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index fc3bfc5c88..471f3bcfd4 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -63,7 +63,7 @@ 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. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -79,7 +79,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 0fa8ce5807..b70206781f 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -54,14 +54,14 @@ flow, e.g. via a profile-unbiased thermostat (PUT) as described in 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 +The *xflag*, *yflag*, *zflag* settings determine which components of average velocity are subtracted out. -The *binstyle* setting and its *Nx*\ , *Ny*\ , *Nz* arguments determine +The *binstyle* setting and its *Nx*, *Ny*, *Nz* arguments determine how bins are setup to perform spatial averaging. "Bins" can be 1d slabs, 2d pencils, or 3d bricks depending on which *binstyle* is used. The simulation box is partitioned conceptually into *Nx* by *Ny* by -*Nz* bins. Depending on the *binstyle*\ , you may only specify one or +*Nz* bins. Depending on the *binstyle*, you may only specify one or two of these values; the others are effectively set to 1 (no binning in that dimension). For non-orthogonal (triclinic) simulation boxes, the bins are "tilted" slabs or pencils or bricks that are parallel to @@ -122,13 +122,13 @@ needed, the subtracted degrees-of-freedom can be altered using the .. note:: - When using the *out* keyword with a value of *bin*\ , the + When using the *out* keyword with a value of *bin*, the calculated temperature for each bin does not include the degrees-of-freedom adjustment described in the preceding paragraph, for fixes that constrain molecular motion. It does include the adjustment due to the *extra* option, which is applied to each bin. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a thermostatting fix, as explained there, will effectively implement a @@ -139,7 +139,7 @@ Output info This compute calculates a global scalar (the temperature). Depending on the setting of the *out* keyword, it also calculates a global -vector or array. For *out* = *tensor*\ , it calculates a vector of +vector or array. For *out* = *tensor*, it calculates a vector of length 6 (KE tensor), which can be accessed by indices 1-6. For *out* = *bin* it calculates a global array which has 2 columns and N rows, where N is the number of bins. The first column contains the number @@ -152,7 +152,7 @@ indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)\*10\*10 + (iy-1)\*10 indices are numbered from 1 to 10 in each dimension. These values can be used by any command that uses global scalar or -vector or array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +vector or array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 078ac66002..9cda8bef30 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -84,7 +84,7 @@ 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. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -94,7 +94,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index 5bf80c8f09..86ae03be9b 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -77,7 +77,7 @@ If needed the number of subtracted degrees-of-freedom can be set explicitly using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -87,7 +87,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index 84baf00aaa..d6623ec02d 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -41,7 +41,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -54,7 +54,7 @@ Restrictions """""""""""" This compute is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index b4adea43bf..a0e2cb14ac 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -62,7 +62,7 @@ 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. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -72,7 +72,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -85,7 +85,7 @@ Restrictions """""""""""" This compute is part of the EXTRA-COMPUTE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index b39bad80c0..b752719741 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -86,7 +86,7 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the :doc:`compute_modify ` command. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -116,7 +116,7 @@ Output info This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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 +vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_uef.rst b/doc/src/compute_temp_uef.rst index 18fc4a9fdf..782b5b9acb 100644 --- a/doc/src/compute_temp_uef.rst +++ b/doc/src/compute_temp_uef.rst @@ -39,7 +39,7 @@ Restrictions """""""""""" This fix is part of the UEF package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This command can only be used when :doc:`fix nvt/uef ` or :doc:`fix npt/uef ` is active. diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index 4a2f9cca21..e377042dcf 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -42,7 +42,7 @@ Description """"""""""" Define a computation that calculates the derivative of the interaction -potential with respect to *lambda*\ , the coupling parameter used in a +potential with respect to *lambda*, the coupling parameter used in a thermodynamic integration. This derivative can be used to infer a free energy difference resulting from an alchemical simulation, as described in :ref:`Eike `. @@ -128,8 +128,8 @@ The scalar value will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +This compute is part of the EXTRA-COMPUTE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst index fd874998ab..190947b087 100644 --- a/doc/src/compute_vcm_chunk.rst +++ b/doc/src/compute_vcm_chunk.rst @@ -64,7 +64,7 @@ This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = 3 for the x,y,z center-of-mass velocity coordinates of each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index 880b1ff3d3..d08217a590 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -108,7 +108,7 @@ 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. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -124,7 +124,7 @@ and the 7-th is the cosine-shaped velocity amplitude :math:`V`, which can be used to calculate the reciprocal viscosity, as shown in the example. 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. +See the :doc:`Howto output ` page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The first 6 elements of vector values are "extensive", diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 8998115841..a84590ff02 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -134,7 +134,7 @@ Voronoi cell. The 3 columns are the atom ID of the atom that owns the cell, the atom ID of the atom in the neighboring cell (or zero if the face is external), and the area of the face. The array can be accessed by any command that uses local values from a compute as -input. See the :doc:`Howto output ` doc page for an +input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. More specifically, the array can be accessed by a :doc:`dump local ` command to write a file containing all the Voronoi neighbors in a system: @@ -196,7 +196,7 @@ columns. In regular dynamic tessellation mode the first column is the Voronoi volume, the second is the neighbor count, as described above (read above for the output data in case the *occupation* keyword is specified). These values can be accessed by any command that uses -per-atom values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. If the *peratom* keyword is set to "no", the per-atom array is still created, but it is not accessible. @@ -216,7 +216,7 @@ Voronoi cell. quantity. This effect can be eliminated by using the *peratom* keyword to turn off the production of the per-atom quantities. For the default value *yes* both quantities are produced. For the value - *no*\ , only the local array is produced. + *no*, only the local array is produced. The Voronoi cell volume will be in distance :doc:`units ` cubed. The Voronoi face area will be in distance :doc:`units ` squared. @@ -225,7 +225,7 @@ Restrictions """""""""""" This compute is part of the VORONOI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. It also requires you have a copy of the Voro++ library built and installed on your system. See instructions on obtaining and diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index a0684109ea..480bee6150 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -224,7 +224,7 @@ Restrictions """""""""""" This compute is part of the DIFFRACTION package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The compute_xrd command does not work for triclinic cells. diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 26da54573a..d10498baf2 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -80,7 +80,7 @@ with units = box or the *random* style. For the remainder of this doc page, a created atom or molecule is referred to as a "particle". If created particles are individual atoms, they are assigned the -specified atom *type*\ , though this can be altered via the *basis* +specified atom *type*, though this can be altered via the *basis* keyword as discussed below. If molecules are being created, the type of each atom in the created molecule is specified in the file read by the :doc:`molecule ` command, and those values are added to @@ -116,7 +116,7 @@ positions. For the *random* style, N particles are added to the system at randomly generated coordinates, which can be useful for generating an amorphous system. The particles are created one by one using the -specified random number *seed*\ , resulting in the same set of particles +specified random number *seed*, resulting in the same set of particles coordinates, independent of how many processors are being used in the simulation. If the *region-ID* argument is specified as NULL, then the created particles will be anywhere in the simulation box. If a @@ -159,7 +159,7 @@ used to remove overlapping atoms or molecules. 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 ` 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. @@ -227,9 +227,9 @@ fashion. Which lattice sites are selected will change with the number of processors used. The *remap* keyword only applies to the *single* style. If it is set -to *yes*\ , then if the specified position is outside the simulation +to *yes*, then if the specified position is outside the simulation box, it will mapped back into the box, assuming the relevant -dimensions are periodic. If it is set to *no*\ , no remapping is done +dimensions are periodic. If it is set to *no*, no remapping is done and no particle is created if its position is outside the box. The *var* and *set* keywords can be used together to provide a @@ -288,7 +288,7 @@ determined by the rotation vector (Rx,Ry,Rz) that goes through the insertion point. The specified *theta* determines the angle of rotation around that axis. Note that the direction of rotation for the atoms around the rotation axis is consistent with the right-hand -rule: if your right-hand's thumb points along *R*\ , then your fingers +rule: if your right-hand's thumb points along *R*, then your fingers wrap around the axis in the direction of rotation. The *units* keyword determines the meaning of the distance units used diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index 056b60c7aa..664d870cb0 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -105,7 +105,7 @@ data file for a complex system of molecules. The *many* style will create bonds between pairs of atoms I,J where I is in one of the two specified groups, and J is in the other. The two groups can be the same, e.g. group "all". The created bonds will be -of bond type *btype*\ , where *btype* must be a value between 1 and the +of bond type *btype*, where *btype* must be a value between 1 and the number of bond types defined. For a bond to be created, an I,J pair of atoms must be a distance D @@ -156,7 +156,7 @@ two atoms with IDs *batom1* and *batom2*\ . *Btype* must be a value 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 +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 ordered linearly within the angle; the central atom is *aatom2*\ . @@ -164,14 +164,14 @@ ordered linearly within the angle; the central atom is *aatom2*\ . defined. The *single/dihedral* style creates a single dihedral of type *dtype* -between four atoms with IDs *datom1*\ , *datom2*\ , *datom3*\ , and *datom4*\ . The +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 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 +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 linearly within the improper. *itype* must be a value between 1 and diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 9b7b5a1a65..aa01be43cd 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -49,11 +49,11 @@ changed by the :doc:`balance ` or :doc:`fix balance ` comm The argument N is the number of atom types that will be used in the simulation. -If the region is not of style *prism*\ , then LAMMPS encloses the region +If the region is not of style *prism*, then LAMMPS encloses the region (block, sphere, etc) with an axis-aligned orthogonal bounding box which becomes the simulation domain. -If the region is of style *prism*\ , LAMMPS creates a non-orthogonal +If the region is of style *prism*, LAMMPS creates a non-orthogonal simulation domain shaped as a parallelepiped with triclinic symmetry. As defined by the :doc:`region prism ` command, the parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3 @@ -76,7 +76,7 @@ factors that exceed these limits, you can use the :doc:`box tilt ` command, with a setting of *large*\ ; a setting of *small* is the default. -See the :doc:`Howto triclinic ` doc page for a +See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 127518535f..d47743071b 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -52,9 +52,9 @@ Delete the specified atoms. This command can be used to carve out voids from a block of material or to delete created atoms that are too close to each other (e.g. at a grain boundary). -For style *group*\ , all atoms belonging to the group are deleted. +For style *group*, all atoms belonging to the group are deleted. -For style *region*\ , all atoms in the region volume are deleted. +For style *region*, all atoms in the region volume are deleted. Additional atoms can be deleted if they are in a molecule for which one or more atoms were deleted within the region; see the *mol* keyword discussion below. @@ -83,7 +83,7 @@ randomly. There is no guarantee that the exact fraction of atoms will be deleted, or that the same atoms will be deleted when running on different numbers of processors. -If the *compress* keyword is set to *yes*\ , then after atoms are +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), @@ -117,7 +117,7 @@ atoms. Note that simply deleting interactions due to dangling bonds (e.g. at a surface) may result in a inaccurate or invalid model for the remaining atoms. -It the *mol* keyword is set to *yes*\ , then for every atom that is +It the *mol* keyword is set to *yes*, then for every atom that is deleted, all other atoms in the same molecule (with the same molecule ID) will also be deleted. This is not done for atoms with molecule ID = 0, since such an ID is assumed to flag isolated atoms that are not diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index ffb06e55b2..5603214b2f 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -52,7 +52,7 @@ For all styles, by default, an interaction is only turned off (or on) if all the atoms involved are in the specified group. See the *any* keyword to change the behavior. -Several of the styles (\ *atom*\ , *bond*\ , *angle*\ , *dihedral*\ , +Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*, *improper*\ ) take a *type* as an argument. The specified *type* should be an integer from 0 to N, where N is the number of relevant types (atom types, bond types, etc). A value of 0 is only relevant for @@ -73,11 +73,11 @@ Style *atom* is the same as style *multi* except that in addition, one or more of the atoms involved in the bond, angle, dihedral, or improper interaction must also be of the specified atom type. -For style *bond*\ , only bonds are candidates for turn-off, and the bond -must also be of the specified type. Styles *angle*\ , *dihedral*\ , and +For style *bond*, only bonds are candidates for turn-off, and the bond +must also be of the specified type. Styles *angle*, *dihedral*, and *improper* are treated similarly. -For style *bond*\ , you can set the type to 0 to delete bonds that have +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. @@ -108,7 +108,7 @@ keyword is used). The *undo* keyword inverts the delete_bonds command so that the specified bonds, angles, etc are turned on if they are currently turned off. This means a negative value is toggled to positive. For -example, for style *angle*\ , if *type* is specified as 2, then all +example, for style *angle*, if *type* is specified as 2, then all angles with current type = -2, are reset to type = 2. Note that the :doc:`fix shake ` command also sets bond and angle types negative, so this option should not be used on those interactions. diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index 9588cf8272..cc792693a2 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -107,7 +107,7 @@ i.e. within the outer cutoff specified for the pair style. The :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 +discussion on the :doc:`CHARMM pair_style ` page for details. Note that for AMBER force fields, which use pair styles with "lj/cut", diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 89258cff35..cd5bed7cd2 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -59,7 +59,7 @@ Restrictions """""""""""" This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the :doc:`Build package ` doc page +EXTRA-MOLECULE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst index c0a803755d..add0d4d282 100644 --- a/doc/src/dihedral_hybrid.rst +++ b/doc/src/dihedral_hybrid.rst @@ -58,7 +58,7 @@ for specifying additional AngleTorsion (and EndBondTorsion, etc) coefficients either via the input script or in the data file. I.e. *class2* must be added to each line after the dihedral type. For lines in the AngleTorsion (or EndBondTorsion, etc) section of the data -file for dihedral types that are not *class2*\ , you must use an +file for dihedral types that are not *class2*, you must use an dihedral style of *skip* as a placeholder, e.g. .. parsed-literal:: diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index 4301824b40..f037d95226 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -93,7 +93,7 @@ command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the :ref:`Commands dihedral ` doc page are followed by one or +The individual style names on the :ref:`Commands dihedral ` page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`none ` - turn off dihedral interactions @@ -124,7 +124,7 @@ Dihedral styles can only be set for atom styles that allow dihedrals to be defined. Most dihedral styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual dihedral potentials tell if it is part of a package. Related commands diff --git a/doc/src/dimension.rst b/doc/src/dimension.rst index be711815a6..d22d3f19fa 100644 --- a/doc/src/dimension.rst +++ b/doc/src/dimension.rst @@ -28,7 +28,7 @@ prior to setting up a simulation box via the :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 +See the discussion on the :doc:`Howto 2d ` page for additional instructions on how to run 2d simulations. .. note:: diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index efc6f9230b..9916126dad 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -93,7 +93,7 @@ The *rotate* style rotates each atom in the group by the angle *theta* around a rotation axis *R* = (Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz). The direction of rotation for the atoms around the rotation axis is consistent with the right-hand rule: if your -right-hand thumb points along *R*\ , then your fingers wrap around the +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 diff --git a/doc/src/dump.rst b/doc/src/dump.rst index a5f11a792a..5bdf38fd4e 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -52,7 +52,7 @@ Syntax *cfg/gz* args = same as *custom* args, see below *cfg/zstd* args = same as *custom* args, see below *cfg/mpiio* args = same as *custom* args, see below - *custom*\ , *custom/gz*\ , *custom/zstd* , *custom/mpiio* args = see below + *custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* args = see below *custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios ` doc page *dcd* args = none *h5md* args = discussed on :doc:`dump h5md ` doc page @@ -185,12 +185,12 @@ or multiple smaller files). parallel, because data for a single snapshot is collected from multiple processors, each of which owns a subset of the atoms. -For the *atom*\ , *custom*\ , *cfg*\ , and *local* styles, sorting is off by -default. For the *dcd*\ , *xtc*\ , *xyz*\ , and *molfile* styles, sorting by +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 page for details. -The *atom/gz*\ , *cfg/gz*\ , *custom/gz*\ , *local/gz*, and *xyz/gz* styles are identical +The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles are identical in command syntax to the corresponding styles without "gz", however, they generate compressed files using the zlib library. Thus the filename suffix ".gz" is mandatory. This is an alternative approach to writing @@ -201,13 +201,13 @@ For the remainder of this doc page, you should thus consider the *atom* and *atom/gz* styles (etc) to be inter-changeable, with the exception of the required filename suffix. -Similarly, the *atom/zstd*\ , *cfg/zstd*\ , *custom/zstd*\ , *local/zstd*, +Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, and *xyz/zstd* styles are identical to the gz styles, but use the Zstd compression library instead and require the ".zst" suffix. See the -:doc:`dump_modify ` doc page for details on how to control +:doc:`dump_modify ` page for details on how to control the compression level in both variants. -As explained below, the *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and +As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles are identical in command syntax and in the format of the dump files they create, to the corresponding styles without "mpiio", except the single dump file they produce is written in @@ -227,13 +227,13 @@ file and in what format. Settings made via the :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 +The *atom*, *local*, and *custom* styles create files in a simple text format that is self-explanatory when viewing a dump file. Some of the LAMMPS post-processing tools described on the :doc:`Tools ` doc page, including `Pizza.py `_, work with this format, as does the :doc:`rerun ` command. -For post-processing purposes the *atom*\ , *local*\ , and *custom* text +For post-processing purposes the *atom*, *local*, and *custom* text files are self-describing in the following sense. The dimensions of the simulation box are included in each snapshot. @@ -272,7 +272,7 @@ This bounding box is convenient for many visualization programs. The meaning of the 6 character flags for "xx yy zz" is the same as above. Note that the first two numbers on each line are now xlo_bound instead -of xlo, etc, since they represent a bounding box. See the :doc:`Howto triclinic ` doc page for a geometric description +of xlo, etc, since they represent a bounding box. See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, simple formulas for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from the triclinic parameters, and how to transform those parameters to and @@ -283,7 +283,7 @@ the per-atom lines that follow. For example, the descriptors would be "id type xs ys zs" for the default *atom* style, and would be the atom attributes you specify in the dump command for the *custom* style. -For style *atom*\ , atom coordinates are written to the file, along with +For style *atom*, atom coordinates are written to the file, along with 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 @@ -295,13 +295,13 @@ Style *custom* allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are listed above and will appear in the order specified. You cannot specify a quantity that is not defined for a particular simulation - -such as *q* for atom style *bond*\ , since that atom style does not +such as *q* for atom style *bond*, since that atom style does not assign charges. Dumps occur at the very end of a timestep, so atom attributes will include effects due to fixes that are applied during the timestep. An explanation of the possible dump custom attributes is given below. -For style *local*\ , local output generated by :doc:`computes ` +For style *local*, local output generated by :doc:`computes ` and :doc:`fixes ` is used to generate lines of output that is written to the dump file. This local data is typically calculated by each processor based on the atoms it owns, but there may be zero or @@ -326,7 +326,7 @@ explicitly in the file). Any remaining attributes will be stored as 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 +coordinates *xsu*, *ysu*, and *zsu* are requested, the nominal AtomEye periodic cell dimensions are expanded by a large factor UNWRAPEXPAND = 10.0, which ensures atoms that are displayed correctly for up to UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond @@ -374,7 +374,7 @@ 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. -Note that *atom*\ , *custom*\ , *dcd*\ , *xtc*\ , and *xyz* style dump files +Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files can be read directly by `VMD `_, a popular molecular viewing program. @@ -417,7 +417,7 @@ with the processor ID from 0 to P-1. For example, tmp.dump.% becomes tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller files and can be a fast mode of output on parallel machines that support parallel I/O for output. This option is not available for the -*dcd*\ , *xtc*\ , and *xyz* styles. +*dcd*, *xtc*, and *xyz* styles. 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 @@ -428,7 +428,7 @@ when running on large numbers of processors. Note that using the "\*" and "%" characters together can produce a large number of small dump files! -For the *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and *xyz/mpiio* +For the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles, a single dump file is written in parallel via the MPI-IO library, which is part of the MPI standard for versions 2.0 and above. Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO @@ -474,7 +474,7 @@ styles. ---------- Note that in the discussion which follows, for styles which can -reference values from a compute or fix, like the *custom*\ , *cfg*\ , or +reference values from a compute or fix, like the *custom*, *cfg*, or *local* styles, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the @@ -557,8 +557,8 @@ the distance and energy of each bond: This section explains the atom attributes that can be specified as part of the *custom* and *cfg* styles. -The *id*\ , *mol*\ , *proc*\ , *procp1*\ , *type*\ , *element*\ , *mass*\ , *vx*\ , -*vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz*\ , *q* attributes are self-explanatory. +The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*, +*vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory. *Id* is the atom ID. *Mol* is the molecule ID, included in the data file for molecular systems. *Proc* is the ID of the processor (0 to @@ -568,31 +568,31 @@ 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 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 +mass. *Vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components of atom velocity and force and atomic charge. -There are several options for outputting atom coordinates. The *x*\ , -*y*\ , *z* attributes write atom coordinates "unscaled", in the +There are several options for outputting atom coordinates. The *x*, +*y*, *z* attributes write atom coordinates "unscaled", in the appropriate distance :doc:`units ` (Angstroms, sigma, etc). Use -*xs*\ , *ys*\ , *zs* if you want the coordinates "scaled" to the box size, +*xs*, *ys*, *zs* if you want the coordinates "scaled" to the box size, so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. I.e. actual unscaled (x,y,z) = xs\*A + ys\*B + zs\*C, where (A,B,C) are the non-orthogonal vectors of the simulation box edges, as discussed on the :doc:`Howto triclinic ` doc page. -Use *xu*\ , *yu*\ , *zu* if you want the coordinates "unwrapped" by the +Use *xu*, *yu*, *zu* if you want the coordinates "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 if it had not been wrapped -back into the periodic box. Note that using *xu*\ , *yu*\ , *zu* means +back into the periodic box. Note that using *xu*, *yu*, *zu* means that the coordinate values may be far outside the box bounds printed -with the snapshot. Using *xsu*\ , *ysu*\ , *zsu* is similar to using -*xu*\ , *yu*\ , *zu*\ , except that the unwrapped coordinates are scaled by +with the snapshot. Using *xsu*, *ysu*, *zsu* is similar to using +*xu*, *yu*, *zu*, except that the unwrapped coordinates are scaled by the box size. Atoms that have passed through a periodic boundary will have the corresponding coordinate increased or decreased by 1.0. -The image flags can be printed directly using the *ix*\ , *iy*\ , *iz* +The image flags can be printed directly using the *ix*, *iy*, *iz* attributes. For periodic dimensions, they specify which image of the simulation box the atom is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths @@ -600,7 +600,7 @@ to get the true value. A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as atoms cross periodic boundaries during the simulation. -The *mux*\ , *muy*\ , *muz* attributes are specific to dipolar systems +The *mux*, *muy*, *muz* attributes are specific to dipolar systems defined with an atom style of *dipole*\ . They give the orientation of the atom's point dipole moment. The *mu* attribute gives the magnitude of the atom's dipole moment. @@ -609,15 +609,15 @@ The *radius* and *diameter* attributes are specific to spherical particles that have a finite size, such as those defined with an atom style of *sphere*\ . -The *omegax*\ , *omegay*\ , and *omegaz* attributes are specific to +The *omegax*, *omegay*, and *omegaz* attributes are specific to finite-size spherical particles that have an angular velocity. Only certain atom styles, such as *sphere* define this quantity. -The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are specific to +The *angmomx*, *angmomy*, and *angmomz* attributes are specific to finite-size aspherical particles that have an angular momentum. Only the *ellipsoid* atom style defines this quantity. -The *tqx*\ , *tqy*\ , *tqz* attributes are for finite-size particles that +The *tqx*, *tqy*, *tqz* attributes are for finite-size particles that can sustain a rotational torque due to interactions with other particles. @@ -673,7 +673,7 @@ The *d_name* and *i_name* attributes allow to output custom per atom floating point or integer properties that are managed by :doc:`fix property/atom `. -See the :doc:`Modify ` doc page for information on how to add +See the :doc:`Modify ` page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files. @@ -684,20 +684,20 @@ Restrictions To write gzipped dump files, you must either compile LAMMPS with the -DLAMMPS_GZIP option or use the styles from the COMPRESS package. -See the :doc:`Build settings ` doc page for details. +See the :doc:`Build settings ` page for details. -The *atom/gz*\ , *cfg/gz*\ , *custom/gz*\ , and *xyz/gz* styles are part of +The *atom/gz*, *cfg/gz*, *custom/gz*, and *xyz/gz* styles are part of the COMPRESS package. They are only enabled if LAMMPS was built with -that package. See the :doc:`Build package ` doc page for +that package. See the :doc:`Build package ` page for more info. -The *atom/mpiio*\ , *cfg/mpiio*\ , *custom/mpiio*\ , and *xyz/mpiio* styles +The *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles are part of the MPIIO package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The *xtc* style is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index 74c8dae189..71ab6a07d9 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -66,7 +66,7 @@ its size is changing every step. The *atom/adios* and *custom/adios* dump styles are part of the ADIOS package. They are only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. ---------- diff --git a/doc/src/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst index 9e33291880..7e95d8f30d 100644 --- a/doc/src/dump_cfg_uef.rst +++ b/doc/src/dump_cfg_uef.rst @@ -43,7 +43,7 @@ Restrictions """""""""""" This fix is part of the UEF package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This command can only be used when :doc:`fix nvt/uef ` or :doc:`fix npt/uef ` is active. diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index 2f66e2863b..202d5fb89d 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -32,7 +32,7 @@ Syntax Note that at least one element must be specified and image may only be present if position is specified first. -For the elements *position*\ , *velocity*\ , *force* and *species*\ , a +For the elements *position*, *velocity*, *force* and *species*, a sub-interval may be specified to write the data only every N_element iterations of the dump (i.e. every N\*N_element time steps). This is specified by this option directly following the element declaration: @@ -66,7 +66,7 @@ another particle group must specify *create_group yes*. .. _h5md: http://nongnu.org/h5md/ -Each data element is written every N\*N_element steps. For *image*\ , no +Each data element is written every N\*N_element steps. For *image*, no sub-interval is needed as it must be present at the same interval as *position*\ . *image* must be given after *position* in any case. The box information (edges in each dimension) is stored at the same @@ -107,8 +107,8 @@ note above). Only orthogonal domains are currently supported. This is a limitation of the present dump h5md command and not of H5MD itself. The *h5md* dump style is part of the H5MD package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. It also requires -(i) building the ch5md library provided with LAMMPS (See the :doc:`Build package ` doc page for more info.) and (ii) having +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. It also requires +(i) building the ch5md library provided with LAMMPS (See the :doc:`Build package ` page for more info.) and (ii) having the `HDF5 `_ library installed (C bindings are sufficient) on your system. The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library. diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 3923d5c2dc..f54b69321b 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -153,7 +153,7 @@ 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 into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG -flag. See the :doc:`Build settings ` doc page for +flag. See the :doc:`Build settings ` page for details. .. note:: @@ -261,7 +261,7 @@ The *atom* keyword allow you to turn off the drawing of all atoms, if the specified value is *no*\ . Note that this will not turn off the drawing of particles that are represented as lines, triangles, or bodies, as discussed below. These particles can be drawn separately -if the *line*\ , *tri*\ , or *body* keywords are used. +if the *line*, *tri*, or *body* keywords are used. The *adiam* keyword allows you to override the *diameter* setting to set a single numeric *size*\ . All atoms will be drawn with that @@ -318,7 +318,7 @@ 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 -currently allowed for the *color* value is *type*\ , which will color +currently allowed for the *color* value is *type*, which will color the lines according to the atom type of the particle. By default the mapping of types to colors is as follows: @@ -345,7 +345,7 @@ or edges (3 lines) or both, depending on the setting for *tflag*\ . If edges are drawn, the *width* setting determines the diameters of the line segments. If this keyword is not used, triangle particles will be drawn as spheres, the same as if they were regular atoms. The only -setting currently allowed for the *color* value is *type*\ , which will +setting currently allowed for the *color* value is *type*, which will color the triangles according to the atom type of the particle. By default the mapping of types to colors is as follows: @@ -367,7 +367,7 @@ is used to define body particles with internal state body style. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. -The :doc:`Howto body ` doc page describes the body styles +The :doc:`Howto body ` page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent and how they are drawn by this dump image command. For all the body styles, individual atoms can be @@ -375,10 +375,10 @@ either a body particle or a usual point (non-body) particle. Non-body particles will be drawn the same way they would be as a regular atom. The *bflag1* and *bflag2* settings are numerical values which are passed to the body style to affect how the drawing of a body particle -is done. See the :doc:`Howto body ` doc page for a +is done. See the :doc:`Howto body ` page for a description of what these parameters mean for each body style. -The only setting currently allowed for the *color* value is *type*\ , +The only setting currently allowed for the *color* value is *type*, which will color the body particles according to the atom type of the particle. By default the mapping of types to colors is as follows: @@ -399,10 +399,10 @@ objects to be drawn. The *fflag1* and *fflag2* settings are numerical values which are passed to the fix to affect how the drawing of its objects is done. -See the individual fix doc page for a description of what these +See the individual fix page for a description of what these parameters mean for a particular fix. -The only setting currently allowed for the *color* value is *type*\ , +The only setting currently allowed for the *color* value is *type*, which will color the fix objects according to their type. By default the mapping of types to colors is as follows: @@ -423,11 +423,11 @@ i.e. the number of pixels in each direction. ---------- -The *view*\ , *center*\ , *up*\ , and *zoom* values determine how +The *view*, *center*, *up*, and *zoom* values determine how 3d simulation space is mapped to the 2d plane of the image. Basically they control how the simulation box appears in the image. -All of the *view*\ , *center*\ , *up*\ , and *zoom* values can be +All of the *view*, *center*, *up*, and *zoom* values can be specified as numeric quantities, whose meaning is explained below. Any of them can also be specified as an :doc:`equal-style variable `, by using v_name as the value, where "name" is @@ -447,13 +447,13 @@ specified via variables, then the variable values should be in degrees. The *center* keyword determines the point in simulation space that -will be at the center of the image. *Cx*\ , *Cy*\ , and *Cz* are +will be at the center of the image. *Cx*, *Cy*, and *Cz* are specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is the center of the simulation box. These values do not have to be between 0.0 and 1.0, if you want the simulation box to be offset from the center of the image. Note, however, that if you choose strange -values for *Cx*\ , *Cy*\ , or *Cz* you may get a blank image. Internally, -*Cx*\ , *Cy*\ , and *Cz* are converted into a point in simulation space. +values for *Cx*, *Cy*, or *Cz* you may get a blank image. Internally, +*Cx*, *Cy*, and *Cz* are converted into a point in simulation space. If *flag* is set to "s" for static, then this conversion is done once, at the time the dump command is issued. If *flag* is set to "d" for dynamic then the conversion is performed every time a new image is @@ -607,7 +607,7 @@ Play the movie: ---------- -See the :doc:`Modify ` doc page for information on how to add +See the :doc:`Modify ` page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files. @@ -626,7 +626,7 @@ building LAMMPS and have the FFmpeg executable available on the machine where LAMMPS is being run. Typically it's name is lowercase, i.e. ffmpeg. -See the :doc:`Build settings ` doc page for details. +See the :doc:`Build settings ` page for details. Note that since FFmpeg is run as an external program via a pipe, LAMMPS has limited control over its execution and no knowledge about diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index a66c571dea..5fea976e70 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -152,8 +152,8 @@ Description Modify the parameters of a previously defined dump command. Not all parameters are relevant to all dump styles. -As explained on the :doc:`dump ` doc page, the *atom/mpiio*\ , -*custom/mpiio*\ , and *xyz/mpiio* dump styles are identical in command +As explained on the :doc:`dump ` doc page, the *atom/mpiio*, +*custom/mpiio*, and *xyz/mpiio* dump styles are identical in command syntax and in the format of the dump files they create, to the corresponding styles without "mpiio", except the single dump file they produce is written in parallel via the MPI-IO library. Thus if a @@ -170,9 +170,9 @@ description gives details. The *append* keyword applies to all dump styles except *cfg* and *xtc* and *dcd*\ . It also applies only to text output files, not to binary -or gzipped or image/movie files. If specified as *yes*\ , then dump +or gzipped or image/movie files. If specified as *yes*, then dump snapshots are appended to the end of an existing dump file. If -specified as *no*\ , then a new dump file will be created which will +specified as *no*, then a new dump file will be created which will overwrite an existing file with the same name. ---------- @@ -180,7 +180,7 @@ overwrite an existing file with the same name. The *at* keyword only applies to the *netcdf* dump style. It can only be used if the *append yes* keyword is also used. The *N* argument is the index of which frame to append to. A negative value can be -specified for *N*\ , which means a frame counted from the end of the +specified for *N*, which means a frame counted from the end of the file. The *at* keyword can only be used if the dump_modify command is before the first command that causes dump snapshots to be output, e.g. a :doc:`run ` or :doc:`minimize ` command. Once the @@ -188,13 +188,13 @@ dump file has been opened, this keyword has no further effect. ---------- -The *buffer* keyword applies only to dump styles *atom*\ , *cfg*\ , -*custom*\ , *local*\ , and *xyz*\ . It also applies only to text output -files, not to binary or gzipped files. If specified as *yes*\ , which +The *buffer* keyword applies only to dump styles *atom*, *cfg*, +*custom*, *local*, and *xyz*\ . It also applies only to text output +files, not to binary or gzipped files. If specified as *yes*, which is the default, then each processor writes its output into an internal text buffer, which is then sent to the processor(s) which perform file writes, and written by those processors(s) as one large chunk of text. -If specified as *no*\ , each processor sends its per-atom data in binary +If specified as *no*, each processor sends its per-atom data in binary format to the processor(s) which perform file wirtes, and those processor(s) format and write it line by line into the output file. @@ -213,16 +213,16 @@ during an equilibration phase. ---------- -The *element* keyword applies only to the dump *cfg*\ , *xyz*\ , and +The *element* keyword applies only to the dump *cfg*, *xyz*, and *image* styles. It associates element names (e.g. H, C, Fe) with LAMMPS atom types. See the list of element names at the bottom of this page. -In the case of dump *cfg*\ , this allows the `AtomEye `_ +In the case of dump *cfg*, this allows the `AtomEye `_ visualization package to read the dump file and render atoms with the appropriate size and color. -In the case of dump *image*\ , the output images will follow the same +In the case of dump *image*, the output images will follow the same `AtomEye `_ convention. An element name is specified for each atom type (1 to Ntype) in the simulation. The same element name can be given to multiple atom types. @@ -298,7 +298,7 @@ the very first timestep after the dump command is invoked. This will always occur if the current timestep is a multiple of N, the frequency specified in the :doc:`dump ` command, including timestep 0. But if this is not the case, a dump snapshot will only be written if the -setting of this keyword is *yes*\ . If it is *no*\ , which is the +setting of this keyword is *yes*\ . If it is *no*, which is the default, then it will not be written. ---------- @@ -312,7 +312,7 @@ performed with dump style *xtc*\ . ---------- The *format* keyword can be used to change the default numeric format output -by the text-based dump styles: *atom*\ , *local*\ , *custom*\ , *cfg*\ , and +by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and *xyz* styles, and their MPIIO variants. Only the *line* or *none* options can be used with the *atom* and *xyz* styles. @@ -381,7 +381,7 @@ The *fileper* keyword is documented below with the *nfile* keyword. ---------- The *image* keyword applies only to the dump *atom* style. If the -image value is *yes*\ , 3 flags are appended to each atom's coords which +image value is *yes*, 3 flags are appended to each atom's coords which are the absolute box image of the atom in each dimension. For example, an x image flag of -2 with a normalized coord of 0.5 means the atom is in the center of the box, but has passed through the box @@ -423,7 +423,7 @@ files produced, even if you run for 1000s of steps. The *nfile* or *fileper* keywords can be used in conjunction with the "%" wildcard character in the specified dump file name, for all dump -styles except the *dcd*\ , *image*\ , *movie*\ , *xtc*\ , and *xyz* styles +styles except the *dcd*, *image*, *movie*, *xtc*, and *xyz* styles (for which "%" is not allowed). As explained on the :doc:`dump ` command doc page, the "%" character causes the dump file to be written in pieces, one piece for each of P processors. By default P = the @@ -461,7 +461,7 @@ slightly outside the simulation box. This is because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, which will not typically coincide with the timesteps dump snapshots are written. If the setting of this keyword is set to -*yes*\ , then all atoms will be remapped to the periodic box before the +*yes*, then all atoms will be remapped to the periodic box before the snapshot is written, then restored to their original position. If it is set to *no* they will not be. The *no* setting is the default because it requires no extra computation. @@ -475,8 +475,8 @@ nanometer accuracy, e.g. for N = 1000, the coordinates are written to ---------- -The *refresh* keyword only applies to the dump *custom*\ , *cfg*\ , -*image*\ , and *movie* styles. It allows an "incremental" dump file to +The *refresh* keyword only applies to the dump *custom*, *cfg*, +*image*, and *movie* styles. It allows an "incremental" dump file to be written, by refreshing a compute that is used as a threshold for determining which atoms are included in a dump snapshot. The specified *c_ID* gives the ID of the compute. It is prefixed by "c\_" @@ -544,8 +544,8 @@ simply do nothing. ---------- -The *region* keyword only applies to the dump *custom*\ , *cfg*\ , -*image*\ , and *movie* styles. If specified, only atoms in the region +The *region* keyword only applies to the dump *custom*, *cfg*, +*image*, and *movie* styles. If specified, only atoms in the region will be written to the dump file or included in the image/movie. Only one region can be applied as a filter (the last one specified). See the :doc:`region ` command for more details. Note that a region @@ -590,7 +590,7 @@ order. The dump *local* style cannot be sorted by atom ID, since there are typically multiple lines of output per atom. Some dump styles, such -as *dcd* and *xtc*\ , require sorting by atom ID to format the output +as *dcd* and *xtc*, require sorting by atom ID to format the output file correctly. If multiple processors are writing the dump file, via the "%" wildcard in the dump filename, then sorting cannot be performed. @@ -610,8 +610,8 @@ identical to the values specified by :doc:`thermo_style `. ---------- -The *thresh* keyword only applies to the dump *custom*\ , *cfg*\ , -*image*\ , and *movie* styles. Multiple thresholds can be specified. +The *thresh* keyword only applies to the dump *custom*, *cfg*, +*image*, and *movie* styles. Multiple thresholds can be specified. Specifying *none* turns off all threshold criteria. If thresholds are specified, only atoms whose attributes meet all the threshold criteria are written to the dump file or included in the image. The possible @@ -626,7 +626,7 @@ produce continuous numeric values or effective Boolean 0/1 values which may be useful for the comparison operator. Boolean values can be generated by variable formulas that use comparison or Boolean math operators or special functions like gmask() and rmask() and grmask(). -See the :doc:`variable ` command doc page for details. +See the :doc:`variable ` command page for details. The specified value must be a simple numeric value or the word LAST. If LAST is used, it refers to the value of the attribute the last time @@ -670,9 +670,9 @@ threshold criterion is met. Otherwise it is not met. ---------- -The *time* keyword only applies to the dump *atom*\ , *custom*\ , and -*local* styles (and their COMPRESS package versions *atom/gz*\ , -*custom/gz* and *local/gz*\ ). If set to *yes*\ , each frame will will +The *time* keyword only applies to the dump *atom*, *custom*, and +*local* styles (and their COMPRESS package versions *atom/gz*, +*custom/gz* and *local/gz*\ ). If set to *yes*, each frame will will contain two extra lines before the "ITEM: TIMESTEP" entry: .. parsed-literal:: @@ -688,9 +688,9 @@ The default setting is *no*\ . ---------- -The *units* keyword only applies to the dump *atom*\ , *custom*\ , and -*local* styles (and their COMPRESS package versions *atom/gz*\ , -*custom/gz* and *local/gz*\ ). If set to *yes*\ , each individual dump +The *units* keyword only applies to the dump *atom*, *custom*, and +*local* styles (and their COMPRESS package versions *atom/gz*, +*custom/gz* and *local/gz*\ ). If set to *yes*, each individual dump file will contain two extra lines at the very beginning with: .. parsed-literal:: @@ -706,7 +706,7 @@ The default setting is *no*\ . ---------- The *unwrap* keyword only applies to the dump *dcd* and *xtc* styles. -If set to *yes*\ , coordinates will be written "unwrapped" by the image +If set to *yes*, coordinates will 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 if it had not been wrapped back into the @@ -723,7 +723,7 @@ images. Some of the keywords only affect the :doc:`dump movie ` sty ---------- The *acolor* keyword can be used with the :doc:`dump image ` -command, when its atom color setting is *type*\ , to set the color that +command, when its atom color setting is *type*, to set the color that atoms of each type will be drawn in the image. The specified *type* should be an integer from 1 to Ntypes = the @@ -747,7 +747,7 @@ of the specified atom types. ---------- The *adiam* keyword can be used with the :doc:`dump image ` -command, when its atom diameter setting is *type*\ , to set the size +command, when its atom diameter setting is *type*, to set the size that atoms of each type will be drawn in the image. The specified *type* should be an integer from 1 to Ntypes. As with the *acolor* keyword, a wildcard asterisk can be used as part of the *type* @@ -776,7 +776,7 @@ There are many possible options for the color map, enabled by the *amap* keyword. Here are the details. The *lo* and *hi* settings determine the range of values allowed for -the atom attribute. If numeric values are used for *lo* and/or *hi*\ , +the atom attribute. If numeric values are used for *lo* and/or *hi*, then values that are lower/higher than that value are set to the value. I.e. the range is static. If *lo* is specified as *min* or *hi* as *max* then the range is dynamic, and the lower and/or @@ -847,7 +847,7 @@ for the color map. Here is how the entries are used to determine the color of an individual atom, given the value X of its atom attribute. The entries are scanned from first to last. The first time that *lo* <= X <= -*hi*\ , X is assigned the color associated with that entry. You can +*hi*, X is assigned the color associated with that entry. You can think of the last entry as assigning a default color (since it will always be matched by X), and the earlier entries as colors that override the default. Also note that no interpolation of a color RGB @@ -894,7 +894,7 @@ name defined by the dump_modify color option. ---------- The *bcolor* keyword can be used with the :doc:`dump image ` -command, with its *bond* keyword, when its color setting is *type*\ , to +command, with its *bond* keyword, when its color setting is *type*, to set the color that bonds of each type will be drawn in the image. The specified *type* should be an integer from 1 to Nbondtypes = the @@ -918,7 +918,7 @@ of the specified bond types. ---------- The *bdiam* keyword can be used with the :doc:`dump image ` -command, with its *bond* keyword, when its diam setting is *type*\ , to +command, with its *bond* keyword, when its diam setting is *type*, to set the diameter that bonds of each type will be drawn in the image. The specified *type* should be an integer from 1 to Nbondtypes. As with the *bcolor* keyword, a wildcard asterisk can be used as part of @@ -1024,7 +1024,7 @@ Default The option defaults are * append = no -* buffer = yes for dump styles *atom*\ , *custom*\ , *loca*\ , and *xyz* +* buffer = yes for dump styles *atom*, *custom*, *loca*, and *xyz* * element = "C" for every atom type * every = whatever it was set to via the :doc:`dump ` command * fileper = # of processors @@ -1040,8 +1040,8 @@ The option defaults are * precision = 1000 * region = none * scale = yes -* sort = off for dump styles *atom*\ , *custom*\ , *cfg*\ , and *local* -* sort = id for dump styles *dcd*\ , *xtc*\ , and *xyz* +* sort = off for dump styles *atom*, *custom*, *cfg*, and *local* +* sort = id for dump styles *dcd*, *xtc*, and *xyz* * thresh = none * units = no * unwrap = no diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst index aa8e04b22c..c1f0b48fe6 100644 --- a/doc/src/dump_molfile.rst +++ b/doc/src/dump_molfile.rst @@ -93,7 +93,7 @@ Restrictions """""""""""" The *molfile* dump style is part of the MOLFILE package. It is -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Molfile plugins provide a consistent programming interface to read and write file formats commonly used in molecular simulations. The diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst index c14ec02871..d53a0a3b12 100644 --- a/doc/src/dump_netcdf.rst +++ b/doc/src/dump_netcdf.rst @@ -70,7 +70,7 @@ Restrictions The *netcdf* and *netcdf/mpiio* dump styles are part of the NETCDF package. They are only enabled if LAMMPS was built with -that package. See the :doc:`Build package ` doc page for +that package. See the :doc:`Build package ` page for more info. The *netcdf* and *netcdf/mpiio* dump styles currently cannot dump diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index 8eea1def94..8eec479292 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -70,7 +70,7 @@ determine the kind of output. 