diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index 4788d93689..800b82645d 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -142,7 +142,7 @@ please refer to its documentation. .. _default-none-issues: -**OpenMP Compiler compatibility info**\ : +**OpenMP Compiler compatibility info**\ : Some compilers do not fully support the 'default(none)' directive and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0 diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index a4064ee812..07adb67a3a 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -53,7 +53,7 @@ This is the list of packages that may require additional steps. * :ref:`USER-QUIP ` * :ref:`USER-SCAFACOS ` * :ref:`USER-SMD ` - * :ref:`USER-VTK ` + * :ref:`USER-VTK ` ---------- @@ -1230,7 +1230,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example. .. parsed-literal:: - CCFLAGS: -fopenmp # for GNU and Clang Compilers + CCFLAGS: -fopenmp # for GNU and Clang Compilers CCFLAGS: -qopenmp -restrict # for Intel compilers on Linux LINKFLAGS: -fopenmp # for GNU and Clang Compilers LINKFLAGS: -qopenmp # for Intel compilers on Linux diff --git a/doc/src/Build_link.rst b/doc/src/Build_link.rst index 365decd54d..fdb98d3785 100644 --- a/doc/src/Build_link.rst +++ b/doc/src/Build_link.rst @@ -101,7 +101,7 @@ change to: gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c g++ -o caller caller.o -L${HOME}/lammps/lib/poems \ - -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps -lpoems -lmpi_stubs + -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps -lpoems -lmpi_stubs Note, that you need to link with "g++" instead of "gcc", since LAMMPS is C++ code. You can display the currently applied settings for building @@ -115,15 +115,15 @@ Which should output something like: .. code-block:: bash - # Compiler: + # Compiler: CXX=g++ - # Linker: + # Linker: LD=g++ - # Compilation: + # Compilation: CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/lammps/lib/poems -I${HOME}/lammps/src/STUBS - # Linking: + # Linking: LDFLAGS=-g -O - # Libraries: + # Libraries: LDLIBS=-L${HOME}/lammps/lib/poems -L${HOME}/lammps/src/STUBS -lpoems -lmpi_stubs From this you can gather the necessary paths and flags. With @@ -165,7 +165,7 @@ traditional make build using "make mode=shlib serial" becomes: g++ -o caller caller.o -L${HOME}/lammps/src -llammps *Locating liblammps.so at runtime*\ : - + However, now the `liblammps.so` file is required at runtime and needs to be in a folder, where the shared linker program of the operating system can find it. This would be either a folder like "/usr/local/lib64" @@ -203,7 +203,7 @@ You can verify whether all required shared libraries are found with the .. code-block:: bash - $ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller + $ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller linux-vdso.so.1 (0x00007ffe729e0000) liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000) @@ -217,7 +217,7 @@ If a required library is missing, you would get a 'not found' entry: .. code-block:: bash - $ ldd caller + $ ldd caller linux-vdso.so.1 (0x00007ffd672fe000) liblammps.so => not found libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000) diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index cd178161b3..f3c98f9bcb 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -221,7 +221,7 @@ package" will list all the these commands. directory src and the sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC), so that the files are included or excluded when LAMMPS is built. Only source files in the src folder will be - compiled. + compiled. The following make commands help manage files that exist in both the src directory and in package sub-directories. You do not normally diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 5f835f76a0..dca5f0f37f 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -12,7 +12,7 @@ explain how to do this for building both with CMake and make. * :ref:`Output of movie files ` via the :doc:`dump_movie ` command * :ref:`Memory allocation alignment ` * :ref:`Workaround for long long integers ` -* :ref:`Error handling exceptions ` when using LAMMPS as a library +* :ref:`Error handling exceptions ` when using LAMMPS as a library ---------- diff --git a/doc/src/Commands_parse.rst b/doc/src/Commands_parse.rst index 83e7d439ef..750369d118 100644 --- a/doc/src/Commands_parse.rst +++ b/doc/src/Commands_parse.rst @@ -116,7 +116,7 @@ LAMMPS: underscores, or punctuation characters. .. _five: - + 5. The first word is the command name. All successive words in the line are arguments. diff --git a/doc/src/Commands_structure.rst b/doc/src/Commands_structure.rst index 9b5a466340..98744efb2a 100644 --- a/doc/src/Commands_structure.rst +++ b/doc/src/Commands_structure.rst @@ -9,7 +9,7 @@ page. A LAMMPS input script typically has 4 parts: 1. :ref:`Initialization ` -2. :ref:`System definition ` +2. :ref:`System definition ` 3. :ref:`Simulation settings ` 4. :ref:`Run a simulation ` diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst index e9b0863a6a..e7ff0bef89 100644 --- a/doc/src/Howto_spc.rst +++ b/doc/src/Howto_spc.rst @@ -20,7 +20,7 @@ atoms and the water molecule to run a rigid SPC model. | LJ epsilon, sigma of OH, HH = 0.0 | r0 of OH bond = 1.0 | theta of HOH angle = 109.47 -| +| Note that as originally proposed, the SPC model was run with a 9 Angstrom cutoff for both LJ and Coulombic terms. It can also be used @@ -33,7 +33,7 @@ the partial charge assignments change: | O charge = -0.8476 | H charge = 0.4238 -| +| See the :ref:`(Berendsen) ` reference for more details on both the SPC and SPC/E models. diff --git a/doc/src/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst index 921dface17..7b36f7f742 100644 --- a/doc/src/Howto_tip3p.rst +++ b/doc/src/Howto_tip3p.rst @@ -30,7 +30,7 @@ set to 0.0, it corresponds to the original 1983 TIP3P model | r0 of OH bond = 0.9572 | K of HOH angle = 55 | theta of HOH angle = 104.52 -| +| These are the parameters to use for TIP3P with a long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) ` for @@ -47,7 +47,7 @@ details: | r0 of OH bond = 0.9572 | K of HOH angle = 55 | theta of HOH angle = 104.52 -| +| Wikipedia also has a nice article on `water models `_. diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 480ddc3bc6..f814496128 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -38,7 +38,7 @@ coefficients. | LJ sigma of O-O = 3.1536 | LJ epsilon, sigma of OH, HH = 0.0 | Coulombic cutoff = 8.5 -| +| For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); http://dx.doi.org/10.1063/1.1931662) these values can be used: @@ -54,7 +54,7 @@ http://dx.doi.org/10.1063/1.1931662) these values can be used: | LJ sigma of O-O = 3.1668 | LJ epsilon, sigma of OH, HH = 0.0 | Coulombic cutoff = 8.5 -| +| For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); http://dx.doi.org/10.1063/1.2121687), these values can be used: @@ -70,7 +70,7 @@ http://dx.doi.org/10.1063/1.2121687), these values can be used: | LJ sigma of O-O = 3.1589 | LJ epsilon, sigma of OH, HH = 0.0 | Coulombic cutoff = 8.5 -| +| These are the parameters to use for TIP4P with a long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS): @@ -85,7 +85,7 @@ solver (e.g. Ewald or PPPM in LAMMPS): | LJ epsilon of O-O = 0.16275 | LJ sigma of O-O = 3.16435 | LJ epsilon, sigma of OH, HH = 0.0 -| +| Note that the when using the TIP4P pair style, the neighbor list cutoff for Coulomb interactions is effectively extended by a distance diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 0e642a4883..ce3792a622 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -78,7 +78,7 @@ The transformation is given by the following equation: \begin{pmatrix} \mathbf{B \times C} \\ \mathbf{C \times A} \\ - \mathbf{A \times B} + \mathbf{A \times B} \end{pmatrix} \cdot \mathbf{X} where *V* is the volume of the box, **X** is the original vector quantity and diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst index 9c06633f2c..6ea0c01b09 100644 --- a/doc/src/Install_patch.rst +++ b/doc/src/Install_patch.rst @@ -32,9 +32,9 @@ up to date. * Apply the patch by typing the following command from your top-level LAMMPS directory, where the redirected file is the name of the patch file. - + .. code-block:: bash - + $ patch -bp1 < patch.12Dec16 * A list of updated files print out to the screen. The -b switch @@ -46,9 +46,9 @@ up to date. successively, you only need to type this once at the end. The purge command removes deprecated src files if any were removed by the patch from package sub-directories. - + .. code-block:: bash - + $ make purge $ make package-update diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index e2b385b243..6c1a2e1ed5 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -37,7 +37,7 @@ For example, the lmp\_mpi executable might be launched as follows: .. _echo: -**-echo style** +**-echo style** Set the style of command echoing. The style can be *none* or *screen* or *log* or *both*\ . Depending on the style, each command read from @@ -52,7 +52,7 @@ set by using the :doc:`echo ` command in the input script itself. .. _help: -**-help** +**-help** Print a brief help summary and a list of options compiled into this executable for each LAMMPS style (atom\_style, fix, compute, @@ -67,7 +67,7 @@ used. .. _file: -**-in file** +**-in file** Specify a file to use as an input script. This is an optional switch when running LAMMPS in one-partition mode. If it is not specified, @@ -85,7 +85,7 @@ stdin. .. _run-kokkos: -**-kokkos on/off keyword/value ...** +**-kokkos on/off keyword/value ...** Explicitly enable or disable KOKKOS support, as provided by the KOKKOS package. Even if LAMMPS is built with this package, as described @@ -190,7 +190,7 @@ traffic which is slow. .. _log: -**-log file** +**-log file** Specify a log file for LAMMPS to write status information to. In one-partition mode, if the switch is not used, LAMMPS writes to the @@ -211,7 +211,7 @@ Option -plog will override the name of the partition log files file.N. .. _mpicolor: -**-mpicolor** color +**-mpicolor** color If used, this must be the first command-line argument after the LAMMPS executable name. It is only used when LAMMPS is launched by an mpirun @@ -238,7 +238,7 @@ links with from the lib/message directory. See the .. _nocite: -**-nocite** +**-nocite** Disable writing the log.cite file which is normally written to list references for specific cite-able features used during a LAMMPS run. @@ -251,7 +251,7 @@ details. .. _package: -**-package style args ....** +**-package style args ....** Invoke the :doc:`package ` command with style and args. The syntax is the same as if the command appeared at the top of the input @@ -271,7 +271,7 @@ having to edit an input script. .. _partition: -**-partition 8x2 4 5 ...** +**-partition 8x2 4 5 ...** Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P processors and this switch is not used, LAMMPS runs in one partition, @@ -302,7 +302,7 @@ in this context. .. _plog: -**-plog file** +**-plog file** Specify the base name for the partition log files, so partition N writes log information to file.N. If file is none, then no partition @@ -320,7 +320,7 @@ command-line option. .. _pscreen: -**-pscreen file** +**-pscreen file** Specify the base name for the partition screen file, so partition N writes screen information to file.N. If file is none, then no @@ -338,7 +338,7 @@ specified by the -screen command-line option. .. _reorder: -**-reorder** +**-reorder** This option has 2 forms: @@ -476,7 +476,7 @@ optional keyword/value settings. .. _restart2dump: -**-restart2dump restartfile [remap] group-ID dumpstyle dumpfile arg1 arg2 ...** +**-restart2dump restartfile [remap] group-ID dumpstyle dumpfile arg1 arg2 ...** Convert the restart file into a dump file and immediately exit. This is the same operation as if the following 2-line input script were @@ -523,7 +523,7 @@ the *nfile* and *fileper* keywords. See the .. _screen: -**-screen file** +**-screen file** Specify a file for LAMMPS to write its screen information to. In one-partition mode, if the switch is not used, LAMMPS writes to the @@ -544,7 +544,7 @@ partition screen files file.N. .. _suffix: -**-suffix style args** +**-suffix style args** Use variants of various styles if they exist. The specified style can be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt*\ , or *hybrid*\ . These @@ -613,7 +613,7 @@ made via the command line. .. _var: -**-var name value1 value2 ...** +**-var name value1 value2 ...** Specify a variable that will be defined for substitution purposes when the input script is read. This switch can be used multiple times to diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index aae517ef08..403c244a5e 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -624,14 +624,14 @@ replica tool -------------------------- The tools/replica directory contains the reorder\_remd\_traj python script which -can be used to reorder the replica trajectories (resulting from the use of the +can be used to reorder the replica trajectories (resulting from the use of the temper command) according to temperature. This will produce discontinuous trajectories with all frames at the same temperature in each trajectory. Additional options can be used to calculate the canonical configurational log-weight for each frame at each temperature using the pymbar package. See the README.md file for further details. Try out the peptide example provided. -This tool was written by (and is maintained by) Tanmoy Sanyal, +This tool was written by (and is maintained by) Tanmoy Sanyal, while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index c15fd635b7..0b0f8087b0 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -32,7 +32,7 @@ The *sdk* angle style is a combination of the harmonic angle potential, .. math:: - E = K (\theta - \theta_0)^2 + E = K (\theta - \theta_0)^2 where :math:`\theta_0` is the equilibrium value of the angle and diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index 147727dd66..28104d129c 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -13,9 +13,9 @@ Syntax * one or more keyword/value pairs may be appended * keyword = *id* or *map* or *first* or *sort* - + .. parsed-literal:: - + *id* value = *yes* or *no* *map* value = *yes* or *array* or *hash* *first* value = group-ID = group whose atoms will appear first in internal atom lists diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 7ae152851f..da371ee59c 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -12,9 +12,9 @@ Syntax atom_style style args * style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *mdpd* or *tdpd* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *spin* or *tri* or *template* or *hybrid* - + .. parsed-literal:: - + args = none for any style except the following *body* args = bstyle bstyle-args bstyle = style of body particles diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 1c667781af..033aa68663 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -14,9 +14,9 @@ Syntax * 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*\ ) * style = *x* or *y* or *z* or *shift* or *rcb* - + .. parsed-literal:: - + *x* args = *uniform* or Px-1 numbers between 0 and 1 *uniform* = evenly spaced cuts between processors in x dimension numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension @@ -37,9 +37,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *weight* or *out* - + .. parsed-literal:: - + *weight* style args = use weighted particle counts for the balancing *style* = *group* or *neigh* or *time* or *var* or *store* *group* args = Ngroup group1 weight1 group2 weight2 ... @@ -351,7 +351,7 @@ particles in that sub-box. .. _weighted\_balance: This sub-section describes how to perform weighted load balancing -using the *weight* keyword. +using the *weight* keyword. By default, all particles have a weight of 1.0, which means each particle is assumed to require the same amount of computation during a diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 2b7ba54708..4284ab2c60 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -69,11 +69,11 @@ commands: coaxial stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding interaction *oxdna/hbond* (see also documentation of :doc:`pair_style oxdna/excv `). For the oxDNA2 - :ref:`(Snodin) ` bond style the analogous pair styles + :ref:`(Snodin) ` bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* , - *oxdna2/hbond* and an additional Debye-Hueckel pair style + *oxdna2/hbond* and an additional Debye-Hueckel pair style *oxdna2/dh* have to be defined. The same applies to the oxRNA2 - :ref:`(Sulc1) ` styles. + :ref:`(Sulc1) ` styles. The coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. @@ -83,17 +83,17 @@ setup tool which creates single straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA duplexes can be found in examples/USER/cgdna/util/. -Please cite :ref:`(Henrich) ` in any publication that uses -this implementation. The article contains general information -on the model, its implementation and performance as well as the structure of +Please cite :ref:`(Henrich) ` in any publication that uses +this implementation. The article contains general information +on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found `here `_. -Please cite also the relevant oxDNA/oxRNA publications. These are -:ref:`(Ouldridge) ` and -:ref:`(Ouldridge-DPhil) ` for oxDNA, -:ref:`(Snodin) ` for oxDNA2, -:ref:`(Sulc1) ` for oxRNA2 -and for sequence-specific hydrogen-bonding and stacking interactions +Please cite also the relevant oxDNA/oxRNA publications. These are +:ref:`(Ouldridge) ` and +:ref:`(Ouldridge-DPhil) ` for oxDNA, +:ref:`(Snodin) ` for oxDNA2, +:ref:`(Sulc1) ` for oxRNA2 +and for sequence-specific hydrogen-bonding and stacking interactions :ref:`(Sulc2) `. @@ -111,7 +111,7 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`pair_style oxdna/excv `, :doc:`pair_style oxdna2/excv `, :doc:`pair_style oxrna2/excv `, +:doc:`pair_style oxdna/excv `, :doc:`pair_style oxdna2/excv `, :doc:`pair_style oxrna2/excv `, :doc:`bond_coeff `, :doc:`fix nve/dotc/langevin ` **Default:** diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index 89b1a0a131..249f8edea2 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -50,7 +50,7 @@ or :doc:`read_restart ` commands: This potential was constructed to mimic the FENE bond potential for coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0` are used, the following choice of parameters gives a quartic potential that -looks nearly like the FENE potential: +looks nearly like the FENE potential: .. math:: @@ -59,7 +59,7 @@ looks nearly like the FENE potential: B_2 &= 0.25 \\ R_c &= 1.3 \\ U_0 &= 34.6878 - + Different parameters can be specified using the :doc:`bond_coeff ` command, but you will need to choose them carefully so they form a suitable bond potential. diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index baf843426e..3d3dac4bd2 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -12,9 +12,9 @@ Syntax boundary x y z * x,y,z = *p* or *s* or *f* or *m*\ , one or two letters - + .. parsed-literal:: - + *p* is periodic *f* is non-periodic and fixed *s* is non-periodic and shrink-wrapped diff --git a/doc/src/box.rst b/doc/src/box.rst index 052057bb90..77a64bd01e 100644 --- a/doc/src/box.rst +++ b/doc/src/box.rst @@ -13,9 +13,9 @@ Syntax * one or more keyword/value pairs may be appended * keyword = *tilt* - + .. parsed-literal:: - + *tilt* value = *small* or *large* diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst index b9bed3a0d6..0701953423 100644 --- a/doc/src/change_box.rst +++ b/doc/src/change_box.rst @@ -13,9 +13,9 @@ Syntax * group-ID = ID of group of atoms to (optionally) displace * one or more parameter/arg pairs may be appended - + .. 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) style = *final* or *delta* or *scale* or *volume* @@ -45,9 +45,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *units* - + .. parsed-literal:: - + *units* value = *lattice* or *box* lattice = distances are defined in lattice units box = distances are defined in simulation box units diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 839b179e8b..65e0c90fe5 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -13,9 +13,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel* - + .. parsed-literal:: - + *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances *cutoff* value = Rcut (distance units) = communicate atoms from this far away *cutoff/multi* type value diff --git a/doc/src/compute_ackland_atom.rst b/doc/src/compute_ackland_atom.rst index f1cabdc3a3..81cd579008 100644 --- a/doc/src/compute_ackland_atom.rst +++ b/doc/src/compute_ackland_atom.rst @@ -15,9 +15,9 @@ Syntax * ackland/atom = style name of this compute command * zero or more keyword/value pairs may be appended * keyword = *legacy* - + .. parsed-literal:: - + *legacy* yes/no = use (\ *yes*\ ) or do not use (\ *no*\ ) legacy ackland algorithm implementation diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index f403f5e5bf..ea5f7c0175 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -23,9 +23,9 @@ Syntax * RkouterN = outer radius of K atom shell for Nth ADF histogram (distance units) * zero or one keyword/value pairs may be appended * keyword = *ordinate* - + .. parsed-literal:: - + *ordinate* value = *degree* or *radian* or *cosine* Choose the ordinate parameter for the histogram diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index 923233fcfc..115808b024 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -15,18 +15,18 @@ Syntax * angle/local = style name of this compute command * one or more values may be appended * value = *theta* or *eng* or *v\_name* - + .. parsed-literal:: - + *theta* = tabulate angles *eng* = tabulate angle energies *v_name* = equal-style variable with name (see below) * zero or more keyword/args pairs may be appended * keyword = *set* - + .. parsed-literal:: - + *set* args = theta name theta = only currently allowed arg name = name of variable to set with theta diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index 47fe6de85b..a245030e6e 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -15,9 +15,9 @@ Syntax * body/local = style name of this compute command * one or more keywords may be appended * keyword = *id* or *type* or *integer* - + .. parsed-literal:: - + *id* = atom ID of the body particle *type* = atom type of the body particle *integer* = 1,2,3,etc = index of fields defined by body style diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index 354aa44d5b..ad03523304 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -13,9 +13,9 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * chunk/atom = style name of this compute command - + .. parsed-literal:: - + style = *bin/1d* or *bin/2d* or *bin/3d* or *bin/sphere* or *type* or *molecule* or c_ID, c_ID[I], f_ID, f_ID[I], v_name *bin/1d* args = dim origin delta dim = *x* or *y* or *z* @@ -51,9 +51,9 @@ Syntax * zero or more keyword/values pairs may be appended * keyword = *region* or *nchunk* or *static* or *compress* or *bound* or *discard* or *pbc* or *units* - + .. parsed-literal:: - + *region* value = region-ID region-ID = ID of region atoms must be in to be part of a chunk *nchunk* value = *once* or *every* diff --git a/doc/src/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst index a1b5cf45e5..c00b7e7478 100644 --- a/doc/src/compute_chunk_spread_atom.rst +++ b/doc/src/compute_chunk_spread_atom.rst @@ -16,9 +16,9 @@ Syntax * chunkID = ID of :doc:`compute chunk/atom ` command * one or more inputs can be listed * input = c\_ID, c\_ID[N], f\_ID, f\_ID[N] - + .. parsed-literal:: - + c_ID = global vector calculated by a compute with ID c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below) f_ID = global vector calculated by a fix with ID diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index b46af08d63..08b688cf67 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * coord/atom = style name of this compute command * cstyle = *cutoff* or *orientorder* - + .. parsed-literal:: - + *cutoff* args = cutoff [group group2-ID] typeN cutoff = distance within which to count coordination neighbors (distance units) group *group2-ID* = select group-ID to restrict which atoms to consider for coordination number (optional) diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index a1dab677ee..554af6724e 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -15,17 +15,17 @@ Syntax * dihedral/local = style name of this compute command * one or more values may be appended * value = *phi* or *v\_name* - + .. parsed-literal:: - + *phi* = tabulate dihedral angles *v_name* = equal-style variable with name (see below) * zero or more keyword/args pairs may be appended * keyword = *set* - + .. parsed-literal:: - + *set* args = phi name phi = only currently allowed arg name = name of variable to set with phi diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index 2d7cdfed3f..08b285a925 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -15,9 +15,9 @@ Syntax * displace/atom = style name of this compute command * zero or more keyword/arg pairs may be appended * keyword = *refresh* - + .. parsed-literal:: - + *replace* arg = name of per-atom variable diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index cb3008a73c..1bf7f73d90 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -38,7 +38,7 @@ relations: .. math:: - U^{cond} = & \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ + U^{cond} = & \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ U^{mech} = & \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\ U^{chem} = & \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\ U = & \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\ diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index 84b62a7f4a..08600c482c 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -16,9 +16,9 @@ Syntax * temp = external temperature (as specified for constant-temperature run) * one or more attributes with args may be appended * attribute = *pair* or *atom* - + .. parsed-literal:: - + *pair* args = pstyle pparam I J v_delta pstyle = pair style name, e.g. lj/cut pparam = parameter to perturb @@ -31,9 +31,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *tail* or *volume* - + .. parsed-literal:: - + *tail* value = *no* or *yes* *no* = ignore tail correction to pair energies (usually small in fep) *yes* = include tail correction to pair energies diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index 01e1d8650a..c85a6326dc 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * global/atom = style name of this compute command * index = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name - + .. parsed-literal:: - + c_ID = per-atom vector calculated by a compute with ID c_ID[I] = Ith column of per-atom array calculated by a compute with ID f_ID = per-atom vector calculated by a fix with ID @@ -25,9 +25,9 @@ Syntax * one or more inputs can be listed * input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name - + .. parsed-literal:: - + c_ID = global vector calculated by a compute with ID c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below) f_ID = global vector calculated by a fix with ID diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index 76766ce755..354f19495f 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -16,9 +16,9 @@ Syntax * group2-ID = group ID of second (or same) group * zero or more keyword/value pairs may be appended * keyword = *pair* or *kspace* or *boundary* or *molecule* - + .. parsed-literal:: - + *pair* value = *yes* or *no* *kspace* value = *yes* or *no* *boundary* value = *yes* or *no* diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index 987cb7fa4c..e40d793980 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -16,9 +16,9 @@ Syntax * chunkID = ID of :doc:`compute chunk/atom ` command * zero or more keyword/value pairs may be appended * keyword = *tensor* - + .. parsed-literal:: - + *tensor* value = none diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index 96c0346926..aca485122f 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -37,11 +37,11 @@ and the relative shape anisotropy, k: c = & l_z - 0.5(l_y+l_x) \\ b = & l_y - l_x \\ - k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} + k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} -where :math:`l_x` <= :math:`l_y` <= :math:`l_z` are the three eigenvalues of the gyration tensor. A general description -of these parameters is provided in :ref:`(Mattice) ` while an application to polymer systems +where :math:`l_x` <= :math:`l_y` <= :math:`l_z` are the three eigenvalues of the gyration tensor. A general description +of these parameters is provided in :ref:`(Mattice) ` while an application to polymer systems can be found in :ref:`(Theodorou) `. The asphericity is always non-negative and zero only when the three principal moments are equal. This zero condition is met when the distribution of particles diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index 72fec2ddc7..80bdbd4200 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -26,8 +26,8 @@ Examples Description """"""""""" -Define a computation that calculates the eigenvalues of the gyration tensor and -three shape parameters of multiple chunks of atoms. The computation includes +Define a computation that calculates the eigenvalues of the gyration tensor and +three shape parameters of multiple chunks of atoms. The computation includes all effects due to atoms passing through periodic boundaries. The three computed shape parameters are the asphericity, b, the acylindricity, c, @@ -37,13 +37,13 @@ and the relative shape anisotropy, k: c = & l_z - 0.5(l_y+l_x) \\ b = & l_y - l_x \\ - k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} + k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} -where :math:`l_x` <= :math:`l_y` <= :math`l_z` are the three eigenvalues of the gyration tensor. A general description -of these parameters is provided in :ref:`(Mattice) ` while an application to polymer systems -can be found in :ref:`(Theodorou) `. The asphericity is always non-negative and zero -only when the three principal moments are equal. This zero condition is met when the distribution +where :math:`l_x` <= :math:`l_y` <= :math`l_z` are the three eigenvalues of the gyration tensor. A general description +of these parameters is provided in :ref:`(Mattice) ` while an application to polymer systems +can be found in :ref:`(Theodorou) `. The asphericity is always non-negative and zero +only when the three principal moments are equal. This zero condition is met when the distribution of particles is spherically symmetric (hence the name asphericity) but also whenever the particle distribution is symmetric with respect to the three coordinate axes, e.g., when the particles are distributed uniformly on a cube, tetrahedron or other Platonic @@ -69,7 +69,7 @@ The tensor keyword must be specified in the compute gyration/chunk command. **Output info:** -This compute calculates a global array with six columns, +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 diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index 45560a2aff..98371f247b 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * hexorder/atom = style name of this compute command * one or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *degree* or *nnn* or *cutoff* *cutoff* value = distance cutoff *nnn* value = number of nearest neighbors diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index 71286d5c9d..ef4bab41a8 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -15,9 +15,9 @@ Syntax * improper/local = style name of this compute command * one or more values may be appended * value = *chi* - + .. parsed-literal:: - + *chi* = tabulate improper angles diff --git a/doc/src/compute_modify.rst b/doc/src/compute_modify.rst index d857472256..f81374d394 100644 --- a/doc/src/compute_modify.rst +++ b/doc/src/compute_modify.rst @@ -14,9 +14,9 @@ Syntax * compute-ID = ID of the compute to modify * one or more keyword/value pairs may be listed * keyword = *extra/dof* or *extra* or *dynamic/dof* or *dynamic* - + .. parsed-literal:: - + *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 diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst index 8ced34f66d..9113ce0331 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -15,9 +15,9 @@ Syntax * msd = style name of this compute command * zero or more keyword/value pairs may be appended * keyword = *com* or *average* - + .. parsed-literal:: - + *com* value = *yes* or *no* *average* value = *yes* or *no* diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst index 8168d25ca6..9bcd90098c 100644 --- a/doc/src/compute_msd_nongauss.rst +++ b/doc/src/compute_msd_nongauss.rst @@ -15,9 +15,9 @@ Syntax * msd/nongauss = style name of this compute command * zero or more keyword/value pairs may be appended * keyword = *com* - + .. parsed-literal:: - + *com* value = *yes* or *no* diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index b864db82a7..5020cd76e4 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * orientorder/atom = style name of this compute command * one or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *cutoff* or *nnn* or *degrees* or *components* *cutoff* value = distance cutoff *nnn* value = number of nearest neighbors diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index 7808253576..1421d4d5da 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -15,9 +15,9 @@ Syntax * pair/local = style name of this compute command * one or more values may be appended * value = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN* - + .. parsed-literal:: - + *dist* = pairwise distance *eng* = pairwise energy *force* = pairwise force @@ -26,9 +26,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *cutoff* - + .. parsed-literal:: - + *cutoff* arg = *type* or *radius* diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index ea7b238db0..905fb5eb68 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -66,7 +66,7 @@ second term uses components of the virial tensor: .. math:: - P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} + + P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} + \frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V} diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index 5aa9ead974..d9968566e2 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * property/atom = style name of this compute command * input = one or more atom attributes - + .. parsed-literal:: - + possible attributes = id, mol, proc, type, mass, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, @@ -36,9 +36,9 @@ Syntax rho, drho, e, de, cv, i_name, d_name - + .. parsed-literal:: - + id = atom ID mol = molecule ID proc = ID of processor that owns atom @@ -66,25 +66,25 @@ Syntax corner123x, corner123y, corner123z = corner points of triangle nbonds = number of bonds assigned to an atom - + .. parsed-literal:: - + PERI package per-atom properties: vfrac = ??? s0 = ??? - + .. parsed-literal:: - + USER-EFF and USER-AWPMD package per-atom properties: spin = electron spin eradius = electron radius ervel = electron radial velocity erforce = electron radial force - + .. parsed-literal:: - + USER-SPH package per-atom properties: rho = ??? drho = ??? @@ -92,9 +92,9 @@ Syntax de = ??? cv = ??? - + .. parsed-literal:: - + :doc:`fix property/atom ` per-atom properties: i_name = custom integer vector with name d_name = custom integer vector with name diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index cd9750f96e..699a675055 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * property/chunk = style name of this compute command * input = one or more attributes - + .. parsed-literal:: - + attributes = count, id, coord1, coord2, coord3 count = # of atoms in chunk id = original chunk IDs before compression by :doc:`compute chunk/atom ` diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index 2e01958194..79d40fae1f 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * property/local = style name of this compute command * one or more attributes may be appended - + .. parsed-literal:: - + possible attributes = natom1 natom2 ntype1 ntype2 patom1 patom2 ptype1 ptype2 batom1 batom2 btype @@ -24,9 +24,9 @@ Syntax datom1 datom2 datom3 datom4 dtype iatom1 iatom2 iatom3 iatom4 itype - + .. parsed-literal:: - + natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff) ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff) patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff) @@ -42,9 +42,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *cutoff* - + .. parsed-literal:: - + *cutoff* arg = *type* or *radius* diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index b35aa54e09..3d7392565f 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -18,9 +18,9 @@ Syntax * jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) * zero or more keyword/value pairs may be appended * keyword = *cutoff* - + .. parsed-literal:: - + *cutoff* value = Rcut Rcut = cutoff distance for RDF computation (distance units) diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index cfd7b27614..416067e0fc 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -16,9 +16,9 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * style = *reduce* or *reduce/region* - + .. parsed-literal:: - + *reduce* arg = none *reduce/region* arg = region-ID region-ID = ID of region to use for choosing atoms @@ -26,9 +26,9 @@ Syntax * mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq* * one or more inputs can be listed * input = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name - + .. parsed-literal:: - + x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) c_ID = per-atom or local vector calculated by a compute with ID c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below) @@ -38,9 +38,9 @@ Syntax * zero or more keyword/args pairs may be appended * keyword = *replace* - + .. parsed-literal:: - + *replace* args = vec1 vec2 vec1 = reduced value from this input vector will be replaced vec2 = replace it with vec1[N] where N is index of max/min value from vec2 diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index 8f850a32c2..2053143c56 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -17,9 +17,9 @@ Syntax * mode = *sum* or *min* or *max* * one or more inputs can be listed * input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_ID - + .. parsed-literal:: - + c_ID = per-atom vector calculated by a compute with ID c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) f_ID = per-atom vector calculated by a fix with ID diff --git a/doc/src/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst index d7e9d4dcdd..825cc3497f 100644 --- a/doc/src/compute_rigid_local.rst +++ b/doc/src/compute_rigid_local.rst @@ -15,9 +15,9 @@ Syntax * rigid/local = style name of this compute command * rigidID = ID of fix rigid/small command or one of its variants * input = one or more rigid body attributes - + .. parsed-literal:: - + possible attributes = id, mol, mass, x, y, z, xu, yu, zu, ix, iy, iz vx, vy, vz, fx, fy, fz, diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index 2a9c05f218..565095daa6 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -17,9 +17,9 @@ Syntax * type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) * zero or more keyword/value pairs may be appended * keyword = *Kmax* or *Zone* or *dR\_Ewald* or *c* or *manual* or *echo* - + .. parsed-literal:: - + *Kmax* value = Maximum distance explored from reciprocal space origin (inverse length units) *Zone* values = z1 z2 z3 diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index 4ed35eb0ff..debae12991 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -17,9 +17,9 @@ Syntax * Nstop = stopping index within input vector(s) * Nskip = extract every Nskip elements from input vector(s) * input = c\_ID, c\_ID[N], f\_ID, f\_ID[N] - + .. parsed-literal:: - + c_ID = global vector calculated by a compute with ID c_ID[I] = Ith column of global array calculated by a compute with ID f_ID = global vector calculated by a fix with ID diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 0fe8acde0c..c821477404 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -20,7 +20,7 @@ Syntax compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... - compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... + compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... * ID, group-ID are documented in :doc:`compute ` command @@ -32,9 +32,9 @@ Syntax * w\_1, w\_2,... = list of neighbor weights, one for each type * zero or more keyword/value pairs may be appended * keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* - + .. parsed-literal:: - + *rmin0* value = parameter in distance to angle conversion (distance units) *switchflag* value = *0* or *1* *0* = do not use switching function @@ -63,7 +63,7 @@ Description Define a computation that calculates a set of quantities related to the bispectrum components of the atoms in a group. These computes are used primarily for calculating the dependence of energy, force, and -stress components on the linear coefficients in the +stress components on the linear coefficients in the :doc:`snap pair\_style `, which is useful when training a SNAP potential to match target data. @@ -103,7 +103,7 @@ coefficient as .. math:: - u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)} + u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)} The *w\_i'* neighbor weights are dimensionless numbers that are chosen @@ -126,7 +126,7 @@ real-valued and invariant under rotation :ref:`(Bartok) `. .. math:: - B_{j_1,j_2,j} = + B_{j_1,j_2,j} = \sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^* H {\scriptscriptstyle \begin{array}{l} {j} {m} {m'} \\ {j_1} {m_1} {m'_1} \\ @@ -175,7 +175,7 @@ section below on output for a detailed explanation. Compute *snap* calculates a global array contains information related 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 +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 out by type. In between these are 3\*\ *N* rows containing the same values @@ -288,12 +288,12 @@ block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ , notation. Each of these sub-blocks contains one column for each bispectrum component, the same as for compute *sna/atom* -Compute *snap* evaluates a global array. +Compute *snap* evaluates a global array. The columns are arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each block contains one column for each bispectrum component, the same as for compute *sna/atom*\ . A final column contains the corresponding energy, force component -on an atom, or virial stress component. The rows of the array appear +on an atom, or virial stress component. The rows of the array appear in the following order: * 1 row: *sna/atom* quantities summed for all atoms of type *I* diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index eef88ebe86..f2faf8c2d5 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -15,9 +15,9 @@ Syntax * temp/asphere = style name of this compute command * zero or more keyword/value pairs may be appended * keyword = *bias* or *dof* - + .. parsed-literal:: - + *bias* value = bias-ID bias-ID = ID of a temperature compute that removes a velocity bias *dof* value = *all* or *rotate* diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index df9ff29f2d..ded3701420 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -15,9 +15,9 @@ Syntax * temp/body = style name of this compute command * zero or more keyword/value pairs may be appended * keyword = *bias* or *dof* - + .. parsed-literal:: - + *bias* value = bias-ID bias-ID = ID of a temperature compute that removes a velocity bias *dof* value = *all* or *rotate* diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index a23ddd0c6d..24ea9ab558 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -16,18 +16,18 @@ Syntax * chunkID = ID of :doc:`compute chunk/atom ` command * zero or more values can be listed as value1,value2,etc * value = *temp* or *kecom* or *internal* - + .. parsed-literal:: - + temp = temperature of each chunk kecom = kinetic energy of each chunk based on velocity of center of mass internal = internal kinetic energy of each chunk * zero or more keyword/value pairs may be appended * keyword = *com* or *bias* or *adof* or *cdof* - + .. parsed-literal:: - + *com* value = *yes* or *no* yes = subtract center-of-mass velocity from each chunk before calculating temperature no = do not subtract center-of-mass velocity diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 9ecf985596..d83e1b009c 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -15,9 +15,9 @@ Syntax * temp/profile = style name of this compute command * xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension * binstyle = *x* or *y* or *z* or *xy* or *yz* or *xz* or *xyz* - + .. parsed-literal:: - + *x* arg = Nx *y* arg = Ny *z* arg = Nz @@ -29,9 +29,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *out* - + .. parsed-literal:: - + *out* value = *tensor* or *bin* diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index 64fc371b50..66cba3f671 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -15,9 +15,9 @@ Syntax * temp/sphere = style name of this compute command * zero or more keyword/value pairs may be appended * keyword = *bias* or *dof* - + .. parsed-literal:: - + *bias* value = bias-ID bias-ID = ID of a temperature compute that removes a velocity bias *dof* value = *all* or *rotate* diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index 9ac5cc5bc3..de8d10e0b7 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -15,9 +15,9 @@ Syntax * ti = style name of this compute command * one or more attribute/arg pairs may be appended * keyword = pair style (lj/cut, gauss, born, etc) or *tail* or *kspace* - + .. parsed-literal:: - + pair style args = atype v_name1 v_name2 atype = atom type (see asterisk form below) v_name1 = variable with name1 that is energy scale factor and function of lambda diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 0e75db4999..58b46fdf39 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -16,9 +16,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *only\_group* or *surface* or *radius* or *edge\_histo* or *edge\_threshold* or *face\_threshold* or *neighbors* or *peratom* - + .. parsed-literal:: - + *only_group* = no arg *occupation* = no arg *surface* arg = sgroup-ID diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index d95fad79e4..382d48dc38 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -17,9 +17,9 @@ Syntax * type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) * zero or more keyword/value pairs may be appended * keyword = *2Theta* or *c* or *LP* or *manual* or *echo* - + .. parsed-literal:: - + *2Theta* values = Min2Theta Max2Theta Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore (radians or degrees) @@ -111,7 +111,7 @@ The analytic approximation is computed using the formula .. math:: - f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4} + f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4} a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )+c Coefficients parameterized by :ref:`(Peng) ` are assigned for each diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index bb3e7ba775..cb4b24f6e3 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -13,9 +13,9 @@ Syntax * type = atom type (1-Ntypes) of atoms to create (offset for molecule creation) * style = *box* or *region* or *single* or *random* - + .. parsed-literal:: - + *box* args = none *region* args = region-ID region-ID = particles will only be created if contained in the region @@ -28,9 +28,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *units* - + .. code-block:: LAMMPS - + *mol* value = template-ID seed template-ID = ID of molecule template specified in a separate :doc:`molecule ` command seed = random # seed (positive integer) diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index ee58323ae9..c167f77ac5 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -15,9 +15,9 @@ Syntax * region-ID = ID of region to use as simulation domain * zero or more keyword/value pairs may be appended * keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* - + .. parsed-literal:: - + *bond/types* value = # of bond types *angle/types* value = # of angle types *dihedral/types* value = # of dihedral types diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 7ad9c75550..c08bba0d72 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -12,9 +12,9 @@ Syntax delete_atoms style args keyword value ... * style = *group* or *region* or *overlap* or *porosity* - + .. parsed-literal:: - + *group* args = group-ID *region* args = region-ID *overlap* args = cutoff group1-ID group2-ID @@ -28,9 +28,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *compress* or *bond* or *mol* - + .. parsed-literal:: - + *compress* value = *no* or *yes* *bond* value = *no* or *yes* *mol* value = *no* or *yes* diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index 37c52f8aff..6b96db4f92 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -13,9 +13,9 @@ Syntax * group-ID = group ID * style = *multi* or *atom* or *bond* or *angle* or *dihedral* or *improper* or *stats* - + .. parsed-literal:: - + *multi* arg = none *atom* arg = an atom type or range of types (see below) *bond* arg = a bond type or range of types (see below) diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 870331944d..06fd754286 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -30,7 +30,7 @@ The *helix* dihedral style uses the potential .. math:: - E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + + E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + C [1 + \cos(\theta + \frac{\pi}{4})] diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index 07d7eb0634..b329f1a2f6 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -30,7 +30,7 @@ The *quadratic* dihedral style uses the potential: .. math:: - E = K (\phi - \phi_0)^2 + E = K (\phi - \phi_0)^2 This dihedral potential can be used to keep a dihedral in a predefined diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index 57e6ac9986..555f0a4fdf 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -13,9 +13,9 @@ Syntax * group-ID = ID of group of atoms to displace * style = *move* or *ramp* or *random* or *rotate* - + .. parsed-literal:: - + *move* args = delx dely delz delx,dely,delz = distance to displace in each dimension (distance units) any of delx,dely,delz can be a variable (see below) @@ -33,9 +33,9 @@ Syntax theta = angle of rotation (degrees) * zero or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *units* value = *box* or *lattice* diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 89a0c53e30..2e4d281fd2 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -42,9 +42,9 @@ Syntax * N = dump every this many timesteps * file = name of file to write dump info to * args = list of arguments for a particular style - + .. parsed-literal:: - + *atom* args = none *atom/gz* args = none *atom/mpiio* args = none @@ -69,9 +69,9 @@ Syntax *xyz/mpiio* args = none * *custom* or *custom/gz* or *custom/mpiio* or *netcdf* or *netcdf/mpiio* args = list of atom attributes - + .. parsed-literal:: - + possible attributes = id, mol, proc, procp1, type, element, mass, x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz, @@ -81,9 +81,9 @@ Syntax angmomx, angmomy, angmomz, tqx, tqy, tqz, c_ID, c_ID[N], f_ID, f_ID[N], v_name - + .. parsed-literal:: - + id = atom ID mol = molecule ID proc = ID of processor that owns atom @@ -114,9 +114,9 @@ Syntax i_name = per-atom integer vector with name, managed by fix property/atom * *local* args = list of local attributes - + .. parsed-literal:: - + possible attributes = index, c_ID, c_ID[I], f_ID, f_ID[I] index = enumeration of local values c_ID = local vector calculated by a compute with ID @@ -716,7 +716,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`dump atom/adios `, :doc:`dump custom/adios `, +:doc:`dump atom/adios `, :doc:`dump custom/adios `, :doc:`dump h5md `, :doc:`dump image `, :doc:`dump molfile `, :doc:`dump_modify `, :doc:`undump ` diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index e891a5e42e..950d453eb2 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -1,5 +1,5 @@ -.. index:: dump atom/adios -.. index:: dump custom/adios +.. index:: dump atom/adios +.. index:: dump custom/adios dump atom/adios command ========================= diff --git a/doc/src/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst index 02e40b7b67..a75476529f 100644 --- a/doc/src/dump_cfg_uef.rst +++ b/doc/src/dump_cfg_uef.rst @@ -15,9 +15,9 @@ Syntax * group-ID = ID of the group of atoms to be dumped * N = dump every this many timesteps * file = name of file to write dump info to - + .. parsed-literal:: - + args = same as args for :doc:`dump custom ` diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index e7e6f0ee44..e6fc008693 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -23,9 +23,9 @@ Syntax * diameter = atom attribute that determines size of each atom * zero or more keyword/value pairs may be appended * keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *persp* or *box* or *axes* or *subbox* or *shiny* or *ssao* - + .. parsed-literal:: - + *atom* = yes/no = do or do not draw atoms *adiam* size = numeric value for atom diameter (distance units) *bond* values = color width = color and width of bonds @@ -568,9 +568,9 @@ To manually convert JPEG, PNG or PPM files into an animated GIF or MPEG or other movie file you can use: * a) Use the ImageMagick convert program. - + .. code-block:: bash - + % convert *.jpg foo.gif % convert -loop 1 *.ppm foo.mpg @@ -596,9 +596,9 @@ MPEG or other movie file you can use: FFmpeg is a command line tool that is available on many platforms and allows extremely flexible encoding and decoding of movies. - + .. code-block:: bash - + cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi @@ -619,18 +619,18 @@ Play the movie: * b) Use the freely available mplayer or ffplay tool to view a movie. Both are available for multiple OSes and support a large variety of file formats and decoders. - + .. code-block:: bash - + % mplayer foo.mpg % ffplay bar.avi * c) Use the `Pizza.py `_ `animate tool `_, which works directly on a series of image files. - + .. code-block:: python - + a = animate("foo*.jpg") * d) QuickTime and other Windows- or MacOS-based media players can diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index c035ea57a3..2c672b4cf0 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -15,9 +15,9 @@ Syntax * one or more keyword/value pairs may be appended * these keywords apply to various dump styles * keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap* - + .. parsed-literal:: - + *append* arg = *yes* or *no* *at* arg = N N = index of frame written upon first dump @@ -68,9 +68,9 @@ Syntax * these keywords apply only to the *image* and *movie* :doc:`styles ` * keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* - + .. parsed-literal:: - + *acolor* args = type color type = atom type or range of types (see below) color = name of color or color1/color2/... diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst index b5ba6f2bf4..d3fba63f1d 100644 --- a/doc/src/dynamical_matrix.rst +++ b/doc/src/dynamical_matrix.rst @@ -15,9 +15,9 @@ Syntax * style = *regular* or *eskm* * gamma = finite different displacement length (distance units) * one or more keyword/arg pairs may be appended - + .. parsed-literal:: - + keyword = *file* or *binary* *file* name = name of output file for the dynamical matrix *binary* arg = *yes* or *no* or *gzip* @@ -51,7 +51,7 @@ matrix defined by \Phi_{ij}^{\alpha\beta} = \frac{\partial^2 U}{\partial x_{i,\alpha} \partial x_{j,\beta}} - + The output for the dynamical matrix is printed three elements at a time. The three elements are the three :math:`\beta` elements for a respective i/:math:`\alpha`/j combination. Each line is printed in order of j diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 0e57ec98c1..102504d3bc 