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 ` page for details. ---------- @@ -88,7 +88,7 @@ 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 -its doc page for a listing and an explanation of each attribute. +its page for a listing and an explanation of each attribute. .. note:: @@ -163,7 +163,7 @@ Restrictions The *vtk* style does not support writing of gzipped dump files. The *vtk* dump style is part of the VTK package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. To use this dump style, you also must link to the VTK library. See the info in lib/vtk/README and insure the Makefile.lammps file in that diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst index 8d17f0aa1e..37b9e5b4a5 100644 --- a/doc/src/dynamical_matrix.rst +++ b/doc/src/dynamical_matrix.rst @@ -65,7 +65,7 @@ for large systems. This command is part of the PHONON package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 07a663c789..81c0c87320 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -34,7 +34,7 @@ positions and velocities due to time integration, controlling temperature, applying constraint forces to atoms, enforcing boundary conditions, computing diagnostics, etc. There are hundreds of fixes defined in LAMMPS and new ones can be added; see the -:doc:`Modify ` doc page for details. +:doc:`Modify ` page for details. Fixes perform their operations at different stages of the timestep. If 2 or more fixes operate at the same stage of the timestep, they are @@ -65,7 +65,7 @@ was. Note that this operation also wipes out any additional changes made to the old fix via the :doc:`fix_modify ` command. The :doc:`fix modify ` command allows settings for some -fixes to be reset. See the doc page for individual fixes for details. +fixes to be reset. See the page for individual fixes for details. Some fixes store an internal "state" which is written to binary restart files via the :doc:`restart ` or @@ -90,7 +90,7 @@ more per atoms. Note that a single fix can produce either global or per-atom or local quantities (or none at all), but not both global and per-atom. It can produce local quantities in tandem with global or per-atom quantities. -The fix doc page will explain. +The fix page will explain. Global, per-atom, and local quantities each come in three kinds: a single scalar value, a vector of values, or a 2d array of values. The @@ -136,7 +136,7 @@ In LAMMPS, the values generated by a fix can be used in several ways: command. Or the per-atom values can be referenced in an :doc:`atom-style variable `. * Local values can be reduced by the :doc:`compute reduce ` command, or histogrammed by the :doc:`fix ave/histo ` command. -See the :doc:`Howto output ` doc page for a summary of +See the :doc:`Howto output ` page for a summary of various LAMMPS output options, many of which involve fixes. The results of fixes that calculate global quantities can be either @@ -149,12 +149,12 @@ values by the number of atoms in the system, depending on the "thermo_modify norm" setting. It will not normalize intensive values. If a fix value is accessed in another way, e.g. by a :doc:`variable `, you may want to know whether it is an -intensive or extensive value. See the doc page for individual fixes +intensive or extensive value. See the page for individual fixes for further info. ---------- -Each fix style has its own doc page which describes its arguments and +Each fix style has its own page which describes its arguments and what it does, as listed below. Here is an alphabetic list of fix styles available in LAMMPS. They are also listed in more compact form on the :doc:`Commands fix ` doc page. @@ -407,7 +407,7 @@ Restrictions """""""""""" Some fix styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual fixes tell if it is part of a package. Related commands diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 58d86f8472..b7151334db 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -85,19 +85,19 @@ variable that is time-dependent. Depending on the value of the *reset* keyword, attributes changed by this fix will or will not be reset back to their original values at -the end of a simulation. Even if *reset* is specified as *yes*\ , a +the end of a simulation. Even if *reset* is specified as *yes*, a restart file written during a simulation will contain the modified settings. -If the *scale* keyword is set to *no*\ , which is the default, then +If the *scale* keyword is set to *no*, which is the default, then the value of the altered parameter will be whatever the variable -generates. If the *scale* keyword is set to *yes*\ , then the value +generates. If the *scale* keyword is set to *yes*, then the value of the altered parameter will be the initial value of that parameter multiplied by whatever the variable generates. I.e. the variable is now a "scale factor" applied in (presumably) a time-varying fashion to the parameter. -Note that whether scale is *no* or *yes*\ , internally, the parameters +Note that whether scale is *no* or *yes*, internally, the parameters themselves are actually altered by this fix. Make sure you use the *reset yes* option if you want the parameters to be restored to their initial values after the run. diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 0f669eade3..affb893117 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -84,13 +84,13 @@ variable that is time-dependent. Depending on the value of the *reset* keyword, attributes changed by this fix will or will not be reset back to their original values at -the end of a simulation. Even if *reset* is specified as *yes*\ , a +the end of a simulation. Even if *reset* is specified as *yes*, a restart file written during a simulation will contain the modified settings. -If the *scale* keyword is set to *no*\ , then the value the parameter is +If the *scale* keyword is set to *no*, then the value the parameter is set to will be whatever the variable generates. If the *scale* -keyword is set to *yes*\ , then the value of the altered parameter will +keyword is set to *yes*, then the value of the altered parameter will be the initial value of that parameter multiplied by whatever the variable generates. I.e. the variable is now a "scale factor" applied in (presumably) a time-varying fashion to the parameter. Internally, @@ -98,7 +98,7 @@ the parameters themselves are actually altered; make sure you use the *reset yes* option if you want the parameters to be restored to their initial values after the run. -If the *after* keyword is set to *yes*\ , then the parameters are +If the *after* keyword is set to *yes*, then the parameters are changed one timestep after the multiple of N. In this manner, if a fix such as "fix ave/time" is used to calculate averages at every N timesteps, all the contributions to the average will be obtained with diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 0137066ff7..15f433f520 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -48,8 +48,8 @@ atoms in a simulation, such as for a simulation of Poiseuille flow in a channel. Any of the 3 quantities defining the force components can be specified -as an equal-style or atom-style :doc:`variable `, namely *fx*\ , -*fy*\ , *fz*\ . If the value is a variable, it should be specified as +as an equal-style or atom-style :doc:`variable `, namely *fx*, +*fy*, *fz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value(s) used to determine the force component. @@ -98,7 +98,7 @@ one or more variables, and you are performing energy minimization via the "minimize" command. The keyword specifies the name of an atom-style :doc:`variable ` which is used to compute the energy of each atom as function of its position. Like variables used -for *fx*\ , *fy*\ , *fz*\ , the energy variable is specified as v_name, +for *fx*, *fy*, *fz*, the energy variable is specified as v_name, where name is the variable name. Note that when the *energy* keyword is used during an energy diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst index e03ed2b160..4e1ca12228 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -37,8 +37,8 @@ the group such that: This command can be used to drive a group of atoms into rotation. Any of the 3 quantities defining the torque components can be specified -as an equal-style :doc:`variable `, namely *Tx*\ , -*Ty*\ , *Tz*\ . If the value is a variable, it should be specified as +as an equal-style :doc:`variable `, namely *Tx*, +*Ty*, *Tz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the torque component. @@ -101,7 +101,7 @@ Restrictions This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst index 754183b55b..c175fa429f 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -31,7 +31,7 @@ Syntax seed = random number seed for langevin kicks extent = extent of thermostatted region (distance units) *random* args = xmax ymax zmax seed - *xmax*\ , *ymax*\ , *zmax* = maximum displacement in particular direction (distance units) + *xmax*, *ymax*, *zmax* = maximum displacement in particular direction (distance units) *seed* = random number seed for random displacement *units* value = *lattice* or *box* *lattice* = the wall position is defined in lattice units @@ -99,7 +99,7 @@ Restrictions """""""""""" This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The boundary on which atoms are added with append/atoms must be shrink/minimum. The opposite boundary may be any boundary type other diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index a2d365dbe2..eb56572db7 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -66,7 +66,7 @@ The *types* keyword is required. At least two atom types must be specified. The *ke* keyword can be set to *no* to turn off kinetic energy -conservation for swaps. The default is *yes*\ , which means that swapped +conservation for swaps. The default is *yes*, which means that swapped atoms have their velocities scaled by the ratio of the masses of the swapped atom types. This ensures that the kinetic energy of each atom is the same after the swap as it was before the swap, even though the @@ -75,12 +75,12 @@ atom masses have changed. The *semi-grand* keyword can be set to *yes* to switch to the semi-grand canonical ensemble as discussed in :ref:`(Sadigh) `. This means that the total number of each particle type does not need to be -conserved. The default is *no*\ , which means that the only kind of swap +conserved. The default is *no*, which means that the only kind of swap allowed exchanges an atom of one type with an atom of a different given type. In other words, the relative mole fractions of the swapped atoms remains constant. Whereas in the semi-grand canonical ensemble, the composition of the system can change. Note that when using -*semi-grand*\ , atoms in the fix group whose type is not listed +*semi-grand*, atoms in the fix group whose type is not listed in the *types* keyword are ineligible for attempted conversion. An attempt is made to switch the selected atom (if eligible) to one of the other listed types @@ -111,7 +111,7 @@ If not using *semi-grand* this fix checks to ensure all atoms of the given types have the same atomic charge. LAMMPS does not enforce this in general, but it is needed for this fix to simplify the swapping procedure. Successful swaps will swap the atom type and charge -of the swapped atoms. Conversely, when using *semi-grand*\ , it is assumed that all the atom +of the swapped atoms. Conversely, when using *semi-grand*, it is assumed that all the atom types involved in switches have the same charge. Otherwise, charge would not be conserved. As a consequence, no checks on atomic charges are performed, and successful switches update the atom type but not the diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index e506b62cfa..7719dfa7e1 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -89,7 +89,7 @@ command creates a per-atom array with 6 columns: ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps that are a multiple of *Nfreq*\ . The average is over *Nrepeat* @@ -136,7 +136,7 @@ appended, the per-atom vector calculated by the fix is used. If a bracketed term containing an index I is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be -compatible with *Nevery*\ , else an error will result. Users can also +compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index ce7fcd1fca..6d5e0b0380 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -102,7 +102,7 @@ a file. In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and the :doc:`Howto chunk ` doc page for details of how chunks can be +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` page and the :doc:`Howto chunk ` page for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -168,7 +168,7 @@ case, a per-atom array with 3 columns: ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be accessed and contribute to the average. The final averaged quantities are generated on timesteps that are a multiples of *Nfreq*\ . The average is over *Nrepeat* @@ -199,14 +199,14 @@ discussed below. remain constant for the duration of the simulation. This fix forces the chunk/atom compute specified by chunkID to hold *Nchunk* constant for the appropriate time windows, by not allowing it to re-calculate - *Nchunk*\ , which can also affect how it assigns chunk IDs to atoms. + *Nchunk*, which can also affect how it assigns chunk IDs to atoms. This is particularly important to understand if the chunks defined by the :doc:`compute chunk/atom ` command are spatial - bins. If its *units* keyword is set to *box* or *lattice*\ , then the + bins. If its *units* keyword is set to *box* or *lattice*, then the number of bins *Nchunk* and size of each bin will be fixed over the *Nfreq* time window, which can affect which atoms are discarded if the simulation box size changes. If its *units* keyword is set to - *reduced*\ , then the number of bins *Nchunk* will still be fixed, but + *reduced*, then the number of bins *Nchunk* will still be fixed, but the size of each bin can vary at each timestep if the simulation box size changes, e.g. for an NPT simulation. @@ -221,7 +221,7 @@ The *density/number* value means the number density is computed for each chunk, i.e. number/volume. The *density/mass* value means the mass density is computed for each chunk, i.e. total-mass/volume. The output values are in units of 1/volume or density (mass/volume). See -the :doc:`units ` command doc page for the definition of density +the :doc:`units ` command page for the definition of density for each choice of units, e.g. gram/cm\^3. If the chunks defined by the :doc:`compute chunk/atom ` command are spatial bins, the volume is the bin volume. Otherwise it is the volume of the @@ -280,7 +280,7 @@ appended, the per-atom vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with -*Nevery*\ , else an error results. Users can also write code for their +*Nevery*, else an error results. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -300,7 +300,7 @@ and its outputs. The *norm* keyword affects how averaging is done for the per-chunk values that are output every *Nfreq* timesteps. -It the *norm* setting is *all*\ , which is the default, a chunk value is +It the *norm* setting is *all*, which is the default, a chunk value is summed over all atoms in all *Nrepeat* samples, as is the count of atoms in the chunk. The averaged output value for the chunk on the *Nfreq* timesteps is Total-sum / Total-count. In other words it is an @@ -311,7 +311,7 @@ the final *Nfreq* timestep. For the *temp* values, degrees of freedom and kinetic energy are summed separately across the entire *Nfreq* timescale, and the output value is calculated by dividing those two sums. -If the *norm* setting is *sample*\ , the chunk value is summed over +If the *norm* setting is *sample*, the chunk value is summed over atoms for each sample, as is the count, and an "average sample value" is computed for each sample, i.e. Sample-sum / Sample-count. The output value for the chunk on the *Nfreq* timesteps is the average of @@ -322,7 +322,7 @@ values, the volume (bin volume or system volume) used in the per-sample normalization will be the current volume at each sampling step. -If the *norm* setting is *none*\ , a similar computation as for the +If the *norm* setting is *none*, a similar computation as for the *sample* setting is done, except the individual "average sample values" are "summed sample values". A summed sample value is simply the chunk value summed over atoms in the sample, without dividing by @@ -335,15 +335,15 @@ normalization will be the current volume at each sampling step. The *ave* keyword determines how the per-chunk values produced every *Nfreq* steps are averaged with values produced on previous steps that -were multiples of *Nfreq*\ , before they are accessed by another output +were multiples of *Nfreq*, before they are accessed by another output command or written to a file. -If the *ave* setting is *one*\ , which is the default, then the chunk +If the *ave* setting is *one*, which is the default, then the chunk values produced on timesteps that are multiples of *Nfreq* are independent of each other; they are output as-is without further averaging. -If the *ave* setting is *running*\ , then the chunk values produced on +If the *ave* setting is *running*, then the chunk values produced on timesteps that are multiples of *Nfreq* are summed and averaged in a cumulative sense before being output. Each output chunk value is thus the average of the chunk value produced on that timestep with all @@ -352,7 +352,7 @@ the fix is defined; it can only be restarted by deleting the fix via the :doc:`unfix ` command, or re-defining the fix by re-specifying it. -If the *ave* setting is *window*\ , then the chunk values produced on +If the *ave* setting is *window*, then the chunk values produced on timesteps that are multiples of *Nfreq* are summed and averaged within a moving "window" of time, so that the last M values for the same chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000, @@ -440,18 +440,18 @@ chunk ID of 3 may correspond to an original chunk ID or molecule ID of 415. The OrigID column will list 415 for the third chunk. The CoordN columns only appear if a *binning* style was used in the -:doc:`compute chunk/atom ` command. For *bin/1d*\ , -*bin/2d*\ , and *bin/3d* styles the column values are the center point +:doc:`compute chunk/atom ` command. For *bin/1d*, +*bin/2d*, and *bin/3d* styles the column values are the center point of the bin in the corresponding dimension. Just Coord1 is used for -*bin/1d*\ , Coord2 is added for *bin/2d*\ , Coord3 is added for *bin/3d*\ . -For *bin/sphere*\ , just Coord1 is used, and it is the radial -coordinate. For *bin/cylinder*\ , Coord1 and Coord2 are used. Coord1 +*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\ . +For *bin/sphere*, just Coord1 is used, and it is the radial +coordinate. For *bin/cylinder*, Coord1 and Coord2 are used. Coord1 is the radial coordinate (away from the cylinder axis), and coord2 is the coordinate along the cylinder axis. -Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*\ , the +Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*, the coordinate values will be in distance :doc:`units `. If the -value of the *units* keyword is *reduced*\ , the coordinate values will +value of the *units* keyword is *reduced*, the coordinate values will be in unitless reduced units (0-1). This is not true for the Coord1 value of style *bin/sphere* or *bin/cylinder* which both represent radial dimensions. Those values are always in distance :doc:`units `. diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 58aff114af..23086d465f 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -130,7 +130,7 @@ values. ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used to calculate correlation data. The input values are sampled every *Nevery* timesteps. The correlation data for the preceding samples is computed on timesteps @@ -194,7 +194,7 @@ be specified with a wildcard asterisk to effectively specify multiple values. Note that some fixes only produce their values on certain timesteps, -which must be compatible with *Nevery*\ , else an error will result. +which must be compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. If a value begins with "v\_", a variable name must follow which has @@ -237,14 +237,14 @@ pair Vi(t)\*Vj(t+delta) is always the one sampled at the later time. The *ave* keyword determines what happens to the accumulation of correlation samples every *Nfreq* timesteps. If the *ave* setting is -*one*\ , then the accumulation is restarted or zeroed every *Nfreq* +*one*, then the accumulation is restarted or zeroed every *Nfreq* timesteps. Thus the outputs on successive *Nfreq* timesteps are essentially independent of each other. The exception is that the Cij(0) = Vi(T)\*Vj(T) value at a timestep T, where T is a multiple of -*Nfreq*\ , contributes to the correlation output both at time T and at +*Nfreq*, contributes to the correlation output both at time T and at time T+Nfreq. -If the *ave* setting is *running*\ , then the accumulation is never +If the *ave* setting is *running*, then the accumulation is never zeroed. Thus the output of correlation data at any timestep is the average over samples accumulated every *Nevery* steps since the fix was defined. it can only be restarted by deleting the fix via the @@ -263,7 +263,7 @@ the size of the time window or other unit conversions. The *file* keyword allows a filename to be specified. Every *Nfreq* steps, an array of correlation data is written to the file. The -number of rows is *Nrepeat*\ , as described above. The number of +number of rows is *Nrepeat*, as described above. The number of columns is the Npair+2, also as described above. Thus the file ends up to be a series of these array sections. @@ -327,19 +327,19 @@ samples contributing to the correlation average, as described above. The remaining Npair columns are for I,J pairs of the N input values, as determined by the *type* keyword, as described above. -* For *type* = *auto*\ , the Npair = N columns are ordered: C11, C22, ..., +* For *type* = *auto*, the Npair = N columns are ordered: C11, C22, ..., CNN. -* For *type* = *upper*\ , the Npair = N\*(N-1)/2 columns are ordered: C12, +* For *type* = *upper*, the Npair = N\*(N-1)/2 columns are ordered: C12, C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N. -* For *type* = *lower*\ , the Npair = N\*(N-1)/2 columns are ordered: C21, +* For *type* = *lower*, the Npair = N\*(N-1)/2 columns are ordered: C21, C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1. -* For *type* = *auto/upper*\ , the Npair = N\*(N+1)/2 columns are ordered: +* For *type* = *auto/upper*, the Npair = N\*(N+1)/2 columns are ordered: C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N, CNN. -* For *type* = *auto/lower*\ , the Npair = N\*(N+1)/2 columns are ordered: +* For *type* = *auto/lower*, the Npair = N\*(N+1)/2 columns are ordered: C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1, CNN. -* For *type* = *full*\ , the Npair = N\^2 columns are ordered: C11, C12, +* For *type* = *full*, the Npair = N\^2 columns are ordered: C11, C12, ..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1, CNN. diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst index e3e118744a..a69d8f5695 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -78,18 +78,18 @@ specified values may represent calculations performed by computes and fixes which store their own "group" definitions. Each listed value can be the result of a compute or fix or the -evaluation of an equal-style variable. See the :doc:`fix ave/correlate ` doc page for details. +evaluation of an equal-style variable. See the :doc:`fix ave/correlate ` page for details. The *Nevery* and *Nfreq* arguments specify on what timesteps the input values will be used to calculate correlation data, and the frequency with which the time correlation functions will be output to a file. Note that there is no *Nrepeat* argument, unlike the :doc:`fix ave/correlate ` command. -The optional keywords *ncorr*\ , *nlen*\ , and *ncount* are unique to this +The optional keywords *ncorr*, *nlen*, and *ncount* are unique to this command and determine the number of correlation points calculated and the memory and CPU overhead used by this calculation. *Nlen* and *ncount* determine the amount of averaging done at longer correlation -times. The default values *nlen=16*\ , *ncount=2* ensure that the +times. The default values *nlen=16*, *ncount=2* ensure that the systematic error of the multiple-tau correlator is always below the level of the statistical error of a typical simulation (which depends on the ensemble size and the simulation length). @@ -128,7 +128,7 @@ Restrictions """""""""""" This compute is part of the EXTRA-FIX package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 3a2857f383..05c63a6faf 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -100,7 +100,7 @@ component) or can be the result of a :doc:`compute ` or atom-style :doc:`variable `. The set of input values can be either all global, all per-atom, or all local quantities. Inputs of different kinds (e.g. global and per-atom) cannot be mixed. Atom -attributes are per-atom vector values. See the doc page for +attributes are per-atom vector values. See the page for individual "compute" and "fix" commands to see what kinds of quantities they generate. See the optional *kind* keyword below for how to force the fix ave/histo command to disambiguate if necessary. @@ -153,7 +153,7 @@ the first vector. ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the histogram. The final histogram is generated on timesteps that are multiple of *Nfreq*\ . It is averaged over *Nrepeat* histograms, @@ -210,7 +210,7 @@ be specified with a wildcard asterisk to effectively specify multiple values. Note that some fixes only produce their values on certain timesteps, -which must be compatible with *Nevery*\ , else an error will result. +which must be compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. If a value begins with "v\_", a variable name must follow which has @@ -223,7 +223,7 @@ atom-style variables can be used, which produce a global or per-atom vector respectively. The vector-style variable must be used without a bracketed term. See the :doc:`variable ` command for details. -Note that variables of style *equal*\ , *vector*\ , and *atom* define a +Note that variables of style *equal*, *vector*, and *atom* define a formula which can reference individual atom properties or thermodynamic keywords, or they can invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of @@ -233,9 +233,9 @@ specifying quantities to histogram. Additional optional keywords also affect the operation of this fix. -If the *mode* keyword is set to *scalar*\ , then all input values must +If the *mode* keyword is set to *scalar*, then all input values must be global scalars, or elements of global vectors. If the *mode* -keyword is set to *vector*\ , then all input values must be global or +keyword is set to *vector*, then all input values must be global or per-atom or local vectors, or columns of global or per-atom or local arrays. @@ -263,14 +263,14 @@ values > *hi* are counted in the last bin (Nbins+2). Values between The *ave* keyword determines how the histogram produced every *Nfreq* steps are averaged with histograms produced on previous steps that -were multiples of *Nfreq*\ , before they are accessed by another output +were multiples of *Nfreq*, before they are accessed by another output command or written to a file. -If the *ave* setting is *one*\ , then the histograms produced on +If the *ave* setting is *one*, then the histograms produced on timesteps that are multiples of *Nfreq* are independent of each other; they are output as-is without further averaging. -If the *ave* setting is *running*\ , then the histograms produced on +If the *ave* setting is *running*, then the histograms produced on timesteps that are multiples of *Nfreq* are summed and averaged in a cumulative sense before being output. Each bin value in the histogram is thus the average of the bin value produced on that timestep with @@ -279,7 +279,7 @@ when the fix is defined; it can only be restarted by deleting the fix via the :doc:`unfix ` command, or by re-defining the fix by re-specifying it. -If the *ave* setting is *window*\ , then the histograms produced on +If the *ave* setting is *window*, then the histograms produced on timesteps that are multiples of *Nfreq* are summed within a moving "window" of time, so that the last M histograms are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then the output on step diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index ad1aca233c..dfa385ea46 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -136,7 +136,7 @@ with 3 columns, each of length 50: ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps that are a multiple of *Nfreq*\ . The average is over *Nrepeat* @@ -185,7 +185,7 @@ for how I can be specified with a wildcard asterisk to effectively specify multiple values. Note that some fixes only produce their values on certain timesteps, -which must be compatible with *Nevery*\ , else an error will result. +which must be compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. If a value begins with "v\_", a variable name must follow which has @@ -207,23 +207,23 @@ quantities to time average. Additional optional keywords also affect the operation of this fix. -If the *mode* keyword is set to *scalar*\ , then all input values must +If the *mode* keyword is set to *scalar*, then all input values must be global scalars, or elements of global vectors. If the *mode* -keyword is set to *vector*\ , then all input values must be global +keyword is set to *vector*, then all input values must be global vectors, or columns of global arrays. They can also be global arrays, which are converted into a series of global vectors (one per column), as explained above. The *ave* keyword determines how the values produced every *Nfreq* steps are averaged with values produced on previous steps that were -multiples of *Nfreq*\ , before they are accessed by another output +multiples of *Nfreq*, before they are accessed by another output command or written to a file. -If the *ave* setting is *one*\ , then the values produced on timesteps +If the *ave* setting is *one*, then the values produced on timesteps that are multiples of *Nfreq* are independent of each other; they are output as-is without further averaging. -If the *ave* setting is *running*\ , then the values produced on +If the *ave* setting is *running*, then the values produced on timesteps that are multiples of *Nfreq* are summed and averaged in a cumulative sense before being output. Each output value is thus the average of the value produced on that timestep with all preceding @@ -231,7 +231,7 @@ values. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the :doc:`unfix ` command, or by re-defining the fix by re-specifying it. -If the *ave* setting is *window*\ , then the values produced on +If the *ave* setting is *window*, then the values produced on timesteps that are multiples of *Nfreq* are summed and averaged within a moving "window" of time, so that the last M values are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then the output @@ -332,7 +332,7 @@ element are "intensive" or "extensive". If the fix produces an array, then all elements in the array must be the same, either "intensive" or "extensive". If a compute or fix provides the value being time averaged, then the compute or fix determines whether the value is -intensive or extensive; see the doc page for that compute or fix for +intensive or extensive; see the page for that compute or fix for further info. Values produced by a variable are treated as intensive. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index 36e1e28ea6..414fa497ed 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -54,7 +54,7 @@ same as specifying a 0.0 value, since that sets all forces to the same average value without adding in any additional force. Any of the 3 quantities defining the force components can be specified -as an equal-style :doc:`variable `, namely *fx*\ , *fy*\ , *fz*\ . +as an equal-style :doc:`variable `, namely *fx*, *fy*, *fz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the average diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 8bab8ebefc..b0f070e5e4 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -222,7 +222,7 @@ once. You should normally only list dimensions where you expect there to be a density variation in the particles. Balancing proceeds by adjusting the cutting planes in each of the -dimensions listed in *dimstr*\ , one dimension at a time. For a single +dimensions listed in *dimstr*, one dimension at a time. For a single dimension, the balancing operation (described below) is iterated on up to *Niter* times. After each dimension finishes, the imbalance factor is re-computed, and the balancing operation halts if the *stopthresh* diff --git a/doc/src/fix_bocs.rst b/doc/src/fix_bocs.rst index c6c7ed41aa..566bf8e68d 100644 --- a/doc/src/fix_bocs.rst +++ b/doc/src/fix_bocs.rst @@ -41,10 +41,10 @@ The first half of the command mimics a standard fix npt command: fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp -The two differences are replacing *npt* with *bocs*\ , and replacing +The two differences are replacing *npt* with *bocs*, and replacing *iso*\ /\ *aniso*\ /\ *etc* with *cgiso*\ . The rest of the command details what form you would like to use for -the pressure correction equation. The choices are: *analytic*\ , *linear_spline*, +the pressure correction equation. The choices are: *analytic*, *linear_spline*, or *cubic_spline*. With either spline method, the only argument that needs to follow it @@ -58,7 +58,7 @@ as a function of volume. The file must be formatted so each line has: Note both the COMMA and the SPACE separating the volume's value and its corresponding pressure correction. The volumes in the file must be uniformly spaced. Both the volumes and the pressure corrections -should be provided in the proper units, e.g. if you are using *units real*\ , +should be provided in the proper units, e.g. if you are using *units real*, the volumes should all be in cubic angstroms, and the pressure corrections should all be in atmospheres. Furthermore, the table should start/end at a volume considerably smaller/larger than you expect your system to sample @@ -72,7 +72,7 @@ With the *analytic* option, the arguments are as follows: ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N Note that *V_avg* and *Coeff_i* should all be in the proper units, e.g. if you -are using *units real*\ , *V_avg* should be in cubic angstroms, and the +are using *units real*, *V_avg* should be in cubic angstroms, and the coefficients should all be in atmospheres \* cubic angstroms. ---------- @@ -125,7 +125,7 @@ XXXX_press, where XXXX is the ID given to the fix bocs command (in the example, the ID of the fix bocs command is 1 ). This fix is part of the BOCS package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Further information """"""""""""""""""" diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index 4f2e2840ab..9538fa8ef3 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -51,7 +51,7 @@ interactions from timestep to timestep as atoms move. A check for possible bond breakage is performed every *Nevery* timesteps. If two bonded atoms I,J are further than a distance *Rmax* -of each other, if the bond is of type *bondtype*\ , and if both I and J +of each other, if the bond is of type *bondtype*, and if both I and J are in the specified fix group, then I,J is labeled as a "possible" bond to break. diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index 34f0d19f8d..c286482f81 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -64,7 +64,7 @@ context, a bond means an interaction between a pair of atoms computed 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* +is part of. See the discussion of the *atype*, *dtype*, and *itype* keywords below. This is different than a :doc:`pairwise ` bond-order @@ -75,7 +75,7 @@ interactions from timestep to timestep as atoms move. A check for possible new bonds is performed every *Nevery* timesteps. If two atoms I,J are within a distance *Rmin* of each other, if I is -of atom type *itype*\ , if J is of atom type *jtype*\ , if both I and J +of atom type *itype*, if J is of atom type *jtype*, if both I and J are in the specified fix group, if a bond does not already exist between I and J, and if both I and J meet their respective *maxbond* requirement (explained below), then I,J is labeled as a "possible" @@ -133,7 +133,7 @@ When a bond is created, data structures within LAMMPS that store bond topology are updated to reflect the creation. If the bond is part of new 3-body (angle) or 4-body (dihedral, improper) interactions, you can choose to create new angles, dihedrals, impropers as well, using -the *atype*\ , *dtype*\ , and *itype* keywords. All of these changes +the *atype*, *dtype*, and *itype* keywords. All of these changes typically affect pairwise interactions between atoms that are now part of new bonds, angles, etc. @@ -147,7 +147,7 @@ of new bonds, angles, etc. If the *atype* keyword is used and if an angle potential is defined 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 +of type *angletype*, with parameters assigned by the corresponding :doc:`angle_coeff ` command. Likewise, the *dtype* and *itype* keywords will create new dihedrals and impropers of type *dihedraltype* and *impropertype*\ . @@ -183,7 +183,7 @@ of type *angletype*\ , with parameters assigned by the corresponding .. note:: - Even if you do not use the *atype*\ , *dtype*\ , or *itype* + Even if you do not use the *atype*, *dtype*, or *itype* 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 diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index baf7985ef5..a48675dcf2 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -424,7 +424,7 @@ The constraint of type 'angle' has the following syntax: angle *ID1* *ID2* *ID3* *amin* *amax* -where 'angle' is the required keyword, *ID1*\ , *ID2* and *ID3* are +where 'angle' is the required keyword, *ID1*, *ID2* and *ID3* are pre-reaction atom IDs (or molecule-fragment IDs, see below), and these three atoms must form an angle between *amin* and *amax* for the reaction to occur (where *ID2* is the central atom). Angles must be @@ -437,7 +437,7 @@ The constraint of type 'dihedral' has the following syntax: dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2* -where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3* +where 'dihedral' is the required keyword, and *ID1*, *ID2*, *ID3* and *ID4* are pre-reaction atom IDs (or molecule-fragment IDs, see below). Dihedral angles are calculated in the interval (-180,180]. Refer to the :doc:`dihedral style ` documentation for @@ -669,7 +669,7 @@ Restrictions This fix is part of the REACTION package. It is only enabled if LAMMPS was built with that package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst index 248c4cc8e9..71bb122c90 100644 --- a/doc/src/fix_bond_swap.rst +++ b/doc/src/fix_bond_swap.rst @@ -67,7 +67,7 @@ initial swap. For each monomer A1, its neighbors are examined to find a possible B1 monomer. Both A1 and B1 must be in the fix group, their separation -must be less than the specified *cutoff*\ , and the molecule IDs of A1 +must be less than the specified *cutoff*, and the molecule IDs of A1 and B1 must be the same (see below). If a suitable partner is found, the energy change due to swapping the 2 bonds is computed. This includes changes in pairwise, bond, and angle energies due to the @@ -117,7 +117,7 @@ ends of a chain swap with each other. This fix computes a temperature each time it is invoked for use by the Boltzmann criterion. To do this, the fix creates its own compute of -style *temp*\ , as if this command had been issued: +style *temp*, as if this command had been issued: .. code-block:: LAMMPS diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst index 7a9abdfe26..5827fe3732 100644 --- a/doc/src/fix_box_relax.rst +++ b/doc/src/fix_box_relax.rst @@ -53,7 +53,7 @@ pressure typically allows the box to expand. ---------- The external pressure tensor is specified using one or more of the -*iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz*\ , and *couple* +*iso*, *aniso*, *tri*, *x*, *y*, *z*, *xy*, *xz*, *yz*, and *couple* keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are @@ -66,25 +66,25 @@ specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. The target pressures *Ptarget* for each of the 6 components of the -stress tensor can be specified independently via the *x*\ , *y*\ , *z*\ , -*xy*\ , *xz*\ , *yz* keywords, which correspond to the 6 simulation box +stress tensor can be specified independently via the *x*, *y*, *z*, +*xy*, *xz*, *yz* keywords, which correspond to the 6 simulation box dimensions. For example, if the *y* keyword is used, the y-box length will change during the minimization. If the *xy* keyword is used, the xy tilt factor will change. A box dimension will not change if that component is not specified. -Note that in order to use the *xy*\ , *xz*\ , or *yz* keywords, the +Note that in order to use the *xy*, *xz*, or *yz* keywords, the simulation box must be triclinic, even if its initial tilt factors are 0.0. When the size of the simulation box changes, all atoms are re-scaled to new positions, unless the keyword *dilate* is specified with a -value of *partial*\ , in which case only the atoms in the fix group are +value of *partial*, in which case only the atoms in the fix group are re-scaled. This can be useful for leaving the coordinates of atoms in a solid substrate unchanged and controlling the pressure of a surrounding fluid. -The *scaleyz*\ , *scalexz*\ , and *scalexy* keywords control whether or +The *scaleyz*, *scalexz*, and *scalexy* keywords control whether or not the corresponding tilt factors are scaled with the associated box dimensions when relaxing triclinic periodic cells. The default values *yes* will turn on scaling, which corresponds to adjusting the @@ -99,7 +99,7 @@ The *fixedpoint* keyword specifies the fixed point for cell relaxation. By default, it is the center of the box. Whatever point is chosen will not move during the simulation. For example, if the lower periodic boundaries pass through (0,0,0), and this point is provided -to *fixedpoint*\ , then the lower periodic boundaries will remain at +to *fixedpoint*, then the lower periodic boundaries will remain at (0,0,0), while the upper periodic boundaries will move twice as far. In all cases, the particle positions at each iteration are unaffected by the chosen value, except that all particles are @@ -107,7 +107,7 @@ displaced by the same amount, different on each iteration. .. note:: - Applying an external pressure to tilt dimensions *xy*\ , *xz*\ , *yz* + Applying an external pressure to tilt dimensions *xy*, *xz*, *yz* can sometimes result in arbitrarily large values of the tilt factors, i.e. a dramatically deformed simulation box. This typically indicates that there is something badly wrong with how the simulation was @@ -149,7 +149,7 @@ simply ignored. ---------- -The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are +The *iso*, *aniso*, and *tri* keywords are simply shortcuts that are equivalent to specifying several other keywords together. The keyword *iso* means couple all 3 diagonal components together when @@ -164,8 +164,8 @@ these 4 keywords: z Ptarget couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Ptarget" is the same as specifying these 4 keywords: @@ -177,7 +177,7 @@ keywords: z Ptarget couple none -The keyword *tri* means *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , and *yz* dimensions +The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions are controlled independently using their individual stress components as the driving forces, and the specified scalar pressure as the external normal stress. Using "tri Ptarget" is the same as specifying @@ -246,7 +246,7 @@ minimization steps, the reference dimensions are set to those of the current simulation domain. Note that resetting the reference dimensions changes the objective function and gradients, which sometimes causes the minimization to fail. This can be resolved by -changing the value of *nreset*\ , or simply continuing the minimization +changing the value of *nreset*, or simply continuing the minimization from a restart file. .. note:: @@ -362,8 +362,8 @@ Restrictions """""""""""" 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 +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 @@ -371,10 +371,10 @@ simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used -for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options +for 2D simulations. *scaleyz yes*, *scalexz yes*, and *scalexy yes* options can only be used if the second dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords -*tri*\ , *yz*\ , *xz*\ , and *xy*\ . +*tri*, *yz*, *xz*, and *xy*\ . Related commands """""""""""""""" diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index 06c1d92b79..9ff28b6ac3 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -227,7 +227,7 @@ Restrictions This fix is part of the MC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. The :doc:`atom_style `, used must contain the charge property, for example, the style could be *charge* or *full*. Only diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst index 3bcc6bdaa5..a688d38e25 100644 --- a/doc/src/fix_client_md.rst +++ b/doc/src/fix_client_md.rst @@ -27,7 +27,7 @@ This fix style enables LAMMPS to run as a "client" code and communicate each timestep with a separate "server" code to perform an MD simulation together. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -101,7 +101,7 @@ Restrictions This fix is part of the MESSAGE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. A script that uses this command must also use the :doc:`message ` command to setup and shut down the messaging diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index e6e8d0c627..6475e538a2 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -73,7 +73,7 @@ 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 ` page for more details. A data file containing CMAP cross-terms can be generated from a PDB @@ -147,7 +147,7 @@ To function as expected this fix command must be issued *before* 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 +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index 6de30a3d84..21b235cb6b 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -80,7 +80,7 @@ that will be used in the colvars module. The *unwrap* keyword controls whether wrapped or unwrapped coordinates are passed to the colvars library for calculation of the collective -variables and the resulting forces. The default is *yes*\ , i.e. to use +variables and the resulting forces. The default is *yes*, i.e. to use the image flags to reconstruct the absolute atom positions. Setting this to *no* will use the current local coordinates that are wrapped back into the simulation cell at each re-neighboring instead. @@ -124,7 +124,7 @@ Restrictions This fix is part of the COLVARS package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. There can only be one colvars fix active at a time. Since the interface communicates only the minimum amount of information and colvars module diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 0b7332cdd7..0ff38ae010 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -127,17 +127,17 @@ When choosing the values of the four constants, it is best to first pick a value and sign for :math:`\alpha` that is consistent with the magnitudes and signs of *pvar* and *cvar*\ . The magnitude of :math:`K_p` should then be tested over a large positive range keeping :math:`K_i = K_d =0`. -A good value for :math:`K_p` will produce a fast response in *pvar*\ , +A good value for :math:`K_p` will produce a fast response in *pvar*, without overshooting the *setpoint*\ . For many applications, proportional feedback is sufficient, and so :math:`K_i` = K_d =0` can be used. In cases where there is a substantial lag time in the response of *pvar* to a change -in *cvar*\ , this can be counteracted by increasing :math:`K_d`. In situations -where *pvar* plateaus without reaching *setpoint*\ , this can be +in *cvar*, this can be counteracted by increasing :math:`K_d`. In situations +where *pvar* plateaus without reaching *setpoint*, this can be counteracted by increasing :math:`K_i`. In the language of Charles Dickens, :math:`K_p` represents the error of the present, :math:`K_i` the error of the past, and :math:`K_d` the error yet to come. -Because this fix updates *cvar*\ , but does not initialize its value, +Because this fix updates *cvar*, but does not initialize its value, the initial value is that assigned by the user in the input script via the :doc:`internal-style variable ` command. This value is used (by the other LAMMPS command that used the variable) until this @@ -162,7 +162,7 @@ used. Users can also write code for their own compute styles and :doc:`add them If *pvar* begins with "f\_", a fix ID must follow which has been previously defined in the input script and which generates a global -scalar or vector. See the individual :doc:`fix ` doc page for +scalar or vector. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when fix controller references the values, or else an error results. If no bracketed integer @@ -215,7 +215,9 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none + +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 90192c6c00..a21a3a6044 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -21,7 +21,7 @@ Syntax .. parsed-literal:: parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* - *x*\ , *y*\ , *z* args = style value(s) + *x*, *y*, *z* args = style value(s) style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* *final* values = lo hi lo hi = box boundaries at end of run (distance units) @@ -43,7 +43,7 @@ Syntax *variable* values = v_name1 v_name2 v_name1 = variable with name1 for box length change as function of time v_name2 = variable with name2 for change rate as function of time - *xy*\ , *xz*\ , *yz* args = style value + *xy*, *xz*, *yz* args = style value style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* *final* value = tilt tilt = tilt factor at end of run (distance units) @@ -102,8 +102,8 @@ of a continuously strained system. See the :doc:`fix nvt/sllod ` that simulation of a continuously extended system (extensional flow) can be modeled using the :ref:`UEF package ` and its :doc:`fix commands `. -For the *x*\ , *y*\ , *z* parameters, the associated dimension cannot be -shrink-wrapped. For the *xy*\ , *yz*\ , *xz* parameters, the associated +For the *x*, *y*, *z* parameters, the associated dimension cannot be +shrink-wrapped. For the *xy*, *yz*, *xz* parameters, the associated second dimension cannot be shrink-wrapped. Dimensions not varied by this command can be periodic or non-periodic. Dimensions corresponding to unspecified parameters can also be controlled by a :doc:`fix npt ` or :doc:`fix nph ` command. @@ -127,29 +127,29 @@ and final values. ---------- -For the *x*\ , *y*\ , and *z* parameters, this is the meaning of their +For the *x*, *y*, and *z* parameters, this is the meaning of their styles and values. -The *final*\ , *delta*\ , *scale*\ , *vel*\ , and *erate* styles all change +The *final*, *delta*, *scale*, *vel*, and *erate* styles all change the specified dimension of the box via "constant displacement" which is effectively a "constant engineering strain rate". This means the box dimension changes linearly with time from its initial to final value. -For style *final*\ , the final lo and hi box boundaries of a dimension +For style *final*, the final lo and hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. See the discussion of the units keyword below. -For style *delta*\ , plus or minus changes in the lo/hi box boundaries +For style *delta*, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box distance units. See the discussion of the units keyword below. -For style *scale*\ , a multiplicative factor to apply to the box length +For style *scale*, a multiplicative factor to apply to the box length of a dimension is specified. For example, if the initial box length is 10, and the factor is 1.1, then the final box length will be 11. A factor less than 1.0 means compression. -For style *vel*\ , a velocity at which the box length changes is +For style *vel*, a velocity at which the box length changes is specified in units of distance/time. This is effectively a "constant engineering strain rate", where rate = V/L0 and L0 is the initial box length. The distance can be in lattice or box distance units. See @@ -207,7 +207,7 @@ triple every picosecond. R = ln(0.99) means the box length will shrink by 1% of its current length every picosecond. Note that for a "true" rate the change is continuous and based on the current length, so running with R = ln(2) for 10 picoseconds does not expand the box -length by a factor of 11 as it would with *erate*\ , but by a factor of +length by a factor of 11 as it would with *erate*, but by a factor of 1024 since the box length will double every picosecond. Note that to change the volume (or cross-sectional area) of the @@ -288,30 +288,30 @@ assume that the current timestep = 0. variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)" fix 2 all deform 1 x variable v_displace v_rate remap v -For the *scale*\ , *vel*\ , *erate*\ , *trate*\ , *volume*\ , *wiggle*\ , and +For the *scale*, *vel*, *erate*, *trate*, *volume*, *wiggle*, and *variable* styles, the box length is expanded or compressed around its mid point. ---------- -For the *xy*\ , *xz*\ , and *yz* parameters, this is the meaning of their +For the *xy*, *xz*, and *yz* parameters, this is the meaning of their styles and values. Note that changing the tilt factors of a triclinic box does not change its volume. -The *final*\ , *delta*\ , *vel*\ , and *erate* styles all change the shear +The *final*, *delta*, *vel*, and *erate* styles all change the shear strain at a "constant engineering shear strain rate". This means the tilt factor changes linearly with time from its initial to final value. -For style *final*\ , the final tilt factor is specified. The value +For style *final*, the final tilt factor is specified. The value can be in lattice or box distance units. See the discussion of the units keyword below. -For style *delta*\ , a plus or minus change in the tilt factor is +For style *delta*, a plus or minus change in the tilt factor is specified. The value can be in lattice or box distance units. See the discussion of the units keyword below. -For style *vel*\ , a velocity at which the tilt factor changes is +For style *vel*, a velocity at which the tilt factor changes is specified in units of distance/time. This is effectively an "engineering shear strain rate", where rate = V/L0 and L0 is the initial box length perpendicular to the direction of shear. The @@ -449,7 +449,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent. To obey this constraint and allow for large shear deformations to be -applied via the *xy*\ , *xz*\ , or *yz* parameters, the following +applied via the *xy*, *xz*, or *yz* parameters, the following algorithm is used. If *prd* is the associated parallel box length (10 in the example above), then if the tilt factor exceeds the accepted range of -5 to 5 during the simulation, then the box is flipped to the @@ -476,13 +476,13 @@ Each time the box size or shape is changed, the *remap* keyword determines whether atom positions are remapped to the new box. If *remap* is set to *x* (the default), atoms in the fix group are remapped; otherwise they are not. Note that their velocities are not -changed, just their positions are altered. If *remap* is set to *v*\ , +changed, just their positions are altered. If *remap* is set to *v*, then any atom in the fix group that crosses a periodic boundary will have a delta added to its velocity equal to the difference in velocities between the lo and hi boundaries. Note that this velocity difference can include tilt components, e.g. a delta in the x velocity when an atom crosses the y periodic boundary. If *remap* is set to -*none*\ , then neither of these remappings take place. +*none*, then neither of these remappings take place. Conceptually, setting *remap* to *x* forces the atoms to deform via an affine transformation that exactly matches the box deformation. This @@ -529,20 +529,20 @@ box without explicit remapping of their coordinates. .. note:: If a :doc:`fix rigid ` is defined for rigid bodies, and - *remap* is set to *x*\ , then the center-of-mass coordinates of rigid + *remap* is set to *x*, then the center-of-mass coordinates of rigid bodies will be remapped to the changing simulation box. This will be done regardless of whether atoms in the rigid bodies are in the fix deform group or not. The velocity of the centers of mass are not - remapped even if *remap* is set to *v*\ , since :doc:`fix nvt/sllod ` does not currently do anything special + remapped even if *remap* is set to *v*, since :doc:`fix nvt/sllod ` does not currently do anything special for rigid particles. If you wish to perform a NEMD simulation of rigid particles, you can either thermostat them independently or include a background fluid and thermostat the fluid via :doc:`fix nvt/sllod `. The *flip* keyword allows the tilt factors for a triclinic box to exceed half the distance of the parallel box length, as discussed -above. If the *flip* value is set to *yes*\ , the bound is enforced by +above. If the *flip* value is set to *yes*, the bound is enforced by flipping the box when it is exceeded. If the *flip* value is set to -*no*\ , the tilt will continue to change without flipping. Note that if +*no*, the tilt will continue to change without flipping. Note that if you apply large deformations, this means the box shape can tilt dramatically LAMMPS will run less efficiently, due to the large volume of communication needed to acquire ghost atoms around a processor's @@ -557,8 +557,8 @@ in lattice spacings. The :doc:`lattice ` command must have 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 ` +does not affect the *variable* style. You should use the *xlat*, +*ylat*, *zlat* keywords of the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. ---------- diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 42975eb0b2..ad3c37b24c 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -220,7 +220,7 @@ ignored if the *global* or *local* keywords are used, since those options choose a z-coordinate for insertion independently. The vx, vy, and vz components of velocity for the inserted particle -are set using the values specified for the *vx*\ , *vy*\ , and *vz* +are set using the values specified for the *vx*, *vy*, and *vz* keywords. Note that normally, new particles should be a assigned a negative vertical velocity so that they move towards the surface. For molecules, the same velocity is given to every particle (no rotation @@ -296,9 +296,6 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. - The specified insertion region cannot be a "dynamic" region, as defined by the :doc:`region ` command. diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index a1e8ef2faf..d6e8dd7230 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -32,7 +32,7 @@ the group at each timestep. It must be used in conjunction with a deterministic integrator (e.g. :doc:`fix nve `) that updates the particle positions and velocities. -For fix *dpd/energy*\ , the particle internal temperature is related to +For fix *dpd/energy*, the particle internal temperature is related to 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 `. @@ -41,9 +41,9 @@ This fix must be used with the :doc:`pair_style dpd/fdt/energy ` com 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 -can be specified by using fix *dpd/energy*\ , fix *nve* and pair_style +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 +be specified by using fix *dpd/energy*, fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the examples/PACKAGES/dpd-react directory. @@ -57,7 +57,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This fix must be used with an additional fix that specifies time integration, e.g. :doc:`fix nve `. diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 5e1b92ae66..ef1a70c3d4 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -78,7 +78,7 @@ Restrictions """""""""""" This fix is part of the DPD-MESO package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` 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. diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst index 6bf9b909c6..3bfc5420de 100644 --- a/doc/src/fix_drag.rst +++ b/doc/src/fix_drag.rst @@ -57,7 +57,9 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none + +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 9943ea0710..bd63a411be 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -152,7 +152,7 @@ temperatures of cores and Drude particles, in center-of-mass and relative coordinates, are calculated using :doc:`compute temp/drude ` In addition, if you want to use a barostat to simulate a system at -constant pressure, only one of the Nose-Hoover fixes must be *npt*\ , +constant pressure, only one of the Nose-Hoover fixes must be *npt*, the other one should be *nvt*\ . You must add a *compute temp/com* and a *fix_modify* command so that the temperature of the *npt* fix be just that of its group (the Drude cores) but the pressure be the overall diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index a413f8f60d..c3aa431e18 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -59,7 +59,7 @@ displace *Xmax* on the next integration step, as a function of its current velocity and force. Since performing this calculation exactly would require the solution to a quartic equation, a cheaper estimate is generated. The estimate is conservative in that the atom's -displacement is guaranteed not to exceed *Xmax*\ , though it may be +displacement is guaranteed not to exceed *Xmax*, though it may be smaller. In addition if the *emax* keyword is used, the specified *Emax* value @@ -72,7 +72,7 @@ across all atoms is computed. Then the *Tmin* and *Tmax* bounds are applied, if specified. If one (or both) is specified as NULL, it is not applied. -When the :doc:`run style ` is *respa*\ , this fix resets the +When the :doc:`run style ` is *respa*, this fix resets the outer loop (largest) timestep, which is the same timestep that the :doc:`timestep ` command sets. diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index 86dcda9bc5..7d958e0afe 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -42,7 +42,7 @@ external electric field. For charges, any of the 3 quantities defining the E-field components can be specified as an equal-style or atom-style -:doc:`variable `, namely *ex*\ , *ey*\ , *ez*\ . If the value is a +:doc:`variable `, namely *ex*, *ey*, *ez*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the E-field component. @@ -100,8 +100,8 @@ minimize the orientation of dipoles in an applied electric field. The *energy* keyword specifies the name of an atom-style :doc:`variable ` which is used to compute the energy of each -atom as function of its position. Like variables used for *ex*\ , -*ey*\ , *ez*\ , the energy variable is specified as v_name, where name +atom as function of its position. Like variables used for *ex*, +*ey*, *ez*, the energy variable is specified as v_name, where name is the variable name. Note that when the *energy* keyword is used during an energy @@ -169,8 +169,7 @@ the iteration count during the minimization. Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +None Related commands """""""""""""""" diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst index 2065ec5033..186ed7065e 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -92,7 +92,7 @@ The thermostatting force is given by where :math:`m_i` is the mass and :math:`k(\mathbf r_i)` maps the particle position to the respective reservoir. The quantity :math:`F_{\Gamma_{k(\mathbf r_i)}}` corresponds to the input parameter -*F*\ , which is the energy flux into the reservoir. Furthermore, +*F*, which is the energy flux into the reservoir. Furthermore, :math:`K_{\Gamma_{k(\mathbf r_i)}}` and :math:`v_{\Gamma_{k(\mathbf r_i)}}` denote the non-translational kinetic energy and the center of mass velocity of that reservoir. The thermostatting force does not affect @@ -176,7 +176,7 @@ Restrictions """""""""""" This fix is part of the RIGID package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index d2bc65608d..fa0fc763f5 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -92,7 +92,7 @@ its velocity and :math:`S_e` is the stopping power of the ion. 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*\ , +friction is not applied to atoms whose kinetic energy is smaller than *Ecut*, or smaller than the lowest energy value given in the table in *file*\ . Electronic stopping should be applied only when a projectile reaches bulk material. This fix scans neighbor list and excludes atoms with fewer than @@ -133,7 +133,7 @@ For example: 750 100 150 If an atom which would have electronic stopping applied to it has a -kinetic energy higher than the largest energy given in *file*\ , LAMMPS +kinetic energy higher than the largest energy given in *file*, LAMMPS will exit with an error message. The stopping power depends on the energy of the ion and the target diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst index 57f8c914ab..c43b5461b1 100644 --- a/doc/src/fix_eos_cv.rst +++ b/doc/src/fix_eos_cv.rst @@ -44,7 +44,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst index 06310e9685..bfb8ec2c3c 100644 --- a/doc/src/fix_eos_table.rst +++ b/doc/src/fix_eos_table.rst @@ -103,7 +103,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index eadac5d56c..2e91b7dd88 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -48,9 +48,9 @@ computed according to the following relation: U_{i} = \displaystyle\sum_{j=1}^{m} c_{i,j}(u_{j} + \Delta H_{f,j}) + \frac{3k_{b}T}{2} + Nk_{b}T \\ where *m* is the number of species, :math:`c_{i,j}` is the -concentration of species *j* in particle *i*\ , :math:`u_j` is the +concentration of species *j* in particle *i*, :math:`u_j` is the internal energy of species j, :math:`\Delta H_{f,j} is the heat of -formation of species *j*\ , N is the number of molecules represented +formation of species *j*, N is the number of molecules represented by the coarse-grained particle, :math:`k_b` is the Boltzmann constant, and *T* is the temperature of the system. Additionally, it is possible to modify the concentration-dependent particle internal @@ -178,7 +178,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst index 5eae16b196..4fa888273c 100644 --- a/doc/src/fix_evaporate.rst +++ b/doc/src/fix_evaporate.rst @@ -41,14 +41,14 @@ fix group and within the specified region are counted. M of these are chosen at random and deleted. If there are less than M eligible particles, then all of them are deleted. -If the setting for the *molecule* keyword is *no*\ , then only single +If the setting for the *molecule* keyword is *no*, then only single atoms are deleted. In this case, you should insure you do not delete only a portion of a molecule (only some of its atoms), or LAMMPS will soon generate an error when it tries to find those atoms. LAMMPS will warn you if any of the atoms eligible for deletion have a non-zero molecule ID, but does not check for this at the time of deletion. -If the setting for the *molecule* keyword is *yes*\ , then when an atom +If the setting for the *molecule* keyword is *yes*, then when an atom is chosen for deletion, the entire molecule it is part of is deleted. The count of deleted atoms is incremented by the number of atoms in the molecule, which may make it exceed *M*\ . If the molecule ID of the @@ -89,8 +89,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +None Related commands """""""""""""""" diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index 938b798ddf..d251eb65e9 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -46,7 +46,7 @@ If mode is *pf/callback* then the fix will make a callback every The external program computes forces on atoms by setting values in an array owned by the fix. The fix then adds these forces to each atom in the group, once every *Napply* steps, similar to the way the :doc:`fix addforce ` command works. Note that if *Ncall* > -*Napply*\ , the force values produced by one callback will persist, and +*Napply*, the force values produced by one callback will persist, and be used multiple times to update atom forces. The callback function "foo" is invoked by the fix as: diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst index 02bcaa710d..6058b0ed3e 100644 --- a/doc/src/fix_ffl.rst +++ b/doc/src/fix_ffl.rst @@ -111,7 +111,7 @@ In order to perform constant-pressure simulations please use equations of motion. This fix is part of the EXTRA-FIX package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst index 6bfcad27e8..c0a2216be3 100644 --- a/doc/src/fix_filter_corotate.rst +++ b/doc/src/fix_filter_corotate.rst @@ -73,7 +73,7 @@ Restrictions """""""""""" This fix is part of the EXTRA-FIX package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Currently, it does not support :doc:`molecule templates `. diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index ce114fdfcd..3697142a37 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -81,7 +81,7 @@ above, see the examples/PACKAGES/flow_gauss directory. velocities of the group-ID atoms are coupled to the velocities of other atoms in the simulation, the flux will not be conserved. For example, in a simulation with fluid atoms and harmonically constrained - wall atoms, if a single thermostat is applied to group *all*\ , the + wall atoms, if a single thermostat is applied to group *all*, the fluid atom velocities will be coupled to the wall atom velocities, and the flux will not be conserved. This issue can be avoided by thermostatting the fluid and wall groups separately. @@ -160,7 +160,7 @@ Restrictions This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index a7370c7f44..ce79ce3caf 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -59,7 +59,7 @@ Restrictions """""""""""" This fix is 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. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. There can only be a single freeze fix defined. This is because other the :doc:`granular pair styles ` treat frozen particles diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index e360fab86e..9955390454 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -24,7 +24,7 @@ Syntax .. parsed-literal:: - keyword = *mol*\ , *region*\ , *maxangle*\ , *pressure*\ , *fugacity_coeff*, *full_energy*, *charge*\ , *group*\ , *grouptype*\ , *intra_energy*, *tfac_insert*, or *overlap_cutoff* + keyword = *mol*, *region*, *maxangle*, *pressure*, *fugacity_coeff*, *full_energy*, *charge*, *group*, *grouptype*, *intra_energy*, *tfac_insert*, or *overlap_cutoff* *mol* value = template-ID template-ID = ID of molecule template specified in a separate :doc:`molecule ` command *mcmoves* values = Patomtrans Pmoltrans Pmolrotate @@ -208,8 +208,8 @@ their bonds or angles constrained via SHAKE, use the *shake* keyword, specifying as its value the ID of a separate :doc:`fix shake ` command which also appears in your input script. Optionally, users may specify the relative amounts of different MC -moves using the *mcmoves* keyword. The values *Patomtrans*\ , -*Pmoltrans*\ , *Pmolrotate* specify the average proportion of +moves using the *mcmoves* keyword. The values *Patomtrans*, +*Pmoltrans*, *Pmolrotate* specify the average proportion of atom translations, molecule translations, and molecule rotations, respectively. The values must be non-negative integers or real numbers, with at least one non-zero value. For example, (10,30,0) @@ -272,7 +272,7 @@ styles except *lj* it is defined as the thermal de Broglie wavelength \Lambda = \sqrt{ \frac{h^2}{2 \pi m k T}} where *h* is Planck's constant, and *m* is the mass of the exchanged atom -or molecule. For unit style *lj*\ , :math:`\Lambda` is simply set to +or molecule. For unit style *lj*, :math:`\Lambda` is simply set to unity. Note that prior to March 2017, :math:`\Lambda` for unit style *lj* was calculated using the above formula with *h* set to the rather specific value of 0.18292026. Chemical potential under the old definition can diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index c47e30a880..d0fd6a4c9e 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -81,7 +81,7 @@ correlated random forces as specified in the third term of the force. Presently, the Prony series coefficients are limited to being greater than or equal to zero, and the time constants are limited to being greater than zero. To this end, the value of series MUST be set to -*pprony*\ , for now. Future updates will allow for negative coefficients +*pprony*, for now. Future updates will allow for negative coefficients and other representations of the memory kernel. It is with these updates in mind that the series option was included. @@ -107,7 +107,7 @@ The keyword/value option pairs are used in the following ways. The keyword *frozen* can be used to specify how the extended variables associated with the GLD memory kernel are initialized. Specifying no (the default), the initial values are drawn at random from an -equilibrium distribution at *Tstart*\ , consistent with the +equilibrium distribution at *Tstart*, consistent with the Fluctuation-Dissipation Theorem. Specifying yes, initializes the extended variables to zero. @@ -116,7 +116,7 @@ thermostat. Because the random forces on different atoms are independent, they do not sum exactly to zero. As a result, this fix applies a small random force to the entire system, and the center-of-mass of the system undergoes a slow random walk. If the -keyword *zero* is set to *yes*\ , the total random force is set exactly +keyword *zero* is set to *yes*, the total random force is set exactly to zero by subtracting off an equal part of it from each atom in the group. As a result, the center-of-mass of a system with zero initial momentum will not drift over time. @@ -146,8 +146,8 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the 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 is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index c7d46c09fa..a42fddf7f5 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -63,7 +63,7 @@ un-correlated Gaussian random forces. The A matrix couples the physical and makes it possible to obtain effectively a history-dependent noise and friction kernel. -The drift matrix should be given as an external file *Afile*\ , +The drift matrix should be given as an external file *Afile*, as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are optimal for a given application and the system of choice can be obtained from :ref:`(GLE4MD) `. @@ -143,7 +143,7 @@ In order to perform constant-pressure simulations please use equations of motion. This fix is part of the EXTRA-FIX package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index bd585b1312..7b0f7669ed 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -77,7 +77,7 @@ Style *vector* imposes an acceleration in the vector direction given by (x,y,z). Only the direction of the vector is important; it's length is ignored. For 2d systems, the *z* component is ignored. -Any of the quantities *magnitude*\ , *angle*\ , *phi*\ , *theta*\ , *x*\ , *y*\ , +Any of the quantities *magnitude*, *angle*, *phi*, *theta*, *x*, *y*, *z* which define the gravitational magnitude and direction, can be specified as an equal-style :doc:`variable `. If the value is a variable, it should be specified as v_name, where name is the diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index 8716fc8cd5..3e3ec02994 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -101,7 +101,7 @@ Restrictions """""""""""" This fix is part of the REPLICA package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 06f068bb7d..d7f7f75515 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -54,7 +54,7 @@ dynamics or minimization iterations, as specified by the :doc:`run The specified group-ID is ignored by this fix. The specified *attribute* can be one of the options listed above, namely -*bondmax*, *tlimit*\ , *diskfree*\ , or an :doc:`equal-style variable +*bondmax*, *tlimit*, *diskfree*, or an :doc:`equal-style variable ` referenced as *v_name*, where "name" is the name of a variable that has been defined previously in the input script. @@ -138,16 +138,16 @@ The specified *avalue* must be a numeric value. ---------- The optional *error* keyword determines how the current run is halted. -If its value is *hard*\ , then LAMMPS will stop with an error message. +If its value is *hard*, then LAMMPS will stop with an error message. -If its value is *soft*\ , LAMMPS will exit the current run, but continue +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. -If its value is *continue*\ , the behavior is the same as for *soft*\ , +If its value is *continue*, the behavior is the same as for *soft*, except subsequent :doc:`run ` or :doc:`minimize ` commands are executed. This allows your script to remedy the condition that triggered the halt, if necessary. Note that you may wish use the diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index 0b46616c5e..c8643b3b86 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -46,7 +46,7 @@ This can lead to a dramatic speed-up in the rate at which events occurs, without altering their relative frequencies, thus leading to an overall increase in the elapsed real time of the simulation as compared to running for the same number of timesteps with normal MD. -See the :doc:`hyper ` doc page for a more general discussion of +See the :doc:`hyper ` page for a more general discussion of hyperdynamics and citations that explain both GHD and LHD. The equations and logic used by this fix and described here to perform @@ -56,8 +56,8 @@ Fichthorn as described in :ref:`(Miron) `. In LAMMPS we use a simplified version of bond-boost GHD where a single bond in the system is biased at any one timestep. -Bonds are defined between each pair of atoms *ij*\ , whose :math:`R^0_{ij}` -distance is less than *cutbond*\ , when the system is in a quenched state +Bonds are defined between each pair of atoms *ij*, whose :math:`R^0_{ij}` +distance is less than *cutbond*, when the system is in a quenched state (minimum) energy. Note that these are not "bonds" in a covalent sense. A bond is simply any pair of atoms that meet the distance criterion. *Cutbond* is an argument to this fix; it is discussed @@ -70,7 +70,7 @@ The current strain of bond *ij* (when running dynamics) is defined as E_{ij} = \frac{R_{ij} - R^0_{ij}}{R^0_{ij}} -where :math:`R_{ij}` is the current distance between atoms *i* and *j*\ , +where :math:`R_{ij}` is the current distance between atoms *i* and *j*, and :math:`R^0_{ij}` is the equilibrium distance in the quenched state. The bias energy :math:`V_{ij}` of any bond between atoms *i* and *j* @@ -136,7 +136,7 @@ Note that in GHD, the boost factor varies from timestep to timestep. Likewise, which bond has :math:`E^{max}` strain and thus which pair of atoms the bias potential is added to, will also vary from timestep to timestep. This is in contrast to local hyperdynamics (LHD) where the boost -factor is an input parameter; see the :doc:`fix hyper/local ` doc page for details. +factor is an input parameter; see the :doc:`fix hyper/local ` page for details. ---------- @@ -192,7 +192,7 @@ beta term in the exponential factor that determines how much boost is achieved as a function of the bias potential. In general, the lower the value of *Tequil* and the higher the value -of *Vmax*\ , the more time boost will be achievable by the GHD +of *Vmax*, the more time boost will be achievable by the GHD algorithm. ---------- @@ -264,7 +264,7 @@ Restrictions """""""""""" This command can only be used if LAMMPS was built with the REPLICA -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 90238e0b4a..22de3bc3ca 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -61,7 +61,7 @@ This can lead to a dramatic speed-up in the rate at which events occurs, without altering their relative frequencies, thus leading to an overall increase in the elapsed real time of the simulation as compared to running for the same number of timesteps with normal MD. -See the :doc:`hyper ` doc page for a more general discussion of +See the :doc:`hyper ` page for a more general discussion of hyperdynamics and citations that explain both GHD and LHD. The equations and logic used by this fix and described here to perform @@ -139,7 +139,7 @@ to this fix. running constant-temperature (NVT) dynamics. LAMMPS does not check that this is done. -Note that if *ij*\ == *kl*\ , then bond *ij* is a biased bond on that +Note that if *ij*\ == *kl*, then bond *ij* is a biased bond on that timestep, otherwise it is not. But regardless, the boost factor :math:`B_{ij}` can be thought of an estimate of time boost currently being applied within a local region centered on bond *ij*. For LHD, @@ -162,15 +162,15 @@ Note that in LHD, the boost factor :math:`B_{target}` is specified by the user. This is in contrast to global hyperdynamics (GHD) where the boost factor varies each timestep and is computed as a function of :math:`V_{max}`, :math:`E_{max}`, and :math:`T_{equil}`; see the -:doc:`fix hyper/global ` doc page for details. +:doc:`fix hyper/global ` page for details. ---------- Here is additional information on the input parameters for LHD. -Note that the *cutbond*\ , *qfactor*\ , and *Tequil* arguments have the +Note that the *cutbond*, *qfactor*, and *Tequil* arguments have the same meaning as for GHD. The *Vmax* argument is slightly different. -The *Dcut*\ , *alpha*\ , and *Btarget* parameters are unique to LHD. +The *Dcut*, *alpha*, and *Btarget* parameters are unique to LHD. The *cutbond* argument is the cutoff distance for defining bonds between pairs of nearby atoms. A pair of I,J atoms in their @@ -310,7 +310,7 @@ Here is additional information on the optional keywords for this fix. The *bound* keyword turns on min/max bounds for bias coefficients :math:`C_{ij}` for all bonds. :math:`C_{ij}` is a prefactor for each bond on the bias potential of maximum strength :math:`V^{max}`. Depending on the -choice of *alpha* and *Btarget* and *Vmax*\ , the boostostatting can cause +choice of *alpha* and *Btarget* and *Vmax*, the boostostatting can cause individual :math:`C_{ij}` values to fluctuate. If the fluctuations are too large :math:`C_{ij} \cdot V^{max}` can exceed low barrier heights and induce bad event dynamics. Bounding the :math:`C_{ij}` values is a way to prevent @@ -326,7 +326,7 @@ The *reset* keyword allow *Vmax* to be adjusted dynamically depending on the average value of all :math:`C_{ij}` prefactors. This can be useful if you are unsure what value of *Vmax* will match the *Btarget* boost for the system. The :math:`C_{ij}` values will then adjust in aggregate (up or down) -so that :math:`C_{ij} \cdot V^{max}` produces a boost of *Btarget*\ , but this +so that :math:`C_{ij} \cdot V^{max}` produces a boost of *Btarget*, but this may conflict with the *bound* keyword settings. By using *bound* and *reset* together, :math:`V^{max}` itself can be reset, and desired bounds still applied to the :math:`C_{ij}` values. @@ -354,7 +354,7 @@ The *check/bias* keyword turns on extra computation and communication to check if any biased bonds are closer than *Dcut* to each other, which should not be the case if LHD is operating correctly. Thus it is a debugging check. The *Nevery* setting determines how often the -check is made. The *error*\ , *warn*\ , or *ignore* setting determines +check is made. The *error*, *warn*, or *ignore* setting determines what is done if the count of too-close bonds is not zero. Either the code will exit, or issue a warning, or silently tally the count. The count can be output as vector value 17, as described below. If this @@ -447,13 +447,13 @@ next event occurs they may move further than *Dcut* away from the sub-box boundary. Value 19 is the furthest (from the sub-box) any ghost atom in the neighbor list with maxstrain < *qfactor* was accessed during the run. Value 20 is the same except that the ghost -atom's maxstrain may be >= *qfactor*\ , which may mean it is about to +atom's maxstrain may be >= *qfactor*, which may mean it is about to participate in an event. Value 21 is a count of how many ghost atoms could not be found on reneighbor steps, presumably because they moved too far away due to their participation in an event (which will likely be detected at the next quench). -Typical values for 19 and 20 should be slightly larger than *Dcut*\ , +Typical values for 19 and 20 should be slightly larger than *Dcut*, which accounts for ghost atoms initially at a *Dcut* distance moving thermally before the next event takes place. diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index 5bb4075873..004bc0b614 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -78,7 +78,7 @@ fixes would be active at the same time, each needs to use a different port number. The *nowait* keyword controls the behavior of the fix when no IMD -client is connected. With the default setting of *off*\ , LAMMPS will +client is connected. With the default setting of *off*, LAMMPS will wait until a connection is made before continuing with the execution. Setting *nowait* to *on* will have the LAMMPS code be ready to connect to a client, but continue with the simulation. This can for @@ -150,7 +150,7 @@ Restrictions """""""""""" This fix is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. When used in combination with VMD, a topology or coordinate file has to be loaded, which matches (in number and ordering of atoms) the diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index e9dab5141f..bb4b450c94 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -96,9 +96,9 @@ the plane's current position will feel no force. Vice versa if *side* is specified as *hi*\ . Any of the 4 quantities defining a spherical indenter's geometry can -be specified as an equal-style :doc:`variable `, namely *x*\ , -*y*\ , *z*\ , or *R*\ . Similarly, for a cylindrical indenter, any of *c1*\ , -*c2*\ , or *R*\ , can be a variable. For a planar indenter, *pos* can be +be specified as an equal-style :doc:`variable `, namely *x*, +*y*, *z*, or *R*\ . Similarly, for a cylindrical indenter, any of *c1*, +*c2*, or *R*, can be a variable. For a planar indenter, *pos* can be a variable. If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to define the @@ -139,10 +139,10 @@ rate. variable rate equal 1.0 variable r equal "v_r0 + step*dt*v_rate" -If the *side* keyword is specified as *out*\ , which is the default, +If the *side* keyword is specified as *out*, which is the default, then particles outside the indenter are pushed away from its outer surface, as described above. This only applies to spherical or -cylindrical indenters. If the *side* keyword is specified as *in*\ , +cylindrical indenters. If the *side* keyword is specified as *in*, the action of the indenter is reversed. Particles inside the indenter are pushed away from its inner surface. In other words, the indenter is now a containing wall that traps the particles inside it. If the @@ -160,7 +160,7 @@ 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 latter case, you should use the *xlat*, *ylat*, *zlat* keywords of the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. @@ -168,7 +168,7 @@ The force constant *K* is not affected by the *units* keyword. It is 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 +contains *xlat*, *ylat*, *zlat* keywords of the :doc:`thermo_style ` command, e.g. .. code-block:: LAMMPS diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index f8ea49c845..bd4b4d84e8 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -14,8 +14,8 @@ Syntax * ipi = style name of this fix command * address = internet address (FQDN or IP), or UNIX socket name * port = port number (ignored for UNIX sockets) -* optional keyword = *unix*\ , if present uses a unix socket -* optional keyword = *reset*\ , if present reset electrostatics at each call +* optional keyword = *unix*, if present uses a unix socket +* optional keyword = *reset*, if present reset electrostatics at each call Examples """""""" @@ -86,7 +86,7 @@ i-PI. This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Because of the use of UNIX domain sockets, this fix will only work in a UNIX environment. diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index 918573fc6b..c8be9afc31 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -112,7 +112,7 @@ thermostatting takes place; see the description below. fix - e.g. by :doc:`fix nvt ` or :doc:`fix temp/rescale ` commands. -See the :doc:`Howto thermostat ` doc page for +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -239,7 +239,7 @@ thermostat. Because the random forces on different atoms are independent, they do not sum exactly to zero. As a result, this fix applies a small random force to the entire system, and the center-of-mass of the system undergoes a slow random walk. If the -keyword *zero* is set to *yes*\ , the total random force is set exactly +keyword *zero* is set to *yes*, the total random force is set exactly to zero by subtracting off an equal part of it from each atom in the group. As a result, the center-of-mass of a system with zero initial momentum will not drift over time. @@ -252,7 +252,7 @@ limit of the integrator), while still producing the correct Boltzmann distribution of atom positions. The current implementation provides the user with the option to output -the velocity in one of two forms: *vfull* or *vhalf*\ , which replaces +the velocity in one of two forms: *vfull* or *vhalf*, which replaces the outdated option *yes*\ . The *gjf* option *vfull* outputs the on-site velocity given in :ref:`Gronbech-Jensen/Farago `; this velocity is shown to be systematically lower @@ -291,8 +291,8 @@ this fix and by the compute should be the same. The cumulative energy change in the system imposed by this fix is included in the :doc:`thermodynamic output ` keywords -*ecouple* and *econserve*\ , but only if the *tally* keyword to set to -*yes*\ . See the :doc:`thermo_style ` doc page for +*ecouple* and *econserve*, but only if the *tally* keyword to set to +*yes*\ . See the :doc:`thermo_style ` page for details. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index 77e59a0848..3486723a67 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -100,7 +100,7 @@ transform: f = \frac m {M'}\, F' + f' This fix also thermostats non-polarizable atoms in the group at -temperature *Tcom*\ , as if they had a massless Drude partner. The +temperature *Tcom*, as if they had a massless Drude partner. The Drude particles themselves need not be in the group. The center of mass and the dipole are thermostatted iff the core atom is in the group. @@ -122,7 +122,7 @@ from them before thermostatting takes place; see the description below. Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix temp/rescale ` commands. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -207,7 +207,7 @@ thermostat on centers of mass. Because the random forces on different centers of mass are independent, they do not sum exactly to zero. As a result, this fix applies a small random force to the entire system, and the momentum of the total center of mass of the system undergoes a -slow random walk. If the keyword *zero* is set to *yes*\ , the total +slow random walk. If the keyword *zero* is set to *yes*, the total random force on the centers of mass is set exactly to zero by subtracting off an equal part of it from each center of mass in the group. As a result, the total center of mass of a system with zero @@ -239,7 +239,7 @@ Comments: * *zero yes* avoids a drift of the center of mass of the system, but is a bit slower. * Use two different random seeds to avoid unphysical correlations. -* Temperature is controlled by the fix *langevin/drude*\ , so the +* Temperature is controlled by the fix *langevin/drude*, so the time-integration fixes do not thermostat. Don't forget to time-integrate both cores and Drude particles. * Pressure is time-integrated only once by using *nve* for Drude @@ -251,7 +251,7 @@ Comments: fix *npt* and :doc:`fix drude/transform `, the *fix_modify* command is not required here, because the fix *nph* computes the global pressure even if its group is *ATOMS*\ . This is - what we want. If we thermostatted *ATOMS* using *npt*\ , the pressure + what we want. If we thermostatted *ATOMS* using *npt*, the pressure should be the global one, but the temperature should be only that of the cores. That's why the command *fix_modify* should be called in that case. diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index 383980b232..506b5052d5 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -83,8 +83,8 @@ this fix and by the compute should be the same. The cumulative energy change in the system imposed by this fix is included in the :doc:`thermodynamic output ` keywords -*ecouple* and *econserve*\ , but only if the *tally* keyword to set to -*yes*\ . See the :doc:`thermo_style ` doc page for +*ecouple* and *econserve*, but only if the *tally* keyword to set to +*yes*\ . See the :doc:`thermo_style ` page for details. This fix computes a global scalar which can be accessed by various @@ -105,7 +105,7 @@ Restrictions none This fix is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst index c73968df48..0926881eef 100644 --- a/doc/src/fix_langevin_spin.rst +++ b/doc/src/fix_langevin_spin.rst @@ -85,7 +85,7 @@ Restrictions """""""""""" The *langevin/spin* fix is part of the SPIN package. This style is -only enabled if LAMMPS was built with this package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with this package. See the :doc:`Build package ` page for more info. The numerical integration has to be performed with *fix nve/spin* when *fix langevin/spin* is enabled. diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index 58a8ddbe20..f75d44e3a4 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -153,7 +153,7 @@ Restrictions This fix is part of the LATTE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. You must use metal units, as set by the :doc:`units ` command to use this fix. @@ -171,7 +171,7 @@ doing 99% or more of the work to compute quantum-accurate forces. NEB calculations can be done using this fix using multiple replicas and running LAMMPS in parallel. However, each replica must be run on a single MPI task. For details, see the :doc:`neb ` - command doc page and the :doc:`-partition command-line switch ` + command page and the :doc:`-partition command-line switch ` Related commands """""""""""""""" diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index 127e846589..21d5d0cb84 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -210,7 +210,7 @@ By default, :math:`\frac{\tau}{dt} = \frac{3\eta dt}{\rho dx^2}` is approximately equal to 1. However, the user has the option of specifying their own values for :math:`dm_{LB}`, and :math:`dx_{LB}`, by using -the optional keywords *dm*\ , and *dx* respectively. +the optional keywords *dm*, and *dx* respectively. .. note:: @@ -224,7 +224,7 @@ the optional keywords *dm*\ , and *dx* respectively. :math:`dx_{LB}` is used, this will automatically be satisfied. Physical parameters describing the fluid are specified through -*viscosity*\ , *density*\ , and *a0*\ . If the force coupling constant is +*viscosity*, *density*, and *a0*\ . If the force coupling constant is set the default way, the surface area associated with the MD particles is specified using the *setArea* keyword. If the user chooses to specify a value for the force coupling constant, this is set using the @@ -342,7 +342,7 @@ Restrictions """""""""""" This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. This fix can only be used with an orthogonal simulation domain. diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index 5a01e1916e..f967c1300a 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -46,7 +46,7 @@ and the fluid velocities at each lattice site. This fix only considers the linear momentum of the system. By default, the subtraction is performed for each dimension. This can -be changed by specifying the keyword *linear*\ , along with a set of +be changed by specifying the keyword *linear*, along with a set of three flags set to 0/1 in order to exclude/ include the corresponding dimension. @@ -67,7 +67,7 @@ Can only be used if a lattice-Boltzmann fluid has been created via the command. This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst index 6ba28ec309..6ba3e72482 100644 --- a/doc/src/fix_lb_pc.rst +++ b/doc/src/fix_lb_pc.rst @@ -24,7 +24,7 @@ Description """"""""""" Update the positions and velocities of the individual particles -described by *group-ID*\ , experiencing velocity-dependent hydrodynamic +described by *group-ID*, experiencing velocity-dependent hydrodynamic forces, using the integration algorithm described in :ref:`Mackay et al. `. This integration algorithm should only be used if a user-specified value for the force-coupling constant used in :doc:`fix lb/fluid ` has been set; do not use this integration algorithm if the force coupling constant has been set by default. @@ -42,7 +42,7 @@ Restrictions """""""""""" This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst index 5ee32c29f0..16e00ba12f 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.rst +++ b/doc/src/fix_lb_rigid_pc_sphere.rst @@ -141,7 +141,7 @@ Restrictions This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst index 5bd6889808..cd3712aac4 100644 --- a/doc/src/fix_lb_viscous.rst +++ b/doc/src/fix_lb_viscous.rst @@ -72,7 +72,7 @@ Restrictions """""""""""" This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst index 964fc1ad1f..2d72743707 100644 --- a/doc/src/fix_manifoldforce.rst +++ b/doc/src/fix_manifoldforce.rst @@ -49,7 +49,7 @@ Restrictions """""""""""" This fix is part of the MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Only use this with *min_style hftn* or *min_style quickmin*. If not, the constraints will not be satisfied very well at all. A warning is diff --git a/doc/src/fix_mdi_engine.rst b/doc/src/fix_mdi_engine.rst index ca667bfe3b..51a4545fd8 100644 --- a/doc/src/fix_mdi_engine.rst +++ b/doc/src/fix_mdi_engine.rst @@ -46,7 +46,7 @@ Restrictions This command is part of the MDI package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst index 6b290382a3..7b3609a8c7 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -125,7 +125,7 @@ notation as where *X0* = (x0,y0,z0) is their position at the time the fix is specified, *A* is the specified amplitude vector with components -(Ax,Ay,Az), *omega* is 2 PI / *period*\ , and *delta* is the time +(Ax,Ay,Az), *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. This style also sets the velocity of each particle to the time derivative of this expression. If any of the amplitude components is specified as NULL, then the @@ -150,7 +150,7 @@ The *rotate* style rotates particles around a rotation axis *R* = (Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz). The *period* of the rotation is also specified. The direction of rotation for the particles around the rotation axis is consistent with the right-hand -rule: if your right-hand thumb points along *R*\ , then your fingers wrap +rule: if your right-hand thumb points along *R*, then your fingers wrap around the axis in the direction of rotation. This style also sets the velocity of each particle to (omega cross @@ -240,7 +240,7 @@ Restrictions This fix is part of the DPD-SMOOTH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This fix requires that atoms store density and internal energy as defined by the :doc:`atom_style sph ` command. diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index a6bac6ac44..47080fcd58 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -85,7 +85,7 @@ appropriate fix. For most fixes that support the *energy* keyword, the default setting is *no*. For a few it is *yes*, when a user would expect - that to be the case. The doc page of each fix gives the default. + that to be the case. The page of each fix gives the default. The *virial* keyword can be used with fixes that support it, which is explained at the bottom of their doc page. *Virial yes* will add a @@ -110,7 +110,7 @@ option to include or exclude the contribution from fixes. For most fixes that support the *virial* keyword, the default setting is *no*. For a few it is *yes*, when a user would expect - that to be the case. The doc page of each fix gives the default. + that to be the case. The page of each fix gives the default. For fixes that set or modify forces, it may be possible to select at which :doc:`r-RESPA ` level the fix operates via the *respa* diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index 71b50ddcdb..7d00a4c67b 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -99,7 +99,7 @@ Restrictions Fix momentum/chunk is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index 7ede1f3050..5d3a9de47f 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -118,7 +118,7 @@ notation as where *X0* = (x0,y0,z0) is their position at the time the fix is specified, *A* is the specified amplitude vector with components -(Ax,Ay,Az), *omega* is 2 PI / *period*\ , and *delta* is the time +(Ax,Ay,Az), *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. This style also sets the velocity of each atom to the time derivative of this expression. If any of the amplitude components is specified as NULL, then the @@ -143,7 +143,7 @@ The *rotate* style rotates atoms around a rotation axis *R* = (Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz). The *period* of the rotation is also specified. The direction of rotation for the atoms around the rotation axis is consistent with the right-hand rule: -if your right-hand thumb points along *R*\ , then your fingers wrap +if your right-hand thumb points along *R*, then your fingers wrap around the axis in the direction of rotation. This style also sets the velocity of each atom to (omega cross Rperp) diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst index fe32acdbd5..5e9bc520b5 100644 --- a/doc/src/fix_mscg.rst +++ b/doc/src/fix_mscg.rst @@ -93,8 +93,8 @@ for more info. ---------- The *range* keyword specifies which MS-CG library functionality should -be invoked. If *on*\ , the step 4 range finder functionality is invoked. -*off*\ , the step 5 force matching functionality is invoked. +be invoked. If *on*, the step 4 range finder functionality is invoked. +*off*, the step 5 force matching functionality is invoked. If the *name* keyword is used, string names are defined to associate with the integer atom types in LAMMPS. *Ntype* names must be diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst index e3996776a1..9502fe21b8 100644 --- a/doc/src/fix_msst.rst +++ b/doc/src/fix_msst.rst @@ -71,7 +71,7 @@ kinetic energy at the start of the simulation. Setting this parameter to a non-zero value may assist in compression at the start of simulations where it is slow to occur. -If keywords *e0*\ , *p0*\ ,or *v0* are not supplied, these quantities will +If keywords *e0*, *p0*,or *v0* are not supplied, these quantities will be calculated on the first step, after the energy specified by *tscale* is removed. The value of *e0* is not used in the dynamical equations, but is used in calculating the deviation from the Hugoniot. @@ -112,7 +112,7 @@ new computes are the fix-ID + "_MSST_temp" or "MSST_press" or The *dftb* keyword is to allow this fix to be used when LAMMPS is being driven by DFTB+, a density-functional tight-binding code. If the -keyword *dftb* is used with a value of *yes*\ , then the MSST equations +keyword *dftb* is used with a value of *yes*, then the MSST equations are altered to account for the electron entropy contribution to the Hugonio relations and total energy. See :ref:`(Reed2) ` and :ref:`(Goldman) ` for details on this contribution. In this case, @@ -152,7 +152,7 @@ integration of the dynamic equations. The global vector contains four values in the following order. The vector values output by this fix are "intensive". -[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*, +[\ *dhugoniot*, *drayleigh*, *lagrangian_speed*, *lagrangian_position*] 1. *dhugoniot* is the departure from the Hugoniot (temperature units). @@ -177,7 +177,7 @@ Restrictions This fix style is part of the SHOCK package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. All cell dimensions must be periodic. This fix can not be used with a triclinic cell. The MSST fix has been tested only for the group-ID diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index 429c1c3bb7..efabab2183 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -91,7 +91,7 @@ Restrictions """""""""""" This fix is part of the DPD-MESO package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 848369d3ea..222e1d5fbf 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -96,7 +96,7 @@ and the relaxation procedure is continued to a new converged MEP. ---------- The keyword *parallel* specifies how the parallel nudging force is -computed. With a value of *neigh*\ , the parallel nudging force is +computed. With a value of *neigh*, the parallel nudging force is computed as in :ref:`(Henkelman1) ` by connecting each intermediate replica with the previous and the next image: @@ -107,7 +107,7 @@ intermediate replica with the previous and the next image: Note that in this case the specified *Kspring* is in force/distance units. -With a value of *ideal*\ , the spring force is computed as suggested in +With a value of *ideal*, the spring force is computed as suggested in ref`(WeinanE) ` .. parsed-literal:: @@ -151,7 +151,7 @@ force is added. By default, no additional forces act on the first and last replicas during the NEB relaxation, so these replicas simply relax toward their -respective local minima. By using the key word *end*\ , additional +respective local minima. By using the key word *end*, additional forces can be applied to the first and/or last replicas, to enable them to relax toward a MEP while constraining their energy E to the target energy ETarget. @@ -166,8 +166,8 @@ If ETarget>E, the interatomic force Fi for the specified replica becomes: The "spring" constant on the difference in energies is the specified *Kspring3* value. -When *estyle* is specified as *first*\ , the force is applied to the -first replica. When *estyle* is specified as *last*\ , the force is +When *estyle* is specified as *first*, the force is applied to the +first replica. When *estyle* is specified as *last*, the force is applied to the last replica. Note that the *end* keyword can be used twice to add forces to both the first and last replicas. @@ -175,13 +175,13 @@ For both these *estyle* settings, the target energy *ETarget* is set to the initial energy of the replica (at the start of the NEB calculation). -If the *estyle* is specified as *last/efirst* or *last/efirst/middle*\ , +If the *estyle* is specified as *last/efirst* or *last/efirst/middle*, force is applied to the last replica, but the target energy *ETarget* is continuously set to the energy of the first replica, as it evolves during the NEB relaxation. The difference between these two *estyle* options is as follows. When -*estyle* is specified as *last/efirst*\ , no change is made to the +*estyle* is specified as *last/efirst*, no change is made to the inter-replica force applied to the intermediate replicas (neither first or last). If the initial path is too far from the MEP, an intermediate replica may relax "faster" and reach a lower energy than @@ -195,7 +195,7 @@ than the first replica. This should effectively prevent the intermediate replicas from over-relaxing. After converging a NEB calculation using an *estyle* of -*last/efirst/middle*\ , you should check that all intermediate replicas +*last/efirst/middle*, you should check that all intermediate replicas have a larger energy than the first replica. If this is not the case, the path is probably not a MEP. diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index f40ce0c463..46b343fdce 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -104,7 +104,7 @@ addition to basic thermostatting and barostatting, these fixes can also create a chain of thermostats coupled to the particle thermostat, and another chain of thermostats coupled to the barostat variables. The barostat can be coupled to the overall box volume, or -to individual dimensions, including the *xy*\ , *xz* and *yz* tilt +to individual dimensions, including the *xy*, *xz* and *yz* tilt dimensions. The external pressure of the barostat can be specified as either a scalar pressure (isobaric ensemble) or as components of a symmetric stress tensor (constant stress ensemble). When used @@ -124,7 +124,7 @@ integrators derived by Tuckerman et al in :ref:`(Tuckerman) `. The thermostat parameters for fix styles *nvt* and *npt* are specified using the *temp* keyword. Other thermostat-related keywords are -*tchain*\ , *tloop* and *drag*\ , which are discussed below. +*tchain*, *tloop* and *drag*, which are discussed below. The thermostat is applied to only the translational degrees of freedom for the particles. The translational degrees of freedom can also have @@ -156,15 +156,15 @@ by the velocity/position update portion of the integration. ---------- The barostat parameters for fix styles *npt* and *nph* is specified -using one or more of the *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , -*xz*\ , *yz*\ , and *couple* keywords. These keywords give you the +using one or more of the *iso*, *aniso*, *tri*, *x*, *y*, *z*, *xy*, +*xz*, *yz*, and *couple* keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during a constant-pressure simulation. -Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , -*nreset*\ , *drag*\ , and *dilate*\ , which are discussed below. +Other barostat-related keywords are *pchain*, *mtk*, *ploop*, +*nreset*, *drag*, and *dilate*, which are discussed below. Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable @@ -173,7 +173,7 @@ specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. The target pressures for each of the 6 components of the stress tensor -can be specified independently via the *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz* +can be specified independently via the *x*, *y*, *z*, *xy*, *xz*, *yz* keywords, which correspond to the 6 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped value during the run from *Pstart* to *Pstop*\ . @@ -184,7 +184,7 @@ the *xy* keyword is used, the xy tilt factor will change. A box dimension will not change if that component is not specified, although you have the option to change that dimension via the :doc:`fix deform ` command. -Note that in order to use the *xy*\ , *xz*\ , or *yz* keywords, the +Note that in order to use the *xy*, *xz*, or *yz* keywords, the simulation box must be triclinic, even if its initial tilt factors are 0.0. @@ -253,13 +253,13 @@ things: the instantaneous stress will be computed as an average of the corresponding diagonal components, and the coupled box dimensions will be changed together in lockstep, meaning coupled dimensions will be dilated or contracted by the same percentage every timestep. The -*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. ---------- -The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are +The *iso*, *aniso*, and *tri* keywords are simply shortcuts that are equivalent to specifying several other keywords together. The keyword *iso* means couple all 3 diagonal components together when @@ -274,8 +274,8 @@ specifying these 4 keywords: z Pstart Pstop Pdamp couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: @@ -287,7 +287,7 @@ these 4 keywords: z Pstart Pstop Pdamp couple none -The keyword *tri* means *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , and *yz* dimensions +The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions are controlled independently using their individual stress components as the driving forces, and the specified scalar pressure as the external normal stress. Using "tri Pstart Pstop Pdamp" is the same as @@ -352,7 +352,7 @@ specified values of the external stress tensor. A value of *nstep* means that every *nstep* timesteps, the reference dimensions are set to those of the current simulation domain. -The *scaleyz*\ , *scalexz*\ , and *scalexy* keywords control whether or +The *scaleyz*, *scalexz*, and *scalexy* keywords control whether or not the corresponding tilt factors are scaled with the associated box dimensions when barostatting triclinic periodic cells. The default values *yes* will turn on scaling, which corresponds to adjusting the @@ -365,9 +365,9 @@ scale keywords to *no*\ . The *flip* keyword allows the tilt factors for a triclinic box to exceed half the distance of the parallel box length, as discussed -below. If the *flip* value is set to *yes*\ , the bound is enforced by +below. If the *flip* value is set to *yes*, the bound is enforced by flipping the box when it is exceeded. If the *flip* value is set to -*no*\ , the tilt will continue to change without flipping. Note that if +*no*, the tilt will continue to change without flipping. Note that if applied stress induces large deformations (e.g. in a liquid), this means the box shape can tilt dramatically and LAMMPS will run less efficiently, due to the large volume of communication needed to @@ -379,7 +379,7 @@ The *fixedpoint* keyword specifies the fixed point for barostat volume changes. By default, it is the center of the box. Whatever point is chosen will not move during the simulation. For example, if the lower periodic boundaries pass through (0,0,0), and this point is provided -to *fixedpoint*\ , then the lower periodic boundaries will remain at +to *fixedpoint*, then the lower periodic boundaries will remain at (0,0,0), while the upper periodic boundaries will move twice as far. In all cases, the particle trajectories are unaffected by the chosen value, except for a time-dependent constant translation of @@ -402,7 +402,7 @@ at only a small additional computational cost. .. note:: - Using a barostat coupled to tilt dimensions *xy*\ , *xz*\ , *yz* can + Using a barostat coupled to tilt dimensions *xy*, *xz*, *yz* can sometimes result in arbitrarily large values of the tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS allows the tilt factors to grow a small amount beyond the normal limit of half the box @@ -410,7 +410,7 @@ at only a small additional computational cost. an equivalent periodic cell. See the discussion of the *flip* keyword above, to allow this bound to be exceeded, if desired. -The flip operation is described in more detail in the doc page for +The flip operation is described in more detail in the page for :doc:`fix deform `. Both the barostat dynamics and the atom trajectories are unaffected by this operation. However, if a tilt factor is incremented by a large amount (1.5 times the box length) on @@ -504,7 +504,7 @@ thermal degrees of freedom, and the bias is added back in. These fixes can be used with either the *verlet* or *respa* :doc:`integrators `. When using one of the barostat fixes -with *respa*\ , LAMMPS uses an integrator constructed +with *respa*, LAMMPS uses an integrator constructed according to the following factorization of the Liouville propagator (for two rRESPA levels): @@ -557,7 +557,7 @@ of the underlying non-Hamiltonian equations of motion. The fix npt and fix nph commands can be used with rigid bodies or mixtures of rigid bodies and non-rigid particles (e.g. solvent). But there are also :doc:`fix rigid/npt ` and :doc:`fix rigid/nph ` commands, which are typically a more natural -choice. See the doc page for those commands for more discussion of +choice. See the page for those commands for more discussion of the various ways to do this. ---------- @@ -599,7 +599,7 @@ compute temperature on a subset of atoms. The cumulative energy change in the system imposed by these fixes, via either thermostatting and/or barostatting, is included in the :doc:`thermodynamic output ` keywords *ecouple* and -*econserve*. See the :doc:`thermo_style ` doc page for +*econserve*. See the :doc:`thermo_style ` page for details. These fixes compute a global scalar which can be accessed by various @@ -613,7 +613,7 @@ vector values are "intensive". The vector stores internal Nose/Hoover thermostat and barostat variables. The number and meaning of the vector values depends on -which fix is used and the settings for keywords *tchain* and *pchain*\ , +which fix is used and the settings for keywords *tchain* and *pchain*, which specify the number of Nose/Hoover chains for the thermostat and barostat. If no thermostatting is done, then *tchain* is 0. If no barostatting is done, then *pchain* is 0. In the following list, @@ -653,10 +653,10 @@ These fixes are not invoked during :doc:`energy minimization `. Restrictions """""""""""" -*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not -periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the +*X*, *y*, *z* cannot be barostatted if the associated dimension is not +periodic. *Xy*, *xz*, and *yz* can only be barostatted if the simulation domain is triclinic and the second dimension in the keyword -(\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be +(\ *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 ` commands specify whether the simulation box is orthogonal or @@ -668,10 +668,10 @@ make the external T = 0.0 at some timestep during the simulation which is not allowed in the Nose/Hoover formulation. The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used -for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options +for 2D simulations. *scaleyz yes*, *scalexz yes*, and *scalexy yes* options can only be used if the second dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords -*tri*\ , *yz*\ , *xz*\ , and *xy*\ . +*tri*, *yz*, *xz*, and *xy*\ . These fixes can be used with dynamic groups as defined by the :doc:`group ` command. Likewise they can be used with groups to diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 2dbd5aa85e..11990d365b 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -68,7 +68,7 @@ domain dimensions (barostatting). In addition to basic thermostatting and barostatting, these fixes can also create a chain of thermostats coupled to the particle thermostat, and another chain of thermostats coupled to the barostat variables. The barostat can be coupled to the -overall box volume, or to individual dimensions, including the *xy*\ , +overall box volume, or to individual dimensions, including the *xy*, *xz* and *yz* tilt dimensions. The external pressure of the barostat can be specified as either a scalar pressure (isobaric ensemble) or as components of a symmetric stress tensor (constant stress ensemble). @@ -110,16 +110,16 @@ to the temperature or kinetic energy from the electron radial velocity. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -See the doc page for the :doc:`fix nvt, npt, and nph ` commands +See the page for the :doc:`fix nvt, npt, and nph ` commands for details. Restrictions """""""""""" This fix is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -Other restriction discussed on the doc page for the :doc:`fix nvt, npt, and nph ` commands also apply. +Other restriction discussed on the page for the :doc:`fix nvt, npt, and nph ` commands also apply. .. note:: diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index e33b2a639d..b51e232a3c 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -16,7 +16,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * style_name = *nvt/uef* or *npt/uef* -* *Tstart*\ , *Tstop*\ , and *Tdamp* are documented in the :doc:`fix npt ` command +* *Tstart*, *Tstop*, and *Tdamp* are documented in the :doc:`fix npt ` command * *edot_x* and *edot_y* are the strain rates in the x and y directions (1/(time units)) * one or more keyword/value pairs may be appended @@ -27,7 +27,7 @@ Syntax sets the external dimensions used to calculate the scalar pressure *strain* values = e_x e_y = initial strain usually not needed, but may be needed to resume a run with a data file. - *iso*\ , *x*\ , *y*\ , *z*\ , *tchain*\ , *pchain*\ , *tloop*\ , *ploop*\ , *mtk* keywords + *iso*, *x*, *y*, *z*, *tchain*, *pchain*, *tloop*, *ploop*, *mtk* keywords documented by the :doc:`fix npt ` command Examples @@ -111,7 +111,7 @@ pressure using this fix. The first method involves using the *ext* keyword along with the *iso* pressure style. With this method, the pressure is controlled by scaling the simulation box isotropically to achieve the average pressure only in the directions specified by -*ext*\ . For example, if the *ext* value is set to *xy*\ , the average +*ext*\ . For example, if the *ext* value is set to *xy*, the average pressure (Pxx+Pyy)/2 will be controlled. This example command will control the total hydrostatic pressure under @@ -130,7 +130,7 @@ drawing with uniaxial tension: fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy The second method for pressure control involves setting the normal -stresses using the *x*\ , *y* , and/or *z* keywords. When using this +stresses using the *x*, *y*, and/or *z* keywords. When using this method, the same pressure must be specified via *Pstart* and *Pstop* for all dimensions controlled. Any choice of pressure conditions that would cause LAMMPS to compute a deviatoric stress are not permissible @@ -200,7 +200,7 @@ Restrictions """""""""""" This fix is part of the UEF package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Due to requirements of the boundary conditions, when the *strain* keyword is set to zero (or unset), the initial simulation box must be diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index 011630a534..a1028efacc 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -41,7 +41,7 @@ point particles and only updates their position and velocity. Additional parameters affecting the barostat are specified by keywords and values documented with the :doc:`fix nph ` command. See, -for example, discussion of the *aniso*\ , and *dilate* keywords. +for example, discussion of the *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -50,7 +50,7 @@ NPH integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -120,7 +120,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/fix_nph_body.rst b/doc/src/fix_nph_body.rst index 4c91d28588..1b740a5ae2 100644 --- a/doc/src/fix_nph_body.rst +++ b/doc/src/fix_nph_body.rst @@ -38,7 +38,7 @@ point particles and only updates their position and velocity. Additional parameters affecting the barostat are specified by keywords and values documented with the :doc:`fix nph ` command. See, -for example, discussion of the *aniso*\ , and *dilate* keywords. +for example, discussion of the *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -47,7 +47,7 @@ NPH integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -117,7 +117,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index 6062faa50e..2ef85953e5 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -54,7 +54,7 @@ moment of inertia, as used in the time integration. Additional parameters affecting the barostat are specified by keywords and values documented with the :doc:`fix nph ` command. See, -for example, discussion of the *aniso*\ , and *dilate* keywords. +for example, discussion of the *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -63,7 +63,7 @@ NPH integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index 776b3e4849..b45cfe964f 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -63,8 +63,8 @@ jump conditions for steady shocks. The compression can be performed either -hydrostatically (using keyword *iso*\ , *aniso*\ , or *tri*\ ) or uniaxially -(using keywords *x*\ , *y*\ , or *z*\ ). In the hydrostatic case, +hydrostatically (using keyword *iso*, *aniso*, or *tri*\ ) or uniaxially +(using keywords *x*, *y*, or *z*\ ). In the hydrostatic case, the cell dimensions change dynamically so that the average axial stress in all three directions converges towards the specified target value. In the uniaxial case, the chosen cell dimension changes dynamically @@ -74,10 +74,10 @@ other two cell dimensions are kept fixed (zero lateral strain). This leads to the following additional restrictions on the keywords: -* One and only one of the following keywords should be used: *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z* +* One and only one of the following keywords should be used: *iso*, *aniso*, *tri*, *x*, *y*, *z* * The specified initial and final target pressures must be the same. -* The keywords *xy*\ , *xz*\ , *yz* may not be used. -* The only admissible value for the couple keyword is *xyz*\ , which has the same effect as keyword *iso* +* The keywords *xy*, *xz*, *yz* may not be used. +* The only admissible value for the couple keyword is *xyz*, which has the same effect as keyword *iso* * The *temp* keyword must be used to specify the time constant for kinetic energy relaxation, but initial and final target temperature values are ignored. Essentially, a Hugoniostat simulation is an NPT simulation in which the @@ -100,8 +100,8 @@ When the system reaches a stable equilibrium, the value of :math:`\Delta` should fluctuate about zero. The values of :math:`E_0`, :math:`V_0`, and :math:`P_0` are the instantaneous values at the start of -the simulation. These can be overridden using the fix_modify keywords *e0*\ , -*v0*\ , and *p0* described below. +the simulation. These can be overridden using the fix_modify keywords *e0*, +*v0*, and *p0* described below. ---------- @@ -159,7 +159,7 @@ as well as the state of all the thermostat and barostat variables to 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 can be +The :doc:`fix_modify ` *e0*, *v0* and *p0* keywords can be used to define the values of :math:`E_0`, :math:`V_0`, and :math:`P_0`. 