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -16,9 +16,9 @@ Syntax * N = adapt simulation settings every this many timesteps * one or more attribute/arg pairs may be appended * attribute = *pair* or *kspace* or *atom* - + .. parsed-literal:: - + *pair* args = pstyle pparam I J v_name pstyle = pair style name, e.g. lj/cut pparam = parameter to adapt over time @@ -37,9 +37,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *scale* or *reset* - + .. parsed-literal:: - + *scale* value = *no* or *yes* *no* = the variable value is the new setting *yes* = the variable value multiplies the original setting diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 2ec43eb5fc..00b498c178 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -16,9 +16,9 @@ Syntax * N = adapt simulation settings every this many timesteps * one or more attribute/arg pairs may be appended * attribute = *pair* or *kspace* or *atom* - + .. parsed-literal:: - + *pair* args = pstyle pparam I J v_name pstyle = pair style name, e.g. lj/cut pparam = parameter to adapt over time @@ -33,9 +33,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *scale* or *reset* or *after* - + .. parsed-literal:: - + *scale* value = *no* or *yes* *no* = the variable value is the new setting *yes* = the variable value multiplies the original setting diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index f85c3f4925..8902a482d9 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -14,16 +14,16 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * addforce = style name of this fix command * fx,fy,fz = force component values (force units) - + .. parsed-literal:: - + any of fx,fy,fz can be a variable (see below) * zero or more keyword/value pairs may be appended to args * keyword = *every* or *region* or *energy* - + .. parsed-literal:: - + *every* value = Nevery Nevery = add force every this many timesteps *region* value = region-ID diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst index ff3fea459f..095be0daaf 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -16,9 +16,9 @@ Syntax * face = *zhi* * zero or more keyword/value pairs may be appended * keyword = *basis* or *size* or *freq* or *temp* or *random* or *units* - + .. parsed-literal:: - + *basis* values = M itype M = which basis atom itype = atom type (1-N) to assign to this basis atom diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index ce6190a58c..79634c0796 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -19,9 +19,9 @@ Syntax * T = scaling temperature of the MC swaps (temperature units) * one or more keyword/value pairs may be appended to args * keyword = *types* or *mu* or *ke* or *semi-grand* or *region* - + .. parsed-literal:: - + *types* values = two or more atom types *mu* values = chemical potential of swap types (energy units) *ke* value = *no* or *yes* diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 4a33a5e85c..70337e9fa2 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -18,9 +18,9 @@ Syntax * Nfreq = calculate averages every this many timesteps one or more input values can be listed * value = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[i], f\_ID, f\_ID[i], v\_name - + .. parsed-literal:: - + x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) c_ID = per-atom vector calculated by a compute with ID c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index f757894c02..d6d813f4e4 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -19,9 +19,9 @@ Syntax * chunkID = ID of :doc:`compute chunk/atom ` command * one or more input values can be listed * value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c\_ID, c\_ID[I], f\_ID, f\_ID[I], v\_name - + .. parsed-literal:: - + vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) density/number, density/mass = number or mass density temp = temperature @@ -33,9 +33,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *title1* or *title2* or *title3* - + .. parsed-literal:: - + *norm* arg = *all* or *sample* or *none* = how output on *Nfreq* steps is normalized all = output is sum of atoms across all *Nrepeat* samples, divided by atom count sample = output is sum of *Nrepeat* sample averages, divided by *Nrepeat* diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 277a7ac25c..6f2aaedc9f 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -18,9 +18,9 @@ Syntax * Nfreq = calculate time window averages every this many timesteps * one or more input values can be listed * value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name - + .. parsed-literal:: - + c_ID = global scalar calculated by a compute with ID c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) f_ID = global scalar calculated by a fix with ID @@ -30,9 +30,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *type* or *ave* or *start* or *prefactor* or *file* or *overwrite* or *title1* or *title2* or *title3* - + .. parsed-literal:: - + *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* auto = correlate each value with itself upper = correlate each value with each succeeding value diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst index d05c29c1a9..2aa33f9040 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -17,9 +17,9 @@ Syntax * Nfreq = save state of the time correlation functions every this many timesteps * one or more input values can be listed * value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name - + .. parsed-literal:: - + c_ID = global scalar calculated by a compute with ID c_ID[I] = Ith component of global vector calculated by a compute with ID f_ID = global scalar calculated by a fix with ID @@ -28,9 +28,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *p* or *m* - + .. parsed-literal:: - + *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* auto = correlate each value with itself upper = correlate each value with each succeeding value diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 2987c25731..ca8c312527 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -23,9 +23,9 @@ Syntax * Nbin = # of histogram bins * one or more input values can be listed * value = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name - + .. parsed-literal:: - + x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) c_ID = scalar or vector calculated by a compute with ID c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below) @@ -36,9 +36,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *mode* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3* - + .. parsed-literal:: - + *mode* arg = *scalar* or *vector* scalar = all input values are scalars vector = all input values are vectors diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 20bd4382c7..9f3f7660c9 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -18,9 +18,9 @@ Syntax * Nfreq = calculate averages every this many timesteps * one or more input values can be listed * value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name - + .. parsed-literal:: - + c_ID = global scalar or vector calculated by a compute with ID c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below) f_ID = global scalar or vector calculated by a fix with ID @@ -30,9 +30,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *title1* or *title2* or *title3* - + .. parsed-literal:: - + *mode* arg = *scalar* or *vector* scalar = all input values are global scalars vector = all input values are global vectors or global arrays diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index d6f67d14c7..c4bb8e79e4 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -14,16 +14,16 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * aveforce = style name of this fix command * fx,fy,fz = force component values (force units) - + .. parsed-literal:: - + any of fx,fy,fz can be a variable (see below) * zero or more keyword/value pairs may be appended to args * keyword = *region* - + .. parsed-literal:: - + *region* value = region-ID region-ID = ID of region atoms must be in to have added force diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 6ba6605377..b407921477 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -16,9 +16,9 @@ Syntax * Nfreq = perform dynamic load balancing every this many steps * thresh = imbalance threshold that must be exceeded to perform a re-balance * style = *shift* or *rcb* - + .. parsed-literal:: - + shift args = dimstr Niter stopthresh dimstr = sequence of letters containing "x" or "y" or "z", each not more than once Niter = # of times to iterate within each dimension of dimstr sequence @@ -27,9 +27,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *weight* or *out* - + .. parsed-literal:: - + *weight* style args = use weighted particle counts for the balancing *style* = *group* or *neigh* or *time* or *var* or *store* *group* args = Ngroup group1 weight1 group2 weight2 ... diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index ce06447f07..fd384cad56 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -18,9 +18,9 @@ Syntax * Rmax = bond longer than Rmax can break (distance units) * zero or more keyword/value pairs may be appended to args * keyword = *prob* - + .. parsed-literal:: - + *prob* values = fraction seed fraction = break a bond with this probability if otherwise eligible seed = random number seed (positive integer) diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index 5ed22bcd58..62815f5f40 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -19,9 +19,9 @@ Syntax * bondtype = type of created bonds * zero or more keyword/value pairs may be appended to args * keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* - + .. parsed-literal:: - + *iparam* values = maxbond, newtype maxbond = max # of bonds of bondtype the itype atom can have newtype = change the itype atom to this type when maxbonds exist diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst index 0c4cad7ad0..7d7c326800 100644 --- a/doc/src/fix_box_relax.rst +++ b/doc/src/fix_box_relax.rst @@ -13,9 +13,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * box/relax = style name of this fix command - + .. parsed-literal:: - + one or more keyword value pairs may be appended keyword = *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *nreset* or *vmax* or *dilate* or *scaleyz* or *scalexz* or *scalexy* or *fixedpoint* *iso* or *aniso* or *tri* value = Ptarget = desired pressure (pressure units) diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index dd4057a346..042edbad6b 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -15,9 +15,9 @@ Syntax * colvars = style name of this fix command * configfile = the configuration file for the colvars module * keyword = *input* or *output* or *seed* or *tstat* - + .. parsed-literal:: - + *input* arg = colvars.state file name or prefix or NULL (default: NULL) *output* arg = output filename prefix (default: out) *seed* arg = seed for random number generator (default: 1966) diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 839c01ef5f..2f7913eb04 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -19,9 +19,9 @@ Syntax * Ki = integral gain in PID equation (unitless) * Kd = derivative gain in PID equation (unitless) * pvar = process variable of form c\_ID, c\_ID[I], f\_ID, f\_ID[I], or v\_name - + .. parsed-literal:: - + c_ID = global scalar calculated by a compute with ID c_ID[I] = Ith component of global vector calculated by a compute with ID f_ID = global scalar calculated by a fix with ID @@ -100,7 +100,7 @@ the following dynamic equation: .. math:: \frac{dc}{dt} = \hat{E} -\alpha (K_p e + K_i \int_0^t e \, dt + K_d \frac{de}{dt} ) - + where *c* is the continuous time analog of the control variable, *e* =\ *pvar*\ -\ *setpoint* is the error in the process variable, and :math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are constants diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 1ddeff6953..308a0cd4d6 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -18,9 +18,9 @@ Syntax * deform = style name of this fix command * N = perform box deformation every this many timesteps * one or more parameter/arg pairs may be appended - + .. parsed-literal:: - + parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* *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* @@ -66,9 +66,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *remap* or *flip* or *units* - + .. parsed-literal:: - + *remap* value = *x* or *v* or *none* x = remap coords of atoms in group into deforming box v = remap velocities of all atoms when they cross periodic boundaries diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 573e9bdf2b..585106e8f7 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -19,9 +19,9 @@ Syntax * seed = random # seed (positive integer) * one or more keyword/value pairs may be appended to args * keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *mol* or *rigid* or *shake* or *units* - + .. parsed-literal:: - + *region* value = region-ID region-ID = ID of region to use as insertion volume *id* value = *max* or *next* diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index a9ae641a41..04ab50dbd8 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -19,9 +19,9 @@ Syntax * edpd/source or tdpd/source = style name of this fix command * index (only specified for tdpd/source) = index of chemical species (1 to Nspecies) * keyword = *sphere* or *cuboid* - + .. parsed-literal:: - + *sphere* values = cx,cy,cz,radius,source cx,cy,cz = x,y,z center of spherical domain (distance units) radius = radius of a spherical domain (distance units) diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index f29f258d27..07db211528 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -54,12 +54,12 @@ Masses: .. math:: - M' = M + m + M' = M + m .. math:: - m' = \frac {M\, m } {M'} + m' = \frac {M\, m } {M'} Positions: @@ -70,7 +70,7 @@ Positions: .. math:: - x' = x - X + x' = x - X Velocities: @@ -81,13 +81,13 @@ Velocities: .. math:: - v' = v - V + v' = v - V Forces: .. math:: - F' = F + f + F' = F + f .. math:: @@ -99,13 +99,13 @@ This transform conserves the total kinetic energy .. math:: \frac 1 2 \, (M\, V^2\ + m\, v^2) - = \frac 1 2 \, (M'\, V'^2\ + m'\, v'^2) + = \frac 1 2 \, (M'\, V'^2\ + m'\, v'^2) and the virial defined with absolute positions .. math:: - X\, F + x\, f = X'\, F' + x'\, f' + X\, F + x\, f = X'\, F' + x'\, f' ---------- diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index a530ccb689..03ad47fcee 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -17,9 +17,9 @@ Syntax * any of ex,ey,ez can be a variable (see below) * zero or more keyword/value pairs may be appended to args * keyword = *region* or *energy* - + .. parsed-literal:: - + *region* value = region-ID region-ID = ID of region atoms must be in to have added force *energy* value = v_name diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst index 9cc02261c7..e981c63b36 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -17,9 +17,9 @@ Syntax * F = energy flux into the reservoir (energy/time units) * zero or more keyword/value pairs may be appended to args * keyword = *region* or *constrain* or *com* or *hex* - + .. parsed-literal:: - + *region* value = region-ID region-ID = ID of region (reservoir) atoms must be in for added thermostatting force *constrain* value = none @@ -88,9 +88,9 @@ The thermostatting force is given by .. math:: \mathbf g_i = \begin{cases} - \frac{m_i}{2} \frac{ F_{\Gamma_{k(\mathbf r_i)}}}{ K_{\Gamma_{k(\mathbf r_i)}}} + \frac{m_i}{2} \frac{ F_{\Gamma_{k(\mathbf r_i)}}}{ K_{\Gamma_{k(\mathbf r_i)}}} \left(\mathbf v_i - \mathbf v_{\Gamma_{k(\mathbf r_i)}} \right) & \mbox{$k(\mathbf r_i)> 0$ (inside a reservoir),} \\ - 0 & \mbox{otherwise, } + 0 & \mbox{otherwise, } \end{cases} where :math:`m_i` is the mass and :math:`k(\mathbf r_i)` maps the particle diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index 095976dc53..09be2e34c7 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -17,9 +17,9 @@ Syntax * file = name of the file containing the electronic stopping power table * zero or more keyword/value pairs may be appended to args * keyword = *region* or *minneigh* - + .. parsed-literal:: - + *region* value = region-ID region-ID = region, whose atoms will be affected by this fix *minneigh* value = minneigh diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index 681b656b53..8f95876bcc 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -47,7 +47,7 @@ computed according to the following relation: .. math:: - U_{i} = \displaystyle\sum_{j=1}^{m} c_{i,j}(u_{j} + \Delta H_{f,j}) + \frac{3k_{b}T}{2} + Nk_{b}T \\ + 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 diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst index c24cb51738..628fd3226e 100644 --- a/doc/src/fix_evaporate.rst +++ b/doc/src/fix_evaporate.rst @@ -18,9 +18,9 @@ Syntax * region-ID = ID of region within which to perform deletions * seed = random number seed to use for choosing atoms to delete * zero or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *molecule* *molecule* value = *no* or *yes* diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index c20b591906..756d896e80 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * external = style name of this fix command * mode = *pf/callback* or *pf/array* - + .. parsed-literal:: - + *pf/callback* args = Ncall Napply Ncall = make callback every Ncall steps Napply = apply callback forces every Napply steps diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst index 37c0985294..56093550f7 100644 --- a/doc/src/fix_ffl.rst +++ b/doc/src/fix_ffl.rst @@ -17,9 +17,9 @@ Syntax * Tstart, Tstop = temperature ramp during the run * seed = random number seed to use for generating noise (positive integer) * one more value may be appended - + .. parsed-literal:: - + flip-type = determines the flipping type, can be chosen between rescale - no_flip - hard - soft, if no flip type is given, rescale will be chosen by default diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst index 8812398bbe..a3dd56d577 100644 --- a/doc/src/fix_filter_corotate.rst +++ b/doc/src/fix_filter_corotate.