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 @@ -205,7 +205,7 @@ Restrictions This fix style is part of the SHOCK package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. All the usual restrictions for :doc:`fix npt ` apply, plus the additional ones mentioned above. diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index f65ecd8d19..28edb59f8d 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -48,8 +48,8 @@ can also have a bias velocity removed from them before thermostatting takes place; see the description below. Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*\ , -*iso*\ , *aniso*\ , and *dilate* keywords. +specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*, +*iso*, *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -58,7 +58,7 @@ NPT integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -143,7 +143,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/fix_npt_body.rst b/doc/src/fix_npt_body.rst index af0a0fb252..d44870a4fb 100644 --- a/doc/src/fix_npt_body.rst +++ b/doc/src/fix_npt_body.rst @@ -46,8 +46,8 @@ takes place; see the description below. Additional parameters affecting the thermostat and barostat are specified by keywords and values documented with the :doc:`fix npt -` command. See, for example, discussion of the *temp*\ , -*iso*\ , *aniso*\ , and *dilate* keywords. +` command. See, for example, discussion of the *temp*, +*iso*, *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -56,7 +56,7 @@ NPT integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -141,7 +141,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index 01bf34927c..13b5b7bf70 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -73,7 +73,7 @@ addition to basic thermostatting and barostatting, this fix can also create a chain of thermostats coupled to the particle thermostat, and another chain of thermostats coupled to the barostat variables. The barostat can be coupled to the overall box volume, or -to individual dimensions, including the *xy*\ , *xz* and *yz* tilt +to individual dimensions, including the *xy*, *xz* and *yz* tilt dimensions. The external pressure of the barostat can be specified as either a scalar pressure (isobaric ensemble) or as components of a symmetric stress tensor (constant stress ensemble). When used @@ -92,7 +92,7 @@ integrators derived by Tuckerman et al in :ref:`(Tuckerman) `. ---------- The thermostat parameters are specified using the *temp* keyword. -Other thermostat-related keywords are *tchain*\ , *tloop* and *drag*\ , +Other thermostat-related keywords are *tchain*, *tloop* and *drag*, which are discussed below. The thermostat is applied to only the translational degrees of freedom @@ -118,15 +118,15 @@ by the velocity/position update portion of the integration. ---------- -The barostat parameters are specified using one or more of the *iso*\ , -*aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz*\ , and *couple* keywords. +The barostat parameters are specified using one or more of the *iso*, +*aniso*, *tri*, *x*, *y*, *z*, *xy*, *xz*, *yz*, and *couple* keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during a constant-pressure simulation. -Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , -*nreset*\ , *drag*\ , and *dilate*\ , which are discussed below. +Other barostat-related keywords are *pchain*, *mtk*, *ploop*, +*nreset*, *drag*, and *dilate*, which are discussed below. Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable @@ -135,7 +135,7 @@ specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. The target pressures for each of the 6 components of the stress tensor -can be specified independently via the *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , *yz* +can be specified independently via the *x*, *y*, *z*, *xy*, *xz*, *yz* keywords, which correspond to the 6 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped value during the run from *Pstart* to *Pstop*\ . @@ -146,7 +146,7 @@ the *xy* keyword is used, the xy tilt factor will change. A box dimension will not change if that component is not specified, although you have the option to change that dimension via the :doc:`fix deform ` command. -Note that in order to use the *xy*\ , *xz*\ , or *yz* keywords, the +Note that in order to use the *xy*, *xz*, or *yz* keywords, the simulation box must be triclinic, even if its initial tilt factors are 0.0. @@ -193,13 +193,13 @@ things: the instantaneous stress will be computed as an average of the corresponding diagonal components, and the coupled box dimensions will be changed together in lockstep, meaning coupled dimensions will be dilated or contracted by the same percentage every timestep. The -*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. ---------- -The *iso*\ , *aniso*\ , and *tri* keywords are simply shortcuts that are +The *iso*, *aniso*, and *tri* keywords are simply shortcuts that are equivalent to specifying several other keywords together. The keyword *iso* means couple all 3 diagonal components together when @@ -214,8 +214,8 @@ specifying these 4 keywords: z Pstart Pstop Pdamp couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: @@ -227,7 +227,7 @@ these 4 keywords: z Pstart Pstop Pdamp couple none -The keyword *tri* means *x*\ , *y*\ , *z*\ , *xy*\ , *xz*\ , and *yz* dimensions +The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions are controlled independently using their individual stress components as the driving forces, and the specified scalar pressure as the external normal stress. Using "tri Pstart Pstop Pdamp" is the same as @@ -292,7 +292,7 @@ specified values of the external stress tensor. A value of *nstep* means that every *nstep* timesteps, the reference dimensions are set to those of the current simulation domain. -The *scaleyz*\ , *scalexz*\ , and *scalexy* keywords control whether or +The *scaleyz*, *scalexz*, and *scalexy* keywords control whether or not the corresponding tilt factors are scaled with the associated box dimensions when barostatting triclinic periodic cells. The default values *yes* will turn on scaling, which corresponds to adjusting the @@ -305,9 +305,9 @@ scale keywords to *no*\ . The *flip* keyword allows the tilt factors for a triclinic box to exceed half the distance of the parallel box length, as discussed -below. If the *flip* value is set to *yes*\ , the bound is enforced by +below. If the *flip* value is set to *yes*, the bound is enforced by flipping the box when it is exceeded. If the *flip* value is set to -*no*\ , the tilt will continue to change without flipping. Note that if +*no*, the tilt will continue to change without flipping. Note that if applied stress induces large deformations (e.g. in a liquid), this means the box shape can tilt dramatically and LAMMPS will run less efficiently, due to the large volume of communication needed to @@ -319,7 +319,7 @@ The *fixedpoint* keyword specifies the fixed point for barostat volume changes. By default, it is the center of the box. Whatever point is chosen will not move during the simulation. For example, if the lower periodic boundaries pass through (0,0,0), and this point is provided -to *fixedpoint*\ , then the lower periodic boundaries will remain at +to *fixedpoint*, then the lower periodic boundaries will remain at (0,0,0), while the upper periodic boundaries will move twice as far. In all cases, the particle trajectories are unaffected by the chosen value, except for a time-dependent constant translation of @@ -329,7 +329,7 @@ positions. .. note:: - Using a barostat coupled to tilt dimensions *xy*\ , *xz*\ , *yz* can + Using a barostat coupled to tilt dimensions *xy*, *xz*, *yz* can sometimes result in arbitrarily large values of the tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS allows the tilt factors to grow a small amount beyond the normal limit of half the box @@ -337,7 +337,7 @@ positions. an equivalent periodic cell. See the discussion of the *flip* keyword above, to allow this bound to be exceeded, if desired. -The flip operation is described in more detail in the doc page for +The flip operation is described in more detail in the page for :doc:`fix deform `. Both the barostat dynamics and the atom trajectories are unaffected by this operation. However, if a tilt factor is incremented by a large amount (1.5 times the box length) on @@ -418,7 +418,7 @@ thermal degrees of freedom, and the bias is added back in. This fix can be used with either the *verlet* or *respa* :doc:`integrators `. When using this fix -with *respa*\ , LAMMPS uses an integrator constructed +with *respa*, LAMMPS uses an integrator constructed according to the following factorization of the Liouville propagator (for two rRESPA levels): @@ -500,7 +500,7 @@ compute temperature on a subset of atoms. The cumulative energy change in the system imposed by this fix, due to thermostatting and/or barostatting, is included in the :doc:`thermodynamic output ` keywords *ecouple* and -*econserve*. See the :doc:`thermo_style ` doc page for +*econserve*. See the :doc:`thermo_style ` page for details. This fix computes a global scalar which can be accessed by various @@ -514,7 +514,7 @@ values are "intensive". The vector stores internal Nose/Hoover thermostat and barostat variables. The number and meaning of the vector values depends on -which fix is used and the settings for keywords *tchain* and *pchain*\ , +which fix is used and the settings for keywords *tchain* and *pchain*, which specify the number of Nose/Hoover chains for the thermostat and barostat. If no thermostatting is done, then *tchain* is 0. If no barostatting is done, then *pchain* is 0. In the following list, @@ -555,12 +555,12 @@ Restrictions """""""""""" This fix is part of the EXTRA-FIX package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not -periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the +*X*, *y*, *z* cannot be barostatted if the associated dimension is not +periodic. *Xy*, *xz*, and *yz* can only be barostatted if the simulation domain is triclinic and the second dimension in the keyword -(\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be +(\ *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 ` commands specify whether the simulation box is orthogonal or @@ -572,10 +572,10 @@ make the external T = 0.0 at some timestep during the simulation which is not allowed in the Nose/Hoover formulation. The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used -for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options +for 2D simulations. *scaleyz yes*, *scalexz yes*, and *scalexy yes* options can only be used if the second dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords -*tri*\ , *yz*\ , *xz*\ , and *xy*\ . +*tri*, *yz*, *xz*, and *xy*\ . The *alpha* keyword modifies the barostat as per Miller et al. (Miller)_"#nc-Miller" so that the Cauchy stress is controlled. diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index dd78cebbf1..75e4c9a4ec 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -61,8 +61,8 @@ The only difference between discs and spheres in this context is their moment of inertia, as used in the time integration. Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*\ , -*iso*\ , *aniso*\ , and *dilate* keywords. +specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*, +*iso*, *aniso*, and *dilate* keywords. The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -71,7 +71,7 @@ NPT integration. Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid. diff --git a/doc/src/fix_numdiff.rst b/doc/src/fix_numdiff.rst index 22c1c59748..b0686f471f 100644 --- a/doc/src/fix_numdiff.rst +++ b/doc/src/fix_numdiff.rst @@ -101,7 +101,9 @@ minimization `. Restrictions """""""""""" - none + +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index c49de34d0b..fbba2bc8dd 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -54,7 +54,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst index 6bc4b98c7f..7d904bef1c 100644 --- a/doc/src/fix_nve_asphere_noforce.rst +++ b/doc/src/fix_nve_asphere_noforce.rst @@ -48,7 +48,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst index a294cebd73..c716a94a84 100644 --- a/doc/src/fix_nve_awpmd.rst +++ b/doc/src/fix_nve_awpmd.rst @@ -46,7 +46,7 @@ Restrictions """""""""""" This fix is part of the AWPMD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_body.rst b/doc/src/fix_nve_body.rst index 7a763e7d42..45beee0659 100644 --- a/doc/src/fix_nve_body.rst +++ b/doc/src/fix_nve_body.rst @@ -26,7 +26,7 @@ Description Perform constant NVE integration to update position, velocity, orientation, and angular velocity for body particles in the group each timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. See the :doc:`Howto body ` doc page for more details on using body +consistent with the microcanonical ensemble. See the :doc:`Howto body ` page for more details on using body particles. This fix differs from the :doc:`fix nve ` command, which @@ -45,7 +45,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst index 26af6efb4b..0a99e11452 100644 --- a/doc/src/fix_nve_dot.rst +++ b/doc/src/fix_nve_dot.rst @@ -47,7 +47,7 @@ Restrictions These pair styles can only be used if LAMMPS was built with the :ref:`CG-DNA ` package and the MOLECULE and ASPHERE package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index 944767ff51..c2835aaccd 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -131,7 +131,7 @@ Restrictions These pair styles can only be used if LAMMPS was built with the :ref:`CG-DNA ` package and the MOLECULE and ASPHERE package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst index 87e64a9661..60bece43d0 100644 --- a/doc/src/fix_nve_eff.rst +++ b/doc/src/fix_nve_eff.rst @@ -43,7 +43,7 @@ Restrictions """""""""""" This fix is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst index b65c543529..5bb6fd4213 100644 --- a/doc/src/fix_nve_line.rst +++ b/doc/src/fix_nve_line.rst @@ -26,7 +26,7 @@ Description Perform constant NVE integration to update position, velocity, orientation, and angular velocity for line segment particles in the group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. See :doc:`Howto spherical ` doc page for an overview of using line +trajectory consistent with the microcanonical ensemble. See :doc:`Howto spherical ` page for an overview of using line segment particles. This fix differs from the :doc:`fix nve ` command, which @@ -45,7 +45,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that particles be line segments as defined by the :doc:`atom_style line ` command. diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index e0c0c10b4a..a9bf07de60 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -84,7 +84,7 @@ Restrictions """""""""""" This fix is part of the MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. ---------- diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst index 167da24475..ee02f795a1 100644 --- a/doc/src/fix_nve_noforce.rst +++ b/doc/src/fix_nve_noforce.rst @@ -48,7 +48,9 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none + +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst index 143ddb2426..e35647aef4 100644 --- a/doc/src/fix_nve_spin.rst +++ b/doc/src/fix_nve_spin.rst @@ -58,7 +58,7 @@ Restrictions """""""""""" This fix style can only be used if LAMMPS was built with the SPIN -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. To use the spin algorithm, it is necessary to define a map with diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst index ad4376e8ec..b511d9b318 100644 --- a/doc/src/fix_nve_tri.rst +++ b/doc/src/fix_nve_tri.rst @@ -27,7 +27,7 @@ Perform constant NVE integration to update position, velocity, orientation, and angular momentum for triangular particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. See the -:doc:`Howto spherical ` doc page for an overview of +:doc:`Howto spherical ` page for an overview of using triangular particles. This fix differs from the :doc:`fix nve ` command, which @@ -46,7 +46,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` page for more info. This fix requires that particles be triangles as defined by the :doc:`atom_style tri ` command. diff --git a/doc/src/fix_nvk.rst b/doc/src/fix_nvk.rst index 30f5a0e004..0d83a4b1be 100644 --- a/doc/src/fix_nvk.rst +++ b/doc/src/fix_nvk.rst @@ -58,7 +58,7 @@ This fix has not yet been implemented to work with the RESPA integrator. This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index 98e8a5b495..00f4588f7f 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -121,7 +121,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst index 02b7d0c66c..28ad3e7857 100644 --- a/doc/src/fix_nvt_body.rst +++ b/doc/src/fix_nvt_body.rst @@ -118,7 +118,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index 3815138064..fe889bda79 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -64,7 +64,7 @@ Restrictions """""""""""" This fix is part of the MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. ---------- diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst index 328ff7d4e5..7500735054 100644 --- a/doc/src/fix_nvt_sllod_eff.rst +++ b/doc/src/fix_nvt_sllod_eff.rst @@ -70,7 +70,7 @@ Restrictions """""""""""" This fix is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This fix works best without Nose-Hoover chain thermostats, i.e. using tchain = 1. Setting tchain to larger values can result in poor diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst index e899703fc1..f54cc42ed0 100644 --- a/doc/src/fix_oneway.rst +++ b/doc/src/fix_oneway.rst @@ -52,7 +52,7 @@ Restrictions """""""""""" This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index 02fda71a0a..68522209b7 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -179,7 +179,7 @@ Restrictions These fixes are part of the ORIENT package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. These fixes should only be used with fcc or bcc lattices. diff --git a/doc/src/fix_orient_eco.rst b/doc/src/fix_orient_eco.rst index b58cf2dd8e..b2fc71f1f7 100644 --- a/doc/src/fix_orient_eco.rst +++ b/doc/src/fix_orient_eco.rst @@ -124,7 +124,7 @@ Restrictions This fix is part of the ORIENT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands diff --git a/doc/src/fix_pafi.rst b/doc/src/fix_pafi.rst index 4c38123dd3..c8830316a2 100644 --- a/doc/src/fix_pafi.rst +++ b/doc/src/fix_pafi.rst @@ -85,7 +85,7 @@ Restrictions """""""""""" This fix is part of the EXTRA-FIX package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Default diff --git a/doc/src/fix_pair_tracker.rst b/doc/src/fix_pair_tracker.rst index 6e544b1c80..5c2ecf5774 100644 --- a/doc/src/fix_pair_tracker.rst +++ b/doc/src/fix_pair_tracker.rst @@ -99,7 +99,7 @@ the array is the number of recorded, lost interactions. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output +that uses local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. The vector or array values will be doubles that correspond to the @@ -111,7 +111,7 @@ Restrictions Must be used in conjunction with :doc:`pair style tracker `. This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index e151d8a671..d1b19173ce 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -138,7 +138,7 @@ code, `latgen `_, can be employed to generate the compatible map file for various crystals. In case one simulates a non-periodic system, where the whole simulation -box is treated as a unit cell, one can set *map_file* as *GAMMA*\ , so +box is treated as a unit cell, one can set *map_file* as *GAMMA*, so that the mapping info will be generated internally and a file is not needed. In this case, the dynamical matrix at only the gamma-point will/can be evaluated. Please keep in mind that fix-phonon is designed @@ -182,9 +182,9 @@ temperature of the system should not exceed the melting temperature to keep the system in its solid state. This fix is part of the PHONON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -This fix requires LAMMPS be built with an FFT library. See the :doc:`Build settings ` doc page for details. +This fix requires LAMMPS be built with an FFT library. See the :doc:`Build settings ` page for details. Related commands """""""""""""""" @@ -204,19 +204,19 @@ the :doc:`dimension ` command, and nasr = 20. **(Campana)** C. Campana and M. H. Muser, *Practical Green's function approach to the -simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) `_ +simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) `_ .. _Kong: **(Kong)** L.T. Kong, G. Bartels, C. Campana, C. Denniston, and Martin H. Muser, *Implementation of Green's -function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). `_ +function molecular dynamics: An extension to LAMMPS*, `Computer Physics Communications [180](6):1004-1010 (2009). `_ L.T. Kong, C. Denniston, and Martin H. Muser, *An improved version of the Green's function molecular dynamics -method*\ , `Computer Physics Communications [182](2):540-541 (2011). `_ +method*, `Computer Physics Communications [182](2):540-541 (2011). `_ .. _Kong2011: **(Kong2011)** L.T. Kong, *Phonon dispersion measured directly from -molecular dynamics simulations*\ , `Computer Physics Communications [182](10):2201-2207, (2011). `_ +molecular dynamics simulations*, `Computer Physics Communications [182](10):2201-2207, (2011). `_ diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index 60e0847eab..9735284280 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -154,7 +154,7 @@ Restrictions This fix is part of the REPLICA package. It is only enabled if LAMMPS was built with that package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` 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 diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index fda37ff64e..c562ecc81d 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -115,7 +115,7 @@ Restrictions This fix is part of the PLUMED package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. There can only be one fix plumed command active at a time. diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index b782b7809e..7ecb4eef7d 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -57,14 +57,14 @@ Each body must have a non-degenerate inertia tensor, which means if must contain at least 3 non-collinear atoms. Which atoms are in which bodies can be defined via several options. -For option *group*\ , each of the listed groups is treated as a rigid +For option *group*, each of the listed groups is treated as a rigid body. Note that only atoms that are also in the fix group are included in each rigid body. -For option *molecule*\ , each set of atoms in the group with a different +For option *molecule*, each set of atoms in the group with a different molecule ID is treated as a rigid body. -For option *file*\ , sets of atoms are read from the specified file and +For option *file*, sets of atoms are read from the specified file and each set is treated as a rigid body. Each line of the file specifies a rigid body in the following format: @@ -136,7 +136,7 @@ Restrictions This fix is part of the :ref:`POEMS ` package. It is only enabled if LAMMPS was built with that package, which also requires the POEMS library be built and linked with LAMMPS. See the :doc:`Build -package ` doc page for more info. +package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_polarize.rst b/doc/src/fix_polarize.rst index bebed3aba0..e130d3010d 100644 --- a/doc/src/fix_polarize.rst +++ b/doc/src/fix_polarize.rst @@ -88,7 +88,7 @@ Restrictions These fixes are part of the DIELECTRIC package. It is only enabled if LAMMPS was built with that package, which requires that also the KSPACE package is installed. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index 7757191482..742648ac76 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -158,10 +158,10 @@ many timesteps until the desired # of particles has been inserted. All other keywords are optional with defaults as shown below. The *diam* option is only used when inserting atoms and specifies the -diameters of inserted particles. There are 3 styles: *one*\ , *range*\ , -or *poly*\ . For *one*\ , all particles will have diameter *D*\ . For -*range*\ , the diameter of each particle will be chosen randomly and -uniformly between the specified *Dlo* and *Dhi* bounds. For *poly*\ , a +diameters of inserted particles. There are 3 styles: *one*, *range*, +or *poly*\ . For *one*, all particles will have diameter *D*\ . For +*range*, the diameter of each particle will be chosen randomly and +uniformly between the specified *Dlo* and *Dhi* bounds. For *poly*, a series of *Npoly* diameters is specified. For each diameter a percentage value from 0.0 to 1.0 is also specified. The *Npoly* percentages must sum to 1.0. For the example shown above with "diam 2 @@ -252,7 +252,7 @@ Restrictions """""""""""" This fix is 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. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. For 3d simulations, a gravity fix in the -z direction must be defined for use in conjunction with this fix. For 2d simulations, gravity diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 6a563bc32f..36a10c8ce6 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -175,7 +175,7 @@ Restrictions The *precession/spin* style is part of the SPIN package. This style is only enabled if LAMMPS was built with this package, and if the atom_style "spin" was declared. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst index eb7adafc57..6d92a00178 100644 --- a/doc/src/fix_press_berendsen.rst +++ b/doc/src/fix_press_berendsen.rst @@ -46,7 +46,7 @@ timestep. Regardless of what atoms are in the fix group, a global pressure is computed for all atoms. Similarly, when the size of the simulation box is changed, all atoms are re-scaled to new positions, unless the -keyword *dilate* is specified with a value of *partial*\ , in which case +keyword *dilate* is specified with a value of *partial*, in which case only the atoms in the fix group are re-scaled. The latter can be useful for leaving the coordinates of atoms in a solid substrate unchanged and controlling the pressure of a surrounding fluid. @@ -61,13 +61,13 @@ unchanged and controlling the pressure of a surrounding fluid. atoms. This fix can be used in conjunction with thermostatting fixes to control the temperature, such as :doc:`fix nvt ` or :doc:`fix langevin ` or :doc:`fix temp/berendsen `. -See the :doc:`Howto baroostat ` doc page for a +See the :doc:`Howto baroostat ` page for a discussion of different ways to perform barostatting. ---------- -The barostat is specified using one or more of the *iso*\ , *aniso*\ , -*x*\ , *y*\ , *z*\ , and *couple* keywords. These keywords give you the +The barostat is specified using one or more of the *iso*, *aniso*, +*x*, *y*, *z*, and *couple* keywords. These keywords give you the ability to specify the 3 diagonal components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during a @@ -77,7 +77,7 @@ constant-pressure simulation. Unlike the :doc:`fix npt ` and general pressure tensor. The target pressures for each of the 3 diagonal components of the -stress tensor can be specified independently via the *x*\ , *y*\ , *z*\ , +stress tensor can be specified independently via the *x*, *y*, *z*, keywords, which correspond to the 3 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped value during the run from *Pstart* to *Pstop*\ . @@ -131,7 +131,7 @@ things: the instantaneous stress will be computed as an average of the corresponding diagonal components, and the coupled box dimensions will be changed together in lockstep, meaning coupled dimensions will be dilated or contracted by the same percentage every timestep. The -*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. @@ -152,8 +152,8 @@ specifying these 4 keywords: z Pstart Pstop Pdamp couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index a086cb442b..863d43b6f2 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -146,7 +146,7 @@ Restrictions """""""""""" With keyword *dipole*, this fix only works when the DIPOLE package is enabled. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. This fix is part of the BROWNIAN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 0768c59ac8..8ac19af25d 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -56,7 +56,7 @@ is read. This fix will augment the set of properties with new custom ones. This can be useful in several scenarios. If the atom style does not define molecule IDs, per-atom charge, -or per-atom mass, they can be added using the *mol*\ , *q* or *rmass* +or per-atom mass, they can be added using the *mol*, *q* or *rmass* keywords. This can be useful, e.g, to define "molecules" to use as rigid bodies with the :doc:`fix rigid ` command, or just to carry around an extra flag with the atoms (stored as a molecule ID) @@ -80,7 +80,7 @@ and second, it may define additional properties that are not needed such as bond lists, which has some overhead when there are no bonds. In the future, we may add additional per-atom properties similar to -*mol*\ , *q* or *rmass*\ , which "turn-on" specific properties defined +*mol*, *q* or *rmass*, which "turn-on" specific properties defined by some atom styles, so they can be used by atom styles that do not define them. @@ -108,7 +108,7 @@ new properties are also defined for the ghost atoms. .. admonition:: Properties on ghost atoms :class: note - If you use this command with the *mol*\ , *q* or *rmass* vectors, + 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 ` that defines them, and many LAMMPS operations that use molecule IDs or diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index 94bad11f00..c82fb91a27 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -70,7 +70,7 @@ Restrictions """""""""""" This fix is part of the PYTHON package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Building LAMMPS with the PYTHON package will link LAMMPS with the Python library on your system. Settings to enable this are in the diff --git a/doc/src/fix_python_move.rst b/doc/src/fix_python_move.rst index 15014ef4fe..b338dcbfac 100644 --- a/doc/src/fix_python_move.rst +++ b/doc/src/fix_python_move.rst @@ -95,7 +95,7 @@ Restrictions """""""""""" This pair style is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index abf8ed1aae..5428eeb637 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -100,10 +100,10 @@ command :doc:`fix qtb ` at constant temperature *T_init* could be used before applying this command to introduce self-consistent quantum nuclear effects into the initial state. -The parameters *q*\ , *mu*\ , *e0*\ , *p0*\ , *v0* and *tscale* are described -in the command :doc:`fix msst `. The values of *e0*\ , *p0*\ , or +The parameters *q*, *mu*, *e0*, *p0*, *v0* and *tscale* are described +in the command :doc:`fix msst `. The values of *e0*, *p0*, or *v0* will be calculated on the first step if not specified. The -parameter of *damp*\ , *f_max*, and *N_f* are described in the command +parameter of *damp*, *f_max*, and *N_f* are described in the command :doc:`fix qtb `. The *fix qbmsst* command couples the shock system to a quantum thermal @@ -152,8 +152,8 @@ Because the state of the random number generator is not written to "exactly" in an uninterrupted fashion. However, in a statistical sense, a restarted simulation should produce similar behaviors of the system as if it is not interrupted. To achieve such a restart, one -should write explicitly the same value for *q*\ , *mu*\ , *damp*\ , -*f_max*, *N_f*, *eta*\ , and *beta* and set *tscale* = 0 if the system +should write explicitly the same value for *q*, *mu*, *damp*, +*f_max*, *N_f*, *eta*, and *beta* and set *tscale* = 0 if the system is compressed during the first run. The cumulative energy change in the system imposed by this fix is @@ -177,7 +177,7 @@ integration of the dynamic equations. The global vector contains five values in the following order. The vector values output by this fix are "intensive". -[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*, *lagrangian_position*, +[\ *dhugoniot*, *drayleigh*, *lagrangian_speed*, *lagrangian_position*, *quantum_temperature*] 1. *dhugoniot* is the departure from the Hugoniot (temperature units). @@ -210,7 +210,7 @@ Restrictions This fix style is part of the QTB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. All cell dimensions must be periodic. This fix can not be used with a triclinic cell. The QBMSST fix has been tested only for the group-ID diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 113692da9b..eab35391b5 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -94,7 +94,7 @@ on the current atom configuration), then remove the fix via the `. The :doc:`fix qeq/reaxff ` command can be used to perform charge equilibration with the :doc:`ReaxFF force field `, although fix qeq/shielded yields the same - results as fix qeq/reaxff if *Nevery*\ , *cutoff*\ , and *tolerance* + results as fix qeq/reaxff if *Nevery*, *cutoff*, and *tolerance* are the same. Eventually the fix qeq/reaxff command will be deprecated. @@ -151,7 +151,7 @@ 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/reaxff `, and can be used with -:doc:`pair_style reaxff `. Only the *chi*\ , *eta*\ , and +:doc:`pair_style reaxff `. Only the *chi*, *eta*, and *gamma* parameters from the *qfile* file are used. When using the string *reaxff* as filename, these parameters are extracted directly from an active *reaxff* pair style. This style solves partial charges on atoms @@ -163,7 +163,7 @@ charge densities centered around atoms via the Slater 1\ *s* orbital, so that the interaction between a pair of charged particles is the product of two Slater 1\ *s* orbitals. The expression for the Slater 1\ *s* orbital is given under equation (6) of the :ref:`Streitz-Mintmire -` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore* +` paper. Only the *chi*, *eta*, *zeta*, and *qcore* parameters from the *qfile* file are used. When using the string *coul/streitz* as filename, these parameters are extracted directly from an active *coul/streitz* pair style. This style solves partial charges @@ -186,16 +186,16 @@ minimization algorithm to solve for equilibrium charges. Keyword *qdamp* can be used to change the damping factor, while keyword *qstep* can be used to change the time step size. -Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe +Note that *qeq/point*, *qeq/shielded*, and *qeq/slater* describe different charge models, whereas the matrix inversion method and the extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are different solvers. -Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all +Note that *qeq/point*, *qeq/dynamic* and *qeq/fire* styles all describe charges as point charges that interact through 1/r relationship, but solve partial charges on atoms using different solvers. These three styles should yield comparable results if the QEq -parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same. +parameters and *Nevery*, *cutoff*, and *tolerance* are the same. Style *qeq/point* is typically faster, *qeq/dynamic* scales better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . @@ -228,7 +228,7 @@ Restrictions These fixes are part of the QEQ package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. The qeq fixes are not compatible with the GPU and USER-INTEL packages. diff --git a/doc/src/fix_qeq_reaxff.rst b/doc/src/fix_qeq_reaxff.rst index 96a20d4ca6..ada9e22ed7 100644 --- a/doc/src/fix_qeq_reaxff.rst +++ b/doc/src/fix_qeq_reaxff.rst @@ -57,7 +57,7 @@ with their neighbors. It requires some parameters for each atom type. If the *params* setting above is the word "reaxff", then these are extracted from the :doc:`pair_style reaxff ` 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 +for *params*, then the parameters are taken from the specified file and the file must contain one line for each atom type. The latter form must be used when performing QeQ with a non-ReaxFF potential. Each line should be formatted as follows: @@ -110,7 +110,7 @@ Restrictions This fix is part of the REAXFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This fix does not correctly handle interactions involving multiple periodic images of the same atom. Hence, it should not be used for diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index acbafccded..a62bd5ab1e 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -56,7 +56,7 @@ Restrictions This fix is part of the QMMM package. It is only enabled if LAMMPS was built with that package. It also requires building a -library provided with LAMMPS. See the :doc:`Build package ` doc page for more info. +library provided with LAMMPS. See the :doc:`Build package ` page for more info. The fix is only functional when LAMMPS is built as a library and linked with a compatible QM program and a QM/MM front end into a QM/MM diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst index 6ea3e97f9a..e6975748c4 100644 --- a/doc/src/fix_qtb.rst +++ b/doc/src/fix_qtb.rst @@ -163,7 +163,7 @@ Restrictions This fix style is part of the QTB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. ---------- diff --git a/doc/src/fix_reaxff_bonds.rst b/doc/src/fix_reaxff_bonds.rst index 5dd4df7765..15b2eb6da9 100644 --- a/doc/src/fix_reaxff_bonds.rst +++ b/doc/src/fix_reaxff_bonds.rst @@ -31,7 +31,7 @@ Description Write out the bond information computed by the ReaxFF potential specified by :doc:`pair_style reaxff ` 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*\ , +is written to *filename* on timesteps that are multiples of *Nevery*, including timestep 0. For time-averaged chemical species analysis, please see the :doc:`fix reaxff/species ` command. @@ -78,7 +78,7 @@ Restrictions The fix reaxff/bonds command requires that the :doc:`pair_style reaxff ` is invoked. This fix is part of the REAXFF package. It is only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. To write gzipped bond files, you must compile LAMMPS with the diff --git a/doc/src/fix_reaxff_species.rst b/doc/src/fix_reaxff_species.rst index bca9c2c726..434e18d8a5 100644 --- a/doc/src/fix_reaxff_species.rst +++ b/doc/src/fix_reaxff_species.rst @@ -87,15 +87,15 @@ chemical formula, total charge, and center-of-mass xyz positions of this molecule. The xyz positions are in fractional coordinates relative to the box dimensions. -For the keyword *position*\ , the *filepos* is the name of the output +For the keyword *position*, the *filepos* is the name of the output file. It can contain the wildcard character "\*". If the "\*" -character appears in *filepos*\ , then one file per snapshot is written +character appears in *filepos*, then one file per snapshot is written at *posfreq* and the "\*" character is replaced with the timestep value. For example, AuO.pos.\* becomes AuO.pos.0, AuO.pos.1000, etc. ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the bond-order values are sampled to get the average bond order. The species analysis is performed using the average bond-order on timesteps that are a multiple of *Nfreq*\ . The average is over @@ -148,7 +148,7 @@ Restrictions The "fix reaxff/species" requires that :doc:`pair_style reaxff ` is used. This fix is part of the REAXFF package. It is only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more info. +package. See the :doc:`Build package ` page for more info. To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option. diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst index 583b4d46c5..a6243e693f 100644 --- a/doc/src/fix_recenter.rst +++ b/doc/src/fix_recenter.rst @@ -58,7 +58,7 @@ example, the COM could be computed on a protein to keep it in the center of the simulation box. But the entire system (protein + water) could be shifted. -If the *units* keyword is set to *box*\ , then the distance units of +If the *units* keyword is set to *box*, then the distance units of x,y,z are defined by the :doc:`units ` command - e.g. Angstroms for *real* units. A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst index f48b562ca8..9d6114328f 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -72,7 +72,7 @@ Restrictions This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 43750d59a1..5b367a48a4 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -253,7 +253,7 @@ differences may accumulate to produce divergent trajectories. they effect any computation of per-atom forces or torques. If the keyword *reinit* is set to *yes* (the default), the rigid body data structures will be recreated at the beginning of each *run* command; - if the keyword *reinit* is set to *no*\ , the rigid body data structures + if the keyword *reinit* is set to *no*, the rigid body data structures will be built only at the very first *run* command and maintained for as long as the rigid fix is defined. For example, you might think you could displace the atoms in a body or add a large velocity to each atom @@ -275,7 +275,7 @@ via several options. .. note:: With the *rigid/small* styles, which require that *bodystyle* be - specified as *molecule* or *custom*\ , you can define a system that has + specified as *molecule* or *custom*, you can define a system that has no rigid bodies initially. This is useful when you are using the *mol* keyword in conjunction with another fix that is adding rigid bodies on-the-fly as molecules, such as :doc:`fix deposit ` @@ -284,7 +284,7 @@ via several options. For bodystyle *single* the entire fix group of atoms is treated as one rigid body. This option is only allowed for the *rigid* styles. -For bodystyle *molecule*\ , atoms are grouped into rigid bodies by their +For bodystyle *molecule*, atoms are grouped into rigid bodies by their respective molecule IDs: each set of atoms in the fix group with the same molecule ID is treated as a different rigid body. This option is allowed for both the *rigid* and *rigid/small* styles. Note that @@ -300,7 +300,7 @@ of atoms that form rigid bodies. An integer vector defined by the :doc:`fix property/atom ` command can be used. Or an :doc:`atom-style or atomfile-style variable ` can be used; the floating-point value produced by the variable is rounded to an -integer. As with bodystyle *molecule*\ , each set of atoms in the fix +integer. As with bodystyle *molecule*, each set of atoms in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all atoms, you should be careful to use a fix group @@ -388,7 +388,7 @@ body. ---------- -The *rigid*\ , *rigid/nve*\ , *rigid/small*\ , and *rigid/small/nve* styles +The *rigid*, *rigid/nve*, *rigid/small*, and *rigid/small/nve* styles perform constant NVE time integration. They are referred to below as the 4 NVE rigid styles. The only difference is that the *rigid* and *rigid/small* styles use an integration technique based on Richardson @@ -404,14 +404,14 @@ of the rigid bodies. They are referred to below as the 2 NVT rigid styles. The rigid-body algorithm used by *rigid/nvt* is described in the paper by :ref:`Kamberaj `. -The *rigid/npt*\ , *rigid/nph*\ , *rigid/npt/small*\ , and *rigid/nph/small* +The *rigid/npt*, *rigid/nph*, *rigid/npt/small*, and *rigid/nph/small* styles perform constant NPT or NPH integration using a Nose/Hoover barostat with chains. They are referred to below as the 4 NPT and NPH rigid styles. For the NPT case, the same Nose/Hoover thermostat is also used as with *rigid/nvt* and *rigid/nvt/small*\ . -The barostat parameters are specified using one or more of the *iso*\ , -*aniso*\ , *x*\ , *y*\ , *z* and *couple* keywords. These keywords give you +The barostat parameters are specified using one or more of the *iso*, +*aniso*, *x*, *y*, *z* and *couple* keywords. These keywords give you the ability to specify 3 diagonal components of the external stress tensor, and to couple these components together so that the dimensions they represent are varied together during a constant-pressure @@ -420,12 +420,12 @@ defined in :doc:`fix npt/nph ` .. note:: - Currently the *rigid/npt*\ , *rigid/nph*\ , *rigid/npt/small*\ , and + Currently the *rigid/npt*, *rigid/nph*, *rigid/npt/small*, and *rigid/nph/small* styles do not support triclinic (non-orthogonal) boxes. The target pressures for each of the 6 components of the stress tensor -can be specified independently via the *x*\ , *y*\ , *z* keywords, which +can be specified independently via the *x*, *y*, *z* keywords, which correspond to the 3 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped value during the run from *Pstart* to *Pstop*\ . If a target pressure is @@ -465,7 +465,7 @@ things: the instantaneous stress will be computed as an average of the corresponding diagonal components, and the coupled box dimensions will be changed together in lockstep, meaning coupled dimensions will be dilated or contracted by the same percentage every timestep. The -*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must be identical. *Couple xyz* can be used for a 2d simulation; the *z* dimension is simply ignored. @@ -484,8 +484,8 @@ specifying these 4 keywords: z Pstart Pstop Pdamp couple xyz -The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled -independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the stress tensor as the driving forces, and the specified scalar external pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying these 4 keywords: @@ -517,8 +517,8 @@ discussed below. The *langevin* keyword applies a Langevin thermostat to the constant NVE time integration performed by any of the 4 NVE rigid styles: -*rigid*\ , *rigid/nve*\ , *rigid/small*\ , *rigid/small/nve*\ . It cannot be -used with the 2 NVT rigid styles: *rigid/nvt*\ , *rigid/small/nvt*\ . The +*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot be +used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ . The desired temperature at each timestep is a ramped value during the run from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in time units and determines how rapidly the temperature is relaxed. For @@ -531,7 +531,7 @@ The way that Langevin thermostatting operates is explained on the :doc:`fix lang damp the rotational motion without thermostatting, you can set *Tstart* and *Tstop* to 0.0, which means only the viscous drag term in the Langevin thermostat will be applied. See the discussion on the -:doc:`fix viscous ` doc page for details. +:doc:`fix viscous ` page for details. .. note:: @@ -851,7 +851,7 @@ Restrictions """""""""""" These fixes are all part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Assigning a temperature via the :doc:`velocity create ` command to a system with :doc:`rigid bodies ` may not have diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index 32ad4aa6c6..0883897aae 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -104,7 +104,7 @@ internal energy and extrapolated velocity are also updated. they effect any computation of per-particle forces or torques. If the keyword *reinit* is set to *yes* (the default), the rigid body data structures will be recreated at the beginning of each *run* command; - if the keyword *reinit* is set to *no*\ , the rigid body data structures + if the keyword *reinit* is set to *no*, the rigid body data structures will be built only at the very first *run* command and maintained for as long as the rigid fix is defined. For example, you might think you could displace the particles in a body or add a large velocity to each particle @@ -126,7 +126,7 @@ defined via several options. For bodystyle *single* the entire fix group of particles is treated as one rigid body. -For bodystyle *molecule*\ , particles are grouped into rigid bodies by their +For bodystyle *molecule*, particles are grouped into rigid bodies by their respective molecule IDs: each set of particles in the fix group with the same molecule ID is treated as a different rigid body. Note that particles with a molecule ID = 0 will be treated as a single rigid body. For a @@ -141,13 +141,13 @@ of particles that form rigid bodies. An integer vector defined by the :doc:`fix property/atom ` command can be used. Or an :doc:`atom-style or atomfile-style variable ` can be used; the floating-point value produced by the variable is rounded to an -integer. As with bodystyle *molecule*\ , each set of particles in the fix +integer. As with bodystyle *molecule*, each set of particles in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all particles, you should be careful to use a fix group that only includes particles you want to be part of rigid bodies. -For bodystyle *group*\ , each of the listed groups is treated as a +For bodystyle *group*, each of the listed groups is treated as a separate rigid body. Only particles that are also in the fix group are included in each rigid body. @@ -346,7 +346,7 @@ Restrictions This fix is part of the DPD-SMOOTH package and also depends on the RIGID package. It is only enabled if LAMMPS was built with both packages. See -the :doc:`Build package ` doc page for more info. +the :doc:`Build package ` page for more info. This fix requires that atoms store density and internal energy as defined by the :doc:`atom_style sph ` command. diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index c3406df5d0..4028a4e7e1 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -62,7 +62,7 @@ in concentration of a given species as a function of time are then constructed based on the *n* reaction rate equations. The ODE systems are solved over the full DPD timestep *dt* using either a fourth -order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified +order Runge-Kutta *rk4* method with a fixed step-size *h*, specified by the *lammps_rk4* keyword, or a fourth order Runge-Kutta-Fehlberg (rkf45) method with an adaptive step-size for *h*\ . The number of ODE steps per DPD timestep for the rk4 method is optionally specified immediately after the rk4 @@ -182,8 +182,8 @@ through its stoichiometric coefficient and a species tag. Reactant species are specified on the left-hand side of the equation and product species are specified on the right-hand side of the equation. After specifying the reactant and product species, the final three -arguments of each line represent the Arrhenius parameter *A*\ , the -temperature exponent *n*\ , and the activation energy *Ea*\ . +arguments of each line represent the Arrhenius parameter *A*, the +temperature exponent *n*, and the activation energy *Ea*\ . Note that the species tags that are defined in the reaction equations are used by the :doc:`fix eos/table/rx ` command to @@ -207,7 +207,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst index 9dd8fb8641..a9e8f154e6 100644 --- a/doc/src/fix_saed_vtk.rst +++ b/doc/src/fix_saed_vtk.rst @@ -72,7 +72,7 @@ values, e.g. ---------- -The *Nevery*\ , *Nrepeat*\ , and *Nfreq* arguments specify on what +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps that are a multiple of *Nfreq*\ . The average is over *Nrepeat* @@ -126,14 +126,14 @@ Additional optional keywords also affect the operation of this fix. The *ave* keyword determines how the values produced every *Nfreq* steps are averaged with values produced on previous steps that were -multiples of *Nfreq*\ , before they are accessed by another output +multiples of *Nfreq*, before they are accessed by another output command or written to a file. -If the *ave* setting is *one*\ , then the values produced on timesteps +If the *ave* setting is *one*, then the values produced on timesteps that are multiples of *Nfreq* are independent of each other; they are output as-is without further averaging. -If the *ave* setting is *running*\ , then the values produced on +If the *ave* setting is *running*, then the values produced on timesteps that are multiples of *Nfreq* are summed and averaged in a cumulative sense before being output. Each output value is thus the average of the value produced on that timestep with all preceding @@ -141,7 +141,7 @@ values. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the :doc:`unfix ` command, or by re-defining the fix by re-specifying it. -If the *ave* setting is *window*\ , then the values produced on +If the *ave* setting is *window*, then the values produced on timesteps that are multiples of *Nfreq* are summed and averaged within a moving "window" of time, so that the last M values are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then the output diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index 406826e5b9..fd1eb70c4a 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -54,8 +54,8 @@ Any of the fx,fy,fz values can be specified as NULL which means do not alter the force component in that dimension. Any of the 3 quantities defining the force components can be specified -as an equal-style or atom-style :doc:`variable `, namely *fx*\ , -*fy*\ , *fz*\ . If the value is a variable, it should be specified as +as an equal-style or atom-style :doc:`variable `, namely *fx*, +*fy*, *fz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the force component. @@ -89,7 +89,7 @@ precession vectors instead of the forces. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -101,13 +101,13 @@ region must be used. See the region :doc:`region ` command for more information. These accelerated styles are part of the r Kokkos package. They are -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 8e8f3e0988..f0c847cb5e 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -71,8 +71,8 @@ required in order to eliminate velocity components along the bonds In order to formulate individual constraints for SHAKE and RATTLE, focus on a single molecule whose bonds are constrained. Let Ri and Vi -be the position and velocity of atom *i* at time *n*\ , for -*i* =1,...,\ *N*\ , where *N* is the number of sites of our reference +be the position and velocity of atom *i* at time *n*, for +*i* =1,...,\ *N*, where *N* is the number of sites of our reference molecule. The distance vector between sites *i* and *j* is given by .. math:: @@ -213,7 +213,7 @@ Restrictions These fixes are part of the RIGID package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. For computational efficiency, there can only be one shake or rattle fix defined in a simulation. diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index 9f60df7e75..94e4b557f5 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -42,9 +42,9 @@ 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 -be specified by using fix *shardlow*\ , fix *nve* and pair_style +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 +using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*\ . DPD under isobaric conditions can be specified by using fix shardlow, fix *nph* and pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can be specified by using fix shardlow, fix *nph* and pair_style @@ -61,7 +61,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This fix is currently limited to orthogonal simulation cell geometries. diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index f59a852be6..93554a4510 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -145,7 +145,7 @@ Restrictions """""""""""" This fix is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst index c1dc008c55..0f1be7ed24 100644 --- a/doc/src/fix_smd_adjust_dt.rst +++ b/doc/src/fix_smd_adjust_dt.rst @@ -55,7 +55,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst index 4f19b98c49..c4f5e61c7e 100644 --- a/doc/src/fix_smd_integrate_tlsph.rst +++ b/doc/src/fix_smd_integrate_tlsph.rst @@ -51,7 +51,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index d6bcdd68a5..8f2e0b2b88 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -59,7 +59,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst index 2da904400a..76f7240007 100644 --- a/doc/src/fix_smd_move_triangulated_surface.rst +++ b/doc/src/fix_smd_move_triangulated_surface.rst @@ -73,7 +73,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index bc475914df..9dcc3c636c 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -42,8 +42,8 @@ alter the velocity component in that dimension. This fix is indented to be used together with a time integration fix. Any of the 3 quantities defining the velocity components can be specified -as an equal-style or atom-style :doc:`variable `, namely *vx*\ , -*vy*\ , *vz*\ . If the value is a variable, it should be specified as +as an equal-style or atom-style :doc:`variable `, namely *vx*, +*vy*, *vz*\ . If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the force component. @@ -82,7 +82,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst index 040cfa7483..192ab7a518 100644 --- a/doc/src/fix_smd_wall_surface.rst +++ b/doc/src/fix_smd_wall_surface.rst @@ -60,7 +60,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535. diff --git a/doc/src/fix_sph.rst b/doc/src/fix_sph.rst index 624209660c..1133142f05 100644 --- a/doc/src/fix_sph.rst +++ b/doc/src/fix_sph.rst @@ -45,7 +45,7 @@ Restrictions """""""""""" This fix is part of the SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_sph_stationary.rst b/doc/src/fix_sph_stationary.rst index a239ce478e..4496a10eca 100644 --- a/doc/src/fix_sph_stationary.rst +++ b/doc/src/fix_sph_stationary.rst @@ -45,7 +45,7 @@ Restrictions """""""""""" This fix is part of the SPH package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst index 21035f9def..aba35c8134 100644 --- a/doc/src/fix_spring_rg.rst +++ b/doc/src/fix_spring_rg.rst @@ -83,7 +83,9 @@ integrator the fix is adding its forces. Default is the outermost level. Restrictions """""""""""" - none + +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 4ff260f575..872bee181c 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -185,7 +185,7 @@ needed. The *radius* keyword scales the effective size of big particles. If big particles will overlap as they undergo dynamics, then this keyword can be used to scale down their effective collision radius by an -amount *rfactor*\ , so that SRD particle will only collide with one big +amount *rfactor*, so that SRD particle will only collide with one big particle at a time. For example, in a Lennard-Jones system at a temperature of 1.0 (in reduced LJ units), the minimum separation between two big particles is as small as about 0.88 sigma. Thus an @@ -267,15 +267,15 @@ vector. The specified random number *shiftseed* is used to generate these vectors. This operation sufficiently randomizes which SRD particles are in the same bin, even if :math:`lambda` is small. -If the *shift* flag is set to *no*\ , then no shifting is performed, but +If the *shift* flag is set to *no*, then no shifting is performed, but bin data will be communicated if bins overlap processor boundaries. An error will be generated if :math:`\lambda < 0.6` of the SRD bin size. -If the *shift* flag is set to *possible*\ , then shifting is performed +If the *shift* flag is set to *possible*, then shifting is performed only if :math:`\lambda < 0.6` of the SRD bin size. A warning is generated to let you know this is occurring. If the *shift* flag is set to *yes* then shifting is performed regardless of the magnitude of :math:`\lambda`. Note that the *shiftseed* is not used if the *shift* -flag is set to *no*\ , but must still be specified. +flag is set to *no*, but must still be specified. Note that shifting of SRD coordinates requires extra communication, hence it should not normally be enabled unless required. diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index 3841ef6359..829a25b517 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -94,7 +94,7 @@ steps. The list of possible attributes is the same as that used by the :doc:`dump custom ` command, which describes their meaning. -If the *com* keyword is set to *yes* then the *xu*\ , *yu*\ , and *zu* +If the *com* keyword is set to *yes* then the *xu*, *yu*, and *zu* inputs store the position of each atom relative to the center-of-mass of the group of atoms, instead of storing the absolute position. diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index 59f4de64a9..89fc2392f4 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/doc/src/fix_temp_berendsen.rst @@ -76,7 +76,7 @@ time. Thus it is easy to specify a time-dependent temperature. be used on atoms that also have their temperature controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix langevin ` commands. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 3652635340..81379f346b 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -85,7 +85,7 @@ time. Thus it is easy to specify a time-dependent temperature. normally be used on atoms that also have their temperature controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix langevin ` commands. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. @@ -178,6 +178,9 @@ Restrictions Fix *temp/csld* is not compatible with :doc:`fix shake `. +These fixes are part of the EXTRA-FIX package. They are only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. + These fixes can be used with dynamic groups as defined by the :doc:`group ` command. Likewise it can be used with groups to which atoms are added or deleted over time, e.g. a deposition diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index 125f74306e..a61773d2a2 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -83,7 +83,7 @@ value. be used on atoms that also have their temperature controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix langevin ` commands. -See the :doc:`Howto thermostat ` doc page for a +See the :doc:`Howto thermostat ` page for a discussion of different ways to compute temperature and perform thermostatting. diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst index 1eaa8cf360..ea3996e9b6 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/doc/src/fix_temp_rescale_eff.rst @@ -67,7 +67,7 @@ Restrictions """""""""""" This fix is part of the EFF package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst index ae8420089a..7eb4d24935 100644 --- a/doc/src/fix_tfmc.rst +++ b/doc/src/fix_tfmc.rst @@ -84,7 +84,7 @@ and the :doc:`simulated time ` as calculated by LAMMPS is meaningless. The critical parameter determining the success of a tfMC simulation is -*Delta*\ , the maximal displacement length of the lightest element in +*Delta*, the maximal displacement length of the lightest element in the system: the larger it is, the longer the effective time scale of the simulation will be (there is an approximately quadratic dependence). However, *Delta* must also be chosen sufficiently small @@ -92,7 +92,7 @@ in order to comply with detailed balance; in general values between 5 and 10 % of the nearest neighbor distance are found to be a good choice. For a more extensive discussion with specific examples, please refer to :ref:`(Bal) `, which also describes how the code calculates -element-specific maximal displacements from *Delta*\ , based on the +element-specific maximal displacements from *Delta*, based on the fourth root of their mass. Because of the uncorrelated movements of the atoms, the center-of-mass diff --git a/doc/src/fix_tgnh_drude.rst b/doc/src/fix_tgnh_drude.rst index 744c7e75f3..7088692353 100644 --- a/doc/src/fix_tgnh_drude.rst +++ b/doc/src/fix_tgnh_drude.rst @@ -139,7 +139,7 @@ The parameter *Tdrude* is the desired temperature for Drude motion at each times Similar to *Tdamp*, the *Tdamp_drude* parameter determines the relaxation speed for Drude motion. Fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the integration. -Other thermostat-related keywords are *tchain*\ and *tloop*\ , +Other thermostat-related keywords are *tchain*\ and *tloop*, which are detailed in :doc:`fix nvt `. .. note:: @@ -158,13 +158,13 @@ which are detailed in :doc:`fix nvt `. ---------- The barostat parameters for fix style *tgnpt/drude* is specified -using one or more of the *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ , -*xz*\ , *yz*\ , and *couple* keywords. These keywords give you the +using one or more of the *iso*, *aniso*, *tri*, *x*, *y*, *z*, *xy*, +*xz*, *yz*, and *couple* keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during a constant-pressure -simulation. Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , -*nreset*\ , *scalexy*\ , *scaleyz*\ , *scalexz*\ , *flip*\ and *fixedpoint*. +simulation. Other barostat-related keywords are *pchain*, *mtk*, *ploop*, +*nreset*, *scalexy*, *scaleyz*, *scalexz*, *flip*\ and *fixedpoint*. The meaning of barostat parameters are detailed in :doc:`fix npt `. Regardless of what atoms are in the fix group (the only atoms which @@ -244,7 +244,7 @@ compute temperature on a subset of atoms. The cumulative energy change in the system imposed by these fixes, due to thermostatting and/or barostatting, are included in the :doc:`thermodynamic output ` keywords *ecouple* and -*econserve*. See the :doc:`thermo_style ` doc page for +*econserve*. See the :doc:`thermo_style ` page for details. These fixes compute a global scalar which can be accessed by various @@ -275,8 +275,8 @@ DRUDE package. These fixes cannot be used with dynamic groups as defined by the :doc:`group ` command. These fixes cannot be used in 2D simulations. -*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not -periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the +*X*, *y*, *z* cannot be barostatted if the associated dimension is not +periodic. *Xy*, *xz*, and *yz* can only be barostatted if the simulation domain is triclinic and the second dimension in the keyword (\ *y* dimension in *xy*\ ) is periodic. The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` @@ -288,10 +288,10 @@ For the *temp* keyword, the final *Tstop* cannot be 0.0 since it would make the external T = 0.0 at some timestep during the simulation which is not allowed in the Nose/Hoover formulation. -The *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options +The *scaleyz yes*, *scalexz yes*, and *scalexy yes* options can only be used if the second dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords -*tri*\ , *yz*\ , *xz*\ , and *xy*\ . +*tri*, *yz*, *xz*, and *xy*\ . Related commands """""""""""""""" diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index 96dbc43540..0652810267 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/doc/src/fix_thermal_conductivity.rst @@ -129,9 +129,6 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. - Swaps conserve both momentum and kinetic energy, even if the masses of the swapped atoms are not equal. Thus you should not need to thermostat the system. If you do use a thermostat, you may want to diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst index e7758350f7..d519f36157 100644 --- a/doc/src/fix_ti_spring.rst +++ b/doc/src/fix_ti_spring.rst @@ -172,7 +172,7 @@ Restrictions This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Default """"""" diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst index 9c9d77820d..b4595d24cd 100644 --- a/doc/src/fix_tmd.rst +++ b/doc/src/fix_tmd.rst @@ -105,6 +105,9 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" +This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. + All TMD fixes must be listed in the input script after all integrator fixes (nve, nvt, npt) are applied. This ensures that atoms are moved before their positions are corrected to comply with the constraint. diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 92a884ee58..ee416304c4 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -324,7 +324,7 @@ Restrictions Fix *ttm* and *ttm/mod* are part of the EXTRA-FIX package. They are only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. These fixes can only be used for 3d simulations and orthogonal simulation boxes. You must also use periodic diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index 744db9dcf3..6a3cba16e4 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -81,7 +81,7 @@ Restrictions """""""""""" This fix is part of the KSPACE package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Do not set "neigh_modify once yes" or else this fix will never be called. Reneighboring is required. diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index b2c05b1af7..f4eee41269 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -75,7 +75,7 @@ be used, since they produce per-atom values. The *Nevery* argument specifies on what timesteps the input values will be used in order to be stored. Only timesteps that are a -multiple of *Nevery*\ , including timestep 0, will contribute values. +multiple of *Nevery*, including timestep 0, will contribute values. Note that if you perform multiple runs, using the "pre no" option of the :doc:`run ` command to avoid initialization on subsequent runs, @@ -107,7 +107,7 @@ bracketed term is appended, the Ith element of the global vector calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, -which must be compatible with *Nevery*\ , else an error will result. +which must be compatible with *Nevery*, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. If a value begins with "v\_", a variable name must follow which has @@ -144,7 +144,7 @@ the vector are "intensive" or "extensive". If the fix produces an array, then all elements in the array must be the same, either "intensive" or "extensive". If a compute or fix provides the value stored, then the compute or fix determines whether the value is -intensive or extensive; see the doc page for that compute or fix for +intensive or extensive; see the page for that compute or fix for further info. Values produced by a variable are treated as intensive. This fix can allocate storage for stored values accumulated over diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index d238c099b5..e077af19f4 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -134,8 +134,8 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the 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 is part of the EXTRA-FIX package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package ` page for more info. Swaps conserve both momentum and kinetic energy, even if the masses of the swapped atoms are not equal. Thus you should not need to diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 2a2aba777d..bcbead8824 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -103,7 +103,7 @@ wall that interacts with the atoms in the group by generating a force on the atom in a direction perpendicular to the wall. The energy of wall-particle interactions depends on the style. -For style *wall/lj93*\ , the energy E is given by the 9/3 potential: +For style *wall/lj93*, the energy E is given by the 9/3 potential: .. math:: @@ -111,7 +111,7 @@ For style *wall/lj93*\ , the energy E is given by the 9/3 potential: \left(\frac{\sigma}{r}\right)^3 \right] \qquad r < r_c -For style *wall/lj126*\ , the energy E is given by the 12/6 potential: +For style *wall/lj126*, the energy E is given by the 12/6 potential: .. math:: @@ -119,7 +119,7 @@ For style *wall/lj126*\ , the energy E is given by the 12/6 potential: \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c -For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: +For style *wall/lj1043*, the energy E is given by the 10/4/3 potential: .. math:: @@ -128,7 +128,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right] \qquad r < r_c -For style *wall/colloid*\ , the energy E is given by an integrated form +For style *wall/colloid*, the energy E is given by an integrated form of the :doc:`pair_style colloid ` potential: .. math:: @@ -138,14 +138,14 @@ of the :doc:`pair_style colloid ` potential: & \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R) \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c -For style *wall/harmonic*\ , the energy E is given by a harmonic spring +For style *wall/harmonic*, the energy E is given by a harmonic spring potential: .. math:: E = \epsilon \quad (r - r_c)^2 \qquad r < r_c -For style *wall/morse*\ , the energy E is given by a Morse potential: +For style *wall/morse*, the energy E is given by a Morse potential: .. math:: @@ -153,13 +153,13 @@ For style *wall/morse*\ , the energy E is given by a Morse potential: \qquad r < r_c In all cases, *r* is the distance from the particle to the wall at -position *coord*\ , and :math:`r_c` is the *cutoff* distance at which the +position *coord*, and :math:`r_c` is the *cutoff* distance at which the particle and wall no longer interact. The energy of the wall potential is shifted so that the wall-particle interaction energy is 0.0 at the cutoff distance. -Up to 6 walls or faces can be specified in a single command: *xlo*\ , -*xhi*\ , *ylo*\ , *yhi*\ , *zlo*\ , *zhi*\ . A *lo* face interacts with +Up to 6 walls or faces can be specified in a single command: *xlo*, +*xhi*, *ylo*, *yhi*, *zlo*, *zhi*\ . A *lo* face interacts with particles near the lower side of the simulation box in that dimension. A *hi* face interacts with particles near the upper side of the simulation box in that dimension. @@ -267,13 +267,13 @@ 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 ` to include the wall force in its calculations. If the setting is -*no*\ , wall forces are imposed after pairwise interactions, in the +*no*, wall forces are imposed after pairwise interactions, in the usual manner. The *pbc* keyword can be used with a *yes* setting to allow walls to be specified in a periodic dimension. See the :doc:`boundary ` command for options on simulation box -boundaries. The default for *pbc* is *no*\ , which means the system +boundaries. The default for *pbc* is *no*, which means the system must be non-periodic when using a wall. But you may wish to use a periodic box. E.g. to allow some particles to interact with the wall via the fix group-ID, and others to pass through it and wrap around a @@ -306,7 +306,7 @@ sigma) could be varied with additional variable definitions. The *ramp(lo,hi)* function adjusts the wall position linearly from *lo* to *hi* over the course of a run. The *vdisplace(c0,velocity)* function does -something similar using the equation *position = c0 + velocity\*delta*\ , +something similar using the equation *position = c0 + velocity\*delta*, where *delta* is the elapsed time. The *swiggle(c0,A,period)* function causes the wall position to diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 079bd633ea..ac0a58f55c 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -51,7 +51,7 @@ particles in the group interact with the wall when they are close enough to touch it. The nature of the interaction between the wall and the polygon particles is the same as that between the polygon particles themselves, which is similar to a Hookean potential. See -the :doc:`Howto body ` doc page for more details on using +the :doc:`Howto body ` page for more details on using body particles. The parameters *k_n*, *c_n*, *c_t* have the same meaning and units as @@ -83,7 +83,7 @@ is set according to this equation: position = coord + A - A cos (omega \* delta) where *coord* is the specified initial position of the wall, *A* is -the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time +the *amplitude*, *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. @@ -100,7 +100,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` page for more info. Any dimension (xy) that has a wall must be non-periodic. diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index ad6540de1d..9930c10f74 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -50,7 +50,7 @@ All particles in the group interact with the wall when they are close enough to touch it. The nature of the interaction between the wall and the polygon particles is the same as that between the polygon particles themselves, which is similar to a Hookean potential. See -the :doc:`Howto body ` doc page for more details on using +the :doc:`Howto body ` page for more details on using body particles. The parameters *k_n*, *c_n*, *c_t* have the same meaning and units as @@ -79,7 +79,7 @@ is set according to this equation: position = coord + A - A cos (omega \* delta) where *coord* is the specified initial position of the wall, *A* is -the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time +the *amplitude*, *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. @@ -96,7 +96,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` page for more info. Any dimension (xyz) that has a wall must be non-periodic. diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index a2aab975ca..13a7935d0d 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -73,7 +73,7 @@ energy of wall-particle interactions E is given by: Introduced by Babadi and Ejtehadi in :ref:`(Babadi) `. Here, *r* is the distance from the particle to the -wall at position *coord*\ , and Rc is the *cutoff* distance at which +wall at position *coord*, and Rc is the *cutoff* distance at which the particle and wall no longer interact. Also, :math:`\sigma_n` is the distance between center of ellipsoid and the nearest point of its surface to the wall as shown below. @@ -162,7 +162,7 @@ Restrictions These fixes are part of the EXTRA-FIX package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. These fixes requires that atoms be ellipsoids as defined by the :doc:`atom_style ellipsoid ` command. diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 57bec679e4..cf8b659df0 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -22,7 +22,7 @@ Syntax .. parsed-literal:: - For *hooke*\ , *hooke/history*\ , and *hertz/history*\ , *fstyle_params* are: + For *hooke*, *hooke/history*, and *hertz/history*, *fstyle_params* are: Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) @@ -33,7 +33,7 @@ Syntax .. parsed-literal:: - For *granular*\ , *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` + For *granular*, *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` * wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder* * args = list of arguments for a particular style @@ -85,7 +85,7 @@ 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 :doc:`pair_style granular ` commands. Currently the -options are *hooke*\ , *hooke/history*\ , or *hertz/history* for 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 @@ -96,12 +96,12 @@ Specifically, delta = radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact = RiRj/Ri+Rj is set to the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +The parameters *Kn*, *Kt*, *gamma_n*, *gamma_t*, *xmu*, *dampflag*, and the optional keyword *limit_damping* have the same meaning and units as those specified with the :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 +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*. @@ -117,7 +117,7 @@ material. .. note:: - As discussed on the doc page for :doc:`pair_style gran/\* `, + As discussed on the 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 @@ -131,7 +131,7 @@ 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 ` 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 @@ -163,13 +163,13 @@ is set according to this equation: position = coord + A - A cos (omega \* delta) where *coord* is the specified initial position of the wall, *A* is -the *amplitude*\ , *omega* is 2 PI / *period*\ , and *delta* is the time +the *amplitude*, *omega* is 2 PI / *period*, and *delta* is the time elapsed since the fix was specified. The velocity of the wall is set to the derivative of this expression. For the *shear* keyword, the wall moves continuously in the specified dimension with velocity *vshear*\ . The dimension must be tangential to -walls with a planar *wallstyle*\ , e.g. in the *y* or *z* directions for +walls with a planar *wallstyle*, e.g. in the *y* or *z* directions for an *xplane* wall. For *zcylinder* walls, a dimension of *z* means the cylinder is moving in the z-direction along it's axis. A dimension of *x* or *y* means the cylinder is spinning around the z-axis, either in @@ -225,7 +225,7 @@ Restrictions """""""""""" This fix is 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. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Any dimension (xyz) that has a granular wall must be non-periodic. diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 35995fedf0..95634238aa 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -22,7 +22,7 @@ Syntax .. parsed-literal:: - For *hooke*\ , *hooke/history*\ , and *hertz/history*\ , *fstyle_params* are: + For *hooke*, *hooke/history*, and *hertz/history*, *fstyle_params* are: Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) @@ -32,7 +32,7 @@ Syntax .. parsed-literal:: - For *granular*\ , *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` + For *granular*, *fstyle_params* are set using the same syntax as for the *pair_coeff* command of :doc:`pair_style granular ` * wallstyle = region (see :doc:`fix wall/gran ` for options for other kinds of walls) * region-ID = region whose boundary will act as wall @@ -106,7 +106,7 @@ or combinations of primitive shapes specified via the *union* or construct particle containers with complex shapes. Regions can also move dynamically via the :doc:`region ` command -keywords (move) and *rotate*\ , or change their shape by use of variables +keywords (move) and *rotate*, or change their shape by use of variables as inputs to the :doc:`region ` command. If such a region is used with this fix, then the region surface will move in time in the corresponding manner. @@ -163,7 +163,7 @@ 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 :doc:`pair_style granular ` commands. Currently the -options are *hooke*\ , *hooke/history*\ , or *hertz/history* for 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 @@ -181,12 +181,12 @@ radius - r = overlap of particle with wall, m_eff = mass of particle, and the effective radius of contact is just the radius of the particle. -The parameters *Kn*\ , *Kt*\ , *gamma_n*, *gamma_t*, *xmu*, *dampflag*, +The parameters *Kn*, *Kt*, *gamma_n*, *gamma_t*, *xmu*, *dampflag*, and the optional keyword *limit_damping* have the same meaning and units as those specified with the :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 +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*. @@ -265,7 +265,7 @@ Restrictions """""""""""" This fix is 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. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index 00cad094eb..af3dece2f5 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -103,7 +103,7 @@ Restrictions """""""""""" This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The face that has the wall/piston must be boundary type 's' (shrink-wrapped). The opposing face can be diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 4f014cc628..8bb895280c 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -62,8 +62,8 @@ divides the corresponding timestep asymmetrically, energy conservation is only satisfied to O(dt), rather than to O(dt\^2) as it would be for velocity-Verlet integration without reflective walls. -Up to 6 walls or faces can be specified in a single command: *xlo*\ , -*xhi*\ , *ylo*\ , *yhi*\ , *zlo*\ , *zhi*\ . A *lo* face reflects particles +Up to 6 walls or faces can be specified in a single command: *xlo*, +*xhi*, *ylo*, *yhi*, *zlo*, *zhi*\ . A *lo* face reflects particles that move to a coordinate less than the wall position, back in the *hi* direction. A *hi* face reflects particles that move to a coordinate higher than the wall position, back in the *lo* direction. @@ -117,7 +117,7 @@ in a time-dependent fashion using equal-style The *ramp(lo,hi)* function adjusts the wall position linearly from *lo* to *hi* over the course of a run. The *vdisplace(c0,velocity)* function does -something similar using the equation *position = c0 + velocity\*delta*\ , +something similar using the equation *position = c0 + velocity\*delta*, where *delta* is the elapsed time. The *swiggle(c0,A,period)* function causes the wall position to diff --git a/doc/src/fix_wall_reflect_stochastic.rst b/doc/src/fix_wall_reflect_stochastic.rst index e03e8db5bc..64e3d759c1 100644 --- a/doc/src/fix_wall_reflect_stochastic.rst +++ b/doc/src/fix_wall_reflect_stochastic.rst @@ -66,25 +66,25 @@ particle is treated stochastically. The randomness can come from many sources: thermal motion of the wall atoms, surface roughness, etc. Three stochastic reflection models are currently implemented. -For rstyle *diffusive*\ , particles are reflected diffusively. Their +For rstyle *diffusive*, particles are reflected diffusively. Their velocity distribution corresponds to an equilibrium distribution of particles at the wall temperature. No accommodation coefficients are specified. -For rstyle *maxwell*\ , particle reflection is Maxwellian which means +For rstyle *maxwell*, particle reflection is Maxwellian which means partially diffusive and partially specular (:ref:`Maxwell `). A single accommodation coeff is specified which must be between 0.0 and 1.0 inclusive. It determines the fraction of the collision which is diffusive versus specular. An accommodation coefficient of 1.0 is fully diffusive; a coefficient of 0.0 is fully specular. -For rstyle *cll*\ , particle collisions are computed by the +For rstyle *cll*, particle collisions are computed by the Cercignani/Lampis model. See :ref:`CL ` and :ref:`To ` for details. Three accommodations coefficient are specified. Each must be between 0.0 and 1.0 inclusive. Two are velocity accommodation coefficients; one is a normal kinetic energy accommodation. The normal coeff is the one corresponding to the normal of the wall itself. For example if -the wall is *ylo* or *yhi*\ , *accomx* and *accomz* are the tangential +the wall is *ylo* or *yhi*, *accomx* and *accomz* are the tangential velocity accommodation coefficients, and *accomy* is the normal kinetic energy accommodation coefficient. @@ -107,7 +107,7 @@ command. The wall velocity must lie on the same plane as the wall itself. This fix is part of the EXTRA-FIX package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index 3803d4b74b..f79a9d6da0 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -127,7 +127,7 @@ region surface will move over time in the corresponding manner. The energy of wall-particle interactions depends on the specified style. -For style *lj93*\ , the energy E is given by the 9/3 potential: +For style *lj93*, the energy E is given by the 9/3 potential: .. math:: @@ -135,7 +135,7 @@ For style *lj93*\ , the energy E is given by the 9/3 potential: \left(\frac{\sigma}{r}\right)^3 \right] \qquad r < r_c -For style *lj126*\ , the energy E is given by the 12/6 potential: +For style *lj126*, the energy E is given by the 12/6 potential: .. math:: @@ -143,7 +143,7 @@ For style *lj126*\ , the energy E is given by the 12/6 potential: \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c -For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: +For style *wall/lj1043*, the energy E is given by the 10/4/3 potential: .. math:: @@ -152,7 +152,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right] \qquad r < r_c -For style *colloid*\ , the energy E is given by an integrated form of +For style *colloid*, the energy E is given by an integrated form of the :doc:`pair_style colloid ` potential: .. math:: @@ -162,14 +162,14 @@ the :doc:`pair_style colloid ` potential: & \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R) \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c -For style *wall/harmonic*\ , the energy E is given by a harmonic spring +For style *wall/harmonic*, the energy E is given by a harmonic spring potential (the distance parameter is ignored): .. math:: E = \epsilon \quad (r - r_c)^2 \qquad r < r_c -For style *wall/morse*\ , the energy E is given by the Morse potential: +For style *wall/morse*, the energy E is given by the Morse potential: .. math:: diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index 72e7c771b7..6363995988 100644 --- a/doc/src/fix_wall_srd.rst +++ b/doc/src/fix_wall_srd.rst @@ -17,11 +17,11 @@ Syntax .. parsed-literal:: - *xlo*\ ,\ *ylo*\ ,\ *zlo* arg = EDGE or constant or variable + *xlo*,\ *ylo*,\ *zlo* arg = EDGE or constant or variable EDGE = current lo edge of simulation box constant = number like 0.0 or -30.0 (distance units) variable = :doc:`equal-style variable ` like v_x or v_wiggle - *xhi*\ ,\ *yhi*\ ,\ *zhi* arg = EDGE or constant or variable + *xhi*,\ *yhi*,\ *zhi* arg = EDGE or constant or variable EDGE = current hi edge of simulation box constant = number like 50.0 or 100.3 (distance units) variable = :doc:`equal-style variable ` like v_x or v_wiggle @@ -72,8 +72,8 @@ tangential direction for the SRD velocity is chosen randomly. This collision style imparts both a normal and tangential force to the wall. -Up to 6 walls or faces can be specified in a single command: *xlo*\ , -*xhi*\ , *ylo*\ , *yhi*\ , *zlo*\ , *zhi*\ . A *lo* face reflects particles +Up to 6 walls or faces can be specified in a single command: *xlo*, +*xhi*, *ylo*, *yhi*, *zlo*, *zhi*\ . A *lo* face reflects particles that move to a coordinate less than the wall position, back in the *hi* direction. A *hi* face reflects particles that move to a coordinate higher than the wall position, back in the *lo* direction. diff --git a/doc/src/fix_widom.rst b/doc/src/fix_widom.rst index 8ec5a1308d..34b9ae44f6 100644 --- a/doc/src/fix_widom.rst +++ b/doc/src/fix_widom.rst @@ -21,7 +21,7 @@ Syntax .. parsed-literal:: - keyword = *mol*\ , *region*\ , *full_energy*, *charge*\ , *intra_energy* + keyword = *mol*, *region*, *full_energy*, *charge*, *intra_energy* *mol* value = template-ID template-ID = ID of molecule template specified in a separate :doc:`molecule ` command *region* value = region-ID diff --git a/doc/src/group.rst b/doc/src/group.rst index 3ce885bdc5..aedf1d39bc 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -113,7 +113,7 @@ Note that this is a static one-time assignment. The atoms remain assigned (or not assigned) to the group even in they later move out of the region volume. -The *type*\ , *id*\ , and *molecule* styles put all atoms with the +The *type*, *id*, and *molecule* styles put all atoms with the specified atom types, atom IDs, or molecule IDs into the group. These 3 styles can use arguments specified in one of two formats. @@ -181,7 +181,7 @@ pe/atom compute was actually invoked during the run. Printing the thermodynamic info for compute 2 insures that this is the case, since it sums the pe/atom compute values (in the reduce compute) to output them to the screen. See the "Variable Accuracy" section of the -:doc:`variable ` doc page for more details on insuring that +:doc:`variable ` page for more details on insuring that variables are current when they are evaluated between runs. The *include* style with its arg *molecule* adds atoms to a group that @@ -236,7 +236,7 @@ per-atom property. The per-atom property is evaluated and atoms whose values are 0.0 are removed from the dynamic group. The assignment of atoms to a dynamic group is done at the beginning of -each run and on every timestep that is a multiple of *N*\ , which is the +each run and on every timestep that is a multiple of *N*, which is the argument for the *every* keyword (N = 1 is the default). For an energy minimization, via the :doc:`minimize ` command, an assignment is made at the beginning of the minimization, but not diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst index 31b46ce2ce..7d66db367b 100644 --- a/doc/src/group2ndx.rst +++ b/doc/src/group2ndx.rst @@ -58,7 +58,7 @@ This command requires that atoms have atom IDs, since this is the information that is written to the index file. These commands are part of the COLVARS package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst index 5b2c931b1f..9266a95523 100644 --- a/doc/src/hyper.rst +++ b/doc/src/hyper.rst @@ -72,7 +72,7 @@ the system and runs dynamics on each independently with a normal unbiased potential until an event occurs in one of the replicas. The time between events is reduced by a factor of Nr replicas. For both methods, per CPU second, more physical time elapses and more events -occur. See the :doc:`prd ` doc page for more info about PRD. +occur. See the :doc:`prd ` page for more info about PRD. An HD run has several stages, which are repeated each time an event occurs, as explained below. The logic for an HD run is as follows: @@ -148,7 +148,7 @@ the specified *dump-ID* to output a snapshot each time an event is detected. It can be specified multiple times with different *dump-ID* values, as in the example above. These snapshots will be for the quenched state of the system on a timestep that is a multiple of -*Nevent*\ , i.e. a timestep after the event has occurred. Note that any +*Nevent*, i.e. a timestep after the event has occurred. Note that any dump command in the input script will also output snapshots at whatever timestep interval it defines via its *N* argument; see the :doc:`dump ` command for details. This means if you only want a diff --git a/doc/src/if.rst b/doc/src/if.rst index e779ec5a04..08ec6f2c3e 100644 --- a/doc/src/if.rst +++ b/doc/src/if.rst @@ -68,7 +68,7 @@ above. If a command itself requires a quoted argument (e.g. a :doc:`print ` command), then double and single quotes can be used and nested in the usual manner, as in the examples above and below. - The :doc:`Commands parse ` doc page has more details on + The :doc:`Commands parse ` page has more details on using quotes in arguments. Only one of level of nesting is allowed, but that should be sufficient for most use cases. diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index 41d533eebe..42cd3b75c5 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -64,7 +64,7 @@ radian\^2. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -74,14 +74,14 @@ produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package -` doc page for more info. +` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst index 0667b8f5b9..ca7c31a923 100644 --- a/doc/src/improper_style.rst +++ b/doc/src/improper_style.rst @@ -70,7 +70,7 @@ command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the :ref:`Commands improper ` doc page are followed by one or +The individual style names on the :ref:`Commands improper ` page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`none ` - turn off improper interactions @@ -99,7 +99,7 @@ Improper styles can only be set for atom_style choices that allow impropers to be defined. Most improper styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual improper potentials tell if it is part of a package. Related commands diff --git a/doc/src/info.rst b/doc/src/info.rst index b3eb6d7000..853e5020fc 100644 --- a/doc/src/info.rst +++ b/doc/src/info.rst @@ -10,9 +10,9 @@ Syntax info args -* args = one or more of the following keywords: *out*\ , *all*\ , *system*\ , *memory*\ , *communication*\ , *computes*\ , *dumps*\ , *fixes*\ , *groups*\ , *regions*\ , *variables*\ , *coeffs*\ , *styles*\ , *time*\ , *accelerator*\ , or *configuration* -* *out* values = *screen*\ , *log*\ , *append* filename, *overwrite* filename -* *styles* values = *all*\ , *angle*\ , *atom*\ , *bond*\ , *compute*\ , *command*\ , *dump*\ , *dihedral*\ , *fix*\ , *improper*\ , *integrate*\ , *kspace*\ , *minimize*\ , *pair*\ , *region* +* args = one or more of the following keywords: *out*, *all*, *system*, *memory*, *communication*, *computes*, *dumps*, *fixes*, *groups*, *regions*, *variables*, *coeffs*, *styles*, *time*, *accelerator*, or *configuration* +* *out* values = *screen*, *log*, *append* filename, *overwrite* filename +* *styles* values = *all*, *angle*, *atom*, *bond*, *compute*, *command*, *dump*, *dihedral*, *fix*, *improper*, *integrate*, *kspace*, *minimize*, *pair*, *region* Examples """""""" diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index fc00a574d2..1be907888c 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -476,7 +476,7 @@ performed. The second required argument *query_function* is the name of the query function to be called (e.g. *get_lattice_constant_cubic*\ ). All following :doc:`arguments ` are parameters handed over to the web query in -the format *keyword=value*\ , where *value* is always an array of one or more +the format *keyword=value*, where *value* is always an array of one or more comma-separated items in brackets. The list of supported keywords and the type and format of their values depend on the query function used. The current list of query functions is available on the OpenKIM webpage at diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index afe3a8c381..5d603782c0 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -75,7 +75,7 @@ relevant to all kspace styles. The *collective* keyword applies only to PPPM. It is set to *no* by default, except on IBM BlueGene machines. If this option is set to -*yes*\ , LAMMPS will use MPI collective operations to remap data for +*yes*, LAMMPS will use MPI collective operations to remap data for 3d-FFT operations instead of the default point-to-point communication. This is faster on IBM BlueGene machines, and may also be faster on other machines if they have an efficient implementation of MPI @@ -131,11 +131,11 @@ always used for MSM. ---------- The *disp/auto* option controls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to *no*\ , parameters have -to be specified using the *gewald/disp*\ , *mesh/disp*\ , +generate PPPM parameters automatically. If set to *no*, parameters have +to be specified using the *gewald/disp*, *mesh/disp*, *force/disp/real* or *force/disp/kspace* keywords, or the code will stop with an error message. When this option is set to -*yes*\ , the error message will not appear and the simulation will start. +*yes*, the error message will not appear and the simulation will start. For a typical application, using the automatic parameter generation will provide simulations that are either inaccurate or slow. Using this option is thus not recommended. For guidelines on how to obtain good @@ -165,8 +165,8 @@ calculated by the long-range solver and is thus specified in force units. A negative value for the accuracy setting means to use the relative accuracy parameter. The accuracy setting is used in conjunction with the pairwise cutoff to determine the number of -K-space vectors for style *ewald*\ , the FFT grid size for style -*pppm*\ , or the real space grid size for style *msm*\ . +K-space vectors for style *ewald*, the FFT grid size for style +*pppm*, or the real space grid size for style *msm*\ . ---------- @@ -223,7 +223,7 @@ The *minorder* keyword allows LAMMPS to reduce the *order* setting if necessary to keep the communication of ghost grid point limited to exchanges between nearest-neighbor processors. See the discussion of the *overlap* keyword for details. If the *overlap* keyword is set to -*yes*\ , which is the default, this is never needed. If it set to *no* +*yes*, which is the default, this is never needed. If it set to *no* and overlap occurs, then LAMMPS will reduce the order setting, one step at a time, until the ghost grid overlap only extends to nearest neighbor processors. The *minorder* keyword limits how small the @@ -237,13 +237,13 @@ MSM. ---------- The *mix/disp* keyword selects the mixing rule for the dispersion -coefficients. With *pair*\ , the dispersion coefficients of unlike +coefficients. With *pair*, the dispersion coefficients of unlike types are computed as indicated with :doc:`pair_modify `. -With *geom*\ , geometric mixing is enforced on the dispersion +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 error in the force computations, as shown in :ref:`(Wennberg) `. -With *none*\ , it is assumed that no mixing rule is +With *none*, it is assumed that no mixing rule is applicable. Splitting of the dispersion coefficients will be performed as described in :ref:`(Isele-Holder) `. @@ -398,8 +398,8 @@ 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*\ , -*ewald/dipole*\ , and *pppm/dipole*\ . +:ref:`(Klapp) ` in :doc:`kspace_style ` *ewald/disp*, +*ewald/dipole*, and *pppm/dipole*\ . .. note:: @@ -419,10 +419,10 @@ optimal performance and accuracy in the results is obtained when these values are different. The *disp/auto* option controls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to *no*\ , parameters -have to be specified using the *gewald/disp*\ , *mesh/disp*\ , +generate PPPM parameters automatically. If set to *no*, parameters +have to be specified using the *gewald/disp*, *mesh/disp*, *force/disp/real* or *force/disp/kspace* keywords, or the code will -stop with an error message. When this option is set to *yes*\ , the +stop with an error message. When this option is set to *yes*, the error message will not appear and the simulation will start. For a typical application, using the automatic parameter generation will provide simulations that are either inaccurate or slow. Using this diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index dc72915b35..055f0b02b2 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -408,7 +408,7 @@ relative RMS error. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -431,9 +431,9 @@ on the CPU when using OpenMP and FFTW3. These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP, and OPT packages respectively. They are only enabled if -LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -445,19 +445,19 @@ Note that the long-range electrostatic solvers in LAMMPS assume conducting metal (tinfoil) boundary conditions for both charge and dipole interactions. Vacuum boundary conditions are not currently supported. -The *ewald/disp*\ , *ewald*\ , *pppm*\ , and *msm* styles support +The *ewald/disp*, *ewald*, *pppm*, and *msm* styles support non-orthogonal (triclinic symmetry) simulation boxes. However, triclinic simulation cells may not yet be supported by all suffix versions of these styles. Most of the base kspace styles are part of the KSPACE package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build -package ` doc page for more info. +package ` page for more info. The *msm/dielectric* and *pppm/dielectric* kspace styles are part of the DIELECTRIC package. They are only enabled if LAMMPS was built with that package **and** the KSPACE package. See the :doc:`Build package -` doc page for more info. +` page for more info. For MSM, a simulation must be 3d and one can use any combination of periodic, non-periodic, or shrink-wrapped boundaries (specified using diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index b87ddaaf70..a03036de1c 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -30,7 +30,7 @@ Syntax i,j,k = integer lattice directions *spacing* values = dx dy dz dx,dy,dz = lattice spacings in the x,y,z box directions - *a1*\ ,\ *a2*\ ,\ *a3* values = x y z + *a1*,\ *a2*,\ *a3* values = x y z x,y,z = primitive vector components that define unit cell *basis* values = x y z x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) @@ -102,7 +102,7 @@ default, a "lattice none 1.0" is defined, which means the lattice spacing is the same as one distance unit, as defined by the :doc:`units ` command. -Lattices of style *sc*\ , *fcc*\ , *bcc*\ , and *diamond* are 3d lattices +Lattices of style *sc*, *fcc*, *bcc*, and *diamond* are 3d lattices that define a cubic unit cell with edge length = 1.0. This means a1 = 1 0 0, a2 = 0 1 0, and a3 = 0 0 1. Style *hcp* has a1 = 1 0 0, a2 = 0 sqrt(3) 0, and a3 = 0 0 sqrt(8/3). The placement of the basis atoms @@ -147,14 +147,14 @@ lattice of the desired size and distance units in the simulation box. The meaning of the *scale* argument depends on the :doc:`units ` being used in your simulation. -For all unit styles except *lj*\ , the scale argument is specified in +For all unit styles except *lj*, the scale argument is specified in the distance units defined by the unit style. For example, in *real* or *metal* units, if the unit cell is a unit cube with edge length 1.0, specifying scale = 3.52 would create a cubic lattice with a spacing of 3.52 Angstroms. In *cgs* units, the spacing would be 3.52 cm. -For unit style *lj*\ , the scale argument is the Lennard-Jones reduced +For unit style *lj*, the scale argument is the Lennard-Jones reduced density, typically written as rho\*. LAMMPS converts this value into the multiplicative factor via the formula "factor\^dim = rho/rho\*", where rho = N/V with V = the volume of the lattice unit cell and N = diff --git a/doc/src/log.rst b/doc/src/log.rst index 2632f34b68..5d4036dc06 100644 --- a/doc/src/log.rst +++ b/doc/src/log.rst @@ -26,7 +26,7 @@ Description This command closes the current LAMMPS log file, opens a new file with the specified name, and begins logging information to it. If the -specified file name is *none*\ , then no new log file is opened. If the +specified file name is *none*, then no new log file is opened. If the optional keyword *append* is specified, then output will be appended to an existing log file, instead of overwriting it. diff --git a/doc/src/mdi_engine.rst b/doc/src/mdi_engine.rst index d26a1f8cd3..e06f571922 100644 --- a/doc/src/mdi_engine.rst +++ b/doc/src/mdi_engine.rst @@ -21,7 +21,7 @@ More specifically, this command causes LAMMPS to begin using the `MDI Library `_ to run as an MDI engine (server), responding to commands made by an external MDI driver code (client). See the :doc:`Howto mdi -` doc page for more information about how LAMMPS can work +` page for more information about how LAMMPS can work as both an MDI driver or engine. General information about launching codes that communicate using the @@ -75,7 +75,7 @@ Restrictions This command is part of the MDI package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/message.rst b/doc/src/message.rst index 718a68f994..83ce965e91 100644 --- a/doc/src/message.rst +++ b/doc/src/message.rst @@ -50,7 +50,7 @@ Description Establish a messaging protocol between LAMMPS and another code for the purpose of client/server coupling. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -73,10 +73,10 @@ are: * md = run dynamics with another code * mc = perform Monte Carlo moves with another code -For protocol *md*\ , LAMMPS can be either a client or server. See the -:doc:`server md ` doc page for details on the protocol. +For protocol *md*, LAMMPS can be either a client or server. See the +:doc:`server md ` page for details on the protocol. -For protocol *mc*\ , LAMMPS can be the server. See the :doc:`server mc ` doc page for details on the protocol. +For protocol *mc*, LAMMPS can be the server. See the :doc:`server mc ` page for details on the protocol. ---------- @@ -84,13 +84,13 @@ The *mode* argument specifies how messages are exchanged between the client and server codes. Both codes must use the same mode and use consistent parameters. -For mode *file*\ , the 2 codes communicate via binary files. They must +For mode *file*, the 2 codes communicate via binary files. They must use the same filename, which is actually a file prefix. Several files with that prefix will be created and deleted as a simulation runs. The filename can include a path. Both codes must be able to access the path/file in a common filesystem. -For mode *zmq*\ , the 2 codes communicate via a socket on the server +For mode *zmq*, the 2 codes communicate via a socket on the server code's machine. Support for socket messaging is provided by the open-source `ZeroMQ library `_, which must be installed on your system. The client specifies an IP address (IPv4 @@ -130,7 +130,7 @@ what the client specifies. Additional explanation is needed here about how to use the *zmq* mode on a parallel machine, e.g. a cluster with many nodes. -For mode *mpi/one*\ , the 2 codes communicate via MPI and are launched +For mode *mpi/one*, the 2 codes communicate via MPI and are launched by the same mpirun command, e.g. with this syntax for OpenMPI: .. code-block:: bash @@ -139,10 +139,10 @@ by the same mpirun command, e.g. with this syntax for OpenMPI: mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server Note the use of the "-mpicolor color" command-line argument with -LAMMPS. See the :doc:`command-line args ` doc page for +LAMMPS. See the :doc:`command-line args ` page for further explanation. -For mode *mpi/two*\ , the 2 codes communicate via MPI, but are launched +For mode *mpi/two*, the 2 codes communicate via MPI, but are launched be 2 separate mpirun commands. The specified *filename* argument is a file the 2 MPI processes will use to exchange info so that an MPI inter-communicator can be established to enable the 2 codes to send @@ -191,7 +191,7 @@ Restrictions """""""""""" This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index 731d2ace62..6b416a9b6a 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -81,8 +81,8 @@ energy after) and that difference may be smaller than machine epsilon even if atoms could move in the gradient direction to reduce forces further. -The choice of a norm can be modified for the min styles *cg*\ , *sd*\ -, *quickmin*\ , *fire*\ , *fire/old*\ , *spin*\ , *spin/cg* and +The choice of a norm can be modified for the min styles *cg*, *sd*\ +, *quickmin*, *fire*, *fire/old*, *spin*, *spin/cg* and *spin/lbfgs* using the *norm* keyword. The default *two* norm computes the 2-norm (Euclidean length) of the global force vector: @@ -104,7 +104,7 @@ all atoms in the system: || \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right) -For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force +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 @@ -138,8 +138,8 @@ minimization is 4fs. Note that parameter defaults has been chosen to be reliable in most cases, but one should consider adjusting :doc:`timestep ` and *tmax* to optimize the minimization for large or complex systems. Other -parameters of the *fire* minimization can be tuned (\ *tmin*\ , -*delaystep*\ , *dtgrow*\ , *dtshrink*\ , *alpha0*\ , and +parameters of the *fire* minimization can be tuned (\ *tmin*, +*delaystep*, *dtgrow*, *dtshrink*, *alpha0*, and *alphashrink*\ ). Please refer to the references describing the :doc:`min_style ` *fire*. An additional stopping criteria *vdfmax* is used by *fire* in order to avoid @@ -176,7 +176,7 @@ Default The option defaults are dmax = 0.1, line = quadratic and norm = two. -For the *spin*\ , *spin/cg* and *spin/lbfgs* styles, the option +For the *spin*, *spin/cg* and *spin/lbfgs* styles, the option defaults are alpha_damp = 1.0, discrete_factor = 10.0, line = spin_none, and norm = euclidean. diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 46fd08b838..4aef3e0fe2 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -81,7 +81,7 @@ The :doc:`min_modify ` command can be used to activate the line search procedure, and to modify the discretization factor *discrete_factor*. -For more information about styles *spin/cg* and *spin/lbfgs*\ , +For more information about styles *spin/cg* and *spin/lbfgs*, see their implementation reported in :ref:`(Ivanov) `. .. note:: diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst index caf2ebd7b2..03a6073994 100644 --- a/doc/src/min_style.rst +++ b/doc/src/min_style.rst @@ -42,7 +42,7 @@ of the energy is not formed directly, but approximated in each conjugate search direction by a finite difference directional 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*\ , +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. @@ -88,14 +88,14 @@ Style *spin/lbfgs* uses an orthogonal spin optimization (OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) approach to minimize spin configurations. -See the :doc:`min/spin ` doc page for more information about -the *spin*\ , *spin/cg* and *spin/lbfgs* styles. +See the :doc:`min/spin ` page for more information about +the *spin*, *spin/cg* and *spin/lbfgs* styles. -Either the *quickmin*\ , *fire* and *fire/old* styles are useful in the +Either the *quickmin*, *fire* and *fire/old* styles are useful in the context of nudged elastic band (NEB) calculations via the :doc:`neb ` command. -Either the *spin*\ , *spin/cg* and *spin/lbfgs* styles are useful in +Either the *spin*, *spin/cg* and *spin/lbfgs* styles are useful in the context of magnetic geodesic nudged elastic band (GNEB) calculations via the :doc:`neb/spin ` command. @@ -110,7 +110,7 @@ calculations via the :doc:`neb/spin ` command. .. note:: - The *quickmin*\ , *fire*\ , *fire/old*\ , *hftn*\ , and *cg/kk* styles do not yet + The *quickmin*, *fire*, *fire/old*, *hftn*, and *cg/kk* styles do not yet support the use of the :doc:`fix box/relax ` command or minimizations involving the electron radius in :doc:`eFF ` models. diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index a9f60fe8f6..14bc4d0d21 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -57,7 +57,7 @@ coordinates of other atoms fixed by applying :doc:`fix setforce ` to the other atoms. See a fuller discussion of using fixes while minimizing below. -The :doc:`minimization styles ` *cg*\ , *sd*\ , and *hftn* +The :doc:`minimization styles ` *cg*, *sd*, and *hftn* involves an outer iteration loop which sets the search direction along which atom coordinates are changed. An inner iteration is then performed using a line search algorithm. The line search typically @@ -68,7 +68,7 @@ be more robust than previous line searches we have tried. The backtracking method is described in Nocedal and Wright's Numerical Optimization (Procedure 3.1 on p 41). -The :doc:`minimization styles ` *quickmin*\ , *fire* and +The :doc:`minimization styles ` *quickmin*, *fire* and *fire/old* perform damped dynamics using an Euler integration step. Thus they require a :doc:`timestep ` be defined. @@ -118,12 +118,12 @@ The minimization procedure stops if any of several criteria are met: .. note:: - the :doc:`minimization style ` *spin*\ , - *spin/cg*\ , and *spin/lbfgs* replace + the :doc:`minimization style ` *spin*, + *spin/cg*, and *spin/lbfgs* replace the force tolerance *ftol* by a torque tolerance. The minimization procedure stops if the 2-norm (length) of the torque vector on atom (defined as the cross product between the - atomic spin and its precession vectors omega) is less than *ftol*\ , + atomic spin and its precession vectors omega) is less than *ftol*, or if any of the other criteria are met. Torque have the same units as the energy. .. note:: diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index b86983766d..f380d82c7d 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -79,7 +79,7 @@ make it easy to use the same molecule file in different molecule templates or in different simulations. You can specify the same file multiple times with different optional keywords. -The *offset*\ , *toff*\ , *boff*\ , *aoff*\ , *doff*\ , *ioff* keywords +The *offset*, *toff*, *boff*, *aoff*, *doff*, *ioff* keywords add the specified offset values to the atom types, bond types, angle types, dihedral types, and/or improper types as they are read from the molecule file. E.g. if *toff* = 2, and the file uses atom types @@ -150,7 +150,7 @@ appear if the value(s) are different than the default. * Xc Yc Zc *com* = coordinates of center-of-mass of molecule * Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule -For *mass*\ , *com*\ , and *inertia*\ , the default is for LAMMPS to +For *mass*, *com*, and *inertia*, the default is for LAMMPS to calculate this quantity itself if needed, assuming the molecules consists of a set of point particles or finite-size particles (with a non-zero diameter) that do not overlap. If finite-size particles in @@ -349,7 +349,7 @@ 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 ` page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds section must also appear. @@ -390,7 +390,7 @@ This section is only needed when molecules created using the template will be constrained by SHAKE via the "fix shake" command. The other two Shake sections must also appear in the file, following this one. -The meaning of the flag for each atom is as follows. See the :doc:`fix shake ` doc page for a further description of SHAKE +The meaning of the flag for each atom is as follows. See the :doc:`fix shake ` page for a further description of SHAKE clusters. * 0 = not part of a SHAKE cluster @@ -432,7 +432,7 @@ and b,c = IDs of other two atoms bonded to the central atom. If flag = 4, a,b,c,d are listed, where a = ID of central atom, and b,c,d = IDs of other three atoms bonded to the central atom. -See the :doc:`fix shake ` doc page for a further description +See the :doc:`fix shake ` page for a further description of SHAKE clusters. ---------- @@ -477,7 +477,7 @@ the second non-central atom (value c in the Shake Atoms section), and c = bondtype of the bond between the central atom and the third non-central atom (value d in the Shake Atoms section). -See the :doc:`fix shake ` doc page for a further description +See the :doc:`fix shake ` page for a further description of SHAKE clusters. ---------- diff --git a/doc/src/neb.rst b/doc/src/neb.rst index fdccdf3d9f..69a0877f3a 100644 --- a/doc/src/neb.rst +++ b/doc/src/neb.rst @@ -114,7 +114,7 @@ closer to the MEP and read them in. ---------- -For a *file-style* setting of *final*\ , a filename is specified which +For a *file-style* setting of *final*, a filename is specified which contains atomic coordinates for zero or more atoms, in the format described below. For each atom that appears in the file, the new coordinates are assigned to that atom in the final replica. Each @@ -143,7 +143,7 @@ case. interpolation is outside the periodic box, the atom will be wrapped back into the box when the NEB calculation begins. -For a *file-style* setting of *each*\ , a filename is specified which is +For a *file-style* setting of *each*, a filename is specified which is assumed to be unique to each replica. This can be done by using a variable in the filename, e.g. @@ -162,7 +162,7 @@ as described below, and for any atom that appears in the file, assign the specified coordinates to its atom. The various files do not need to contain the same set of atoms. -For a *file-style* setting of *none*\ , no filename is specified. Each +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 @@ -185,13 +185,13 @@ 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*\ , -*sd*\ , and *hftn* styles cannot be used, since they perform iterative +: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. The minimizer tolerances for energy and force are set by *etol* and -*ftol*\ , the same as for the :doc:`minimize ` command. +*ftol*, the same as for the :doc:`minimize ` command. A non-zero *etol* means that the NEB calculation will terminate if the energy criterion is met by every replica. The energies being compared diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 10b08f674b..9f714096dc 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -114,7 +114,7 @@ closer to the MEP and read them in. ---------- -For a *file-style* setting of *final*\ , a filename is specified which +For a *file-style* setting of *final*, a filename is specified which contains atomic and spin coordinates for zero or more atoms, in the format described below. For each atom that appears in the file, the new coordinates are @@ -168,12 +168,12 @@ opposite directions, an arbitrary rotation vector belonging to the plane perpendicular to initial and final spins is chosen. In this case, a warning message is displayed. -For a *file-style* setting of *each*\ , a filename is specified which is +For a *file-style* setting of *each*, a filename is specified which is assumed to be unique to each replica. See the :doc:`neb ` documentation page for more information about this option. -For a *file-style* setting of *none*\ , no filename is specified. Each +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 @@ -196,14 +196,14 @@ 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*\ , -*spin/cg*\ , or *spin/lbfgs* style (see +:doc:`min_style `, using either the *spin*, +*spin/cg*, or *spin/lbfgs* style (see :doc:`min_spin ` for more information). The other styles cannot be used, since they relax the lattice degrees of freedom instead of the spins. The minimizer tolerances for energy and force are set by *etol* and -*ttol*\ , the same as for the :doc:`minimize ` command. +*ttol*, the same as for the :doc:`minimize ` command. A non-zero *etol* means that the GNEB calculation will terminate if the energy criterion is met by every replica. The energies being compared diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 25c2c2ac77..d6fa12f713 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -75,13 +75,13 @@ pairwise neighbor lists. Depending on what pair interactions and other commands are defined, a simulation may require one or more neighbor lists. -The *every*\ , *delay*\ , *check*\ , and *once* options affect how often +The *every*, *delay*, *check*, and *once* options affect how often lists are built as a simulation runs. The *delay* setting means never build new lists until at least N steps after the previous build. The *every* setting means build lists every M steps (after the delay has -passed). If the *check* setting is *no*\ , the lists are built on the +passed). If the *check* setting is *no*, the lists are built on the first step that satisfies the *delay* and *every* settings. If the -*check* setting is *yes*\ , then the *every* and *delay* settings +*check* setting is *yes*, then the *every* and *delay* settings determine when a build may possibly be performed, but an actual build only occurs if some atom has moved more than half the skin distance (specified in the :doc:`neighbor ` command) since the last @@ -112,7 +112,7 @@ 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 -that to save time, the default *cluster* setting is *no*\ , so that this +that to save time, the default *cluster* setting is *no*, so that this check is not performed. The *include* option limits the building of pairwise neighbor lists to diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 1b10ec8998..0cfedfc090 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -87,7 +87,7 @@ stored in the list. When a run is finished, counts of the number of neighbors stored in the pairwise list and the number of times neighbor lists were built -are printed to the screen and log file. See the :doc:`Run output ` doc page for details. +are printed to the screen and log file. See the :doc:`Run output ` page for details. Restrictions """""""""""" diff --git a/doc/src/next.rst b/doc/src/next.rst index 2b578a43f5..46d39660eb 100644 --- a/doc/src/next.rst +++ b/doc/src/next.rst @@ -37,8 +37,8 @@ be used in an input script command as $a or $z. If it is multiple letters, it can be used as ${myTemp}. If multiple variables are used as arguments to the *next* command, -then all must be of the same variable style: *index*\ , *loop*\ , *file*\ , -*universe*\ , or *uloop*\ . An exception is that *universe*\ - and +then all must be of the same variable style: *index*, *loop*, *file*, +*universe*, or *uloop*\ . An exception is that *universe*\ - and *uloop*\ -style variables can be mixed in the same *next* command. All the variables specified with the next command are incremented by @@ -93,7 +93,7 @@ directories run1 through run8. next d jump in.polymer -If the variable "d" were of style *universe*\ , and the same in.polymer +If the variable "d" were of style *universe*, and the same in.polymer input script were run on 3 partitions of processors, then the first 3 simulations would begin, one on each set of processors. Whichever partition finished first, it would assign variable "d" the fourth value diff --git a/doc/src/package.rst b/doc/src/package.rst index 54cf74f5be..cbff28cee3 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -166,7 +166,7 @@ intel", or "package omp" command with default settings. set, either to default values or to specified settings. I.e. settings from previous invocations do not persist across multiple invocations. -See the :doc:`Speed packages ` doc page for more details +See the :doc:`Speed packages ` page for more details about using the various accelerator packages for speeding up LAMMPS simulations. @@ -192,8 +192,8 @@ Optional keyword/value pairs can also be specified. Each has a default value as listed below. The *neigh* keyword specifies where neighbor lists for pair style -computation will be built. If *neigh* is *yes*\ , which is the default, -neighbor list building is performed on the GPU. If *neigh* is *no*\ , +computation will be built. If *neigh* is *yes*, which is the default, +neighbor list building is performed on the GPU. If *neigh* is *no*, neighbor list building is performed on the CPU. GPU neighbor list building currently cannot be used with a triclinic box. GPU neighbor lists are not compatible with commands that are not GPU-enabled. When @@ -202,7 +202,7 @@ built on the CPU. In these cases, it will typically be more efficient to only use CPU neighbor list builds. The *newton* keyword sets the Newton flags for pairwise (not bonded) -interactions to *off* or *on*\ , the same as the :doc:`newton ` +interactions to *off* or *on*, the same as the :doc:`newton ` command allows. Currently, only an *off* value is allowed, since all the GPU package pair styles require this setting. This means more computation is done, but less communication. In the future a value of @@ -288,7 +288,7 @@ The *Nthreads* value for the *omp* keyword sets the number of OpenMP threads allocated for each MPI task. This setting controls OpenMP parallelism only for routines run on the CPUs. For more details on setting the number of OpenMP threads, see the discussion of the -*Nthreads* setting on this doc page for the "package omp" command. +*Nthreads* setting on this page for the "package omp" command. The meaning of *Nthreads* is exactly the same for the GPU, INTEL, and GPU packages. @@ -350,14 +350,14 @@ The *Nthreads* value for the *omp* keyword sets the number of OpenMP threads allocated for each MPI task. This setting controls OpenMP parallelism only for routines run on the CPUs. For more details on setting the number of OpenMP threads, see the discussion of the -*Nthreads* setting on this doc page for the "package omp" command. +*Nthreads* setting on this page for the "package omp" command. The meaning of *Nthreads* is exactly the same for the GPU, INTEL, and GPU packages. The *mode* keyword determines the precision mode to use for computing pair style forces, either on the CPU or on the co-processor, when using a INTEL supported :doc:`pair style `. It -can take a value of *single*\ , *mixed* which is the default, or +can take a value of *single*, *mixed* which is the default, or *double*\ . *Single* means single precision is used for the entire force calculation. *Mixed* means forces between a pair of atoms are computed in single precision, but accumulated and stored in double @@ -451,11 +451,11 @@ often faster, just as it is for non-accelerated pair styles. Similarly, the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reaxff/kk `. -If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package +If the *neigh/thread* keyword is set to *off*, then the KOKKOS package threads only over atoms. However, for small systems, this may not expose -enough parallelism to keep a GPU busy. When this keyword is set to *on*\ , +enough parallelism to keep a GPU busy. When this keyword is set to *on*, the KOKKOS package threads over both atoms and neighbors of atoms. When -using *neigh/thread* *on*\ , a full neighbor list must also be used. Using +using *neigh/thread* *on*, a full neighbor list must also be used. Using *neigh/thread* *on* may be slower for large systems, so this this option is turned on by default only when there are 16K atoms or less owned by an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled @@ -464,7 +464,7 @@ simple pair-wise potentials such as Lennard-Jones do support threading over both atoms and neighbors. The *newton* keyword sets the Newton flags for pairwise and bonded -interactions to *off* or *on*\ , the same as the :doc:`newton ` +interactions to *off* or *on*, the same as the :doc:`newton ` command allows. The default for GPUs is *off* because this will almost always give better performance for the KOKKOS package. This means more computation is done, but less communication. However, when running on @@ -531,7 +531,7 @@ performing the exchange pack/unpack on the host CPU can give speedup since it reduces the number of CUDA kernel launches. The *gpu/aware* keyword chooses whether GPU-aware MPI will be used. When -this keyword is set to *on*\ , buffers in GPU memory are passed directly +this keyword is set to *on*, buffers in GPU memory are passed directly through MPI send/receive calls. This reduces overhead of first copying the data to the host CPU. However GPU-aware MPI is not supported on all systems, which can lead to segmentation faults and would require using a @@ -539,7 +539,7 @@ value of *off*\ . If LAMMPS can safely detect that GPU-aware MPI is not available (currently only possible with OpenMPI v2.0.0 or later), then the *gpu/aware* keyword is automatically set to *off* by default. When the *gpu/aware* keyword is set to *off* while any of the *comm* -keywords are set to *device*\ , the value for these *comm* keywords will +keywords are set to *device*, the value for these *comm* keywords will be automatically changed to *no*\ . This setting has no effect if not running on GPUs or if using only one MPI rank. GPU-aware MPI is available for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the @@ -643,7 +643,7 @@ with the GPU package. See the :doc:`Build package ` doc page for more info. The intel style of this command can only be invoked if LAMMPS was -built with the INTEL package. See the :doc:`Build package ` doc page for more info. +built with the INTEL package. See the :doc:`Build package ` page for more info. The kk style of this command can only be invoked if LAMMPS was built with the KOKKOS package. See the :doc:`Build package ` diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index abc8cb3c4c..87493724b0 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -72,7 +72,7 @@ where :math:`N` is the number of LAMMPS atom types: * filename * :math:`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 ` page for alternate ways to specify the path for the potential file. As an example, the potentials/AlCu.adp file, included in the @@ -156,7 +156,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index 2e4d95760f..8e91e57b72 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -57,7 +57,7 @@ pair_coeff command, where :math:`N` is the number of LAMMPS atom types: * filename * :math:`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 ` 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 @@ -74,13 +74,13 @@ the same arguments and should produce the same results, except for round-off and precision issues. The accelerated style is part of the OPENMP. They are only enabled -if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. You can specify the accelerated style explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -97,7 +97,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -113,7 +113,7 @@ It should work with damped dynamics based minimizers like *fire* or integration of the forces as discussed in :ref:`(Botu3) `. This pair style is part of the MISC package. It is only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. The AGNI force field files provided with LAMMPS (see the diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index d631d0a3d0..28d7811f06 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -122,7 +122,7 @@ would be 10.2 Angstroms. By default, the longer-ranged interaction is smoothly switched off between 2.16 and 3.0 :math:`\sigma`. By specifying *cutoff_min* in addition -to *cutoff*\ , the switching can be configured to take place between +to *cutoff*, the switching can be configured to take place between *cutoff_min* and *cutoff*\ . *cutoff_min* can only be specified if all optional arguments are given. @@ -131,7 +131,7 @@ various dihedral angle preferences in hydrocarbon configurations. ---------- -Only a single pair_coeff command is used with the *airebo*\ , *airebo* +Only a single pair_coeff command is used with the *airebo*, *airebo* or *rebo* style which specifies an AIREBO, REBO, or AIREBO-M potential file with parameters for C and H. Note that as of LAMMPS version 15 May 2019 the *rebo* style in LAMMPS uses its own potential @@ -142,7 +142,7 @@ where N is the number of LAMMPS atom types: * filename * :math:`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 ` 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 @@ -211,13 +211,13 @@ 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 -*inner* , *middle*, *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair potentials require the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_atm.rst b/doc/src/pair_atm.rst index 0bdfecd517..18c66961fb 100644 --- a/doc/src/pair_atm.rst +++ b/doc/src/pair_atm.rst @@ -155,7 +155,7 @@ 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 -*inner* , *middle* , *outer* keywords. +*inner*, *middle*, and *outer* keywords. ---------- @@ -163,7 +163,7 @@ Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst index 919656a8f5..604baceb8a 100644 --- a/doc/src/pair_awpmd.rst +++ b/doc/src/pair_awpmd.rst @@ -52,7 +52,7 @@ Rc is the cutoff. The pair_style command allows for several optional keywords to be specified. -The *hartree*\ , *dproduct*\ , and *uhf* keywords specify the form of the +The *hartree*, *dproduct*, and *uhf* keywords specify the form of the initial trial wave function for the system. If the *hartree* keyword is used, then a Hartree multielectron trial wave function is used. If the *dproduct* keyword is used, then a trial function which is a @@ -60,7 +60,7 @@ product of two determinants for each spin type is used. If the *uhf* keyword is used, then an unrestricted Hartree-Fock trial wave function is used. -The *free*\ , *pbc*\ , and *fix* keywords specify a width constraint on +The *free*, *pbc*, and *fix* keywords specify a width constraint on the electron wave packets. If the *free* keyword is specified, then there is no constraint. If the *pbc* keyword is used and *Plen* is specified as -1, then the maximum width is half the shortest box length. If *Plen* @@ -91,7 +91,7 @@ commands, or by mixing as described below: * cutoff (distance units) -For *awpmd/cut*\ , the cutoff coefficient is optional. If it is not +For *awpmd/cut*, the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default global value specified in the pair_style command is used. @@ -108,7 +108,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index 44bc317138..d220e0abdd 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -78,7 +78,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_body_nparticle.rst b/doc/src/pair_body_nparticle.rst index 963f9f4b50..24d5beeb3d 100644 --- a/doc/src/pair_body_nparticle.rst +++ b/doc/src/pair_body_nparticle.rst @@ -31,7 +31,7 @@ for more details on using body particles. This pair style is designed for use with the "nparticle" body style, which is specified as an argument to the "atom-style body" command. -See the :doc:`Howto body ` doc page for more details about +See the :doc:`Howto body ` page for more details about the body styles LAMMPS supports. The "nparticle" style treats a body particle as a rigid body composed of N sub-particles. @@ -74,7 +74,7 @@ interaction, using the standard formula where :math:`R_c` is the cutoff. As explained above, an interaction involving one or two body sub-particles may be computed even for :math:`r > R_c`. -For style *body*\ , the following coefficients must be defined for each +For style *body*, 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 ` @@ -104,7 +104,7 @@ This pair style does not write its information to :doc:`binary restart files ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -112,7 +112,7 @@ Restrictions """""""""""" 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. +was built with that package. See the :doc:`Build package ` 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. diff --git a/doc/src/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst index 6301bf23b1..6757d9d60e 100644 --- a/doc/src/pair_body_rounded_polygon.rst +++ b/doc/src/pair_body_rounded_polygon.rst @@ -34,7 +34,7 @@ Style *body/rounded/polygon* is for use with 2d models of body particles of style *rounded/polygon*\ . It calculates pairwise body/body interactions which can include body particles modeled as 1-vertex circular disks with a specified diameter. See the -:doc:`Howto body ` doc page for more details on using body +:doc:`Howto body ` page for more details on using body rounded/polygon particles. This pairwise interaction between rounded polygons is described in @@ -127,13 +127,13 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" These pair styles are part of the BODY package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst index 3ef4fb7ca2..f2f7c1676a 100644 --- a/doc/src/pair_body_rounded_polyhedron.rst +++ b/doc/src/pair_body_rounded_polyhedron.rst @@ -34,7 +34,7 @@ Style *body/rounded/polygon* is for use with 3d models of body particles of style *rounded/polyhedron*\ . It calculates pairwise body/body interactions which can include body particles modeled as 1-vertex spheres with a specified diameter. See the -:doc:`Howto body ` doc page for more details on using body +:doc:`Howto body ` page for more details on using body rounded/polyhedron particles. This pairwise interaction between the rounded polyhedra is described @@ -122,13 +122,13 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" These pair styles are part of the BODY package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index f566d41e2c..42b9c54406 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -372,7 +372,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -380,7 +380,7 @@ Restrictions """""""""""" These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair potentials require the :doc:`newtion ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 65be948f82..555e78eecd 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -147,7 +147,7 @@ The second coefficient, rho, must be greater than zero. The last coefficient is optional. If not specified, the global A,C,D cutoff specified in the pair_style command is used. -For *born/coul/long*\ , *born/coul/wolf* and *born/coul/dsf* no +For *born/coul/long*, *born/coul/wolf* and *born/coul/dsf* no Coulombic cutoff can be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. @@ -179,8 +179,8 @@ 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*\ , -*middle*\ , *outer* keywords. +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. ---------- @@ -188,7 +188,13 @@ Restrictions """""""""""" The *born/coul/long* style is part of the KSPACE package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. + +The *born/coul/dsf* and *born/coul/wolf* pair styles are part of the +EXTRA-PAIR package. They are only enabled if LAMMPS was built with +that package. See the :doc:`Build package ` page +for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index 43c17c9087..780a181a69 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -50,7 +50,7 @@ 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 when dissipative lubrication forces are acting. Thus the parameters -*mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , and *cutoff* should be +*mu*, *flaglog*, *flagfld*, *cutinner*, and *cutoff* should be specified consistent with the settings in the lubrication pair styles. For details, refer to either of the lubrication pair styles. @@ -104,7 +104,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -112,7 +112,7 @@ Restrictions """""""""""" These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Only spherical monodisperse particles are allowed for pair_style brownian. diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 5f255ece39..eb88d09fd0 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -100,7 +100,7 @@ where :math:`\rho` is an ionic-pair dependent length parameter, and 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 +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* or *msm* option. The Coulombic cutoff specified for this style means @@ -145,7 +145,7 @@ A,C and Coulombic cutoffs are used. If only one cutoff is specified, it is used as the cutoff for both A,C and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the A,C and Coulombic cutoffs for this type pair. You cannot specify -2 cutoffs for style *buck*\ , since it has no Coulombic terms. +2 cutoffs for style *buck*, since it has no Coulombic terms. For *buck/coul/long* only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the @@ -177,14 +177,14 @@ 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*\ , -*middle*\ , *outer* keywords. +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 """""""""""" The *buck/coul/long* style is part of the KSPACE package. They are -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 740ed0292f..be23f11416 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -136,7 +136,7 @@ Restrictions """""""""""" These styles are part of the MOFFF package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index 0e19873500..82dd41ff6f 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -64,22 +64,22 @@ settings. The :ref:`Ismail ` paper has more details on when it is appropriate to include long-range 1/r\^6 interactions, using this potential. -If *flag_buck* is set to *long*\ , no cutoff is used on the Buckingham +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 ` 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 +the Kspace style. If *flag_buck* is set to *cut*, the Buckingham interactions are simply cutoff, as with :doc:`pair_style buck `. -If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic +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 *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 -Coulombic interactions. If *flag_coul* is set to *off*\ , Coulombic +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 @@ -102,9 +102,9 @@ are used. If only one cutoff is specified, it is used as the cutoff for both Buckingham and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the Buckingham and Coulombic cutoffs for this type pair. Note that if you are using -*flag_buck* set to *long*\ , you cannot specify a Buckingham cutoff for +*flag_buck* set to *long*, you cannot specify a Buckingham cutoff for an atom type pair, since only one global Buckingham cutoff is allowed. -Similarly, if you are using *flag_coul* set to *long*\ , you cannot +Similarly, if you are using *flag_coul* set to *long*, you cannot specify a Coulombic cutoff for an atom type pair, since only one global Coulombic cutoff is allowed. @@ -135,7 +135,7 @@ the long-range Coulombic and dispersion interactions. This pair style write 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* +This pair style supports the use of the *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. See the :doc:`run_style ` command for @@ -147,7 +147,7 @@ Restrictions """""""""""" This style is part of the KSPACE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index b3d2a2b878..d45ef58060 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -169,7 +169,7 @@ where S(r) is the energy switching function mentioned above for the functional forms of the force switching and force shifting functions used in the *charmmfsw* and *charmmfsh* styles. -When using the *lj/charmm/coul/charmm styles*\ , both the LJ and +When using the *lj/charmm/coul/charmm styles*, both the LJ and Coulombic terms require an inner and outer cutoff. They can be the same for both formulas or different depending on whether 2 or 4 arguments are used in the pair_style command. For the @@ -193,7 +193,7 @@ biomolecule (no explicit water molecules). Styles *lj/charmm/coul/long* and *lj/charmm/coul/msm* compute the same 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 +*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 *ewald* or *pppm* or *msm* option. Only one Coulombic cutoff is @@ -260,7 +260,7 @@ pair_coeff commands do not need to be specified in an input script 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 +support the use of the *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 diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index f88663d36b..8c6f90efa8 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -100,7 +100,7 @@ class 2 and Coulombic cutoffs are used. If only one cutoff is specified, it is used as the cutoff for both class 2 and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the class 2 and Coulombic cutoffs for this type pair. -You cannot specify 2 cutoffs for style *lj/class2*\ , since it has no +You cannot specify 2 cutoffs for style *lj/class2*, since it has no Coulombic terms. For *lj/class2/coul/long* only the class 2 cutoff can be specified @@ -120,10 +120,10 @@ for mixing the cutoff distance. ---------- -A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in +A version of these styles with a soft core, *lj/cut/soft*, suitable for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is -only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only available if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. ---------- @@ -158,7 +158,7 @@ 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. @@ -167,7 +167,7 @@ Restrictions """""""""""" These styles are part of the CLASS2 package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index ea62d839ab..147b9177ec 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -78,7 +78,7 @@ 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 this option as it pertains to individual potentials are described on -the doc page for the potential. +the page for the potential. Many pair styles, typically for many-body potentials, use tabulated potential files as input, when specifying the pair_coeff command. diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index 040bea2487..9e68e65778 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -187,7 +187,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -195,7 +195,7 @@ Restrictions """""""""""" 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. +LAMMPS was built with that package. See the :doc:`Build package ` 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, diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index 2e164d46fc..aff28cd892 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -52,7 +52,7 @@ total energy :math:`E_T` of a system of atoms is given by where :math:`E_i^{self}` is the self-energy of atom *i* (including atomic ionization energies and electron affinities), :math:`E_{ij}^{short}` is the bond-order potential between atoms *i* and -*j*\ , :math:`E_{ij}^{Coul}` is the Coulomb interactions, +*j*, :math:`E_{ij}^{Coul}` is the Coulomb interactions, :math:`E^{polar}` is the polarization term for organic systems (style *comb3* only), :math:`E^{vdW}` is the van der Waals energy (style *comb3* only), :math:`E^{barr}` is a charge barrier function, and @@ -93,10 +93,10 @@ This can be used when a *comb* potential is used as part of the *hybrid* pair style. The NULL values are placeholders for atom types that will be used with other potentials. -For style *comb*\ , the provided potential file *ffield.comb* contains +For style *comb*, the provided potential file *ffield.comb* contains all currently-available second generation COMB parameterizations: for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style -*comb3*\ , the potential file *ffield.comb3* contains all +*comb3*, the potential file *ffield.comb3* contains all currently-available third generation COMB parameterizations: O, Cu, N, C, H, Ti, Zn and Zr. The status of the optimization of the compounds, for example Cu2O, TiN and hydrocarbons, are given in the @@ -126,8 +126,8 @@ following table: * M = Only optimized for dimer molecule * P = in progress, but have it from mixing rule -For style *comb3*\ , in addition to ffield.comb3, a special parameter -file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be +For style *comb3*, in addition to ffield.comb3, a special parameter +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 directories listed in the environment variable ``LAMMPS_POTENTIALS``, as @@ -139,7 +139,7 @@ has not yet been implemented, it can only set polar_off at present. .. note:: - You can not use potential file *ffield.comb* with style *comb3*\ , + You can not use potential file *ffield.comb* with style *comb3*, nor file *ffield.comb3* with style *comb*\ . ---------- @@ -164,7 +164,7 @@ restart file. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -172,7 +172,7 @@ Restrictions """""""""""" These pair styles are part of the MANYBODY package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair styles requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index 185bffff99..f68df419a4 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -93,14 +93,14 @@ Mixing, shift, table, tail correction, restart, rRESPA info Mixing is not supported for this style. -The *shift*\ , *table* and *tail* options are not relevant for this style. +The *shift*, *table* and *tail* options are not relevant for this 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. These pair 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -108,7 +108,7 @@ Restrictions """""""""""" The *cosine/squared* style is part of the EXTRA-PAIR package. It is only -enabled if LAMMPS is build with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS is build with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index b8303622aa..990458887d 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -283,7 +283,7 @@ Coulombic solver (Ewald or PPPM). atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the :doc:`Howto tip4p ` doc page for more information +See the :doc:`Howto tip4p ` page for more information on how to use the TIP4P pair styles and lists of parameters to set. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2\*qdist when using the TIP4P pair @@ -311,14 +311,14 @@ commands, or by mixing as described below: * cutoff (distance units) -For *coul/cut* and *coul/debye*\ , the cutoff coefficient is optional. +For *coul/cut* and *coul/debye* the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default global value specified in the pair_style command is used. -For *coul/long* and *coul/msm* no cutoff can be specified for an -individual I,J type pair via the pair_coeff command. All type pairs -use the same global Coulomb cutoff specified in the pair_style -command. +For *coul/cut/global*, *coul/long* and *coul/msm* no cutoff can be +specified for an individual I,J type pair via the pair_coeff command. +All type pairs use the same global Coulomb cutoff specified in the +pair_style command. ---------- @@ -349,17 +349,17 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -The *coul/long*\ , *coul/msm* and *tip4p/long* styles are part of the -KSPACE package. They are only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more -info. +The *coul/cut/global*, *coul/long*, *coul/msm*, *coul/streitz*, and *tip4p/long* styles +are part of the KSPACE package. They are only enabled if LAMMPS was built +with that package. See the :doc:`Build package ` doc page +for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index 573329a1bb..7dc245f449 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -90,13 +90,13 @@ pressure. 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. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" This style is part of the EXTRA-PAIR package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index 0ca656092e..a7f99500f5 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -77,14 +77,14 @@ pressure. 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. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" This pair style is part of the INTERLAYER package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul_slater.rst b/doc/src/pair_coul_slater.rst index f3dab4c778..443de4262b 100644 --- a/doc/src/pair_coul_slater.rst +++ b/doc/src/pair_coul_slater.rst @@ -93,7 +93,7 @@ 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. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" @@ -101,7 +101,7 @@ Restrictions The *coul/slater/long* style requires the long-range solvers included in the KSPACE package. These styles are part of the EXTRA-PAIR package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_coul_tt.rst b/doc/src/pair_coul_tt.rst index d1465ef147..f6c3a1f6f2 100644 --- a/doc/src/pair_coul_tt.rst +++ b/doc/src/pair_coul_tt.rst @@ -70,7 +70,7 @@ interactions between the (non-polarizable part of the) charge of a core, The :math:`b_{ij}` and :math:`c_{ij}` are equal to :math:`b_{ji}` and :math:`c_{ji}` in the case of core-core interactions. -For pair_style *coul/tt*\ , the following coefficients must be defined for +For pair_style *coul/tt*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the example above. @@ -97,7 +97,7 @@ Restrictions These pair styles are part of the DRUDE package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair_style should currently not be used with the :doc:`charmm dihedral style ` if the latter has non-zero 1-4 weighting diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index f41d840216..ef40eb310f 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -115,7 +115,7 @@ Description These pair styles are designed to be used with the adiabatic core/shell model of :ref:`(Mitchell and Finchham) `. See -the :doc:`Howto coreshell ` doc page for an overview of +the :doc:`Howto coreshell ` page for an overview of the model as implemented in LAMMPS. All the styles are identical to the corresponding pair style without @@ -181,7 +181,7 @@ Restrictions """""""""""" These pair styles are part of the CORESHELL package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_dielectric.rst b/doc/src/pair_dielectric.rst index 1af26a0921..c1f28c2089 100644 --- a/doc/src/pair_dielectric.rst +++ b/doc/src/pair_dielectric.rst @@ -105,13 +105,13 @@ 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. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" These styles are part of the DIELECTRIC package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 7645966229..372ea26794 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -242,19 +242,19 @@ dipole-charge, and charge-charge interactions are all supported, along with the standard 12/6 Lennard-Jones interactions. LJ interactions can be cutoff or long-ranged. -For style *lj/long/dipole/long*\ , if *flag_lj* is set to *long*\ , no +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 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 +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 are not computed at all. -If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic or +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 -*flag_coul* is set to *off*\ , Coulombic and dipole interactions are not +*flag_coul* is set to *off*, Coulombic and dipole interactions are not computed at all. Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere update dipole ` or the :doc:`fix nvt/sphere update dipole ` command to rotate the @@ -320,15 +320,15 @@ 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. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" -The *lj/cut/dipole/cut*\ , *lj/cut/dipole/long*\ , *lj/long/dipole/long*, +The *lj/cut/dipole/cut*, *lj/cut/dipole/long*, *lj/long/dipole/long*, and lj/sf/dipole/sf* styles are part of the DIPOLE package. They are only enabled if LAMMPS was built with that package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Using dipole pair styles with *electron* :doc:`units ` is not currently supported. diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index aa8323379a..8a8b35e50a 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -57,7 +57,7 @@ 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 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 +For style *dpd*, the force on atom I due to atom J is given as a sum of 3 terms .. math:: @@ -79,18 +79,18 @@ is set equal to :math:`\sqrt{2 k_B T \gamma}`, where :math:`k_B` is the Boltzmann constant and T is the temperature parameter in the pair_style command. -For style *dpd/tstat*\ , the force on atom I due to atom J is the same +For style *dpd/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative Fc term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. -For style *dpd*\ , the pairwise energy associated with style *dpd* is +For style *dpd*, the pairwise energy associated with style *dpd* is only due to the conservative force term Fc, and is shifted to be zero at the cutoff distance Rc. The pairwise virial is calculated using 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 +For style *dpd*, 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 ` @@ -105,7 +105,7 @@ 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 ` command so it does not need to be specified. -For style *dpd/tstat*\ , the coefficients defined for each pair of +For style *dpd/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. @@ -165,7 +165,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. The *dpd/tstat* style can ramp its target temperature over multiple runs, using the *start* and *stop* keywords of the :doc:`run ` @@ -179,7 +179,7 @@ Restrictions These styles are part of the DPD-BASIC package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index 0523a19e0b..7512f8e688 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -49,7 +49,7 @@ 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 the style *dpd/ext*\ , the force on atom I due to atom J is given as +For the style *dpd/ext*, the force on atom I due to atom J is given as a sum of 3 terms .. math:: @@ -78,12 +78,12 @@ unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. -For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is +For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. -For the style *dpd/ext*\ , the pairwise energy associated with style +For the style *dpd/ext*, the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three @@ -95,7 +95,7 @@ same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. -For the style *dpd/ext*\ , the pairwise energy associated with style +For the style *dpd/ext*, the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three @@ -157,7 +157,7 @@ energy and pressure. The pair styles can only be used via the pair keyword of the :doc:`run_style respa ` command. They do not support the -*inner*\ , *middle*\ , and *outer*\ keywords. +*inner*, *middle*, and *outer*\ keywords. The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` @@ -171,7 +171,7 @@ Restrictions These styles are part of the DPD-BASIC package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index 8767c5b99e..25fe2581db 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -77,7 +77,7 @@ following functional form: Note that alternative definitions of the weighting function exist, but would have to be implemented as a separate pair style command. -For style *dpd/fdt*\ , the fluctuation-dissipation theorem defines :math:`\gamma` +For style *dpd/fdt*, the fluctuation-dissipation theorem defines :math:`\gamma` to be set equal to :math:`\sigma^2/(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 @@ -163,7 +163,7 @@ Restrictions """""""""""" These commands are part of the DPD-REACT package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` 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 diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst index 39a5e8bbef..f7b01eee25 100644 --- a/doc/src/pair_drip.rst +++ b/doc/src/pair_drip.rst @@ -119,7 +119,7 @@ Restrictions This pair style is part of the INTERLAYER package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_dsmc.rst b/doc/src/pair_dsmc.rst index d7542ea801..b0a508b054 100644 --- a/doc/src/pair_dsmc.rst +++ b/doc/src/pair_dsmc.rst @@ -131,7 +131,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -139,7 +139,7 @@ Restrictions """""""""""" This style is part of the MC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index 9aeebfc020..b75fb8450c 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -98,7 +98,7 @@ The *preset 2015* option should be used with the :doc:`TIP4P/2005 water model ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index a8b67e7f41..fd05d7189e 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -145,7 +145,7 @@ provides EAM potentials that can be used directly in LAMMPS with the ---------- -For style *eam*\ , potential values are read from a file that is in the +For style *eam*, potential values are read from a file that is in the DYNAMO single-element *funcfl* format. If the DYNAMO file was created by a Fortran program, it cannot have "D" values in it for exponents. C only recognizes "e" or "E" for scientific notation. @@ -225,7 +225,7 @@ above, *setfl* files contain explicit tabulated values for alloy interactions. Thus they allow more generality than *funcfl* files for modeling alloys. -For style *eam/alloy*\ , potential values are read from a file that is +For style *eam/alloy*, potential values are read from a file that is in the DYNAMO multi-element *setfl* format, except that element names (Ni, Cu, etc) are added to one of the lines in the file. If the DYNAMO file was created by a Fortran program, it cannot have "D" @@ -372,7 +372,7 @@ require that; the user can tabulate any functional form desired in the FS potential files. For style *eam/fs* and *eam/he* the form of the pair_coeff command is exactly -the same as for style *eam/alloy*\ , e.g. +the same as for style *eam/alloy*, e.g. .. code-block:: LAMMPS @@ -383,13 +383,13 @@ 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 -with *eam/alloy*\ , if a mapping value is NULL, the mapping is not +with *eam/alloy*, if a mapping value is NULL, the mapping is not performed. This can be used when an *eam/fs* or *eam/he* potential is used as part of a *hybrid* pair style. The NULL values are used as placeholders for atom types that will be used with other potentials. FS EAM and HE EAM files include more information than the DYNAMO *setfl* -format files read by *eam/alloy*\ , in that i,j density functionals for +format files read by *eam/alloy*, in that i,j density functionals for all pairs of elements are included as needed by the Finnis/Sinclair formulation of the EAM. @@ -465,7 +465,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -473,7 +473,7 @@ Restrictions """""""""""" All of these styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index b57ba3d162..6b6bfbb11b 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -69,7 +69,7 @@ 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 ` 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. @@ -142,7 +142,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index ceb571a58d..b104b01b40 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -141,7 +141,7 @@ commands, or by mixing as described below: * cutoff (distance units) -For *eff/cut*\ , the cutoff coefficient is optional. If it is not used +For *eff/cut*, the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default global value specified in the pair_style command is used. @@ -283,7 +283,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -292,7 +292,7 @@ Restrictions These pair styles will only be enabled if LAMMPS is built with the EFF package. It will only be enabled if LAMMPS was built with -that package. See the :doc:`Build package ` doc page for +that package. See the :doc:`Build package ` page for more info. These pair styles require that particles store electron attributes diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index 8360dbab64..c84bce9d53 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -105,7 +105,7 @@ 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 ` 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 diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index e9550c2152..55395bcd0d 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -71,7 +71,7 @@ to be the internal chemical energy (uChem). The fourth argument specifies the type of scaling that will be used to scale the EXP-6 parameters as reactions occur. Currently, there -are three scaling options: *exponent*\ , *polynomial* and *none*\ . +are three scaling options: *exponent*, *polynomial* and *none*\ . Exponent scaling requires two additional arguments for scaling the :math:`R_m` and :math:`\epsilon` parameters, respectively. The scaling factor @@ -179,7 +179,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index 6f8954a0a7..400ad0cc4a 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -259,7 +259,7 @@ LJ and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both LJ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. You cannot specify 2 cutoffs for style *lj/cut/soft*\ , +type pair. You cannot specify 2 cutoffs for style *lj/cut/soft*, since it has no Coulombic terms. For the *coul/cut/soft* and *coul/long/soft* only lambda and the optional cutoff2 are to be specified. @@ -290,7 +290,7 @@ activation parameter lambda is introduced as an argument of the the :doc:`pair_coeff ` command, after :math:`\epsilon` and :math:`\sigma` and before the optional cutoffs. -The *coul/cut/soft*\ , *coul/long/soft* and *tip4p/long/soft* sub-styles are +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 they have no repulsive core. Hence, if used by themselves, there will be no repulsion to keep two @@ -304,7 +304,7 @@ the second coefficient. .. note:: When using the soft-core Coulomb potentials with long-range solvers (\ - *coul/long/soft*\ , *lj/cut/coul/long/soft*\ , etc.) in a free energy + *coul/long/soft*, *lj/cut/coul/long/soft*, etc.) in a free energy calculation in which sites holding electrostatic charges are being created or annihilated (using :doc:`fix adapt/fep ` and :doc:`compute fep `) it is important to adapt both the :math:`\lambda` activation @@ -417,7 +417,7 @@ The pair styles with soft core are only enabled if LAMMPS was built with the FEP package. The *long* versions also require the KSPACE package to be installed. The soft *tip4p* versions also require the MOLECULE package to be installed. These styles are only enabled if LAMMPS was built with those -packages. See the :doc:`Build package ` doc page for more +packages. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index 71b8df6e3a..4eb45a416b 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -143,7 +143,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. The *gauss* pair style tallies an "occupancy" count of how many Gaussian-well sites have an atom within the distance at which the force is a maximum @@ -165,7 +165,7 @@ Restrictions The *gauss* and *gauss/cut* styles are part of the EXTRA-PAIR package. They are only enabled if LAMMPS is build with that package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. The *gauss* style does not apply :doc:`special_bonds ` factors. When using this pair style on a system that has bonds, the diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 448f3a26de..09bc3706c2 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -178,7 +178,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -186,7 +186,7 @@ Restrictions """""""""""" The *gayberne* 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. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair styles require that atoms store torque and a quaternion to represent their orientation, as defined by the diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index fbcacb5c76..c4024a391a 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -101,7 +101,7 @@ damping force. The tangential force also has 2 terms: a shear force and a damping force. The shear force is a "history" effect that accounts for the tangential displacement between the particles for the duration of the time they are in contact. This term is included in -pair styles *hooke/history* and *hertz/history*\ , but is not included +pair styles *hooke/history* and *hertz/history*, but is not included in pair style *hooke*\ . The tangential damping force term is included in all three pair styles if *dampflag* is set to 1; it is not included if *dampflag* is set to 0. @@ -240,7 +240,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. The single() function of these pair styles returns 0.0 for the energy of a pairwise interaction, since energy is not conserved in these @@ -254,7 +254,7 @@ normal direction (along the line joining the 2 sphere centers). The last 3 (8-10) the components of the relative velocity in the tangential direction. -These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*\ , *p2*\ , ..., +These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*, *p2*, ..., *p10*\ . ---------- @@ -263,7 +263,7 @@ Restrictions """""""""""" 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. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` 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 diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index dea862b62d..b7f9da9f8b 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -99,8 +99,8 @@ Where :math:`\delta_{ij} = R_i + R_j - \|\mathbf{r}_{ij}\|` is the particle overlap, :math:`R_i, R_j` are the particle radii, :math:`\mathbf{r}_{ij} = \mathbf{r}_i - \mathbf{r}_j` is the vector separating the two particle centers (note the i-j ordering so that :math:`F_{ne}` is positive for repulsion), and :math:`\mathbf{n} = \frac{\mathbf{r}_{ij}}{\|\mathbf{r}_{ij}\|}`. Therefore, -for *hooke*\ , the units of the spring constant :math:`k_n` are -*force*\ /\ *distance*\ , or equivalently *mass*\ /*time\^2*. +for *hooke*, the units of the spring constant :math:`k_n` are +*force*\ /\ *distance*, or equivalently *mass*\ /*time\^2*. For the *hertz* model, the normal component of force is given by: @@ -109,7 +109,7 @@ For the *hertz* model, the normal component of force is given by: \mathbf{F}_{ne, Hertz} = k_n R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n} Here, :math:`R_{eff} = \frac{R_i R_j}{R_i + R_j}` is the effective -radius, denoted for simplicity as *R* from here on. For *hertz*\ , the +radius, denoted for simplicity as *R* from here on. For *hertz*, the units of the spring constant :math:`k_n` are *force*\ /\ *length*\ \^2, or equivalently *pressure*\ . @@ -188,7 +188,7 @@ for the damping model currently supported are: If the *damping* keyword is not specified, the *viscoelastic* model is used by default. -For *damping velocity*\ , the normal damping is simply equal to the +For *damping velocity*, the normal damping is simply equal to the user-specified damping coefficient in the *normal* model: .. math:: @@ -219,8 +219,8 @@ damping is given by: \eta_n = \eta_{n0}\ a m_{eff} Here, *a* is the contact radius, given by :math:`a =\sqrt{R\delta}` -for all models except *jkr*\ , for which it is given implicitly according -to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`. For *damping viscoelastic*\ , +for all models except *jkr*, for which it is given implicitly according +to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`. For *damping viscoelastic*, :math:`\eta_{n0}` is in units of 1/(\ *time*\ \*\ *distance*\ ). The *tsuji* model is based on the work of :ref:`(Tsuji et al) `. Here, the damping coefficient specified as part of @@ -302,14 +302,14 @@ The direction of the applied force is :math:`\mathbf{t} = \mathbf{v_{t,rel}}/\|\ The normal force value :math:`F_{n0}` used to compute the critical force depends on the form of the contact model. For non-cohesive models -(\ *hertz*\ , *hertz/material*\ , *hooke*\ ), it is given by the magnitude of +(\ *hertz*, *hertz/material*, *hooke*\ ), it is given by the magnitude of the normal force: .. math:: F_{n0} = \|\mathbf{F}_n\| -For cohesive models such as *jkr* and *dmt*\ , the critical force is +For cohesive models such as *jkr* and *dmt*, the critical force is adjusted so that the critical tangential force approaches :math:`\mu_t F_{pulloff}`, see :ref:`Marshall `, equation 43, and :ref:`Thornton `. For both models, :math:`F_{n0}` takes the form: @@ -318,7 +318,7 @@ form: F_{n0} = \|\mathbf{F}_{ne} + 2 F_{pulloff}\| -Where :math:`F_{pulloff} = 3\pi \gamma R` for *jkr*\ , and +Where :math:`F_{pulloff} = 3\pi \gamma R` for *jkr*, and :math:`F_{pulloff} = 4\pi \gamma R` for *dmt*\ . The remaining tangential options all use accumulated tangential @@ -392,7 +392,7 @@ overlap region) to induce a torque on each particle according to: \mathbf{\tau}_j = -(R_j - 0.5 \delta) \mathbf{n} \times \mathbf{F}_t -For *tangential mindlin*\ , the :ref:`Mindlin ` no-slip solution +For *tangential mindlin*, the :ref:`Mindlin ` no-slip solution is used which differs from the *linear_history* option by an additional factor of :math:`a`, the radius of the contact region. The tangential force is given by: @@ -402,7 +402,7 @@ of :math:`a`, the radius of the contact region. The tangential force is given by Here, :math:`a` is the radius of the contact region, given by :math:`a =\sqrt{R\delta}` -for all normal contact models, except for *jkr*\ , where it is given +for all normal contact models, except for *jkr*, where it is given implicitly by :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`, see discussion above. To match the Mindlin solution, one should set :math:`k_t = 8G_{eff}`, where :math:`G_{eff}` is the effective shear modulus given by: @@ -415,7 +415,7 @@ where :math:`G` is the shear modulus, related to Young's modulus :math:`E` and Poisson's ratio :math:`\nu` by :math:`G = E/(2(1+\nu))`. This can also be achieved by specifying *NULL* for :math:`k_t`, in which case a normal contact model that specifies material parameters :math:`E` and -:math:`\nu` is required (e.g. *hertz/material*\ , *dmt* or *jkr*\ ). In this +:math:`\nu` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this case, mixing of the shear modulus for different particle types *i* and *j* is done according to the formula above. @@ -455,7 +455,7 @@ the critical force: The same rules as those described for *mindlin* apply regarding the tangential stiffness and mixing of the shear modulus for different particle types. -The *mindlin_rescale* option uses the same form as *mindlin*\ , but the +The *mindlin_rescale* option uses the same form as *mindlin*, but the magnitude of the tangential displacement is re-scaled as the contact unloads, i.e. if :math:`a < a_{t_{n-1}}`: @@ -504,7 +504,7 @@ pure rolling motion of particles. The options currently supported are: If the *rolling* keyword is not specified, the model defaults to *none*\ . -For *rolling sds*\ , rolling friction is computed via a +For *rolling sds*, rolling friction is computed via a spring-dashpot-slider, using a 'pseudo-force' formulation, as detailed by :ref:`Luding `. Unlike the formulation in :ref:`Marshall `, this allows for the required adjustment of @@ -564,7 +564,7 @@ supported are: If the *twisting* keyword is not specified, the model defaults to *none*\ . -For both *twisting sds* and *twisting marshall*\ , a history-dependent +For both *twisting sds* and *twisting marshall*, a history-dependent spring-dashpot-slider is used to compute the twisting torque. Because twisting displacement is a scalar, there is no need to adjust for changes in the frame of reference due to rotations of the particle @@ -591,7 +591,7 @@ if the twisting torque exceeds this critical value: \xi_{twist} = \frac{1}{k_{twist}} (\mu_{twist} F_{n,0}sgn(\Omega_{twist}) - \gamma_{twist}\Omega_{twist}) -For *twisting sds*\ , the coefficients :math:`k_{twist}, \gamma_{twist}` +For *twisting sds*, the coefficients :math:`k_{twist}, \gamma_{twist}` and :math:`\mu_{twist}` are simply the user input parameters that follow the *twisting sds* keywords in the *pair_coeff* command. @@ -684,7 +684,7 @@ interactions is set to :math:`\mu_1`, and friction coefficient for type for type1-type2 interactions is computed as :math:`\sqrt{\mu_1\mu_2}` (unless explicitly specified to a different value by a *pair_coeff 1 2 ...* command). The exception to this is elastic modulus, only -applicable to *hertz/material*\ , *dmt* and *jkr* normal contact +applicable to *hertz/material*, *dmt* and *jkr* normal contact models. In that case, the effective elastic modulus is computed as: .. math:: @@ -709,7 +709,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. The single() function of these pair styles returns 0.0 for the energy of a pairwise interaction, since energy is not conserved in these @@ -725,7 +725,7 @@ about the vector connecting the two particle centers. The last 3 (10-12) are the components of the vector connecting the centers of the two particles (x_I - x_J). -These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*\ , *p2*\ , ..., +These extra quantities can be accessed by the :doc:`compute pair/local ` command, as *p1*, *p2*, ..., *p12*\ . ---------- @@ -734,7 +734,7 @@ Restrictions """""""""""" 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. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` 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 @@ -759,7 +759,7 @@ Related commands Default """"""" -For the *pair_coeff* settings: *damping viscoelastic*\ , *rolling none*\ , +For the *pair_coeff* settings: *damping viscoelastic*, *rolling none*, *twisting none*\ . References diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index 88cb4ce880..ed24b481f9 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -140,13 +140,16 @@ 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 -support the *inner*\ , *middle*\ , *outer* keywords. +support the *inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" - none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index d0a7e69b00..6945356ecd 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -51,7 +51,7 @@ 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 ` 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. @@ -96,7 +96,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -104,7 +104,7 @@ Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 5e7183a348..f9b2a010fd 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -88,7 +88,7 @@ potential for the Donor-Acceptor interactions. :ref:`(Liu) ` showed that the Morse form gives improved results for Dendrimer simulations, when n = 2. -See the :doc:`Howto bioFF ` doc page for more information +See the :doc:`Howto bioFF ` page for more information on the DREIDING force field. .. note:: @@ -170,11 +170,11 @@ 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 ` -command doc page for details. +command page for details. -If the donor flag is *i*\ , then the atom of type I in the pair_coeff +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 +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. @@ -219,7 +219,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. These pair styles tally a count of how many hydrogen bonding interactions they calculate each timestep and the hbond energy. These diff --git a/doc/src/pair_hdnnp.rst b/doc/src/pair_hdnnp.rst index ff1739aa9a..1bd3030bf5 100644 --- a/doc/src/pair_hdnnp.rst +++ b/doc/src/pair_hdnnp.rst @@ -182,7 +182,7 @@ 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*\ , *middle*\ , *outer* +` command. It does not support the *inner*, *middle*, *outer* keywords. Restrictions diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index b9b51e04c0..972c30c36f 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -83,7 +83,7 @@ general any combination of pair potentials can be used together in to produce an interaction that is not encoded in any single pair_style file, e.g. adding Coulombic forces between granular particles. -If the *hybrid/scaled* style is used instead of *hybrid/overlay*\ , +If the *hybrid/scaled* style is used instead of *hybrid/overlay*, contributions from sub-styles are weighted by their scale factors, which may be fractional or even negative. Furthermore the scale factors may be variables that may change during a simulation. This enables @@ -288,7 +288,7 @@ 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 ` page for details on the specific syntax, requirements and restrictions. ---------- @@ -375,7 +375,7 @@ coefficients to 0.0. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -391,13 +391,13 @@ exist. Otherwise the non-accelerated version will be used. The individual accelerated sub-styles are part of the GPU, KOKKOS, INTEL, OPENMP, and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build -package ` doc page for more info. +package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -422,7 +422,7 @@ generated, even if the sub-styles support mixing, and I,J pair coefficients must be explicitly defined. See the :doc:`pair_modify ` command for -details of mixing rules. See the See the doc page for the sub-style to +details of mixing rules. See the See the page for the sub-style to see if allows for mixing. The hybrid pair styles supports the :doc:`pair_modify ` @@ -439,7 +439,7 @@ style *hybrid/scaled* also the names of any variables used as scale factors are restored, but not the variables themselves, so those may need to be redefined when continuing from a restart. -These pair styles support the use of the *inner*\ , *middle*\ , and +These pair styles support the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, if their sub-styles do. diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index 63357dc926..c188b4011e 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -77,7 +77,7 @@ calculating the normals. The parameter file (e.g. BNCH.ILP), is intended for use with *metal* :doc:`units `, with energies in meV. Two additional parameters, -*S*\ , and *rcut* are included in the parameter file. *S* is designed to +*S*, and *rcut* are included in the parameter file. *S* is designed to facilitate scaling of energies. *rcut* is designed to build the neighbor list for calculating the normals for each atom pair. @@ -141,7 +141,7 @@ Restrictions This pair style is part of the INTERLAYER package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair style requires the newton setting to be *on* for pair interactions. diff --git a/doc/src/pair_kim.rst b/doc/src/pair_kim.rst index 551a0bc46e..fcc86e0d77 100644 --- a/doc/src/pair_kim.rst +++ b/doc/src/pair_kim.rst @@ -99,7 +99,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index 9408148e72..1a33a3f4bb 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -64,7 +64,7 @@ can be found in pair style :doc:`ilp/graphene/hbn `. thus a data file with the "full" atom style is required to use this potential. The parameter file (e.g. CH.KC), is intended for use with *metal* -:doc:`units `, with energies in meV. Two additional parameters, *S*\ , +:doc:`units `, with energies in meV. Two additional parameters, *S*, and *rcut* are included in the parameter file. *S* is designed to facilitate scaling of energies. *rcut* is designed to build the neighbor list for calculating the normals for each atom pair. @@ -121,7 +121,7 @@ Restrictions This pair style is part of the INTERLAYER package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair style requires the newton setting to be *on* for pair interactions. diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index 60c012c47c..937d868b55 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -48,7 +48,7 @@ each layer should have a separate atom type and interactions should only be computed between atom types of neighboring layers. The parameter file (e.g. CC.KC), is intended for use with metal -:doc:`units `, with energies in meV. An additional parameter, *S*\ , +:doc:`units `, with energies in meV. An additional parameter, *S*, is available to facilitate scaling of energies in accordance with :ref:`(vanWijk) `. @@ -60,7 +60,7 @@ Restrictions This fix is part of the INTERLAYER package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst index c44ad1f8a4..e8a6ccd7a4 100644 --- a/doc/src/pair_lcbop.rst +++ b/doc/src/pair_lcbop.rst @@ -34,7 +34,7 @@ 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 ` 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 @@ -70,14 +70,14 @@ 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. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. This pair potential requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst index 369828784c..5afd0da92c 100644 --- a/doc/src/pair_lebedeva_z.rst +++ b/doc/src/pair_lebedeva_z.rst @@ -44,7 +44,7 @@ that the exponential part of :math:`V_{ij}` (first term) decays sufficiently fas This shift is achieved by the last term in the equation for :math:`V_{ij}` above. The parameter file (e.g. CC.Lebedeva), is intended for use with metal -:doc:`units `, with energies in meV. An additional parameter, *S*\ , +:doc:`units `, with energies in meV. An additional parameter, *S*, is available to facilitate scaling of energies. This potential must be used in combination with hybrid/overlay. @@ -55,7 +55,7 @@ Restrictions This pair style is part of the INTERLAYER package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst index c803d327e2..bfea7d172a 100644 --- a/doc/src/pair_line_lj.rst +++ b/doc/src/pair_line_lj.rst @@ -32,7 +32,7 @@ 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 interactions. +` page for the definition of Lennard-Jones interactions. The set of non-overlapping spherical sub-particles that represent a line segment are generated in the following manner. Their size is a @@ -76,7 +76,7 @@ the pair of particles to be included in the neighbor list. setting that is consistent with the length of the line segments you are using and the sub-particle cutoff settings. -For style *line/lj*\ , the following coefficients must be defined for +For style *line/lj*, 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 or restart files read by the :doc:`read_data ` or :doc:`read_restart ` @@ -126,7 +126,7 @@ This pair style does not write its information to :doc:`binary restart files ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -134,7 +134,7 @@ Restrictions """""""""""" 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. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Defining particles to be line segments so they participate in line/line or line/particle interactions requires the use the diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst index ea0ac282da..321bf61be9 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -125,7 +125,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -143,7 +143,7 @@ atom J (assuming the images are within the cutoff distance), but only with the nearest image. This style is part of the MISC package. It is only enabled if -LAMMPS is build with that package. See the :doc:`Build package ` doc page on for more info. +LAMMPS is build with that package. See the :doc:`Build package ` page on for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index c42f3ffbb8..939756e550 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -72,7 +72,7 @@ LJ cutoff specified in the pair_style command are used. ---------- -A version of these styles with a soft core, *lj/cut/soft*\ , suitable +A version of these styles with a soft core, *lj/cut/soft*, suitable for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. @@ -104,7 +104,7 @@ 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* 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. diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 3f1172618b..47000fe70a 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -79,7 +79,7 @@ pressure of the pair interaction. 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* +This pair style supports the use of the *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. See the :doc:`run_style ` command for @@ -89,7 +89,10 @@ details. Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index e220e6e67c..d6470b26be 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -98,13 +98,16 @@ not need to be specified in an input script that reads a restart file. The lj/cubic 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. +support the *inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" - none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst index 30ea469071..e04da852dd 100644 --- a/doc/src/pair_lj_cut_coul.rst +++ b/doc/src/pair_lj_cut_coul.rst @@ -244,7 +244,7 @@ the pair_style command. ---------- A version of these styles with a soft core, *lj/cut/coul/soft*\ and -*lj/cut/coul/long/soft*\ , suitable for use in free energy calculations, is +*lj/cut/coul/long/soft*, suitable for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. ---------- @@ -278,7 +278,7 @@ 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/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. @@ -288,9 +288,13 @@ See the :doc:`run_style ` command for details. Restrictions """""""""""" -The *lj/cut/coul/long* styles are part of the KSPACE package. -These styles are only enabled if LAMMPS was built with those -packages. See the :doc:`Build package ` doc page for +The *lj/cut/coul/long* and *lj/cut/coul/msm* styles are part of the KSPACE package. + +The *lj/cut/coul/debye*, *lj/cut/coul/dsf*, and *lj/cut/coul/wolf* styles are part +of the EXTRA-PAIR package. + +These styles are only enabled if LAMMPS was built with those respective +packages. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_lj_cut_tip4p.rst b/doc/src/pair_lj_cut_tip4p.rst index 273483c941..7198b60159 100644 --- a/doc/src/pair_lj_cut_tip4p.rst +++ b/doc/src/pair_lj_cut_tip4p.rst @@ -109,7 +109,7 @@ long-range Coulombic solver (Ewald or PPPM). atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the :doc:`Howto tip4p ` doc page for more information +See the :doc:`Howto tip4p ` page for more information on how to use the TIP4P pair styles and lists of parameters to set. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2\*qdist when using the TIP4P pair @@ -163,7 +163,7 @@ the pair_style command. ---------- -A version of these styles with a soft core, *lj/cut/tip4p/long/soft*\ , suitable +A version of these styles with a soft core, *lj/cut/tip4p/long/soft*, suitable for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. @@ -199,7 +199,7 @@ 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. @@ -212,7 +212,7 @@ Restrictions The *lj/cut/tip4p/long* styles are part of the KSPACE package. The *lj/cut/tip4p/cut* style is part of the MOLECULE package. These styles are only enabled if LAMMPS was built with those -packages. See the :doc:`Build package ` doc page for +packages. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 4d619a67e2..dca7a2dd2f 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -108,7 +108,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index f190d7b502..f7bdf49189 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -113,7 +113,7 @@ massless charge site are specified as pair_style arguments. atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the :doc:`Howto tip4p ` doc page for more +See the :doc:`Howto tip4p ` page for more information on how to use the TIP4P pair style. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2\*qdist when using the TIP4P pair style, to account for @@ -123,22 +123,22 @@ LJ cutoff >= Coulombic cutoff + 2\*qdist, 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. -If *flag_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6 +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 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 +*flag_lj* is set to *cut*, the LJ interactions are simply cutoff, as with :doc:`pair_style lj/cut `. -If *flag_coul* is set to *long*\ , no cutoff is used on the Coulombic +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 *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 -interactions. If *flag_coul* is set to *off*\ , Coulombic interactions +interactions. If *flag_coul* is set to *off*, Coulombic interactions are not computed. The following coefficients must be defined for each pair of atoms @@ -163,10 +163,10 @@ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this type pair. -Note that if you are using *flag_lj* set to *long*\ , you +Note that if you are using *flag_lj* set to *long*, you cannot specify a LJ cutoff for an atom type pair, since only one global LJ cutoff is allowed. Similarly, if you are using *flag_coul* -set to *long*\ , you cannot specify a Coulombic cutoff for an atom type +set to *long*, you cannot specify a Coulombic cutoff for an atom type pair, since only one global Coulombic cutoff is allowed. For *lj/long/tip4p/long* only the LJ cutoff can be specified @@ -176,10 +176,10 @@ specified in the pair_style command. ---------- -A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in +A version of these styles with a soft core, *lj/cut/soft*, suitable for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is -only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only available if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. ---------- @@ -210,8 +210,8 @@ Lennard-Jones portion of the energy and pressure. 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. -The pair lj/long/coul/long styles support the use of the *inner*\ , -*middle*\ , and *outer* keywords of the :doc:`run_style respa ` +The pair lj/long/coul/long styles support the use of the *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. See the :doc:`run_style ` command for details. @@ -222,7 +222,7 @@ Restrictions """""""""""" These styles are part of the KSPACE package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_relres.rst b/doc/src/pair_lj_relres.rst index 20a705d876..df5227ebbb 100644 --- a/doc/src/pair_lj_relres.rst +++ b/doc/src/pair_lj_relres.rst @@ -235,7 +235,7 @@ For atom type pairs :math:`I,\:J` with :math:`I\;!=J`, the :math:`\sigma^{CG}`, :math:`r_{si}`, :math:`r_{so}`, :math:`r_{ci}`, and :math:`r_{co}` parameters for this pair style can be mixed, if not defined explicitly. All parameters are mixed according to the -pair_modify mix option. The default mix value is *geometric*\ , +pair_modify mix option. The default mix value is *geometric*, and it is recommended to use with this *lj/relres* style. See the "pair_modify" command for details. @@ -259,13 +259,16 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index a77eefd023..4799ca3277 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -102,13 +102,16 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index b105fc4911..7a3ba7a3d5 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -82,13 +82,16 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" - none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index 631addeb57..19ca8df973 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -130,14 +130,14 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" These styles are part of the YAFF package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst index c2bae5ced9..f7e26389c3 100644 --- a/doc/src/pair_local_density.rst +++ b/doc/src/pair_local_density.rst @@ -114,8 +114,8 @@ with the LD expressed as \rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij}) -where :math:`\alpha` gives the type of atom *i*\ , :math:`\beta` the -type of atom *j*\ , and the coefficients *a* and *b* filter for atom +where :math:`\alpha` gives the type of atom *i*, :math:`\beta` the +type of atom *j*, and the coefficients *a* and *b* filter for atom types as specified by the user. *a* is called the central atom filter as it determines to which atoms the potential applies; :math:`a_{\alpha} = 1` if the LD potential applies to atom type :math:`\alpha` else zero. On the @@ -222,7 +222,7 @@ Restrictions The local/density pair style is a part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index e83a16c80b..49872c31f2 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -139,8 +139,8 @@ 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 -and the brownian style should use consistent parameters for *mu*\ , -*flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ . +and the brownian style should use consistent parameters for *mu*, +*flaglog*, *flagfld*, *cutinner*, *cutoff*, *flagHI* and *flagVF*\ . ---------- @@ -185,7 +185,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -193,7 +193,7 @@ Restrictions """""""""""" These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Only spherical monodisperse particles are allowed for pair_style lubricate. diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index a9382556c5..2706291da1 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -137,15 +137,15 @@ for with the following types of walls: :doc:`wall/lj93 `, volume fraction will be used when walls do not coincide with the box boundary, as well as when walls move and thereby cause a change in the volume fraction. To use these wall styles with pair_style *lubricateU* -or *lubricateU/poly*\ , the *fld yes* option must be specified in the +or *lubricateU/poly*, the *fld yes* option must be specified in the 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 -and the brownian style should use consistent parameters for *mu*\ , -*flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ . +and the brownian style should use consistent parameters for *mu*, +*flaglog*, *flagfld*, *cutinner*, *cutoff*, *flagHI* and *flagVF*\ . ---------- @@ -186,7 +186,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -194,7 +194,7 @@ Restrictions """""""""""" These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Currently, these pair styles assume that all other types of forces/torques on the particles have been already been computed when diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 1e4ad1f8d6..dc2667dba7 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -53,7 +53,7 @@ Examples Description """"""""""" -The *lj/mdf*\ , *buck/mdf* and *lennard/mdf* compute the standard 12-6 +The *lj/mdf*, *buck/mdf* and *lennard/mdf* compute the standard 12-6 Lennard-Jones and Buckingham potential with the addition of a taper function that ramps the energy and force smoothly to zero between an inner and outer cutoff. @@ -62,7 +62,7 @@ inner and outer cutoff. E_{smooth}(r) = E(r)*f(r) -The tapering, *f(r)*\ , is done by using the Mei, Davenport, Fernando +The tapering, *f(r)*, is done by using the Mei, Davenport, Fernando function :ref:`(Mei) `. .. math:: @@ -82,7 +82,7 @@ outer cutoff radius. ---------- -For the *lj/mdf* pair_style, the potential energy, *E(r)*\ , is the +For the *lj/mdf* pair_style, the potential energy, *E(r)*, is the standard 12-6 Lennard-Jones written in the epsilon/sigma form: .. math:: @@ -104,7 +104,7 @@ described below: ---------- -For the *buck/mdf* pair_style, the potential energy, *E(r)*\ , is the +For the *buck/mdf* pair_style, the potential energy, *E(r)*, is the standard Buckingham potential with three required coefficients. The two cutoffs can be omitted and default to the corresponding global values: @@ -121,7 +121,7 @@ global values: ---------- -For the *lennard/mdf* pair_style, the potential energy, *E(r)*\ , is the +For the *lennard/mdf* pair_style, the potential energy, *E(r)*, is the standard 12-6 Lennard-Jones written in the A/B form: .. math:: @@ -158,8 +158,8 @@ 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*\ , -*middle*\ , *outer* keywords. +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. ---------- diff --git a/doc/src/pair_meam.rst b/doc/src/pair_meam.rst index c55967a756..d091496325 100644 --- a/doc/src/pair_meam.rst +++ b/doc/src/pair_meam.rst @@ -79,7 +79,7 @@ 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 ` page for alternate ways to specify the path for the potential files. As an example, the potentials/library.meam file has generic MEAM @@ -376,7 +376,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -385,7 +385,7 @@ Restrictions The *meam* style is provided in the MEAM package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. The maximum number of elements, that can be read from the MEAM library file, is determined at compile time. The default is 5. diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index e7680ddc15..9f231cb78c 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -50,7 +50,7 @@ the total energy E is given by where the five functions :math:`\phi, U, \rho, f,` and *g* depend on the chemistry of the atoms in the interaction. In particular, if there are -N different chemistries, there are N different *U*\ , :math:`\rho`, and +N different chemistries, there are N different *U*, :math:`\rho`, and *f* functions, while there are N(N+1)/2 different :math:`\phi` and *g* functions. The new style multicomponent MEAM potential files are indicated by the second line in the file starts with "meam/spline" @@ -81,7 +81,7 @@ 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 ` 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). @@ -132,7 +132,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -145,7 +145,7 @@ for pair interactions. This pair style does not support mapping multiple atom types to the same element. This pair style is only enabled if LAMMPS was built with the MANYBODY -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index 79236819b9..686081e854 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -67,7 +67,7 @@ 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 ` 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. @@ -114,7 +114,7 @@ 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 -support the *inner*\ , *middle*\ , *outer* keywords. +support the *inner*, *middle*, *outer* keywords. ---------- @@ -125,7 +125,7 @@ This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. This pair style is only enabled if LAMMPS was built with the MANYBODY -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_mesocnt.rst b/doc/src/pair_mesocnt.rst index ca461aee7a..78a6680b6b 100644 --- a/doc/src/pair_mesocnt.rst +++ b/doc/src/pair_mesocnt.rst @@ -115,7 +115,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -123,7 +123,7 @@ Restrictions """""""""""" This style is part of the MESONT package. It is only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair potential requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 567c14f0ea..e5cd2643dd 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -284,13 +284,13 @@ concentration profiles of the two chemical species as Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not support +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 styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* do not support the :doc:`pair_modify ` shift, table, and tail options. -The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not write +The styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* do 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. @@ -298,9 +298,9 @@ that reads a restart file. Restrictions """""""""""" -The pair styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* are part of +The pair styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* are part of the DPD-MESO package. It is only enabled if LAMMPS was built with -that package. See the :doc:`Build package ` doc page for +that package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index ea6621a3fd..6ef9f52fac 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -161,7 +161,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -169,7 +169,7 @@ Restrictions """""""""""" This pair style is part of the MGPT package and is only enabled -if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS is built with that package. See the :doc:`Build package ` page for more info. The MGPT potentials require the :doc:`newtion ` setting to be "on" for pair style interactions. diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index e1a34893c9..089f8d3d29 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -82,7 +82,7 @@ pressure of the pair interaction. 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* +This pair style supports the use of the *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. See the :doc:`run_style ` command for @@ -92,7 +92,10 @@ details. Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_mliap.rst b/doc/src/pair_mliap.rst index 199f23e1b2..900a2c2e6a 100644 --- a/doc/src/pair_mliap.rst +++ b/doc/src/pair_mliap.rst @@ -156,7 +156,7 @@ contains a few more arguments (e.g., *nmax* and *alpha*). The preparation of SO3 descriptor and model files can be done with the `Pyxtal_FF `_ package. -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for these *model* and *descriptor* files. .. note:: @@ -185,7 +185,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -196,7 +196,7 @@ This pair style is part of the ML-IAP package. It is only enabled if LAMMPS was built with that package. In addition, building LAMMPS with the ML-IAP package requires building LAMMPS with the ML-SNAP package. The *mliappy* model requires building LAMMPS with the PYTHON package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index 9c021e60a4..1a62a4c1a0 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -82,7 +82,7 @@ as sigma. Note that not all pair styles support mixing and some mix options are not available for certain pair styles. Also, there are additional restrictions when using :doc:`pair style hybrid or hybrid/overlay `. -See the doc page for individual pair styles for those restrictions. Note also that the +See the page for individual pair styles for those restrictions. Note also that the :doc:`pair_coeff ` command also can be used to directly set coefficients for a specific I != J pairing, in which case no mixing is performed. @@ -117,7 +117,7 @@ option. The *table* and *table/disp* keywords apply to pair styles with a long-range Coulombic term or long-range dispersion term respectively; -see the doc page for individual styles to see which potentials support +see the page for individual styles to see which potentials support these options. If N is non-zero, a table of length 2\^N is pre-computed for forces and energies, which can shrink their computational cost by up to a factor of 2. The table is indexed via a @@ -149,11 +149,11 @@ pairwise interactions are computed via table lookup for simulations with "real" units, but some close pairs may be computed directly (non-table) for simulations with "lj" units. -When the *tail* keyword is set to *yes*\ , certain pair styles will +When the *tail* keyword is set to *yes*, certain pair styles will add a long-range VanderWaals tail "correction" to the energy and pressure. 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 +See the 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 ` command). Their effect will also be included in diff --git a/doc/src/pair_momb.rst b/doc/src/pair_momb.rst index 71dfe84087..982ef86603 100644 --- a/doc/src/pair_momb.rst +++ b/doc/src/pair_momb.rst @@ -57,7 +57,7 @@ Restrictions This style is part of the EXTRA-PAIR package. It is only enabled if LAMMPS is built with that package. See the :doc:`Build package -` doc page on for more info. +` page on for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index b977c58eaa..686dd6e511 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -85,12 +85,12 @@ the *morse* and *morse/smooth/linear* styles. ---------- -A version of the *morse* style with a soft core, *morse/soft*\ , +A version of the *morse* style with a soft core, *morse/soft*, suitable for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. ---------- @@ -119,7 +119,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -128,7 +128,7 @@ Restrictions The *morse/smooth/linear* pair style is only enabled if LAMMPS was built with the EXTRA-PAIR package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index 8f65d8f438..c8c8551df5 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -11,7 +11,7 @@ Syntax pair_style multi/lucy style N keyword ... * style = *lookup* or *linear* = method of interpolation -* N = use N values in *lookup*\ , *linear* tables +* N = use N values in *lookup*, *linear* tables Examples """""""" @@ -186,7 +186,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -194,7 +194,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index b39bd02b6d..6cb56360ba 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -14,7 +14,7 @@ Syntax pair_style multi/lucy/rx style N keyword ... * style = *lookup* or *linear* = method of interpolation -* N = use N values in *lookup*\ , *linear* tables +* N = use N values in *lookup*, *linear* tables * weighting = fractional or molecular (optional) Examples @@ -214,7 +214,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -226,7 +226,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index 853da9d821..203c707ec0 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -30,7 +30,7 @@ energy E of a system of atoms as where :math:`\theta_0` is the equilibrium value of the angle and *K* is a prefactor. Note that the usual 1/2 factor is included in *K*\ . The form -of the potential is identical to that used in angle_style *harmonic*\ , +of the potential is identical to that used in angle_style *harmonic*, but in this case, the atoms do not need to be explicitly bonded. Only a single pair_coeff command is used with this style which @@ -42,7 +42,7 @@ 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 ` page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.nb3b.harmonic has potential values @@ -100,7 +100,7 @@ Restrictions """""""""""" This pair style can only be used if LAMMPS was built with the MANYBODY -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Related commands diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index d38e21fd15..2c356bb4ca 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -114,7 +114,7 @@ N-M and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both N-M and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the N-M and Coulombic cutoffs for this -type pair. You cannot specify 2 cutoffs for style *nm*\ , since it +type pair. You cannot specify 2 cutoffs for style *nm*, since it has no Coulombic terms. For *nm/cut/coul/long* only the N-M cutoff can be specified since a @@ -147,7 +147,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -156,8 +156,9 @@ the :doc:`run_style respa ` command. They do not support the Restrictions """""""""""" -These pair styles are part of the MISC 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 are part of the EXTRA-PAIR package. They are only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_none.rst b/doc/src/pair_none.rst index b2f27c355e..3dc87a7815 100644 --- a/doc/src/pair_none.rst +++ b/doc/src/pair_none.rst @@ -30,7 +30,7 @@ skin distance is large enough to acquire atoms needed for computing bonds, angles, etc. A pair style of *none* will also prevent pairwise neighbor lists from -being built. However if the :doc:`neighbor ` style is *bin*\ , +being built. However if the :doc:`neighbor ` style is *bin*, data structures for binning are still allocated. If the neighbor skin distance is small, then these data structures can consume a large amount of memory. So you should either set the neighbor style to diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index 38fb19a8b0..fcc7dc2e49 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -63,7 +63,7 @@ Description The *oxdna* pair styles compute the pairwise-additive parts of the oxDNA force field for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction *oxdna/excv*\ , the stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk* +excluded volume interaction *oxdna/excv*, the stacking *oxdna/stk*, cross-stacking *oxdna/xstk* and coaxial stacking interaction *oxdna/coaxstk* as well as the hydrogen-bonding interaction *oxdna/hbond* between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths @@ -120,7 +120,7 @@ Restrictions These pair styles can only be used if LAMMPS was built with the CG-DNA package and the MOLECULE and ASPHERE package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 3dce3c2d1b..f253c4ae10 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -72,8 +72,8 @@ Description The *oxdna2* pair styles compute the pairwise-additive parts of the oxDNA force field for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction *oxdna2/excv*\ , the stacking *oxdna2/stk*\ , cross-stacking *oxdna2/xstk* -and coaxial stacking interaction *oxdna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxdna2/dh* +excluded volume interaction *oxdna2/excv*, the stacking *oxdna2/stk*, cross-stacking *oxdna2/xstk* +and coaxial stacking interaction *oxdna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxdna2/dh* as well as the hydrogen-bonding interaction *oxdna2/hbond* between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths are supported :ref:`(Sulc) `. Quasi-unique base-pairing between nucleotides can be achieved by using @@ -127,7 +127,7 @@ Restrictions These pair styles can only be used if LAMMPS was built with the CG-DNA package and the MOLECULE and ASPHERE package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 63a5c9308b..7b8220740c 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -73,8 +73,8 @@ Description The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross-stacking *oxrna2/xstk* -and coaxial stacking interaction *oxrna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxrna2/dh* +excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*, cross-stacking *oxrna2/xstk* +and coaxial stacking interaction *oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh* as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths are supported :ref:`(Sulc2) `. Quasi-unique base-pairing between nucleotides can be achieved by using @@ -128,7 +128,7 @@ Restrictions These pair styles can only be used if LAMMPS was built with the CG-DNA package and the MOLECULE and ASPHERE package. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index e737072e7b..ad66febdf5 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -64,7 +64,7 @@ The pair_style *pace* command may be followed by an optional keyword is used for the calculation of basis functions and derivatives. The default is *recursive*. -See the :doc:`pair_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` page for alternate ways to specify the path for the ACE coefficient file. Mixing, shift, table, tail correction, restart, rRESPA info @@ -84,7 +84,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -93,7 +93,7 @@ Restrictions This pair style is part of the ML-PACE package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index 2a1c7f6aa5..45b406dd61 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -170,7 +170,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -178,7 +178,7 @@ Restrictions """""""""""" All of these styles are part of the PERI package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index 3df70a017c..8968c9d7d2 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -195,7 +195,7 @@ atom types: * filename * N element names = mapping of polymorphic potential elements to atom types -See the pair_coeff doc page for alternate ways to specify the path for +See the pair_coeff page for alternate ways to specify the path for the potential file. Several files for polymorphic potentials are included in the potentials directory of the LAMMPS distribution. They have a "poly" suffix. @@ -317,7 +317,7 @@ atomic structure data file. This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair potential requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index 99b8ebd766..3d087565be 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -184,7 +184,7 @@ always **append** to a table file, while pair style table will use the class, the table pair style will still read the old variant unless the table file is first deleted. -After switching the pair style to *table*\ , the potential tables need +After switching the pair style to *table*, the potential tables need to be assigned to the LAMMPS atom types like this: .. code-block:: LAMMPS @@ -215,7 +215,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -223,7 +223,7 @@ Restrictions """""""""""" This pair style is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index 5f520f3d03..c150561cb1 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -42,7 +42,7 @@ 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 ` page for alternate ways to specify the path for the potential file. A QUIP potential is fully specified by the filename which contains the @@ -70,13 +70,13 @@ 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. +*inner*, *middle*, *outer* keywords. Restrictions """""""""""" This pair style is part of the ML-QUIP package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. QUIP potentials are parameterized in electron-volts and Angstroms and therefore should be used with LAMMPS metal :doc:`units `. diff --git a/doc/src/pair_reaxff.rst b/doc/src/pair_reaxff.rst index 0389742ea5..a3a9c81cb8 100644 --- a/doc/src/pair_reaxff.rst +++ b/doc/src/pair_reaxff.rst @@ -140,7 +140,7 @@ control file. Note: Force field files are different for the original or lg corrected pair styles, using the wrong ffield file generates an error. -Using the optional keyword *enobonds* with the value *yes*\ , the energy +Using the optional keyword *enobonds* with the value *yes*, the energy of atoms with no bonds (i.e. isolated atoms) is included in the total potential energy and the per-atom energy of that atom. If the value *no* is specified then the energy of atoms with no bonds is set to @@ -148,7 +148,7 @@ zero. The latter behavior is usual not desired, as it causes discontinuities in the potential energy when the bonding of an atom drops to zero. -Optional keywords *safezone*\ , *mincap*\ , and *minhbonds* are used +Optional keywords *safezone*, *mincap*, and *minhbonds* are used for allocating reaxff arrays. Increasing these values can avoid memory problems, such as segmentation faults and bondchk failed errors, that could occur under certain conditions. These keywords are not used by @@ -327,7 +327,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -340,7 +340,7 @@ Restrictions This pair style is part of the REAXFF package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. The ReaxFF potential files provided with LAMMPS in the potentials directory are parameterized for *real* :doc:`units `. You can use diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 0932730469..8d7b5eca5b 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -191,7 +191,7 @@ 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 `. +*inner*, *middle*, *outer* keywords of the :doc:`run_style command `. ---------- @@ -199,7 +199,7 @@ Restrictions """""""""""" 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. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires that atoms be ellipsoids as defined by the :doc:`atom_style ellipsoid ` command. diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index a89a833998..f389079e15 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -141,7 +141,7 @@ All of the lj/sdk pair styles write their information to :doc:`binary restart fi 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. ---------- diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst index 15a4eb5374..7eaab203c9 100644 --- a/doc/src/pair_sdpd_taitwater_isothermal.rst +++ b/doc/src/pair_sdpd_taitwater_isothermal.rst @@ -91,14 +91,14 @@ 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*\ , -*middle*\ , *outer* keywords. +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 """""""""""" This pair style is part of the DPD-SMOOTH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst index a10edde6b0..deb3f69ec5 100644 --- a/doc/src/pair_smd_hertz.rst +++ b/doc/src/pair_smd_hertz.rst @@ -51,7 +51,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst index cab156167e..3884b0fec3 100644 --- a/doc/src/pair_smd_tlsph.rst +++ b/doc/src/pair_smd_tlsph.rst @@ -66,7 +66,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 957ff1ca19..76385ae7fb 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -52,7 +52,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index c69fbf2a43..fd63908e3d 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -77,7 +77,7 @@ Restrictions """""""""""" This fix is part of the MACHDYN package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index 96ccc5c4c7..50b4afaf2d 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -94,8 +94,8 @@ ffield.SMTBQ.Syst. The energy band term is given by: \delta Q_i \bigl( 2\frac{n_0}{\eta_i} - \delta Q_i \bigr) \biggr\}^{1/2} \\ \delta Q_i & = | Q_i^{F} | - | Q_i | -where :math:`\eta_i` is the stoichiometry of atom *i*\ , -:math:`\delta Q_i` is the charge delocalization of atom *i*\ , +where :math:`\eta_i` is the stoichiometry of atom *i*, +:math:`\delta Q_i` is the charge delocalization of atom *i*, compared to its formal charge :math:`Q^F_i`. :math:`n_0`, the number of hybridized orbitals, is calculated with to the atomic orbitals shared @@ -161,7 +161,7 @@ For the anion (oxygen) * Name of element (char) and stoichiometry in oxide * Formal charge and mass of element * Principal quantum number of outer orbital n), electronegativity (:math:`\chi^0_i`) and hardness (:math:`J^0_i`) -* Ionic radius parameters : max coordination number (\ *coordBB* = 6 by default), bulk coordination number *(coordB)*\ , surface coordination number *(coordS)* and *rBB, rB and rS* the slater radius for each coordination number. (**note : If you don't want to change the slater radius, use three identical radius values**) +* Ionic radius parameters : max coordination number (\ *coordBB* = 6 by default), bulk coordination number *(coordB)*, surface coordination number *(coordS)* and *rBB, rB and rS* the slater radius for each coordination number. (**note : If you don't want to change the slater radius, use three identical radius values**) * Number of orbital shared by the element in the oxide (:math:`d_i`) * Divider line @@ -169,7 +169,7 @@ For each cations (metal): * Name of element (char) and stoichiometry in oxide * Formal charge and mass of element -* Number of electron in outer orbital *(ne)*\ , electronegativity (:math:`\chi^0_i`), hardness (:math:`J^0_i`) and :math:`r_{Slater}` the slater radius for the cation. +* Number of electron in outer orbital *(ne)*, electronegativity (:math:`\chi^0_i`), hardness (:math:`J^0_i`) and :math:`r_{Slater}` the slater radius for the cation. * Number of orbitals shared by the elements in the oxide (:math:`d_i`) * Divider line @@ -244,7 +244,7 @@ For each cations (metal): :math:`N_{Energy}` time steps. If the value is 'false' then :math:`N_{Energy} = 0`. The file takes into account the possibility to have several QEq groups *g* then it writes: time step, number of atoms - in group *g*\ , electrostatic part of energy, :math:`E_{ES}`, the + in group *g*, electrostatic part of energy, :math:`E_{ES}`, the interaction between oxygen, :math:`E_{OO}`, and short range metal-oxygen interaction, :math:`E_{MO}`. * If you want to print to the file 'Electroneg_component.txt' the @@ -252,9 +252,9 @@ For each cations (metal): Q_i}`) or not: 'true' or 'false' and :math:`N_{Electroneg}`. This option writes to the file every :math:`N_{Electroneg}` time steps. If the value is 'false' then :math:`N_{Electroneg} = 0`. The file - consist of atom number *i*\ , atom type (1 for oxygen and # higher - than 1 for metal), atom position: *x*\ , *y* and *z*\ , atomic charge - of atom *i*\ , electrostatic part of atom *i* electronegativity, + consist of atom number *i*, atom type (1 for oxygen and # higher + than 1 for metal), atom position: *x*, *y* and *z*, atomic charge + of atom *i*, electrostatic part of atom *i* electronegativity, covalent part of atom *i* electronegativity, the hopping integral of atom *i* :math:`(Z\beta^2)_i` and box electronegativity. @@ -277,7 +277,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -285,7 +285,7 @@ Restrictions """""""""""" This pair style is part of the SMTBQ package and is only enabled -if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS is built with that package. See the :doc:`Build package ` page for more info. This potential requires using atom type 1 for oxygen and atom type higher than 1 for metal atoms. diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 5638087d78..381250f57b 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -40,7 +40,7 @@ atom *i* is expressed as a weighted sum over bispectrum components. E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\mu_i}_0 + \sum_{k=1}^K \beta_k^{\mu_i} B_k^i -where :math:`B_k^i` is the *k*\ -th bispectrum component of atom *i*\ , +where :math:`B_k^i` is the *k*\ -th bispectrum component of atom *i*, and :math:`\beta_k^{\mu_i}` is the corresponding linear coefficient that depends on :math:`\mu_i`, the SNAP element of atom *i*\ . The number of bispectrum components used and their definitions depend on the value of @@ -90,7 +90,7 @@ elements not in the pair_coeff command, except when using *chemflag* (see below). 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 to specify the path for these +` page for alternate ways to specify the path for these files. SNAP potentials are quite commonly combined with one or more other @@ -133,9 +133,9 @@ This line is followed by *ncoeff* coefficients, one per line. The SNAP parameter file can contain blank and comment lines (start with #) anywhere. Each non-blank non-comment line must contain one keyword/value pair. The required keywords are *rcutfac* and -*twojmax*\ . Optional keywords are *rfac0*\ , *rmin0*\ , -*switchflag*\ , *bzeroflag*\ , *quadraticflag*\ , *chemflag*\ , -*bnormflag*\ , *wselfallflag*\ , and *chunksize*\ . +*twojmax*\ . Optional keywords are *rfac0*, *rmin0*, +*switchflag*, *bzeroflag*, *quadraticflag*, *chemflag*, +*bnormflag*, *wselfallflag*, and *chunksize*\ . The default values for these keywords are @@ -225,7 +225,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -238,7 +238,7 @@ Restrictions This style is part of the ML-SNAP package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index cc024cb6dd..7986b1286e 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -113,7 +113,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst index 03e9606750..4716ed54fb 100644 --- a/doc/src/pair_sph_heatconduction.rst +++ b/doc/src/pair_sph_heatconduction.rst @@ -48,14 +48,14 @@ 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*\ , -*middle*\ , *outer* keywords. +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 """""""""""" This pair style is part of the SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst index a62db85133..02949849c4 100644 --- a/doc/src/pair_sph_idealgas.rst +++ b/doc/src/pair_sph_idealgas.rst @@ -57,14 +57,14 @@ 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*\ , -*middle*\ , *outer* keywords. +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 """""""""""" This pair style is part of the SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst index ca25dedbbf..b5c02c41ff 100644 --- a/doc/src/pair_sph_lj.rst +++ b/doc/src/pair_sph_lj.rst @@ -52,8 +52,8 @@ 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*\ , -*middle*\ , *outer* keywords. +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 """""""""""" @@ -62,7 +62,7 @@ As noted above, the Lennard-Jones parameters epsilon and sigma are set to unity. This pair style is part of the SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst index 42c5c2d222..ecbff98486 100644 --- a/doc/src/pair_sph_rhosum.rst +++ b/doc/src/pair_sph_rhosum.rst @@ -49,14 +49,14 @@ 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*\ , -*middle*\ , *outer* keywords. +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 """""""""""" This pair style is part of the SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst index 88fa65eb90..34eb65f005 100644 --- a/doc/src/pair_sph_taitwater.rst +++ b/doc/src/pair_sph_taitwater.rst @@ -61,14 +61,14 @@ 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*\ , -*middle*\ , *outer* keywords. +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 """""""""""" This pair style is part of the SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst index b9c1710a3d..cd8346364b 100644 --- a/doc/src/pair_sph_taitwater_morris.rst +++ b/doc/src/pair_sph_taitwater_morris.rst @@ -60,14 +60,14 @@ 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*\ , -*middle*\ , *outer* keywords. +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 """""""""""" This pair style is part of the SPH package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index d1bbf3b699..c38bba03ae 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -97,7 +97,7 @@ Restrictions The *spin/dipole/cut* and *spin/dipole/long* styles are part of the SPIN package. They are only enabled if LAMMPS was built with that -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. Using dipole/spin pair styles with *electron* :doc:`units ` is not diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index eb945acc04..3d1498b769 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -81,7 +81,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index 630ec6608e..553af72983 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -196,7 +196,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the atom_style "spin" was declared. -See the :doc:`Build package ` doc page for more info. +See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 1860ed4677..b422b6a070 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -60,7 +60,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_spin_neel.rst b/doc/src/pair_spin_neel.rst index c0df74187d..e5d655f196 100644 --- a/doc/src/pair_spin_neel.rst +++ b/doc/src/pair_spin_neel.rst @@ -80,7 +80,7 @@ Restrictions All the *pair/spin* styles are part of the SPIN package. These styles are only enabled if LAMMPS was built with this package, and if the -atom_style "spin" was declared. See the :doc:`Build package ` doc page for more info. +atom_style "spin" was declared. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index c1e8403022..ea094aa720 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -91,7 +91,7 @@ is used. .. note:: Pair style srp considers each bond of type *btype* to be a - fictitious "particle" of type *bptype*\ , where *bptype* is either the + fictitious "particle" of type *bptype*, where *bptype* is either the largest atom type in the system, or the type set by the *bptype* flag. 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 @@ -108,7 +108,7 @@ is used. The optional *exclude* keyword determines if forces are computed between first neighbor (directly connected) bonds. For a setting of -*no*\ , first neighbor forces are computed; for *yes* they are not +*no*, first neighbor forces are computed; for *yes* they are not computed. A setting of *no* cannot be used with the *min* option for distance calculation because the minimum distance between directly connected bonds is zero. @@ -143,7 +143,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 50f49c87c9..7677cd9535 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -358,7 +358,7 @@ This command must be used before any coefficients are set by the :doc:`read_restart ` commands. Some pair styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The doc pages for +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. The doc pages for individual pair potentials tell if it is part of a package. Related commands diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index a4b39be3c9..f207b25863 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -57,7 +57,7 @@ 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 ` 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 @@ -155,11 +155,11 @@ parameters used only for two-body interactions (A, B, p, and q) in entries whose second and third element are different (e.g. SiCSi) are not used for anything and can be set to 0.0 if desired. This is also true for the parameters in :math:`\phi_3` that are -taken from the ij and ik pairs (:math:`\sigma`, *a*\ , :math:`\gamma`) +taken from the ij and ik pairs (:math:`\sigma`, *a*, :math:`\gamma`) ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -168,7 +168,7 @@ produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with those packages. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the @@ -179,7 +179,7 @@ additional 5 to 10 percent performance improvement when the Stillinger-Weber parameters p and q are set to 4 and 0 respectively. These parameters are common for modeling silicon and water. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -200,7 +200,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -208,7 +208,7 @@ Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 39ed690551..79eb8f5b42 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -16,7 +16,7 @@ Syntax pair_style table style N keyword ... * style = *lookup* or *linear* or *spline* or *bitmap* = method of interpolation -* N = use N values in *lookup*\ , *linear*\ , *spline* tables +* N = use N values in *lookup*, *linear*, *spline* tables * N = use 2\^N values in *bitmap* tables * zero or more keywords may be appended * keyword = *ewald* or *pppm* or *msm* or *dispersion* or *tip4p* @@ -47,7 +47,7 @@ cubic splines to the file values and interpolating energy and force values at each of *N* distances. During a simulation, the tables are used to interpolate energy and force values as needed for each pair of particles separated by a distance *R*\ . The interpolation is done in -one of 4 styles: *lookup*\ , *linear*\ , *spline*\ , or *bitmap*\ . +one of 4 styles: *lookup*, *linear*, *spline*, or *bitmap*\ . For the *lookup* style, the distance *R* is used to find the nearest table entry, which is the energy or force. @@ -240,7 +240,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index 1c860b90ad..094107d9ef 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -14,7 +14,7 @@ Syntax pair_style table style N ... * style = *lookup* or *linear* or *spline* or *bitmap* = method of interpolation -* N = use N values in *lookup*\ , *linear*\ , *spline* tables +* N = use N values in *lookup*, *linear*, *spline* tables * weighting = fractional or molecular (optional) Examples @@ -47,7 +47,7 @@ The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and force values at each of *N* distances. During a simulation, these tables are used to interpolate energy and force values as needed. The interpolation is done in one -of 4 styles: *lookup*\ , *linear*\ , *spline*\ , or *bitmap*\ . +of 4 styles: *lookup*, *linear*, *spline*, or *bitmap*\ . For the *lookup* style, the distance between 2 atoms is used to find the nearest table entry, which is the energy or force. @@ -221,7 +221,7 @@ 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 -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -233,7 +233,7 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 4fa77fc032..ab88806ca6 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -90,7 +90,7 @@ 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 ` 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 @@ -288,7 +288,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -297,7 +297,7 @@ Restrictions This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index e59005c2b0..8c9605d62c 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -189,7 +189,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -197,7 +197,7 @@ Restrictions """""""""""" This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index 345ebf3e03..276905163f 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -101,7 +101,7 @@ 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 ` 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 @@ -270,7 +270,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -279,7 +279,7 @@ Restrictions This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package -` doc page for more info. +` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 68966a3d9b..5a1e72f569 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -107,7 +107,7 @@ 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 +For pair_style *thole*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the example above. @@ -120,7 +120,7 @@ Thole damping parameter or global cutoff specified in the pair_style 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 +For pair style *lj/cut/thole/long*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command. @@ -156,7 +156,7 @@ Restrictions """""""""""" These pair styles are part of the DRUDE package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This pair_style should currently not be used with the :doc:`charmm dihedral style ` if the latter has non-zero 1-4 weighting factors. This is because the *thole* pair style does not know which diff --git a/doc/src/pair_tracker.rst b/doc/src/pair_tracker.rst index 5a85a7f048..d2cee1d879 100644 --- a/doc/src/pair_tracker.rst +++ b/doc/src/pair_tracker.rst @@ -84,7 +84,7 @@ This pair style is currently incompatible with granular pair styles that extend beyond the contact (e.g. JKR and DMT). This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst index 5516f60408..d72a061bf3 100644 --- a/doc/src/pair_tri_lj.rst +++ b/doc/src/pair_tri_lj.rst @@ -66,7 +66,7 @@ using only sigma_II values, specific to the triangles's type, this means that any specified sigma_IJ values (for I != J) are effectively ignored. -For style *tri/lj*\ , the following coefficients must be defined for +For style *tri/lj*, 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 ` @@ -96,7 +96,7 @@ This pair style does not write its information to :doc:`binary restart files ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords. +*inner*, *middle*, *outer* keywords. ---------- @@ -104,7 +104,7 @@ Restrictions """""""""""" 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. +LAMMPS was built with that package. See the :doc:`Build package ` 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. diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index 140bb75ee7..22438d559b 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -107,13 +107,16 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- Restrictions """""""""""" -none + +This pair style is part of the EXTRA-PAIR package. It is only enabled if +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index 9edb77ecbe..d38ac02a96 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -93,7 +93,7 @@ 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 ` page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.vashishta has parameters for @@ -156,13 +156,13 @@ unambiguous, general, and simple to code, LAMMPS uses a slightly confusing method for specifying parameters. All parameters are divided into two classes: two-body and three-body. Two-body and three-body parameters are handled differently, as described below. -The two-body parameters are *H*\ , :math:`\eta`, :math:`\lambda_1`, -*D*\ , :math:`\lambda_4`, *W*, :math:`r_c`, :math:`\gamma`, +The two-body parameters are *H*, :math:`\eta`, :math:`\lambda_1`, +*D*, :math:`\lambda_4`, *W*, :math:`r_c`, :math:`\gamma`, and :math:`r_0`. They appear in the above formulae with two subscripts. The parameters :math:`Z_i` and :math:`Z_j` are also classified as two-body parameters, even -though they only have 1 subscript. The three-body parameters are *B*\ , -*C*\ , :math:`\cos\theta_0`. They appear in the above formulae with +though they only have 1 subscript. The three-body parameters are *B*, +*C*, :math:`\cos\theta_0`. They appear in the above formulae with three subscripts. Two-body and three-body parameters are handled differently, as described below. @@ -210,7 +210,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -218,7 +218,7 @@ Restrictions """""""""""" These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. These pair styles requires the :doc:`newton ` setting to be "on" for pair interactions. diff --git a/doc/src/pair_wf_cut.rst b/doc/src/pair_wf_cut.rst index 6ae1c3e897..8f6e352665 100644 --- a/doc/src/pair_wf_cut.rst +++ b/doc/src/pair_wf_cut.rst @@ -91,7 +91,7 @@ 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 does not support the use of the *inner*\ , *middle*\ , +This pair style does not support the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command. ---------- diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 340c151226..1d88137255 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -44,13 +44,13 @@ will refuse to add a table if the units are not the same. 