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * one or more constraint/value pairs are appended * constraint = *b* or *a* or *t* or *m* - + .. parsed-literal:: - + *b* values = one or more bond types *a* values = one or more angle types *t* values = one or more atom types diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index 4077d45e01..510336f4d2 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -14,17 +14,17 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * flow/gauss = style name of this fix command * xflag,yflag,zflag = 0 or 1 - + .. parsed-literal:: - + 0 = do not conserve current in this dimension 1 = conserve current in this dimension * zero or more keyword/value pairs may be appended * keyword = *energy* - + .. parsed-literal:: - + *energy* value = no or yes no = do not compute work done by this fix yes = compute work done by this fix diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index dd06d074a4..ac14b2bcc4 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -22,9 +22,9 @@ Syntax * mu = chemical potential of the ideal gas reservoir (energy units) * displace = maximum Monte Carlo translation distance (length units) * zero or more keyword/value pairs may be appended to args - + .. parsed-literal:: - + 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 @@ -265,7 +265,7 @@ pressure of the fictitious gas reservoir by: .. math:: \mu^{id} = & k T \ln{\rho \Lambda^3} \\ - = & k T \ln{\frac{\phi P \Lambda^3}{k T}} + = & k T \ln{\frac{\phi P \Lambda^3}{k T}} where *k* is Boltzman's constant, *T* is the user-specified @@ -394,9 +394,9 @@ place any pair of atoms closer than the specified overlap cutoff distance. The *max* and *min* keywords allow for the restriction of the number -of atoms in the simulation. They automatically reject all insertion +of atoms in the simulation. They automatically reject all insertion or deletion moves that would take the system beyond the set boundaries. -Should the system already be beyond the boundary, only moves that bring +Should the system already be beyond the boundary, only moves that bring the system closer to the bounds may be accepted. The *group* keyword adds all inserted atoms to the diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index 8dc2b9dd98..9a2538d6be 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -20,9 +20,9 @@ Syntax * c\_k = the weight of the kth term in the Prony series (mass per time units) * tau\_k = the time constant of the kth term in the Prony series (time units) * zero or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *frozen* or *zero* *frozen* value = *no* or *yes* *no* = initialize extended variables using values drawn from equilibrium distribution at Tstart @@ -65,7 +65,7 @@ With this fix active, the force on the *j*\ th atom is given as .. math:: {\bf F}_{j}(t) = & {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\ - \Gamma_j(t-s) = & \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ + \Gamma_j(t-s) = & \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ \langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s) diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index e4aadfa401..6f95b6030a 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -18,9 +18,9 @@ Syntax * Amatrix = file to read the drift matrix A from * seed = random number seed to use for generating noise (positive integer) * zero or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *noneq* or *every* *noneq* Cmatrix = file to read the non-equilibrium covariance matrix from *every* stride = apply the GLE once every time steps. Reduces the accuracy diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index 6fbf9a80c5..3466bb393a 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -22,9 +22,9 @@ Syntax * magnitude = size of acceleration (force/mass units) * magnitude can be a variable (see below) * style = *chute* or *spherical* or *gradient* or *vector* - + .. parsed-literal:: - + *chute* args = angle angle = angle in +x away from -z or -y axis in 3d/2d (in degrees) angle can be a variable (see below) diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 296be3aa10..ab0918a63d 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -15,9 +15,9 @@ Syntax * halt = style name of this fix command * N = check halt condition every N steps * attribute = *bondmax* or *tlimit* or v\_name - + .. parsed-literal:: - + bondmax = length of longest bond in the system tlimit = elapsed CPU time v_name = name of :doc:`equal-style variable ` @@ -26,9 +26,9 @@ Syntax * avalue = numeric value to compare attribute to * zero or more keyword/value pairs may be appended * keyword = *error* or *message* - + .. parsed-literal:: - + *error* value = *hard* or *soft* or *continue* *message* value = *yes* or *no* diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst index 86850a2db7..5cc8504ff2 100644 --- a/doc/src/fix_heat.rst +++ b/doc/src/fix_heat.rst @@ -18,9 +18,9 @@ Syntax * eflux can be a variable (see below) * zero or more keyword/value pairs may be appended to args * keyword = *region* - + .. parsed-literal:: - + *region* value = region-ID region-ID = ID of region atoms must be in to have added force diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 7512f34ab7..87bb71e4f0 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -22,9 +22,9 @@ Syntax * Btarget = desired time boost factor (unitless) * zero or more keyword/value pairs may be appended * keyword = *bound* or *reset* or *check/ghost* or *check/bias* - + .. parsed-literal:: - + *bound* value = Bfrac Bfrac = -1 or a value >= 0.0 *reset* value = Rfreq diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index d7931e1666..14246d90e1 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -15,9 +15,9 @@ Syntax * imd = style name of this fix command * port = port number on which the fix listens for an IMD client * keyword = *unwrap* or *fscale* or *trate* - + .. parsed-literal:: - + *unwrap* arg = *on* or *off* off = coordinates are wrapped back into the principal unit cell (default) on = "unwrapped" coordinates using the image flags used diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index 51a90bc3cc..8eabfd4447 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -16,9 +16,9 @@ Syntax * K = force constant for indenter surface (force/distance\^2 units) * one or more keyword/value pairs may be appended * keyword = *sphere* or *cylinder* or *plane* or *side* or *units* - + .. parsed-literal:: - + *sphere* args = x y z R x,y,z = initial position of center of indenter (distance units) R = sphere radius of indenter (distance units) diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index 2b764ef908..b176d39651 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -22,9 +22,9 @@ Syntax * seed = random number seed to use for white noise (positive integer) * zero or more keyword/value pairs may be appended * keyword = *angmom* or *omega* or *scale* or *tally* or *zero* - + .. parsed-literal:: - + *angmom* value = *no* or factor *no* = do not thermostat rotational degrees of freedom via the angular momentum factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index b87c8ef226..56a0861003 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -21,9 +21,9 @@ Syntax * seed\_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer) * zero or more keyword/value pairs may be appended * keyword = *zero* - + .. parsed-literal:: - + *zero* value = *no* or *yes* *no* = do not set total random force on centers of mass to zero *yes* = set total random force on centers of mass to zero @@ -60,34 +60,34 @@ Velocities: .. math:: - V' = \frac {M\, V + m\, v} {M'} + V' = \frac {M\, V + m\, v} {M'} .. math:: - v' = v - V + v' = v - V Masses: .. math:: - M' = M + m + M' = M + m .. math:: - m' = \frac {M\, m } {M'} + m' = \frac {M\, m } {M'} The Langevin forces are computed as .. math:: - F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' + F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' .. math:: - f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' + f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' :math:`F_r'` is a random force proportional to :math:`\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'} {\mathrm dt\, \mathtt{damp\_com} } }`. @@ -98,12 +98,12 @@ transform: .. math:: - F = \frac M {M'}\, F' - f' + F = \frac M {M'}\, F' - f' .. math:: - f = \frac m {M'}\, F' + f' + 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 diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index 5057ea1e8a..cde59b39ab 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -17,9 +17,9 @@ Syntax * damp = damping parameter (time units) * seed = random number seed to use for white noise (positive integer) * zero or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *scale* or *tally* or *zero* *scale* values = type ratio type = atom type (1-N) @@ -28,9 +28,9 @@ Syntax *no* = do not tally the energy added/subtracted to atoms *yes* = do tally the energy added/subtracted to atoms - + .. parsed-literal:: - + *zero* value = *no* or *yes* *no* = do not set total random force to zero *yes* = set total random force to zero diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index 5f487906bd..09cec05750 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -20,9 +20,9 @@ Syntax * density = the fluid density. * zero or more keyword/value pairs may be appended * keyword = *setArea* or *setGamma* or *scaleGamma* or *dx* or *dm* or *a0* or *noise* or *calcforce* or *trilinear* or *D3Q19* or *read\_restart* or *write\_restart* or *zwall\_velocity* or *bodyforce* or *printfluid* - + .. parsed-literal:: - + *setArea* values = type node_area type = atom type (1-N) node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default). @@ -70,7 +70,7 @@ The lattice-Boltzmann algorithm solves for the fluid motion governed by the Navier Stokes equations, .. math:: - + \partial_t \rho + \partial_{\beta}\left(\rho u_{\beta}\right)= & 0 \\ \partial_t\left(\rho u_{\alpha}\right) + \partial_{\beta}\left(\rho u_{\alpha} u_{\beta}\right) = & \partial_{\beta}\sigma_{\alpha \beta} + F_{\alpha} + \partial_{\beta}\left(\eta_{\alpha \beta \gamma \nu}\partial_{\gamma} u_{\nu}\right) diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index 8eb4fa094b..d498e06f7d 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -16,9 +16,9 @@ Syntax * nevery = adjust the momentum every this many timesteps * zero or more keyword/value pairs may be appended * keyword = *linear* - + .. parsed-literal:: - + *linear* values = xflag yflag zflag xflag,yflag,zflag = 0/1 to exclude/include each dimension. diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst index 34336f0940..90059b5cac 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.rst +++ b/doc/src/fix_lb_rigid_pc_sphere.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * lb/rigid/pc/sphere = style name of this fix command * bodystyle = *single* or *molecule* or *group* - + .. parsed-literal:: - + *single* args = none *molecule* args = none *group* args = N groupID1 groupID2 ... @@ -24,9 +24,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *force* or *torque* or *innerNodes* - + .. parsed-literal:: - + *force* values = M xflag yflag zflag M = which rigid body from 1-Nbody (see asterisk form below) xflag,yflag,zflag = off/on if component of center-of-mass force is active diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst index eb60f18146..81074d306a 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * meso/move = style name of this fix command * style = *linear* or *wiggle* or *rotate* or *variable* - + .. parsed-literal:: - + *linear* args = Vx Vy Vz Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL *wiggle* args = Ax Ay Az period @@ -32,9 +32,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *units* - + .. parsed-literal:: - + *units* value = *box* or *lattice* diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index 02b0de3a7a..1a728d6c88 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -14,9 +14,9 @@ Syntax * fix-ID = ID of the fix to modify * one or more keyword/value pairs may be appended * keyword = *temp* or *press* or *energy* or *virial* or *respa* or *dynamic/dof* or *bodyforces* - + .. parsed-literal:: - + *temp* value = compute ID that calculates a temperature *press* value = compute ID that calculates a pressure *energy* value = *yes* or *no* diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index f2730e54e4..b0e2e2a456 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -19,16 +19,16 @@ Syntax * N = adjust the momentum every this many timesteps one or more keyword/value pairs may be appended * keyword = *linear* or *angular* or *rescale* - + .. parsed-literal:: - + *linear* values = xflag yflag zflag xflag,yflag,zflag = 0/1 to exclude/include each dimension *angular* values = none - + .. parsed-literal:: - + *rescale* values = none diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index 82b5b585a0..f4cd1b0231 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * move = style name of this fix command * style = *linear* or *wiggle* or *rotate* or *variable* - + .. parsed-literal:: - + *linear* args = Vx Vy Vz Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL *wiggle* args = Ax Ay Az period @@ -32,9 +32,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *units* - + .. parsed-literal:: - + *units* value = *box* or *lattice* diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst index e6b09d9cc6..76819c8598 100644 --- a/doc/src/fix_mscg.rst +++ b/doc/src/fix_mscg.rst @@ -16,9 +16,9 @@ Syntax * N = envoke this fix every this many timesteps * zero or more keyword/value pairs may be appended * keyword = *range* or *name* or *max* - + .. parsed-literal:: - + *range* arg = *on* or *off* *on* = range finding functionality is performed *off* = force matching functionality is performed diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst index 80bfaf24bd..7bbbe95202 100644 --- a/doc/src/fix_msst.rst +++ b/doc/src/fix_msst.rst @@ -17,9 +17,9 @@ Syntax * shockvel = shock velocity (strictly positive, distance/time units) * zero or more keyword value pairs may be appended * keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *beta* or *dftb* - + .. parsed-literal:: - + *q* value = cell mass-like parameter (mass\^2/distance\^4 units) *mu* value = artificial viscosity (mass/length/time units) *p0* value = initial pressure in the shock equations (pressure units) diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 2b79185551..63cdfb4be1 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -115,7 +115,7 @@ 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 -ref`(WeinanE) ` +ref`(WeinanE) ` .. parsed-literal:: diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 88ece95e95..7d45272ae0 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -44,9 +44,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * style\_name = *nvt* or *npt* or *nph* * one or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update* *temp* values = Tstart Tstop Tdamp Tstart,Tstop = external temperature at start/end of run @@ -518,7 +518,7 @@ according to the following factorization of the Liouville propagator \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\ - &\times \left[ + &\times \left[ \exp \left(\mathrm{i} L_{2}^{(1)} \frac{\Delta t}{2n} \right) \exp \left(\mathrm{i} L_{\epsilon , 1} \frac{\Delta t}{2n} \right) \exp \left(\mathrm{i} L_1 \frac{\Delta t}{n} \right) @@ -527,12 +527,12 @@ according to the following factorization of the Liouville propagator \right]^n \\ &\times \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ &+ \mathcal{O} \left(\Delta t^3 \right) - + This factorization differs somewhat from that of Tuckerman et al, in that the barostat is only updated at the outermost rRESPA level, whereas Tuckerman's factorization requires splitting the pressure into diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 1f07d13625..78aae45ad6 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -19,9 +19,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * style\_name = *nvt/eff* or *npt/eff* or *nph/eff* - + .. parsed-literal:: - + one or more keyword value pairs may be appended keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* *temp* values = Tstart Tstop Tdamp diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 2732087800..6724597e13 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -19,9 +19,9 @@ Syntax * *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 - + .. parsed-literal:: - + keyword = *ext* or *strain* or *iso* or *x* or *y* or *z* or *tchain* or *pchain* or *tloop* or *ploop* or *mtk* *ext* value = *x* or *y* or *z* or *xy* or *yz* or *xz* = external dimensions sets the external dimensions used to calculate the scalar pressure diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index d7322aa46d..ebda193f51 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -17,9 +17,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * nph/sphere = style name of this fix command * keyword = *disc* - + .. parsed-literal:: - + *disc* value = none = treat particles as 2d discs, not spheres * additional barostat related keyword/value pairs from the :doc:`fix nph ` command can be appended diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index 1d946e5f83..e47debdfb9 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -15,9 +15,9 @@ Syntax fix ID group-ID nphug keyword value ... * ID, group-ID are documented in :doc:`fix ` command - + .. parsed-literal:: - + one or more keyword value pairs may be appended keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scaleyz* or *scalexz* or *scalexy* *temp* values = Value1 Value2 Tdamp diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index e9a98b813f..cf1425e6e4 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -451,7 +451,7 @@ according to the following factorization of the Liouville propagator \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\ - &\times \left[ + &\times \left[ \exp \left(\mathrm{i} L_{2}^{(1)} \frac{\Delta t}{2n} \right) \exp \left(\mathrm{i} L_{\epsilon , 1} \frac{\Delta t}{2n} \right) \exp \left(\mathrm{i} L_1 \frac{\Delta t}{n} \right) @@ -460,8 +460,8 @@ according to the following factorization of the Liouville propagator \right]^n \\ &\times \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) - \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right) + \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right) \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\ &+ \mathcal{O} \left(\Delta t^3 \right) diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index e360e70c23..bda47d4901 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -17,9 +17,9 @@ Syntax * damp = damping parameter (time units) * seed = random number seed to use for white noise (positive integer) * keyword = *angmom* - + .. parsed-literal:: - + *angmom* value = factor factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index 68c2d7b574..be73bd1abc 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -18,9 +18,9 @@ Syntax * manifold = name of the manifold * manifold-args = parameters for the manifold * one or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *every* *every* values = N N = print info about iteration every N steps. N = 0 means no output diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index b5460fa1e0..4419a6b8ad 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -21,9 +21,9 @@ Syntax * nve/sphere = style name of this fix command * zero or more keyword/value pairs may be appended * keyword = *update* or *disc* - + .. parsed-literal:: - + *update* value = *dipole* or *dipole/dlm* dipole = update orientation of dipole moment during integration dipole/dlm = use DLM integrator to update dipole orientation diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst index c66d107089..b583121a2b 100644 --- a/doc/src/fix_nve_spin.rst +++ b/doc/src/fix_nve_spin.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * nve/spin = style name of this fix command * keyword = *lattice* - + .. parsed-literal:: - + *lattice* value = *moving* or *frozen* moving = integrate both spin and atomic degress of freedom frozen = integrate spins on a fixed lattice diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index 6fb9d8de3a..8bd7307cbf 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -18,9 +18,9 @@ Syntax * manifold = name of the manifold * manifold-args = parameters for the manifold * one or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *temp* or *tchain* or *every* *temp* values = Tstart Tstop Tdamp Tstart, Tstop = external temperature at start/end of run diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index 7bf80307ae..3d08b5a910 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -18,9 +18,9 @@ Syntax * nvt/sphere = style name of this fix command * zero or more keyword/value pairs may be appended * keyword = *disc* - + .. parsed-literal:: - + *disc* value = none = treat particles as 2d discs, not spheres * additional thermostat related keyword/value pairs from the :doc:`fix nvt ` command can be appended diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index 57579b0fce..1e302fa28d 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -17,14 +17,14 @@ Syntax * Noutput = output the dynamical matrix every this many measurements * Nwait = wait this many timesteps before measuring * map\_file = *file* or *GAMMA* - + .. parsed-literal:: - + *file* is the file that contains the mapping info between atom ID and the lattice indices. - + .. parsed-literal:: - + *GAMMA* flags to treate the whole simulation box as a unit cell, so that the mapping info can be generated internally. In this case, dynamical matrix at only the gamma-point will/can be evaluated. @@ -32,9 +32,9 @@ Syntax * prefix = prefix for output files * one or none keyword/value pairs may be appended * keyword = *sysdim* or *nasr* - + .. parsed-literal:: - + *sysdim* value = d d = dimension of the system, usually the same as the MD model dimension *nasr* value = n diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index d71c969acf..dfdb9eb36e 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -15,9 +15,9 @@ Syntax * pimd = style name of this fix command * zero or more keyword/value pairs may be appended * keyword = *method* or *fmass* or *sp* or *temp* or *nhc* - + .. parsed-literal:: - + *method* value = *pimd* or *nmpimd* or *cmd* *fmass* value = scaling factor on mass *sp* value = scaling factor on Planck constant diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index 0f6ccf4d31..98c126a421 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * plumed = style name of this fix command * keyword = *plumedfile* or *outfile* - + .. parsed-literal:: - + *plumedfile* arg = name of PLUMED input file to use (default: NULL) *outfile* arg = name of file on which to write the PLUMED log (default: NULL) diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index 38b4794237..43bbdd09e7 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -13,9 +13,9 @@ Syntax: * ID, group-ID are documented in :doc:`fix ` command * poems = style name of this fix command * keyword = *group* or *file* or *molecule* - + .. parsed-literal:: - + *group* values = list of group IDs *molecule* values = none *file* values = filename diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index d5933ba296..2537b836ac 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -18,9 +18,9 @@ Syntax * seed = random # seed (positive integer) * one or more keyword/value pairs may be appended to args * keyword = *region* or *diam* or *vol* or *rate* or *dens* or *vel* or *mol* or *rigid* or *shake* or *ignore* - + .. parsed-literal:: - + *region* value = region-ID region-ID = ID of region to use as insertion volume *diam* values = dstyle args diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 9cd15119bd..07bbe40bfb 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -14,9 +14,9 @@ Syntax * ID, group are documented in :doc:`fix ` command * precession/spin = style name of this fix command * style = *zeeman* or *anisotropy* or *cubic* - + .. parsed-literal:: - + *zeeman* args = H x y z H = intensity of the magnetic field (in Tesla) x y z = vector direction of the field @@ -24,9 +24,9 @@ Syntax K = intensity of the magnetic anisotropy (in eV) x y z = vector direction of the anisotropy - + .. parsed-literal:: - + *cubic* args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z K1 and K2c = intensity of the magnetic anisotropy (in eV) n1x to n3z = three direction vectors of the cubic anisotropy @@ -73,11 +73,11 @@ rad.THz (in metal units and with :math:`\mu_B = 5.788 eV/T`). As a comparison, the figure below displays the simulation of a single spin (of norm :math:`\mu_i = 1.0`) submitted to an external magnetic field of :math:`\vert B_{ext}\vert = 10.0\; \mathrm{Tesla}` (and oriented along the z -axis). +axis). The upper plot shows the average magnetization along the external magnetic field axis and the lower plot the Zeeman energy, both as a function of temperature. -The reference result is provided by the plot of the Langevin +The reference result is provided by the plot of the Langevin function for the same parameters. .. image:: JPG/zeeman_langevin.jpg @@ -85,7 +85,7 @@ function for the same parameters. The temperature effects are accounted for by connecting the spin :math:`i` to a thermal bath using a Langevin thermostat (see -:doc:`fix langevin/spin ` for the definition of +:doc:`fix langevin/spin ` for the definition of this thermostat). Style *anisotropy* is used to simulate an easy axis or an easy plane diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst index fd45553713..0107302c94 100644 --- a/doc/src/fix_press_berendsen.rst +++ b/doc/src/fix_press_berendsen.rst @@ -13,9 +13,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * press/berendsen = style name of this fix command - + .. parsed-literal:: - + one or more keyword value pairs may be appended keyword = *iso* or *aniso* or *x* or *y* or *z* or *couple* or *dilate* or *modulus* *iso* or *aniso* values = Pstart Pstop Pdamp diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst index 1b97a3f879..ab81edd773 100644 --- a/doc/src/fix_print.rst +++ b/doc/src/fix_print.rst @@ -17,9 +17,9 @@ Syntax * string = text string to print with optional variable names * zero or more keyword/value pairs may be appended * keyword = *file* or *append* or *screen* or *title* - + .. parsed-literal:: - + *file* value = filename *append* value = filename *screen* value = *yes* or *no* diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 799d62a0aa..bddb742aaa 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -17,9 +17,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * property/atom = style name of this fix command * vec1,vec2,... = *mol* or *q* or *rmass* or *i\_name* or *d\_name* - + .. parsed-literal:: - + *mol* = molecule IDs *q* = charge *rmass* = per-atom mass @@ -28,9 +28,9 @@ Syntax * zero of more keyword/value pairs may be appended * keyword = *ghost* - + .. parsed-literal:: - + *ghost* value = *no* or *yes* for whether ghost atom info in communicated diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index f45f3f8f5b..600fa4aedc 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -15,9 +15,9 @@ Syntax * python/invoke = style name of this fix command * N = execute every N steps * callback = *post\_force* or *end\_of\_step* - + .. parsed-literal:: - + *post_force* = callback after force computations on atoms every N time steps *end_of_step* = callback after every N time steps diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index 984c0ca793..5b4e70a5dd 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -17,9 +17,9 @@ Syntax * shockvel = shock velocity (strictly positive, velocity units) * zero or more keyword/value pairs may be appended * keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *damp* or *seed*\ or *f\_max* or *N\_f* or *eta* or *beta* or *T\_init* - + .. parsed-literal:: - + *q* value = cell mass-like parameter (mass\^2/distance\^4 units) *mu* value = artificial viscosity (mass/distance/time units) *p0* value = initial pressure in the shock equations (pressure units) diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 6ac647dad9..19b0741e7b 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -32,9 +32,9 @@ Syntax * qfile = a filename with QEq parameters or *coul/streitz* or *reax/c* * zero or more keyword/value pairs may be appended * keyword = *alpha* or *qdamp* or *qstep* - + .. parsed-literal:: - + *alpha* value = Slater type orbital exponent (qeq/slater only) *qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only) *qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only) diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index dcd0950bf2..4947165265 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -20,9 +20,9 @@ Syntax * precision = convergence criterion for charge equilibration * zero or more keyword/value pairs may be appended * keyword = *file* - + .. parsed-literal:: - + *file* value = filename filename = name of file to write QEQ equilibration info to diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst index 7242d0739b..77b00cdcbc 100644 --- a/doc/src/fix_qtb.rst +++ b/doc/src/fix_qtb.rst @@ -15,9 +15,9 @@ Syntax * qtb = style name of this fix * zero or more keyword/value pairs may be appended * keyword = *temp* or *damp* or *seed* or *f\_max* or *N\_f* - + .. parsed-literal:: - + *temp* value = target quantum temperature (temperature units) *damp* value = damping parameter (time units) inverse of friction *gamma* *seed* value = random number seed (positive integer) diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index a709ddaa35..1725f2aeef 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -22,9 +22,9 @@ Syntax * filename = name of output file * zero or more keyword/value pairs may be appended * keyword = *cutoff* or *element* or *position* - + .. parsed-literal:: - + *cutoff* value = I J Cutoff I, J = atom types Cutoff = Bond-order cutoff value for this pair of atom types diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst index 6c63ead911..9639890060 100644 --- a/doc/src/fix_recenter.rst +++ b/doc/src/fix_recenter.rst @@ -16,9 +16,9 @@ Syntax * x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below) * zero or more keyword/value pairs may be appended * keyword = *shift* or *units* - + .. parsed-literal:: - + *shift* value = group-ID group-ID = group of atoms whose coords are shifted *units* value = *box* or *lattice* or *fraction* diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index 04d7a01c07..1eeb632da7 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -15,9 +15,9 @@ Syntax * restrain = style name of this fix command * one or more keyword/arg pairs may be appended * keyword = *bond* or *angle* or *dihedral* - + .. parsed-literal:: - + *bond* args = atom1 atom2 Kstart Kstop r0 atom1,atom2 = IDs of 2 atoms in bond Kstart,Kstop = restraint coefficients at start/end of run (energy units) diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 15f7c41b60..aad626a66f 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -59,9 +59,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * style = *rigid* or *rigid/nve* or *rigid/nvt* or *rigid/npt* or *rigid/nph* or *rigid/small* or *rigid/nve/small* or *rigid/nvt/small* or *rigid/npt/small* or *rigid/nph/small* * bodystyle = *single* or *molecule* or *group* - + .. parsed-literal:: - + *single* args = none *molecule* args = none *custom* args = *i_propname* or *v_varname* @@ -73,9 +73,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *langevin* or *reinit* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* - + .. parsed-literal:: - + *langevin* values = Tstart Tstop Tperiod seed Tstart,Tstop = desired temperature at start/stop of run (temperature units) Tdamp = temperature damping parameter (time units) diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index 3f6796c4c6..b0a6629c48 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * rigid/meso = style name of this fix command * bodystyle = *single* or *molecule* or *group* - + .. parsed-literal:: - + *single* args = none *molecule* args = none *custom* args = *i_propname* or *v_varname* @@ -28,9 +28,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *reinit* or *force* or *torque* or *infile* - + .. parsed-literal:: - + *reinit* = *yes* or *no* *force* values = M xflag yflag zflag M = which rigid body from 1-Nbody (see asterisk form below) diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst index c2f57618ed..e89641363c 100644 --- a/doc/src/fix_saed_vtk.rst +++ b/doc/src/fix_saed_vtk.rst @@ -17,9 +17,9 @@ Syntax * Nrepeat = # of times to use input values for calculating averages * Nfreq = calculate averages every this many timesteps * c\_ID = saed compute ID - + .. parsed-literal:: - + keyword = *file* or *ave* or *start* or *file* or *overwrite*\ :l *ave* args = *one* or *running* or *window M* one = output a new average value every Nfreq steps diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index 3e358aef31..0257d6dedf 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -23,9 +23,9 @@ Syntax * any of fx,fy,fz can be a variable (see below) * zero or more keyword/value pairs may be appended to args * keyword = *region* - + .. parsed-literal:: - + *region* value = region-ID region-ID = ID of region atoms must be in to have added force diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 624d5cf455..ce0739900f 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -21,9 +21,9 @@ Syntax * N = print SHAKE statistics every this many timesteps (0 = never) * one or more constraint/value pairs are appended * constraint = *b* or *a* or *t* or *m* - + .. parsed-literal:: - + *b* values = one or more bond types *a* values = one or more angle types *t* values = one or more atom types @@ -31,9 +31,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *mol* - + .. parsed-literal:: - + *mol* value = template-ID template-ID = ID of molecule template specified in a separate :doc:`molecule ` command diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index 5c8496c2a8..2bd41cfa84 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * smd = style name of this fix command * mode = *cvel* or *cfor* to select constant velocity or constant force SMD - + .. parsed-literal:: - + *cvel* values = K vel K = spring constant (force/distance units) vel = velocity of pulling (distance/time units) @@ -24,9 +24,9 @@ Syntax force = pulling force (force units) * keyword = *tether* or *couple* - + .. parsed-literal:: - + *tether* values = x y z R0 x,y,z = point to which spring is tethered R0 = distance of end of spring from tether point (distance units) diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst index 87e7d303b3..c6332753ea 100644 --- a/doc/src/fix_smd_adjust_dt.rst +++ b/doc/src/fix_smd_adjust_dt.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * smd/adjust\_dt = style name of this fix command * arg = *s\_fact* - + .. parsed-literal:: - + *s_fact* = safety factor diff --git a/doc/src/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst index d5796e0c99..f3e1417f4b 100644 --- a/doc/src/fix_smd_move_triangulated_surface.rst +++ b/doc/src/fix_smd_move_triangulated_surface.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * smd/move\_tri\_surf keyword = style name of this fix command * keyword = *\*LINEAR* or *\*WIGGLE* or *\*ROTATE* - + .. parsed-literal:: - + *\*LINEAR* args = Vx Vy Vz Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL *\*WIGGLE* args = Vx Vy Vz max_travel diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index 9c860f2766..b98b334a40 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -17,9 +17,9 @@ Syntax * any of vx,vy,vz can be a variable (see below) * zero or more keyword/value pairs may be appended to args * keyword = *region* - + .. parsed-literal:: - + *region* value = region-ID region-ID = ID of region particles must be in to have their velocities set diff --git a/doc/src/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst index a75a75ab27..60ad5bfd35 100644 --- a/doc/src/fix_smd_wall_surface.rst +++ b/doc/src/fix_smd_wall_surface.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * smd/wall\_surface = style name of this fix command * arg = *file* - + .. parsed-literal:: - + *file* = file name of a triangular mesh in stl format * type = particle type to be given to the new particles created by this fix diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst index e7db053d57..1a3469ccc8 100644 --- a/doc/src/fix_spring.rst +++ b/doc/src/fix_spring.