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 -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. +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. -For example, for N = 7, style = *r*\ , inner = 1.0, and outer = 4.0, +For example, for N = 7, style = *r*, inner = 1.0, and outer = 4.0, 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 +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 reasonable accuracy in a bitmapped table, choose N >= 12, an *inner* diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 057adbd60f..2b832f187a 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -79,7 +79,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index 4d21d8e8c3..6611ea04e4 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -112,7 +112,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- @@ -120,7 +120,7 @@ Restrictions """""""""""" 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. +LAMMPS was built with that package. See the :doc:`Build package ` 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 ` diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index e01cbf45f2..bbf9f6bc29 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -117,7 +117,7 @@ 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. +*inner*, *middle*, *outer* keywords. ---------- diff --git a/doc/src/pair_zero.rst b/doc/src/pair_zero.rst index 416958de1b..062b5204f8 100644 --- a/doc/src/pair_zero.rst +++ b/doc/src/pair_zero.rst @@ -72,7 +72,7 @@ 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*\ , +This pair style supports the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command. ---------- diff --git a/doc/src/partition.rst b/doc/src/partition.rst index e63a4941bb..f05c3fa446 100644 --- a/doc/src/partition.rst +++ b/doc/src/partition.rst @@ -42,7 +42,7 @@ script operate differently on different partitions. It is basically a prefix on any LAMMPS command. The command will only be invoked on the partition(s) specified by the *style* and *N* arguments. -If the *style* is *yes*\ , the command will be invoked on any partition +If the *style* is *yes*, the command will be invoked on any partition which matches the *N* argument. If the *style* is *no* the command will be invoked on all the partitions which do not match the Np argument. diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst index 02228636bc..7995ddc369 100644 --- a/doc/src/plugin.rst +++ b/doc/src/plugin.rst @@ -62,7 +62,7 @@ Restrictions The *plugin* command is part of the PLUGIN package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for +See the :doc:`Build package ` page for more info. Plugins are not available on Windows. For the loading of plugins to work the LAMMPS library must be diff --git a/doc/src/prd.rst b/doc/src/prd.rst index d1acaf645e..758aa4f570 100644 --- a/doc/src/prd.rst +++ b/doc/src/prd.rst @@ -30,8 +30,8 @@ Syntax *temp* value = Tdephase Tdephase = target temperature for velocity randomization, used in dephasing *vel* values = loop dist - loop = *all* or *local* or *geom*\ , used in dephasing - dist = *uniform* or *gaussian*\ , used in dephasing + loop = *all* or *local* or *geom*, used in dephasing + dist = *uniform* or *gaussian*, used in dephasing *time* value = *steps* or *clock* *steps* = simulation runs for N timesteps on each replica (default) *clock* = simulation runs for N timesteps across all replicas @@ -72,7 +72,7 @@ reduced by a factor of Nr replicas. HD uses a single replica of the system and accelerates time by biasing the interaction potential in a manner such that each timestep is effectively longer. For both methods, per CPU second, more physical time elapses and more events -occur. See the :doc:`hyper ` doc page for more info about HD. +occur. See the :doc:`hyper ` page for more info about HD. In PRD, each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the :doc:`-partition command-line switch `. Note that if you have MPI @@ -171,8 +171,8 @@ dynamics have been performed. Note that *N* only includes the dynamics of stages 2 and 3, not the steps taken during dephasing or the minimization iterations of quenching. The specified *N* is interpreted in one of two ways, depending on the *time* keyword. If -the *time* value is *steps*\ , which is the default, then each replica -runs for *N* timesteps. If the *time* value is *clock*\ , then the +the *time* value is *steps*, which is the default, then each replica +runs for *N* timesteps. If the *time* value is *clock*, then the simulation runs until *N* aggregate timesteps across all replicas have elapsed. This aggregate time is the "clock" time defined below, which typically advances nearly M times faster than the timestepping on a diff --git a/doc/src/processors.rst b/doc/src/processors.rst index 899c87f4b0..d717fa9b73 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -85,7 +85,7 @@ communication costs due to the high surface area of each processor's sub-domain. Also note that if multiple partitions are being used then P is the -number of processors in this partition; see the :doc:`-partition command-line switch ` doc page for details. Also note +number of processors in this partition; see the :doc:`-partition command-line switch ` page for details. Also note that you can prefix the processors command with the :doc:`partition ` command to easily specify different Px,Py,Pz values for different partitions. @@ -140,7 +140,7 @@ For example if *Nc* is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections of the 3d grid will correspond to the cores of each node. This affects both the factorization and mapping steps. -The *Cx*\ , *Cy*\ , *Cz* settings are similar to the *Px*\ , *Py*\ , *Pz* +The *Cx*, *Cy*, *Cz* settings are similar to the *Px*, *Py*, *Pz* settings, only their product should equal *Nc*\ . Any of the 3 parameters can be specified with an asterisk "\*", which means LAMMPS will choose the number of cores in that dimension of the node's @@ -222,7 +222,7 @@ The *cart/reorder* style does the same thing as the *cart* style except it sets the reorder flag to 1, so that MPI can reorder processors if it desires. -The *xyz*\ , *xzy*\ , *yxz*\ , *yzx*\ , *zxy*\ , and *zyx* styles are all +The *xyz*, *xzy*, *yxz*, *yzx*, *zxy*, and *zyx* styles are all similar. If the style is IJK, then it maps the P processors to the grid so that the processor ID in the I direction varies fastest, the processor ID in the J direction varies next fastest, and the processor @@ -275,7 +275,7 @@ regular 3d grid and will use the sender's Px,Py,Pz values as a constraint. The nature of the constraint is determined by the *cstyle* argument. -For a *cstyle* of *multiple*\ , each dimension of the sender's processor +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. diff --git a/doc/src/python.rst b/doc/src/python.rst index a4c3d7097c..aad2f636d3 100644 --- a/doc/src/python.rst +++ b/doc/src/python.rst @@ -185,12 +185,12 @@ output as a string, then the default maximum length of that string is a longer string, the *length* keyword can be specified with its *Nlen* value set to a larger number (the code allocates space for Nlen+1 to include the string terminator). If the Python function generates a -string longer than the default 63 or the specified *Nlen*\ , it will be +string longer than the default 63 or the specified *Nlen*, it will be truncated. ---------- -Either the *file*\ , *here*\ , or *exists* keyword must be used, but only +Either the *file*, *here*, or *exists* keyword must be used, but only one of them. These keywords specify what Python code to load into the Python interpreter. The *file* keyword gives the name of a file, which should end with a ".py" suffix, which contains Python code. The @@ -340,7 +340,7 @@ to the screen and log file. Note that since the LAMMPS print command itself takes a string in quotes as its argument, the Python string must be delimited with a different style of quotes. -The :doc:`Python_head` doc page describes the syntax +The :doc:`Python_head` page describes the syntax for how Python wraps the various functions included in the LAMMPS library interface. @@ -495,7 +495,7 @@ Restrictions """""""""""" This command is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Building LAMMPS with the PYTHON package will link LAMMPS with the Python library on your system. Settings to enable this are in the diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index bd7c480af2..e0cd38416e 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -70,7 +70,7 @@ Also see the explanation of the :doc:`-restart command-line switch file. This command can be used multiple times to add new atoms and their -properties to an existing system by using the *add*\ , *offset*\ , and +properties to an existing system by using the *add*, *offset*, and *shift* keywords. See more details below, which includes the use case for the *extra* keywords. @@ -105,7 +105,7 @@ other side of the fluid. The third set of atoms could be rotated to 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 +The *add*, *offset*, *shift*, *extra*, and *group* keywords are useful in this context. If a simulation box does not yet exist, the *add* keyword cannot be @@ -249,7 +249,7 @@ a fix that will be used to process a specific portion of the data file. Any header line containing *header-string* and any section with a name containing *section-string* will be passed to the specified fix. See the :doc:`fix property/atom ` command for -an example of a fix that operates in this manner. The doc page for +an example of a fix that operates in this manner. The page for the fix defines the syntax of the header line(s) and section(s) that it reads from the data file. Note that the *header-string* can be specified as NULL, in which case no header lines are passed to the @@ -332,7 +332,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, with tilt factors that exceed these limits, you can use the :doc:`box tilt ` command, with a setting of *large*\ ; a setting of *small* is the default. -See the :doc:`Howto triclinic ` doc page for a +See the :doc:`Howto triclinic ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. @@ -460,9 +460,9 @@ are point particles. See the discussion of ellipsoidflag and the 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 - file, nor can you define *Bonds*\ , *Angles*\ , etc sections as discussed - below. You can set the *bond types*\ , *angle types*\ , etc header + cannot set the *bonds*, *angles*, etc header keywords in the data + file, nor can you define *Bonds*, *Angles*, etc sections as discussed + below. You can set the *bond types*, *angle types*, etc header keywords, though it is not necessary. If specified, they must match the maximum values defined in any of the template molecules. @@ -491,7 +491,7 @@ For example, these lines: Pair Coeffs # lj/cut will check if the currently-defined :doc:`atom_style ` is -*sphere*\ , and the current :doc:`pair_style ` is *lj/cut*\ . +*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. @@ -722,8 +722,8 @@ The ellipsoidflag, lineflag, triangleflag, and bodyflag determine whether the particle is a finite-size ellipsoid or line or triangle or body of finite size, or whether the particle is a point particle. Additional attributes must be defined for each ellipsoid, line, -triangle, or body in the corresponding *Ellipsoids*\ , *Lines*\ , -*Triangles*\ , or *Bodies* section. +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 @@ -1051,7 +1051,7 @@ The 3 shape values specify the 3 diameters or aspect ratios of a finite-size ellipsoidal particle, when it is oriented along the 3 coordinate axes. They must all be non-zero values. -The values *quatw*\ , *quati*\ , *quatj*\ , and *quatk* set the orientation +The values *quatw*, *quati*, *quatj*, and *quatk* set the orientation of the atom as a quaternion (4-vector). Note that the shape attributes specify the aspect ratios of an ellipsoidal particle, which is oriented by default with its x-axis along the simulation box's diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index 5a51e9ad7a..c873156a38 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -17,11 +17,11 @@ Syntax .. parsed-literal:: field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz* - *x*\ ,\ *y*\ ,\ *z* = atom coordinates - *vx*\ ,\ *vy*\ ,\ *vz* = velocity components + *x*,\ *y*,\ *z* = atom coordinates + *vx*,\ *vy*,\ *vz* = velocity components *q* = charge - *ix*\ ,\ *iy*\ ,\ *iz* = image flags in each dimension - *fx*\ ,\ *fy*\ ,\ *fz* = force components + *ix*,\ *iy*,\ *iz* = image flags in each dimension + *fx*,\ *fy*,\ *fz* = force components * zero or more keyword/value pairs may be appended * keyword = *nfile* or *box* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format* @@ -197,11 +197,11 @@ always work perfectly. Per-atom information from the dump file snapshot is then read from the dump file snapshot. This corresponds to the specified *fields* listed in the read_dump command. It is an error to specify a z-dimension -field, namely *z*\ , *vz*\ , or *iz*\ , for a 2d simulation. +field, namely *z*, *vz*, or *iz*, for a 2d simulation. For dump files in *native* format, each column of per-atom data has a text label listed in the file. A matching label for each field must -appear, e.g. the label "vy" for the field *vy*\ . For the *x*\ , *y*\ , *z* +appear, e.g. the label "vy" for the field *vy*\ . For the *x*, *y*, *z* fields any of the following labels are considered a match: .. parsed-literal:: @@ -217,7 +217,7 @@ file, in order, until a match is found. The dump file must also contain atom IDs, with a column label of "id". -If the *add* keyword is specified with a value of *yes* or *keep*\ , as +If the *add* keyword is specified with a value of *yes* or *keep*, as discussed below, the dump file must contain atom types, with a column label of "type". @@ -230,7 +230,7 @@ will then have a label corresponding to the fix-ID rather than "x" or "xs". The *label* keyword can also be used to specify new column labels for fields *id* and *type*\ . -For dump files in *xyz* format, only the *x*\ , *y*\ , and *z* fields are +For dump files in *xyz* format, only the *x*, *y*, and *z* fields are 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 @@ -238,7 +238,7 @@ consistent from snapshot to snapshot in the XYZ dump file. See 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 +For dump files in *molfile* format, the *x*, *y*, *z*, *vx*, *vy*, and *vz* fields can be specified. However, not all molfile formats store velocities, or their respective plugins may not support reading of velocities. The molfile dump files do not store atom IDs, so these @@ -277,7 +277,7 @@ current simulation box is unchanged. If the *purge* keyword is specified with a *yes* value, then all current atoms in the system are deleted before any of the operations -invoked by the *replace*\ , *trim*\ , or *add* keywords take place. +invoked by the *replace*, *trim*, or *add* keywords take place. If the *replace* keyword is specified with a *yes* value, then atoms with IDs that are in both the current system and the dump snapshot @@ -330,7 +330,7 @@ atom will be lost if it is outside the simulation box. For *native* format dump files, the 3 xyz image flags for an atom in the dump file are set to the corresponding values appearing in the -dump file if the *ix*\ , *iy*\ , *iz* fields are specified. If not +dump file if the *ix*, *iy*, *iz* fields are specified. If not specified, the image flags for replaced atoms are not changed and image flags for new atoms are set to default values. If coordinates read from the dump file are in unwrapped format (e.g. *xu*\ ) then the @@ -343,13 +343,13 @@ conditions are applied to remap an atom back into the simulation box. If you get a warning about inconsistent image flags after reading in a dump snapshot, it means one or more pairs of bonded atoms - now have inconsistent image flags. As discussed on the :doc:`Errors common ` doc page this may or may not cause problems + now have inconsistent image flags. As discussed on the :doc:`Errors common ` page this may or may not cause problems for subsequent simulations. One way this can happen is if you read image flag fields from the dump file but do not also use the dump file box parameters. LAMMPS knows how to compute unscaled and remapped coordinates for the -snapshot column labels discussed above, e.g. *x*\ , *xs*\ , *xu*\ , *xsu*\ . +snapshot column labels discussed above, e.g. *x*, *xs*, *xu*, *xsu*\ . If another column label is assigned to the *x* or *y* or *z* field via the *label* keyword, e.g. for coordinates output by the :doc:`fix ave/atom ` command, then LAMMPS needs to know whether the coordinate information in the dump file is scaled and/or wrapped. @@ -359,10 +359,10 @@ the value of the *scaled* and *wrapped* keywords is ignored for fields column label to that field. The scaled/unscaled and wrapped/unwrapped setting must be identical -for any of the *x*\ , *y*\ , *z* fields that are specified. Thus you +for any of the *x*, *y*, *z* fields that are specified. Thus you cannot read *xs* and *yu* from the dump file. Also, if the dump file coordinates are scaled and the simulation box is triclinic, then all 3 -of the *x*\ , *y*\ , *z* fields must be specified, since they are all +of the *x*, *y*, *z* fields must be specified, since they are all needed to generate absolute, unscaled coordinates. ---------- @@ -378,7 +378,7 @@ doc page for details. The *molfile* dump file formats are part of the MOLFILE package. They are only enabled if LAMMPS was built with that packages. See the -:doc:`Build package ` doc page for more info. +:doc:`Build package ` page for more info. To write and read adios .bp files, you must compile LAMMPS with the :ref:`ADIOS ` package. diff --git a/doc/src/region.rst b/doc/src/region.rst index 9f2d996b20..d891a69410 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -147,24 +147,24 @@ non-zero, then xlo and xhi cannot both be INF, nor can ylo and yhi. define the region so that its intersection with the 2d x-y plane of the simulation has the 2d geometric extent you want. -For style *cone*\ , an axis-aligned cone is defined which is like a +For style *cone*, an axis-aligned cone is defined which is like a *cylinder* except that two different radii (one at each end) can be defined. Either of the radii (but not both) can be 0.0. -For style *cone* and *cylinder*\ , the c1,c2 params are coordinates in +For style *cone* and *cylinder*, the c1,c2 params are coordinates in the 2 other dimensions besides the cylinder axis dimension. For dim = x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y. Thus the third example above specifies a cylinder with its axis in the y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and extending in the y-direction from -5.0 to the upper box boundary. -For style *plane*\ , a plane is defined which contain the point +For style *plane*, a plane is defined which contain the point (px,py,pz) and has a normal vector (nx,ny,nz). The normal vector does not have to be of unit length. The "inside" of the plane is the half-space in the direction of the normal vector; see the discussion of the *side* option below. -For style *prism*\ , a parallelepiped is defined (it's too hard to spell +For style *prism*, a parallelepiped is defined (it's too hard to spell parallelepiped in an input script!). The parallelepiped 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 = (xy,yhi-ylo,0); C = @@ -200,7 +200,7 @@ 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. -See the :doc:`Howto tricilinc ` doc page for a +See the :doc:`Howto tricilinc ` page for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. @@ -239,25 +239,25 @@ A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacings which are used as follows: -* For style *block*\ , the lattice spacing in dimension x is applied to +* For style *block*, the lattice spacing in dimension x is applied to xlo and xhi, similarly the spacings in dimensions y,z are applied to ylo/yhi and zlo/zhi. -* For style *cone*\ , the lattice spacing in argument *dim* is applied to +* For style *cone*, the lattice spacing in argument *dim* is applied to lo and hi. The spacings in the two radial dimensions are applied to c1 and c2. The two cone radii are scaled by the lattice spacing in the dimension corresponding to c1. -* For style *cylinder*\ , the lattice spacing in argument *dim* is applied +* For style *cylinder*, the lattice spacing in argument *dim* is applied to lo and hi. The spacings in the two radial dimensions are applied to c1 and c2. The cylinder radius is scaled by the lattice spacing in the dimension corresponding to c1. -* For style *plane*\ , the lattice spacing in dimension x is applied to +* For style *plane*, the lattice spacing in dimension x is applied to px and nx, similarly the spacings in dimensions y,z are applied to py/ny and pz/nz. -* For style *prism*\ , the lattice spacing in dimension x is applied to +* For style *prism*, the lattice spacing in dimension x is applied to xlo and xhi, similarly for ylo/yhi and zlo/zhi. The lattice spacing in dimension x is applied to xy and xz, and the spacing in dimension y to yz. -* For style *sphere*\ , the lattice spacing in dimensions x,y,z are +* For style *sphere*, the lattice spacing in dimensions x,y,z are applied to the sphere center x,y,z. The spacing in dimension x is applied to the sphere radius. @@ -311,7 +311,7 @@ angle is calculated, presumably as a function of time, by a variable specified as v_theta, where theta is the variable name. The variable should generate its result in radians. The direction of rotation for the region around the rotation axis is consistent with the right-hand -rule: if your right-hand thumb points along *R*\ , then your fingers +rule: if your right-hand thumb points along *R*, then your fingers wrap around the axis in the direction of rotation. The *move* and *rotate* keywords can be used together. In this case, @@ -341,25 +341,25 @@ sub-regions that use them. The indices specified as part of the *open* keyword have the following meanings: -For style *block*\ , indices 1-6 correspond to the xlo, xhi, ylo, yhi, +For style *block*, indices 1-6 correspond to the xlo, xhi, ylo, yhi, zlo, zhi surfaces of the block. I.e. 1 is the yz plane at x = xlo, 2 is the yz-plane at x = xhi, 3 is the xz plane at y = ylo, 4 is the xz plane at y = yhi, 5 is the xy plane at z = zlo, 6 is the xy plane at z = zhi). In the second-to-last example above, the region is a box open at both xy planes. -For style *prism*\ , values 1-6 have the same mapping as for style -*block*\ . I.e. in an untilted *prism*\ , *open* indices correspond to +For style *prism*, values 1-6 have the same mapping as for style +*block*\ . I.e. in an untilted *prism*, *open* indices correspond to the xlo, xhi, ylo, yhi, zlo, zhi surfaces. -For style *cylinder*\ , index 1 corresponds to the flat end cap at the +For style *cylinder*, index 1 corresponds to the flat end cap at the low coordinate along the cylinder axis, index 2 corresponds to the high-coordinate flat end cap along the cylinder axis, and index 3 is the curved cylinder surface. For example, a *cylinder* region with *open 1 open 2* keywords will be open at both ends (e.g. a section of pipe), regardless of the cylinder orientation. -For style *cone*\ , the mapping is the same as for style *cylinder*\ . +For style *cone*, the mapping is the same as for style *cylinder*\ . Index 1 is the low-coordinate flat end cap, index 2 is the high-coordinate flat end cap, and index 3 is the curved cone surface. In the last example above, a *cone* region is defined along the z-axis @@ -371,7 +371,7 @@ sub-regions can be defined with the *open* keyword. ---------- -Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the :doc:`Speed packages ` doc @@ -383,13 +383,13 @@ by Kokkos or no acceleration will occur. Currently, only *block* style regions are supported by Kokkos. These accelerated styles are part of the Kokkos package. They are -only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index e9e23afba8..21c6f68643 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -114,11 +114,11 @@ Note that the dump files specified as part of the *dump* keyword can be parallel files, i.e. written as multiple files either per processor and/or per snapshot. If that is the case they will also be read in parallel which can make the rerun command operate dramatically faster -for large systems. See the doc page for the :doc:`read_dump +for large systems. See the page for the :doc:`read_dump ` and :doc:`dump ` commands which describe how to read and write parallel dump files. -The *first*\ , *last*\ , *every*\ , *skip* keywords determine which +The *first*, *last*, *every*, *skip* keywords determine which snapshots are read from the dump file(s). Snapshots are skipped until they have a timestep >= *Nfirst*\ . When a snapshot with a timestep > *Nlast* is encountered, the rerun command finishes. Note that @@ -145,7 +145,7 @@ do for the :doc:`run ` command. They only need to be defined if (a) you are using a :doc:`fix ` command that changes some value over time, and (b) you want the reference point for elapsed time (from start to stop) to be different than the *first* and *last* settings. -See the doc page for individual fixes to see which ones can be used +See the page for individual fixes to see which ones can be used with the *start/stop* keywords. Note that if you define neither of the *start*\ /\ *stop* or *first*\ /\ *last* keywords, then LAMMPS treats the pseudo run as going from 0 to a huge value (effectively infinity). @@ -163,7 +163,7 @@ The *dump* keyword is required and must be the last keyword specified. 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 :doc:`read_dump ` 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. @@ -192,14 +192,14 @@ 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 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 +defined. See its 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 command. If time-averaging fixes like :doc:`fix ave/time ` are used, they are invoked on timesteps that are a function of their -*Nevery*\ , *Nrepeat*\ , and *Nfreq* settings. As an example, see the -:doc:`fix ave/time ` doc page for details. You must +*Nevery*, *Nrepeat*, and *Nfreq* settings. As an example, see the +:doc:`fix ave/time ` page for details. You must insure those settings are consistent with the snapshot timestamps that 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. diff --git a/doc/src/run.rst b/doc/src/run.rst index 6c47721e91..75c3bc93f0 100644 --- a/doc/src/run.rst +++ b/doc/src/run.rst @@ -45,7 +45,7 @@ Description Run or continue dynamics for a specified number of timesteps. -When the :doc:`run style ` is *respa*\ , N refers to outer +When the :doc:`run style ` is *respa*, N refers to outer loop (largest) timesteps. A value of N = 0 is acceptable; only the thermodynamics of the system @@ -64,7 +64,7 @@ completes. The *start* or *stop* keywords can be used if multiple runs are being performed and you want a :doc:`fix ` command that changes some value over time (e.g. temperature) to make the change across the -entire set of runs and not just a single run. See the doc page for +entire set of runs and not just a single run. See the page for individual fixes to see which ones can be used with the *start/stop* keywords. @@ -136,7 +136,7 @@ be useful for invoking a command you have added to LAMMPS that wraps some other code (e.g. as a library) to perform a computation periodically during a long LAMMPS run. See the :doc:`Modify ` doc page for info about how to add new commands to LAMMPS. See the -:doc:`Howto couple ` doc page for ideas about how to +:doc:`Howto couple ` page for ideas about how to couple LAMMPS to other codes. With the *every* option, N total steps are simulated, in shorter runs @@ -203,7 +203,7 @@ Restrictions When not using the *upto* keyword, the number of specified timesteps N must fit in a signed 32-bit integer, so you are limited to slightly -more than 2 billion steps (2\^31) in a single run. When using *upto*\ , +more than 2 billion steps (2\^31) in a single run. When using *upto*, N can be larger than a signed 32-bit integer, however the difference between N and the current timestep must still be no larger than 2\^31 steps. diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index 3cb5e28597..bcfa3d7b54 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -125,7 +125,7 @@ screen.0 by default; see the :doc:`-plog and -pscreen command-line switches ` doc page for performance +See the :doc:`Speed packages ` page for performance details of the speed-up offered by the *verlet/split* style. One important performance consideration is the assignment of logical processors in the 2 partitions to the physical cores of a parallel @@ -298,7 +298,7 @@ can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -See the :doc:`Speed packages ` doc page for more +See the :doc:`Speed packages ` page for more instructions on how to use the accelerated styles effectively. ---------- @@ -308,7 +308,7 @@ Restrictions The *verlet/split* style can only be used if LAMMPS was built with the REPLICA package. Correspondingly the *respa/omp* style is available -only if the OPENMP package was included. See the :doc:`Build package ` doc page for more info. +only if the OPENMP package was included. See the :doc:`Build package ` page for more info. Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are diff --git a/doc/src/server.rst b/doc/src/server.rst index f305f314c1..7423653c14 100644 --- a/doc/src/server.rst +++ b/doc/src/server.rst @@ -28,7 +28,7 @@ message back to the client. The specified *protocol* determines the format and content of messages LAMMPS expects to receive and how it responds. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -47,9 +47,9 @@ are: * :doc:`md ` = run dynamics with another code * :doc:`mc ` = perform Monte Carlo moves with another code -For protocol *md*\ , LAMMPS can be either a client (via the :doc:`fix client/md ` command) or server. See the :doc:`server md ` doc page for details on the protocol. +For protocol *md*, LAMMPS can be either a client (via the :doc:`fix client/md ` command) or server. See the :doc:`server md ` page for details on the protocol. -For protocol *mc*\ , LAMMPS can be the server. See the :doc:`server mc ` doc page for details on the protocol. +For protocol *mc*, LAMMPS can be the server. See the :doc:`server mc ` page for details on the protocol. ---------- @@ -57,7 +57,7 @@ Restrictions """""""""""" This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. A script that uses this command must also use the :doc:`message ` command to setup the messaging protocol with diff --git a/doc/src/server_mc.rst b/doc/src/server_mc.rst index eae3ead5b4..f5ddf2f468 100644 --- a/doc/src/server_mc.rst +++ b/doc/src/server_mc.rst @@ -27,7 +27,7 @@ expect messages from a separate "client" code that match the *mc* protocol for format and content explained below. For each message LAMMPS receives it will send a message back to the client. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -39,7 +39,7 @@ signals when it is done sending messages to LAMMPS, at which point the loop will exit, and the remainder of the LAMMPS script will be processed. -The :doc:`server ` doc page gives other options for using LAMMPS +The :doc:`server ` page gives other options for using LAMMPS See an example of how this command is used in examples/COUPLE/lammps_mc/in.server. @@ -109,7 +109,7 @@ Restrictions """""""""""" This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. A script that uses this command must also use the :doc:`message ` command to setup the messaging protocol with diff --git a/doc/src/server_md.rst b/doc/src/server_md.rst index 86a8225e7a..f9a25a4718 100644 --- a/doc/src/server_md.rst +++ b/doc/src/server_md.rst @@ -27,7 +27,7 @@ expect messages from a separate "client" code that match the *md* protocol for format and content explained below. For each message LAMMPS receives it will send a message back to the client. -The :doc:`Howto client/server ` doc page gives an +The :doc:`Howto client/server ` page gives an overview of client/server coupling of LAMMPS with another code where one code is the "client" and sends request messages to a "server" code. The server responds to each request with a reply message. This @@ -39,7 +39,7 @@ signals when it is done sending messages to LAMMPS, at which point the loop will exit, and the remainder of the LAMMPS script will be processed. -The :doc:`server ` doc page gives other options for using LAMMPS +The :doc:`server ` page gives other options for using LAMMPS in server mode. See an example of how this command is used in examples/message/in.message.server. @@ -148,7 +148,7 @@ Restrictions """""""""""" This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/set.rst b/doc/src/set.rst index dd136f867e..e61c288a74 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -42,9 +42,9 @@ Syntax seed = random # seed (positive integer) *mol* value = molecule ID value can be an atom-style variable (see below) - *x*\ ,\ *y*\ ,\ *z* value = atom coordinate (distance units) + *x*,\ *y*,\ *z* value = atom coordinate (distance units) value can be an atom-style variable (see below) - *vx*\ ,\ *vy*\ ,\ *vz* value = atom velocity (velocity units) + *vx*,\ *vy*,\ *vz* value = atom velocity (velocity units) value can be an atom-style variable (see below) *charge* value = atomic charge (charge units) value can be an atom-style variable (see below) @@ -175,12 +175,12 @@ style *type* selects all the atoms in a range of types. The style In each of the range cases, the range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For -example, for the style *type*\ , if N = the number of atom types, then +example, for the style *type*, if N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). For all the styles except -*mol*\ , the lowest value for the wildcard is 1; for *mol* it is 0. +*mol*, the lowest value for the wildcard is 1; for *mol* it is 0. The style *group* selects all the atoms in the specified group. The style *region* selects all the atoms in the specified geometric @@ -250,10 +250,10 @@ Keyword *mol* sets the molecule ID for all selected atoms. The :doc:`atom style ` being used must support the use of molecule IDs. -Keywords *x*\ , *y*\ , *z*\ , and *charge* set the coordinates or -charge of all selected atoms. For *charge*\ , the :doc:`atom style +Keywords *x*, *y*, *z*, and *charge* set the coordinates or +charge of all selected atoms. For *charge*, the :doc:`atom style ` being used must support the use of atomic -charge. Keywords *vx*\ , *vy*\ , and *vz* set the velocities of all +charge. Keywords *vx*, *vy*, and *vz* set the velocities of all selected atoms. Keyword *dipole* uses the specified x,y,z values as components of a @@ -303,7 +303,7 @@ 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 -*quat*\ , for ellipsoidal particles, the 3 shape values must be non-zero +*quat*, for ellipsoidal particles, the 3 shape values must be non-zero for each particle set by this command. This keyword does not allow use of an atom-style variable. @@ -316,7 +316,7 @@ 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 +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 @@ -430,16 +430,16 @@ up analysis of the trajectories if a LAMMPS diagnostic or your own analysis relies on the image flags to unwrap a molecule which straddles the periodic box. -Keywords *bond*\ , *angle*\ , *dihedral*\ , and *improper*\ , set the bond +Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond type (angle type, etc) of all bonds (angles, etc) of selected atoms to 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 +etc) was set by the *bond types* (\ *angle types*, etc) field in the header of the data file read by the :doc:`read_data ` command. These keywords do not allow use of an atom-style variable. -Keywords *sph/e*\ , *sph/cv*\ , and *sph/rho* set the energy, heat +Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity, and density of smoothed particle hydrodynamics (SPH) particles. See `this PDF guide `_ to using SPH in LAMMPS. diff --git a/doc/src/shell.rst b/doc/src/shell.rst index 95f72a27ba..af5c110fee 100644 --- a/doc/src/shell.rst +++ b/doc/src/shell.rst @@ -58,7 +58,7 @@ of the input script. Or you can run a program that pre-processes data for input into LAMMPS. Or you can run a program that post-processes LAMMPS output data. -With the exception of *cd*\ , all commands, including ones invoked via a +With the exception of *cd*, all commands, including ones invoked via a system() call, are executed by only a single processor, so that files/directories are not being manipulated by multiple processors. diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index 779056f87a..4b197fbf3a 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -148,7 +148,7 @@ LJ and Coulombic interactions, which is consistent with a coarse-grained polymer model with :doc:`FENE bonds `. See :ref:`(Kremer) ` for a description of FENE bonds. -The *lj/coul*\ , *lj*\ , and *coul* keywords allow the 3 coefficients to +The *lj/coul*, *lj*, and *coul* keywords allow the 3 coefficients to be set explicitly. The *lj/coul* keyword sets both the LJ and Coulombic coefficients to the same 3 values. The *lj* and *coul* keywords only set either the LJ or Coulombic coefficients. Use both @@ -165,7 +165,7 @@ as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a dihedral, then the pairwise interaction between atoms 1 and 3 will always be weighted by 0.5, but different force fields use different rules for weighting the pairwise interaction between atoms 2 and 4. -If the *angle* keyword is specified as *yes*\ , then the pairwise +If the *angle* keyword is specified as *yes*, then the pairwise interaction between atoms 2 and 4 will be unaffected (full weighting of 1.0). If the *angle* keyword is specified as *no* which is the default, then the 2,4 interaction will also be weighted by 0.5. @@ -179,7 +179,7 @@ defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a dihedral, then the pairwise interaction between atoms 1 and 4 will always be weighted by 0.5, but different force fields use different rules for weighting the pairwise interaction between atoms 2 and 5. -If the *dihedral* keyword is specified as *yes*\ , then the pairwise +If the *dihedral* keyword is specified as *yes*, then the pairwise interaction between atoms 2 and 5 will be unaffected (full weighting of 1.0). If the *dihedral* keyword is specified as *no* which is the default, then the 2,5 interaction will also be weighted by 0.5. diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst index 1ece739f55..4789229800 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -32,7 +32,7 @@ This command allows you to use variants of various styles if they exist. In that respect it operates the same as the :doc:`-suffix command-line switch `. It also has options to turn off or back on any suffix setting made via the command line. -The specified style can be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt* or +The specified style can be *gpu*, *intel*, *kk*, *omp*, *opt* or *hybrid*\ . These refer to optional packages that LAMMPS can be built with, as described on the :doc:`Build package ` doc page. The "gpu" style corresponds to the GPU package, the "intel" style to @@ -78,9 +78,9 @@ example, "hybrid intel omp" will use styles from the INTEL package as a first choice and styles from the OPENMP package as a second choice if no INTEL variant is available. -If the specified style is *off*\ , then any previously specified suffix +If the specified style is *off*, then any previously specified suffix is temporarily disabled, whether it was specified by a command-line -switch or a previous suffix command. If the specified style is *on*\ , +switch or a previous suffix command. If the specified style is *on*, a disabled suffix is turned back on. The use of these 2 commands lets your input script use a standard LAMMPS style (i.e. a non-accelerated variant), which can be useful for testing or benchmarking purposes. diff --git a/doc/src/tad.rst b/doc/src/tad.rst index c3cd3b825b..b36ad2e431 100644 --- a/doc/src/tad.rst +++ b/doc/src/tad.rst @@ -160,7 +160,7 @@ events must be generated before one is finally executed. Conversely, if this criterion is too aggressive, high-entropy high-barrier events will be over-sampled, while low-entropy low-barrier events will be under-sampled. If the lowest pre-exponential factor is known fairly -accurately, then it can be used to estimate *tmax*\ , and the value of +accurately, then it can be used to estimate *tmax*, and the value of *delta* can be set to the desired confidence level e.g. *delta* = 0.05 corresponds to 95% confidence. However, for systems where the dynamics are not well characterized (the most common case), it will be @@ -181,7 +181,7 @@ files, and restart files. Event statistics are printed to the screen and master log.lammps file each time an event is executed. The quantities are the timestep, CPU -time, global event number *N*\ , local event number *M*\ , event status, +time, global event number *N*, local event number *M*, event status, energy barrier, time margin, *t_lo* and *delt_lo*. The timestep is the usual LAMMPS timestep, which corresponds to the high-temperature time at which the event was detected, in units of timestep. The CPU @@ -204,7 +204,7 @@ high-temperature time since entering the current basin, scaled by an exponential factor that depends on the hi/lo temperature ratio and the energy barrier for that event. -On lines for executed events, with status *E*\ , the global event number +On lines for executed events, with status *E*, the global event number is incremented by one, the local event number and time margin are reset to zero, while the global event number, energy barrier, and @@ -304,7 +304,7 @@ Default """"""" The option defaults are *min* = 0.1 0.1 40 50, *neb* = 0.01 100 100 -10, *neb_style* = *quickmin*\ , *neb_step* = the same timestep set by +10, *neb_style* = *quickmin*, *neb_step* = the same timestep set by the :doc:`timestep ` command, and *neb_log* = "none". ---------- diff --git a/doc/src/temper.rst b/doc/src/temper.rst index bdc0e426ec..363e0102fc 100644 --- a/doc/src/temper.rst +++ b/doc/src/temper.rst @@ -45,7 +45,7 @@ Each replica's temperature is controlled at a different value by a fix with *fix-ID* that controls temperature. Most thermostat fix styles (with and without included time integration) are supported. The command will print an error message and abort, if the chosen fix is unsupported. -The desired temperature is specified by *temp*\ , which is typically a +The desired temperature is specified by *temp*, which is typically a variable previously set in the input script, so that each partition is assigned a different temperature. See the :doc:`variable ` command for more details. For example: diff --git a/doc/src/temper_grem.rst b/doc/src/temper_grem.rst index f45755da50..312df21254 100644 --- a/doc/src/temper_grem.rst +++ b/doc/src/temper_grem.rst @@ -48,7 +48,7 @@ discussed there in greater detail. Instead of temperature, this command performs replica exchanges in lambda as per the generalized ensemble enforced by :doc:`fix grem -`. The desired lambda is specified by *lambda*\ , which is +`. The desired lambda is specified by *lambda*, which is typically a variable previously set in the input script, so that each partition is assigned a different temperature. See the :doc:`variable ` command for more details. For example: diff --git a/doc/src/temper_npt.rst b/doc/src/temper_npt.rst index 9c5ba242e9..a8f5999dbe 100644 --- a/doc/src/temper_npt.rst +++ b/doc/src/temper_npt.rst @@ -52,7 +52,7 @@ Restrictions """""""""""" This command can only be used if LAMMPS was built with the REPLICA -package. See the :doc:`Build package ` doc page for more +package. See the :doc:`Build package ` page for more info. This command should be used with a fix that maintains the diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 1815a7cb76..31de925492 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -59,8 +59,8 @@ simulation box :doc:`boundary ` or if it moves more than a box length outside the simulation domain (or more than a processor sub-domain length) before reneighboring occurs. The latter case is typically due to bad dynamics, e.g. too large a timestep or huge -forces and velocities. If the value is *ignore*\ , LAMMPS does not -check for lost atoms. If the value is *error* or *warn*\ , LAMMPS +forces and velocities. If the value is *ignore*, LAMMPS does not +check for lost atoms. If the value is *error* or *warn*, LAMMPS checks and either issues an error or warning. The code will exit with an error and continue with a warning. A warning will only be issued once, the first time an atom is lost. This can be a useful debugging @@ -117,15 +117,15 @@ The *norm* keyword determines whether various thermodynamic output values are normalized by the number of atoms or not, depending on whether it is set to *yes* or *no*\ . Different unit styles have different defaults for this setting (see below). Even if *norm* is -set to *yes*\ , a value is only normalized if it is an "extensive" +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 +system. For the thermo keywords described by the page for the :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 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 @@ -174,7 +174,7 @@ settings, reverting all values to their default format. a "%d"-style format identifier in the format string and LAMMPS will convert this to the corresponding 8-byte form when it is applied to those keywords. However, when specifying the *line* option or *format - M string* option for *step* and *natoms*\ , you should specify a format + M string* option for *step* and *natoms*, you should specify a format string appropriate for an 8-byte signed integer, e.g. one with "%ld". The *temp* keyword is used to determine how thermodynamic temperature @@ -222,7 +222,7 @@ Default """"""" The option defaults are lost = error, warn = 100, norm = yes for unit -style of *lj*\ , norm = no for unit style of *real* and *metal*\ , +style of *lj*, norm = no for unit style of *real* and *metal*, flush = no, and temp/press = compute IDs defined by thermo_style. The defaults for the line and format options depend on the thermo diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 8ea487fd0a..a04504b1a6 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -117,7 +117,7 @@ thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are references to :doc:`computes `, :doc:`fixes `, and equal-style :doc:`variables ` that have been defined elsewhere in the input script or can even be new styles which users have added -to LAMMPS. See the :doc:`Modify ` doc page for details on the +to LAMMPS. See the :doc:`Modify ` page for details on the latter. Thus the *custom* style provides a flexible means of outputting essentially any desired quantity as a simulation proceeds. @@ -218,16 +218,16 @@ to see which ones contribute and whether their default A long-range tail correction *etail* for the van der Waals pairwise 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 +included in *evdwl*, *epair*, *pe*, and *etotal*, and the corresponding tail correction to the pressure is included in *press* -and *pxx*\ , *pyy*\ , etc. +and *pxx*, *pyy*, etc. ---------- Here is more information on other keywords whose meaning may not be clear: -The *step*\ , *elapsed*\ , and *elaplong* keywords refer to timestep +The *step*, *elapsed*, and *elaplong* keywords refer to timestep count. *Step* is the current timestep, or iteration count when a :doc:`minimization ` is being performed. *Elapsed* is the number of timesteps elapsed since the beginning of this run. @@ -318,13 +318,13 @@ to reduce the delay factor to insure no force interactions are missed by atoms moving beyond the neighbor skin distance before a rebuild takes place. -The keywords *cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , -*cellbeta*\ , *cellgamma*\ , correspond to the usual crystallographic +The keywords *cella*, *cellb*, *cellc*, *cellalpha*, +*cellbeta*, *cellgamma*, correspond to the usual crystallographic quantities that define the periodic unit cell of a crystal. See the -:doc:`Howto triclinic ` doc page for a geometric +:doc:`Howto triclinic ` page for a geometric description of triclinic periodic cells, including a precise definition of these quantities in terms of the internal LAMMPS cell -dimensions *lx*\ , *ly*\ , *lz*\ , *yz*\ , *xz*\ , *xy*\ . +dimensions *lx*, *ly*, *lz*, *yz*, *xz*, *xy*\ . ---------- diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index 513d96b9e8..f020511aad 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -56,7 +56,7 @@ The command collects a 9 times the number of atoms in the group on every single so the memory requirements can be very significant for large systems. This command is part of the PHONON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/timer.rst b/doc/src/timer.rst index eac86656af..a604cc2212 100644 --- a/doc/src/timer.rst +++ b/doc/src/timer.rst @@ -81,7 +81,7 @@ which can be set with the *every* keyword. Default is checking every 10 steps. After the timer timeout has expired all subsequent run or minimize commands in the input script will be skipped. The remaining time or timer status can be accessed with the -:doc:`thermo ` variable *timeremain*\ , which will be +:doc:`thermo ` variable *timeremain*, which will be zero, if the timeout is inactive (default setting), it will be negative, if the timeout time is expired and positive if there is time remaining and in this case the value of the variable are diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst index e512eed1b2..3142509611 100644 --- a/doc/src/timestep.rst +++ b/doc/src/timestep.rst @@ -30,7 +30,7 @@ each choice of units that LAMMPS supports. The default value for the timestep size also depends on the choice of units for the simulation; see the default values below. -When the :doc:`run style ` is *respa*\ , dt is the timestep for +When the :doc:`run style ` is *respa*, dt is the timestep for the outer loop (largest) timestep. Restrictions diff --git a/doc/src/units.rst b/doc/src/units.rst index 3c0f4a220a..da81c17078 100644 --- a/doc/src/units.rst +++ b/doc/src/units.rst @@ -29,7 +29,7 @@ and data file, as well as quantities output to the screen, log file, and dump files. Typically, this command is used at the very beginning of an input script. -For all units except *lj*\ , LAMMPS uses physical constants from +For all units except *lj*, LAMMPS uses physical constants from www.physics.nist.gov. For the definition of Kcal in real units, LAMMPS uses the thermochemical calorie = 4.184 J. @@ -60,7 +60,7 @@ automatic conversion has happened is printed to the screen. ---------- -For style *lj*\ , all quantities are unitless. Without loss of +For style *lj*, all quantities are unitless. Without loss of generality, LAMMPS sets the fundamental quantities mass, :math:`\sigma`, :math:`\epsilon`, and the Boltzmann constant :math:`k_B = 1`. The masses, distances, energies you specify are multiples of these @@ -97,7 +97,7 @@ 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. -For style *real*\ , these are the units: +For style *real*, these are the units: * mass = grams/mole * distance = Angstroms @@ -114,7 +114,7 @@ For style *real*\ , these are the units: * electric field = volts/Angstrom * density = gram/cm\^dim -For style *metal*\ , these are the units: +For style *metal*, these are the units: * mass = grams/mole * distance = Angstroms @@ -131,7 +131,7 @@ For style *metal*\ , these are the units: * electric field = volts/Angstrom * density = gram/cm\^dim -For style *si*\ , these are the units: +For style *si*, these are the units: * mass = kilograms * distance = meters @@ -148,7 +148,7 @@ For style *si*\ , these are the units: * electric field = volts/meter * density = kilograms/meter\^dim -For style *cgs*\ , these are the units: +For style *cgs*, these are the units: * mass = grams * distance = centimeters @@ -165,7 +165,7 @@ For style *cgs*\ , these are the units: * electric field = statvolt/cm or dyne/esu * density = grams/cm\^dim -For style *electron*\ , these are the units: +For style *electron*, these are the units: * mass = atomic mass units * distance = Bohr @@ -179,7 +179,7 @@ For style *electron*\ , these are the units: * dipole moment = Debye * electric field = volts/cm -For style *micro*\ , these are the units: +For style *micro*, these are the units: * mass = picograms * distance = micrometers @@ -196,7 +196,7 @@ For style *micro*\ , these are the units: * electric field = volt/micrometer * density = picograms/micrometer\^dim -For style *nano*\ , these are the units: +For style *nano*, these are the units: * mass = attograms * distance = nanometers diff --git a/doc/src/variable.rst b/doc/src/variable.rst index f24c262e58..25861ae17b 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -189,7 +189,7 @@ executed. override a corresponding index variable setting in the input script. There are two exceptions to this rule. First, variables of style -*string*\ , *getenv*\ , *internal*\ , *equal*\ , *vector*\ , *atom*\ , and +*string*, *getenv*, *internal*, *equal*, *vector*, *atom*, and *python* ARE redefined each time the command is encountered. This allows these style of variables to be redefined multiple times in an input script. In a loop, this means the formula associated with an @@ -204,14 +204,14 @@ the same thing. ---------- -The :doc:`Commands parse ` doc page explains how +The :doc:`Commands parse ` page explains how occurrences of a variable name in an input script line are replaced by the variable's string. The variable name can be referenced as $x if the name "x" is a single character, or as ${LoopVar} if the name "LoopVar" is one or more characters. -As described below, for variable styles *index*\ , *loop*\ , *file*\ , -*universe*\ , and *uloop*\ , which string is assigned to a variable can be +As described below, for variable styles *index*, *loop*, *file*, +*universe*, and *uloop*, which string is assigned to a variable can be incremented via the :doc:`next ` command. When there are no more strings to assign, the variable is exhausted and a flag is set that causes the next :doc:`jump ` command encountered in the input @@ -439,7 +439,7 @@ compute, fix, or other vector-style variable. For *atom*\ -style variables the formula computes one quantity for each atom whenever it is evaluated. -Note that *equal*\ , *vector*\ , and *atom* variables can produce +Note that *equal*, *vector*, and *atom* variables can produce different values at different stages of the input script or at different times during a run. For example, if an *equal* variable is used in a :doc:`fix print ` command, different values could @@ -451,7 +451,7 @@ of Variables". The next command cannot be used with *equal* or *vector* or *atom* style variables, since there is only one string. -The formula for an *equal*\ , *vector*\ , or *atom* variable can contain a +The formula for an *equal*, *vector*, or *atom* variable can contain a variety of quantities. The syntax for each kind of quantity is simple, but multiple quantities can be nested and combined in various ways to build up formulas of arbitrary complexity. For example, this @@ -527,8 +527,8 @@ Numbers can contain digits, scientific notation (3.0e20,3.0e-20,3.0E20,3.0E-20), and leading minus signs. Constants are set at compile time and cannot be changed. *PI* will -return the number 3.14159265358979323846; *on*\ , *true* or *yes* will -return 1.0; *off*\ , *false* or *no* will return 0.0; *version* will +return the number 3.14159265358979323846; *on*, *true* or *yes* will +return 1.0; *off*, *false* or *no* will return 0.0; *version* will return a numeric version code of the current LAMMPS version (e.g. version 2 Sep 2015 will return the number 20150902). The corresponding value for newer versions of LAMMPS will be larger, for older versions @@ -788,7 +788,7 @@ Group and Region Functions Group functions are specified as keywords followed by one or two parenthesized arguments. The first argument *ID* is the group-ID. The *dim* argument, if it exists, is *x* or *y* or *z*\ . The *dir* -argument, if it exists, is *xmin*\ , *xmax*\ , *ymin*\ , *ymax*\ , *zmin*\ , or +argument, if it exists, is *xmin*, *xmax*, *ymin*, *ymax*, *zmin*, or *zmax*\ . The *dimdim* argument, if it exists, is *xx* or *yy* or *zz* or *xy* or *yz* or *xz*\ . @@ -958,21 +958,21 @@ Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, othe timestep $(2.0*(1.0+2.0*is_active(pair,respa)) if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3" -The *is_defined()* function allows to query categories like *compute*\ , -*dump*\ , *fix*\ , *group*\ , *region*\ , and *variable* whether an entry +The *is_defined()* function allows to query categories like *compute*, +*dump*, *fix*, *group*, *region*, and *variable* whether an entry with the provided name or id is defined. The *is_available(category,name)* function allows to query whether a specific optional feature is available, i.e. compiled in. -This currently works for the following categories: *command*\ , -*compute*\ , *fix*\ , *pair_style* and *feature*\ . For all categories +This currently works for the following categories: *command*, +*compute*, *fix*, *pair_style* and *feature*\ . For all categories except *command* and *feature* also appending active suffixes is tried before reporting failure. The *feature* category is used to check the availability of compiled in features such as GZIP support, PNG support, JPEG support, FFMPEG support, and C++ exceptions for error handling. Corresponding values for name are -*gzip*\ , *png*\ , *jpeg*\ , *ffmpeg* and *exceptions*\ . +*gzip*, *png*, *jpeg*, *ffmpeg* and *exceptions*\ . This enables writing input scripts which only dump using a given format if the compiled binary supports it. @@ -1025,7 +1025,7 @@ Compute References Compute references access quantities calculated by a :doc:`compute `. The ID in the reference should be replaced by the ID of a compute defined elsewhere in the input script. As -discussed in the doc page for the :doc:`compute ` command, +discussed in the page for the :doc:`compute ` command, computes can produce global, per-atom, or local values. Only global and per-atom values can be used in a variable. Computes can also produce a scalar, vector, or array. @@ -1086,7 +1086,7 @@ Fix References Fix references access quantities calculated by a :doc:`fix `. The ID in the reference should be replaced by the ID of a fix defined -elsewhere in the input script. As discussed in the doc page for the +elsewhere in the input script. As discussed in the page for the :doc:`fix ` command, fixes can produce global, per-atom, or local values. Only global and per-atom values can be used in a variable. Fixes can also produce a scalar, vector, or array. An equal-style @@ -1198,7 +1198,7 @@ Immediate Evaluation of Variables If you want an equal-style variable to be evaluated immediately, it may be the case that you do not need to define a variable at all. See -the :doc:`Commands parse ` doc page for info on how to +the :doc:`Commands parse ` page for info on how to use "immediate" variables in an input script, specified as $(formula) with parenthesis, where the formula has the same syntax as equal-style variables described on this page. This effectively evaluates a diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index d8823d6b7e..0c8de5b854 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -115,7 +115,7 @@ body. All temperatures specified in the velocity command are in temperature units; see the :doc:`units ` command. The units of velocities and coordinates depend on whether the *units* keyword is set to *box* or -*lattice*\ , as discussed below. +*lattice*, as discussed below. For all styles, no atoms are assigned z-component velocities if the simulation is 2d; see the :doc:`dimension ` command. @@ -161,12 +161,12 @@ appropriate fix command must be specified before the velocity command is issued. The *bias* keyword with a *yes* setting is used by *create* and -*scale*\ , but only if the *temp* keyword is also used to specify a +*scale*, but only if the *temp* keyword is also used to specify a :doc:`compute ` that calculates temperature in a desired way. If the temperature compute also calculates a velocity bias, the bias is subtracted from atom velocities before the *create* and *scale* operations are performed. After the operations, the bias is -added back to the atom velocities. See the :doc:`Howto thermostat ` doc page for more discussion of +added back to the atom velocities. See the :doc:`Howto thermostat ` page for more discussion of temperature computes with biases. Note that the velocity bias is only applied to atoms in the temperature compute specified with the *temp* keyword. diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index 0aa26f8bbf..e14d1b7f4c 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -107,7 +107,7 @@ from :doc:`fix property/atom `. The *pair* keyword lets you specify in what format the pair coefficient information is written into the data file. If the value -is specified as *ii*\ , then one line per atom type is written, to +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 @@ -116,7 +116,7 @@ behavior can be overridden in the input script after reading the data 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 +If the value is specified as *ij*, then one line of coefficients is written for all I,J pairs where I <= J. These coefficients will include any specific settings made in the input script up to that point. The presence of these I != J coefficients in the data file diff --git a/src/EXTRA-PAIR/pair_coul_streitz.cpp b/src/KSPACE/pair_coul_streitz.cpp similarity index 100% rename from src/EXTRA-PAIR/pair_coul_streitz.cpp rename to src/KSPACE/pair_coul_streitz.cpp diff --git a/src/EXTRA-PAIR/pair_coul_streitz.h b/src/KSPACE/pair_coul_streitz.h similarity index 100% rename from src/EXTRA-PAIR/pair_coul_streitz.h rename to src/KSPACE/pair_coul_streitz.h