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * spring = style name of this fix command * keyword = *tether* or *couple* - + .. parsed-literal:: - + *tether* values = K x y z R0 K = spring constant (force/distance units) x,y,z = point to which spring is tethered diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 63d93a1c48..0a9f0bd1ab 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -21,9 +21,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *lamda* or *collision* or *overlap* or *inside* or *exact* or *radius* or *bounce* or *search* or *cubic* or *shift* or *tstat* or *rescale* - + .. parsed-literal:: - + *lamda* value = mean free path of SRD particles (distance units) *collision* value = *noslip* or *slip* = collision model *overlap* value = *yes* or *no* = whether big particles may overlap diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index d480a45d60..d1f61b7c1e 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -15,9 +15,9 @@ Syntax * store/state = style name of this fix command * N = store atom attributes every N steps, N = 0 for initial store only * input = one or more atom attributes - + .. parsed-literal:: - + possible attributes = id, mol, type, mass, x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz, vx, vy, vz, fx, fy, fz, @@ -27,9 +27,9 @@ Syntax c_ID, c_ID[N], f_ID, f_ID[N], v_name, d_name, i_name - + .. parsed-literal:: - + id = atom ID mol = molecule ID type = atom type @@ -58,9 +58,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *com* - + .. parsed-literal:: - + *com* value = *yes* or *no* diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index 6351bb947b..5f0b83b63a 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/doc/src/fix_temp_berendsen.rst @@ -14,9 +14,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * temp/berendsen = style name of this fix command * Tstart,Tstop = desired temperature at start/end of run - + .. parsed-literal:: - + Tstart can be a variable (see below) * Tdamp = temperature damping parameter (time units) diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index d57c0e2583..445b5cc676 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -19,9 +19,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * temp/csvr or temp/csld = style name of this fix command * Tstart,Tstop = desired temperature at start/end of run - + .. parsed-literal:: - + Tstart can be a variable (see below) * Tdamp = temperature damping parameter (time units) diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index b8713d6c85..4b524c2e23 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -15,9 +15,9 @@ Syntax * temp/rescale = style name of this fix command * N = perform rescaling every N steps * Tstart,Tstop = desired temperature at start/end of run (temperature units) - + .. parsed-literal:: - + Tstart can be a variable (see below) * window = only rescale if temperature is outside this window (temperature units) diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst index 2b111a4288..750207a567 100644 --- a/doc/src/fix_tfmc.rst +++ b/doc/src/fix_tfmc.rst @@ -18,9 +18,9 @@ Syntax * seed = random number seed (positive integer) * zero or more keyword/arg pairs may be appended * keyword = *com* or *rot* - + .. parsed-literal:: - + *com* args = xflag yflag zflag xflag,yflag,zflag = 0/1 to exclude/include each dimension *rot* args = none diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index 4c62ccd9be..ede20b2ad9 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/doc/src/fix_thermal_conductivity.rst @@ -18,9 +18,9 @@ Syntax * Nbin = # of layers in edim direction (must be even number) * zero or more keyword/value pairs may be appended * keyword = *swap* - + .. parsed-literal:: - + *swap* value = Nswap = number of swaps to perform every N steps diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst index 152e3fbcac..6b7f59fa92 100644 --- a/doc/src/fix_ti_spring.rst +++ b/doc/src/fix_ti_spring.rst @@ -18,9 +18,9 @@ Syntax * t\_s = number of steps for the switching procedure * zero or more keyword/value pairs may be appended to args * keyword = *function* - + .. parsed-literal:: - + *function* value = function-ID function-ID = ID of the switching function (1 or 2) diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 022afc67b5..1a3fcf2ad9 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -19,9 +19,9 @@ Syntax * style = *ttm* or *ttm\_mod* * seed = random number seed to use for white noise (positive integer) * remaining arguments for fix ttm: - + .. parsed-literal:: - + C_e = electronic specific heat (energy/(electron\*temperature) units) rho_e = electronic density (electrons/volume units) kappa_e = electronic thermal conductivity (energy/(time\*distance\*temperature) units) @@ -36,9 +36,9 @@ Syntax T_outfile = filename to write TTM temperatures to (only needed if N > 0) * remaining arguments for fix ttm/mod: - + .. parsed-literal:: - + init_file = file with the parameters to TTM Nx = number of thermal solve grid points in the x-direction (positive integer) Ny = number of thermal solve grid points in the y-direction (positive integer) @@ -111,8 +111,8 @@ transfer between the subsystems: .. math:: - C_e \rho_e \frac{\partial T_e}{\partial t} = - \bigtriangledown (\kappa_e \bigtriangledown T_e) - + C_e \rho_e \frac{\partial T_e}{\partial t} = + \bigtriangledown (\kappa_e \bigtriangledown T_e) - g_p (T_e - T_a) + g_s T_a' @@ -200,8 +200,8 @@ heat sources (e.g. laser heating in ablation simulations): .. math:: - C_e \rho_e \frac{\partial T_e}{\partial t} = - \bigtriangledown (\kappa_e \bigtriangledown T_e) - + C_e \rho_e \frac{\partial T_e}{\partial t} = + \bigtriangledown (\kappa_e \bigtriangledown T_e) - g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin}) diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 92ebffba1e..752d794728 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -16,9 +16,9 @@ Syntax * Nevery = use input values every this many timesteps * one or more input values can be listed * value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name - + .. parsed-literal:: - + c_ID = global scalar calculated by a compute with ID c_ID[I] = Ith component of global vector calculated by a compute with ID f_ID = global scalar calculated by a fix with ID diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index 9dd1cf3557..db54257df9 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -19,9 +19,9 @@ Syntax * Nbin = # of layers in pdim direction (must be even number) * zero or more keyword/value pairs may be appended * keyword = *swap* or *target* - + .. parsed-literal:: - + *swap* value = Nswap = number of swaps to perform every N steps *vtarget* value = V or INF = target velocity of swap partners (velocity units) diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst index 427ff06cfd..5163872e65 100644 --- a/doc/src/fix_viscous.rst +++ b/doc/src/fix_viscous.rst @@ -15,9 +15,9 @@ Syntax * viscous = style name of this fix command * gamma = damping coefficient (force/velocity units) * zero or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *scale* *scale* values = type ratio type = atom type (1-N) diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index c76b0c8905..c44a6cbb81 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -34,9 +34,9 @@ Syntax * one or more face/arg pairs may be appended * face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* * args for styles *lj93* or *lj126* or *lj1043* or *colloid* or *harmonic* - + .. parsed-literal:: - + args = coord epsilon sigma cutoff coord = position of wall = EDGE or constant or variable EDGE = current lo or hi edge of simulation box @@ -49,9 +49,9 @@ Syntax cutoff = distance from wall at which wall-particle interaction is cut off (distance units) * args for style *morse* - + .. parsed-literal:: - + args = coord D_0 alpha r_0 cutoff coord = position of wall = EDGE or constant or variable EDGE = current lo or hi edge of simulation box @@ -67,9 +67,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *units* or *fld* - + .. parsed-literal:: - + *units* value = *lattice* or *box* *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units @@ -106,7 +106,7 @@ For style *wall/lj93*\ , the energy E is given by the 9/3 potential: .. math:: - E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} - + E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} - \left(\frac{\sigma}{r}\right)^3 \right] \qquad r < r_c @@ -115,7 +115,7 @@ For style *wall/lj126*\ , the energy E is given by the 12/6 potential: .. math:: - E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c @@ -124,7 +124,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: .. math:: - E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} - + E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} - \left(\frac{\sigma}{r}\right)^4 - \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right] \qquad r < r_c @@ -135,10 +135,10 @@ of the :doc:`pair_style colloid ` potential: .. math:: - E = & \epsilon \left[ \frac{\sigma^{6}}{7560} + E = & \epsilon \left[ \frac{\sigma^{6}}{7560} \left(\frac{6R-D}{D^{7}} + \frac{D+8R}{(D+2R)^{7}} \right) \right. \\ & \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 + \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 diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 6b0ba4b130..4847d58e0f 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -18,9 +18,9 @@ Syntax * c\_t = tangential damping coefficient (force/distance or pressure units) * wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder* * args = list of arguments for a particular style - + .. parsed-literal:: - + *xplane* or *yplane* args = lo hi lo,hi = position of lower and upper plane (distance units), either can be NULL) *zcylinder* args = radius @@ -28,9 +28,9 @@ Syntax * zero or more keyword/value pairs may be appended to args * keyword = *wiggle* - + .. parsed-literal:: - + *wiggle* values = dim amplitude period dim = *x* or *y* or *z* amplitude = size of oscillation (distance units) diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index 38e75de13a..13283b0a50 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -18,9 +18,9 @@ Syntax * c\_t = tangential damping coefficient (force/distance units or pressure units - see discussion below) * wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder* * args = list of arguments for a particular style - + .. parsed-literal:: - + *xplane* or *yplane* args = lo hi lo,hi = position of lower and upper plane (distance units), either can be NULL) *zcylinder* args = radius @@ -28,9 +28,9 @@ Syntax * zero or more keyword/value pairs may be appended to args * keyword = *wiggle* - + .. parsed-literal:: - + *wiggle* values = dim amplitude period dim = *x* or *y* or *z* amplitude = size of oscillation (distance units) diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index 334228d85b..d77880f2c4 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -16,9 +16,9 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * style = *wall/ees* or *wall/region/ees* - + .. parsed-literal:: - + args for style *wall/ees*\ : one or more *face parameters* groups may be appended face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* parameters = coord epsilon sigma cutoff @@ -32,9 +32,9 @@ Syntax sigma can be a variable (see below) cutoff = distance from wall at which wall-particle interaction is cut off (distance units) - + .. parsed-literal:: - + args for style *wall/region/ees*\ : *region-ID* *epsilon* *sigma* *cutoff* region-ID = region whose boundary will act as wall epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units) diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index dde9af0f94..3a1ed6a2fb 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -14,15 +14,15 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * wall/gran = style name of this fix command * fstyle = style of force interactions between particles and wall - + .. parsed-literal:: - + possible choices: hooke, hooke/history, hertz/history, granular * fstyle\_params = parameters associated with force interaction style - + .. parsed-literal:: - + 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) @@ -31,16 +31,16 @@ Syntax xmu = static yield criterion (unitless value between 0.0 and 1.0e4) dampflag = 0 or 1 if tangential damping force is excluded or included - + .. parsed-literal:: - + 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 - + .. parsed-literal:: - + *xplane* or *yplane* or *zplane* args = lo hi lo,hi = position of lower and upper plane (distance units), either can be NULL) *zcylinder* args = radius @@ -48,9 +48,9 @@ Syntax * zero or more keyword/value pairs may be appended to args * keyword = *wiggle* or *shear* - + .. parsed-literal:: - + *wiggle* values = dim amplitude period dim = *x* or *y* or *z* amplitude = size of oscillation (distance units) diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 6f82bfd85a..c02179a958 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -14,15 +14,15 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * wall/region = style name of this fix command * fstyle = style of force interactions between particles and wall - + .. parsed-literal:: - + possible choices: hooke, hooke/history, hertz/history, granular * fstyle\_params = parameters associated with force interaction style - + .. parsed-literal:: - + 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) @@ -31,9 +31,9 @@ Syntax xmu = static yield criterion (unitless value between 0.0 and 1.0e4) dampflag = 0 or 1 if tangential damping force is excluded or included - + .. parsed-literal:: - + 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) diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index cb5c611f61..7cc577ca7d 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -16,9 +16,9 @@ Syntax * face = *zlo* * zero or more keyword/value pairs may be appended * keyword = *pos* or *vel* or *ramp* or *units* - + .. parsed-literal:: - + *pos* args = z z = z coordinate at which the piston begins (distance units) *vel* args = vz diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 7a7cc6425b..4d8dbdcd0c 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -18,9 +18,9 @@ Syntax * wall/reflect = style name of this fix command * one or more face/arg pairs may be appended * face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* - + .. parsed-literal:: - + arg = EDGE or constant or variable EDGE = current lo edge of simulation box constant = number like 0.0 or 30.0 (distance units) @@ -28,9 +28,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *units* - + .. parsed-literal:: - + *units* value = *lattice* or *box* *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units diff --git a/doc/src/fix_wall_reflect_stochastic.rst b/doc/src/fix_wall_reflect_stochastic.rst index bf254945a1..696d1a465c 100644 --- a/doc/src/fix_wall_reflect_stochastic.rst +++ b/doc/src/fix_wall_reflect_stochastic.rst @@ -17,9 +17,9 @@ Syntax * seed = random seed for stochasticity (positive integer) * one or more face/args pairs may be appended * face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* - + .. parsed-literal:: - + args = pos temp velx vely velz accomx accomy accomz pos = EDGE or constant EDGE = current lo or hi edge of simulation box @@ -33,9 +33,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *units* - + .. parsed-literal:: - + *units* value = *lattice* or *box* *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index a6f719e142..932f82dfde 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -16,16 +16,16 @@ Syntax * region-ID = region whose boundary will act as wall * style = *lj93* or *lj126* or *lj1043* or *colloid* or *harmonic* or *morse* * args for styles *lj93* or *lj126* or *lj1043* or *colloid* or *harmonic* = - + .. parsed-literal:: - + epsilon = strength factor for wall-particle interaction (energy or energy/distance\^2 units) sigma = size factor for wall-particle interaction (distance units) * args for style *morse* = - + .. parsed-literal:: - + D_0 = depth of the potential (energy units) alpha = width parameter (1/distance units) r_0 = distance of the potential minimum from wall position (distance units) @@ -134,7 +134,7 @@ For style *lj93*\ , the energy E is given by the 9/3 potential: .. math:: - E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} - + E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} - \left(\frac{\sigma}{r}\right)^3 \right] \qquad r < r_c @@ -143,7 +143,7 @@ For style *lj126*\ , the energy E is given by the 12/6 potential: .. math:: - E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c @@ -152,7 +152,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: .. math:: - E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} - + E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} - \left(\frac{\sigma}{r}\right)^4 - \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right] \qquad r < r_c @@ -163,10 +163,10 @@ the :doc:`pair_style colloid ` potential: .. math:: - E = & \epsilon \left[ \frac{\sigma^{6}}{7560} + E = & \epsilon \left[ \frac{\sigma^{6}}{7560} \left(\frac{6R-D}{D^{7}} + \frac{D+8R}{(D+2R)^{7}} \right) \right. \\ & \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 + \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 diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index 8685b39fff..1553844875 100644 --- a/doc/src/fix_wall_srd.rst +++ b/doc/src/fix_wall_srd.rst @@ -15,9 +15,9 @@ Syntax * wall/srd = style name of this fix command * one or more face/arg pairs may be appended * face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* - + .. parsed-literal:: - + *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) @@ -29,9 +29,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *units* - + .. parsed-literal:: - + *units* value = *lattice* or *box* *lattice* = the wall position is defined in lattice units *box* = the wall position is defined in simulation box units diff --git a/doc/src/group.rst b/doc/src/group.rst index 9246f432c8..bb78921e65 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -13,9 +13,9 @@ Syntax * ID = user-defined name of the group * style = *delete* or *clear* or *empty* or *region* or *type* or *id* or *molecule* or *variable* or *include* or *subtract* or *union* or *intersect* or *dynamic* or *static* - + .. parsed-literal:: - + *delete* = no args *clear* = no args *empty* = no args diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst index eab9cf8973..0324e8301e 100644 --- a/doc/src/hyper.rst +++ b/doc/src/hyper.rst @@ -17,9 +17,9 @@ Syntax * compute-ID = ID of a compute that identifies when an event has occurred * zero or more keyword/value pairs may be appended * keyword = *min* or *dump* or *rebond* - + .. parsed-literal:: - + *min* values = etol ftol maxiter maxeval etol = stopping tolerance for energy, used in quenching ftol = stopping tolerance for force, used in quenching diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index 4d1e0be059..644caa1a92 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -33,7 +33,7 @@ The *cvff* improper style uses the potential .. math:: - E = K [1 + d \cos (n \phi) ] + E = K [1 + d \cos (n \phi) ] where phi is the improper dihedral angle. diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 18876e69c6..f85eb4784d 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -30,7 +30,7 @@ The *fourier* improper style uses the following potential: .. math:: - E = K [C_0 + C_1 \cos ( \omega) + C_2 \cos( 2 \omega) ] + E = K [C_0 + C_1 \cos ( \omega) + C_2 \cos( 2 \omega) ] where K is the force constant, C0, C1, C2 are dimensionless coefficients, diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index aeab9fae56..99a4735427 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -34,9 +34,9 @@ Syntax * typeargs = atom type to species mapping (one entry per atom type) or *fixed\_types* for models with a preset fixed mapping * variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command. * formatarg = *list, split, or explicit* (optional): - + .. parsed-literal:: - + *list* = returns a single string with a list of space separated values (e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as defined by the *variable* argument. [default for *kim_query*] diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index 9c692997c9..5d2293fb2c 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -13,9 +13,9 @@ Syntax * one or more keyword/value pairs may be listed * keyword = *collective* or *compute* or *cutoff/adjust* or *diff* or *disp/auto* or *fftbench* or *force/disp/kspace* or *force/disp/real* or *force* or *gewald/disp* or *gewald* or *kmax/ewald* or *mesh* or *minorder* or *mix/disp* or *order/disp* or *order* or *overlap* or *scafacos* or *slab* or *splittol* - + .. parsed-literal:: - + *collective* value = *yes* or *no* *compute* value = *yes* or *no* *cutoff/adjust* value = *yes* or *no* diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index 6969ae8aa5..a1b643ce14 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -13,17 +13,17 @@ Syntax * style = *none* or *sc* or *bcc* or *fcc* or *hcp* or *diamond* or *sq* or *sq2* or *hex* or *custom* * scale = scale factor between lattice and simulation box - + .. parsed-literal:: - + scale = reduced density rho\* (for LJ units) scale = lattice constant in distance units (for all other units) * zero or more keyword/value pairs may be appended * keyword = *origin* or *orient* or *spacing* or *a1* or *a2* or *a3* or *basis* - + .. parsed-literal:: - + *origin* values = x y z x,y,z = fractions of a unit cell (0 <= x,y,z < 1) *orient* values = dim i j k diff --git a/doc/src/message.rst b/doc/src/message.rst index 2552991318..4792c064d8 100644 --- a/doc/src/message.rst +++ b/doc/src/message.rst @@ -14,9 +14,9 @@ Syntax * which = *client* or *server* or *quit* * protocol = *md* or *mc* * mode = *file* or *zmq* or *mpi/one* or *mpi/two* - + .. parsed-literal:: - + *file* arg = filename filename = file used for message exchanges *zmq* arg = socket-ID diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index 5628c65710..bad1b1366d 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -12,14 +12,14 @@ Syntax min_modify keyword values ... * one or more keyword/value pairs may be listed - + .. parsed-literal:: - + keyword = *dmax* or *line* or *norm* or *alpha_damp* or *discrete_factor* or *integrator* or *tmax* *dmax* value = max max = maximum distance for line search to move (distance units) *line* value = *backtrack* or *quadratic* or *forcezero* or *spin_cubic* or *spin_none* - backtrack,quadratic,forcezero,spin_cubic,spin_none = style of linesearch to use + backtrack,quadratic,forcezero,spin_cubic,spin_none = style of linesearch to use *norm* value = *two* or *max* two = Euclidean two-norm (length of 3N vector) inf = max force component across all 3-vectors @@ -86,16 +86,16 @@ 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 -*spin/lbfgs* using the *norm* keyword. The default *two* norm computes +, *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: .. math:: || \vec{F} ||_{2} = \sqrt{\vec{F}_1+ \cdots + \vec{F}_N} -The *max* norm computes the length of the 3-vector force -for each atom (2-norm), and takes the maximum value of those across +The *max* norm computes the length of the 3-vector force +for each atom (2-norm), and takes the maximum value of those across all atoms .. math:: @@ -139,8 +139,8 @@ adaptive timestep during a *fire* minimization. It is a multiplication factor applied to the current :doc:`timestep ` (not in time unit). For example, *tmax* = 4.0 with a :doc:`timestep ` of 2fs, means that the maximum value the timestep can reach during a *fire* -minimization is 4fs. -Note that parameter defaults has been chosen to be reliable in most cases, +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*\ , @@ -150,12 +150,12 @@ parameters of the *fire* minimization can be tuned (\ *tmin*\ , An additional stopping criteria *vdfmax* is used by *fire* in order to avoid unnecessary looping when it is reasonable to think the system will not be relaxed further. Note that in this case the system will NOT have -reached your minimization criteria. This could happen when the system -comes to be stuck in a local basin of the phase space. *vdfmax* is +reached your minimization criteria. This could happen when the system +comes to be stuck in a local basin of the phase space. *vdfmax* is the maximum number of consecutive iterations with P(t) < 0. The :doc:`min_style ` *fire* is an optimized implementation of -:doc:`min_style ` *fire/old*. It can however behave similarly +:doc:`min_style ` *fire/old*. It can however behave similarly to the *fire/old* style by using the following set of parameters: .. code-block:: LAMMPS diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 49db5c783a..2dc29c7544 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -15,8 +15,8 @@ Syntax .. code-block:: LAMMPS - min_style spin - min_style spin/cg + min_style spin + min_style spin/cg min_style spin/lbfgs Examples @@ -63,11 +63,11 @@ the definition of this timestep. *discrete\_factor* can be defined with the :doc:`min_modify ` command. Style *spin/cg* defines an orthogonal spin optimization -(OSO) combined to a conjugate gradient (CG) algorithm. +(OSO) combined to a conjugate gradient (CG) algorithm. The :doc:`min_modify ` command can be used to -couple the *spin/cg* to a line search procedure, and to modify the +couple the *spin/cg* to a line search procedure, and to modify the discretization factor *discrete\_factor*. -By default, style *spin/cg* does not employ the line search procedure +By default, style *spin/cg* does not employ the line search procedure and uses the adaptive time-step technique in the same way as style *spin*\ . Style *spin/lbfgs* defines an orthogonal spin optimization (OSO) @@ -83,7 +83,7 @@ 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/molecule.rst b/doc/src/molecule.rst index ba57aed2ca..36980cd568 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -15,9 +15,9 @@ Syntax * file1,file2,... = names of files containing molecule descriptions * zero or more keyword/value pairs may be appended after each file * keyword = *offset* or *toff* or *boff* or *aoff* or *doff* or *ioff* or *scale* - + .. parsed-literal:: - + *offset* values = Toff Boff Aoff Doff Ioff Toff = offset to add to atom types Boff = offset to add to bond types diff --git a/doc/src/neb.rst b/doc/src/neb.rst index 5b1e4570bc..0ad7718d78 100644 --- a/doc/src/neb.rst +++ b/doc/src/neb.rst @@ -17,9 +17,9 @@ Syntax * N2 = max # of iterations (timesteps) to run barrier-climbing NEB * Nevery = print replica energies and reaction coordinates every this many timesteps * file-style = *final* or *each* or *none* - + .. parsed-literal:: - + *final* arg = filename filename = file with initial coords for final replica coords for intermediate replicas are linearly interpolated diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 523f32652c..9a8e538a14 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -17,9 +17,9 @@ Syntax * N2 = max # of iterations (timesteps) to run barrier-climbing NEB * Nevery = print replica energies and reaction coordinates every this many timesteps * file-style = *final* or *each* or *none* - + .. parsed-literal:: - + *final* arg = filename filename = file with initial coords for final replica coords for intermediate replicas are linearly interpolated @@ -160,7 +160,7 @@ with :math:`\nu` the image number, Q the total number of images, and .. math:: - \vec{k}_i = \frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I \times \vec{m}_i^F\right|} + \vec{k}_i = \frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I \times \vec{m}_i^F\right|} if the initial and final spins are not aligned. If the initial and final spins are aligned, then their cross @@ -204,7 +204,7 @@ 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_spin ` for more information). +:doc:`min_spin ` for more information). The other styles cannot be used, since they relax the lattice degrees of freedom instead of the spins. diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index dbf08d6726..1d36350366 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -12,9 +12,9 @@ Syntax neigh_modify keyword values ... * one or more keyword/value pairs may be listed - + .. parsed-literal:: - + keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* *delay* value = N N = delay building until this many steps since last build diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index a8b70cb731..ba391c0250 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -86,5 +86,5 @@ Default | 0.3 bin for units = lj, skin = 0.3 sigma | 2.0 bin for units = real or metal, skin = 2.0 Angstroms | 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm -| 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm -| +| 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm +| diff --git a/doc/src/package.rst b/doc/src/package.rst index 4a8b3dcdcd..db40602f81 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -13,9 +13,9 @@ Syntax * style = *gpu* or *intel* or *kokkos* or *omp* * args = arguments specific to the style - + .. parsed-literal:: - + *gpu* args = Ngpu keyword value ... Ngpu = # of GPUs per node zero or more keyword/value pairs may be appended diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index e2ef285f91..922f213051 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -84,8 +84,8 @@ The AIREBO potential consists of three terms: .. math:: - E & = \frac{1}{2} \sum_i \sum_{j \neq i} - \left[ E^{\text{REBO}}_{ij} + E^{\text{LJ}}_{ij} + + E & = \frac{1}{2} \sum_i \sum_{j \neq i} + \left[ E^{\text{REBO}}_{ij} + E^{\text{LJ}}_{ij} + \sum_{k \neq i,j} \sum_{l \neq i,j,k} E^{\text{TORSION}}_{kijl} \right] \\ By default, all three terms are included. For the *airebo* style, if diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst index 8e353960f0..5626ac37e3 100644 --- a/doc/src/pair_awpmd.rst +++ b/doc/src/pair_awpmd.rst @@ -14,9 +14,9 @@ Syntax * Rc = global cutoff, -1 means cutoff of half the shortest box length * zero or more keyword/value pairs may be appended * keyword = *hartree* or *dproduct* or *uhf* or *free* or *pbc* or *fix* or *harm* or *ermscale* or *flex\_press* - + .. parsed-literal:: - + *hartree* value = none *dproduct* value = none *uhf* value = none diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 1e0dfc5611..a5c51c0cb6 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -104,7 +104,7 @@ potential described in :ref:`(Fumi and Tosi) `, given by .. math:: - E = A \exp \left(\frac{\sigma - r}{\rho} \right) - + E = A \exp \left(\frac{\sigma - r}{\rho} \right) - \frac{C}{r^6} + \frac{D}{r^8} \qquad r < r_c diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index 1c6701463b..711d8b2b82 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -15,16 +15,16 @@ Syntax pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2) * flag\_buck = *long* or *cut* - + .. parsed-literal:: - + *long* = use Kspace long-range summation for the dispersion term 1/r\^6 *cut* = use a cutoff * flag\_coul = *long* or *off* - + .. parsed-literal:: - + *long* = use Kspace long-range summation for the Coulombic term 1/r *off* = omit the Coulombic term diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index 78de46d23f..a9c18291f8 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -168,11 +168,11 @@ artifacts. E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\ = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ - LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \\ C(r) = & \frac{C q_i q_j}{ \epsilon r} \\ - S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 - \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} + S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 + \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 3b005ed517..33c6487af0 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -84,7 +84,7 @@ The *lj/class2* styles compute a 6/9 Lennard-Jones potential given by .. math:: - E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 - + E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 - 3 \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index f94c163e1d..102c3f0b94 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -47,7 +47,7 @@ The colloid-colloid interaction energy is given by \frac{2 a_1 a_2}{r^2-\left(a_1+a_2\right)^2} + \frac{2 a_1 a_2}{r^2 - \left(a_1 - a_2\right)^2} + \mathrm{ln} - \left( + \left( \frac{r^2-\left(a_1+a_2\right)^2}{r^2-\left(a_1-a_2\right)^2} \right) \right] \\ @@ -75,9 +75,9 @@ The colloid-solvent interaction energy is given by .. math:: - U = \frac{2 ~ a^3 ~ \sigma^3 ~ A_{cs}}{9 \left( a^2 - r^2 \right)^3} + U = \frac{2 ~ a^3 ~ \sigma^3 ~ A_{cs}}{9 \left( a^2 - r^2 \right)^3} \left[ 1 - \frac{\left(5 ~ a^6+45~a^4~r^2+63~a^2~r^4+15~r^6\right) \sigma^6} - {15 \left(a-r\right)^6 \left( a+r \right)^6} \right], \quad r < r_c + {15 \left(a-r\right)^6 \left( a+r \right)^6} \right], \quad r < r_c where :math:A_{cs}` is the Hamaker constant, *a* is the radius of the colloidal particle, and :math:`r_c` is the cutoff. This formula is derived from the diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index b893f56502..782ef5d5ad 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -51,7 +51,7 @@ total energy :math:`E_T` of a system of atoms is given by .. math:: E_T = & \sum_i [ E_i^{self} (q_i) + \sum_{j>i} [E_{ij}^{short} (r_{ij}, q_i, q_j) + E_{ij}^{Coul} (r_{ij}, q_i, q_j)] + \\ - & E^{polar} (q_i, r_{ij}) + E^{vdW} (r_{ij}) + E^{barr} (q_i) + E^{corr} (r_{ij}, \theta_{jik})] + & E^{polar} (q_i, r_{ij}) + E^{vdW} (r_{ij}) + E^{barr} (q_i) + E^{corr} (r_{ij}, \theta_{jik})] where :math:`E_i^{self}` is the self-energy of atom *i* (including diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index c29dda8224..b92d7bb3e4 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -46,7 +46,7 @@ Style *cosine/squared* computes a potential of the form .. math:: - E = + E = \begin{cases} -\epsilon& \quad r < \sigma \\ -\epsilon\cos\left(\frac{\pi\left(r - \sigma\right)}{2\left(r_c - \sigma\right)}\right)&\quad \sigma \leq r < r_c \\ @@ -72,7 +72,7 @@ specifically the following: .. math:: - E = \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + E = \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 2\left(\frac{\sigma}{r}\right)^6 + 1\right] , \quad r < \sigma diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index ac4aa4e8d5..59a95db2a6 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -174,8 +174,8 @@ shifted force model described in :ref:`Fennell `, given by: .. math:: - E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + - \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c + E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + + \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c where :math:`\alpha` is the damping parameter and erfc() is the @@ -193,9 +193,9 @@ summation method, described in :ref:`Wolf `, given by: .. math:: - E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + - \frac{1}{2} \sum_{j \neq i} + E_i = \frac{1}{2} \sum_{j \neq i} + \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{1}{2} \sum_{j \neq i} \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index 47b93387d3..1c2ddd7f91 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -41,7 +41,7 @@ in the Coulomb correction term for small ion separations as follows .. math:: E = & \frac{Cq_iq_j}{\epsilon r} \left( \frac{\epsilon}{\epsilon_D(r)}-1\right) \qquad r < r_c \\ - \epsilon_D(r) = & \frac{5.2+\epsilon}{2} + \frac{\epsilon-5.2}{2}\tanh\left(\frac{r-r_{me}}{\sigma_e}\right) + \epsilon_D(r) = & \frac{5.2+\epsilon}{2} + \frac{\epsilon-5.2}{2}\tanh\left(\frac{r-r_{me}}{\sigma_e}\right) where :math:`r_{me}` is the inflection point of :math:`\epsilon_D(r)` and :math:`\sigma_e` is a slope diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 6d685f27c3..8d42371a7a 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -41,17 +41,17 @@ Syntax * cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units) * cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units) * flag\_lj = *long* or *cut* or *off* - + .. parsed-literal:: - + *long* = use long-range damping on dispersion 1/r\^6 term *cut* = use a cutoff on dispersion 1/r\^6 term *off* = omit disperion 1/r\^6 term entirely * flag\_coul = *long* or *off* - + .. parsed-literal:: - + *long* = use long-range damping on Coulombic 1/r and point-dipole terms *off* = omit Coulombic and point-dipole terms entirely @@ -92,29 +92,29 @@ interactions are computed by these formulas for the energy (E), force .. math:: - E_{LJ} = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + E_{LJ} = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \\ E_{qq} = & \frac{q_i q_j}{r} \\ E_{qp} = & \frac{q}{r^3} (p \bullet \vec{r}) \\ - E_{pp} = & \frac{1}{r^3} (\vec{p_i} \bullet \vec{p_j}) - + E_{pp} = & \frac{1}{r^3} (\vec{p_i} \bullet \vec{p_j}) - \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r}) \\ & \\ F_{qq} = & \frac{q_i q_j}{r^3} \vec{r} \\ - F_{qp} = & -\frac{q}{r^3} \vec{p} + \frac{3q}{r^5} + F_{qp} = & -\frac{q}{r^3} \vec{p} + \frac{3q}{r^5} (\vec{p} \bullet \vec{r}) \vec{r} \\ F_{pp} = & \frac{3}{r^5} (\vec{p_i} \bullet \vec{p_j}) \vec{r} - - \frac{15}{r^7} (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \bullet \vec{r}) \vec{r} + - \frac{3}{r^5} \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + + \frac{15}{r^7} (\vec{p_i} \bullet \vec{r}) + (\vec{p_j} \bullet \vec{r}) \vec{r} + + \frac{3}{r^5} \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + (\vec{p_i} \bullet \vec{r}) \vec{p_j} \right] \\ & \\ T_{pq} = T_{ij} = & \frac{q_j}{r^3} (\vec{p_i} \times \vec{r}) \\ T_{qp} = T_{ji} = & - \frac{q_i}{r^3} (\vec{p_j} \times \vec{r}) \\ - T_{pp} = T_{ij} = & -\frac{1}{r^3} (\vec{p_i} \times \vec{p_j}) + + T_{pp} = T_{ij} = & -\frac{1}{r^3} (\vec{p_i} \times \vec{p_j}) + \frac{3}{r^5} (\vec{p_j} \bullet \vec{r}) (\vec{p_i} \times \vec{r}) \\ - T_{pp} = T_{ji} = & -\frac{1}{r^3} (\vec{p_j} \times \vec{p_i}) + - \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) + T_{pp} = T_{ji} = & -\frac{1}{r^3} (\vec{p_j} \times \vec{p_i}) + + \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \times \vec{r}) @@ -151,7 +151,7 @@ potentials are computed by these formulas for the energy (E), force E_{LJ} = & 4\epsilon \left\{ \left[ \left( \frac{\sigma}{r} \right)^{\!12} - \left( \frac{\sigma}{r} \right)^{\!6} \right] + - \left[ 6\left( \frac{\sigma}{r_c} \right)^{\!12} - + \left[ 6\left( \frac{\sigma}{r_c} \right)^{\!12} - 3\left(\frac{\sigma}{r_c}\right)^{\!6}\right]\left(\frac{r}{r_c}\right)^{\!2} - 7\left( \frac{\sigma}{r_c} \right)^{\!12} + 4\left( \frac{\sigma}{r_c} \right)^{\!6}\right\} \\ @@ -163,14 +163,14 @@ potentials are computed by these formulas for the energy (E), force 3\left(\frac{r}{r_c}\right)^{\!2} + 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\ E_{pp} = & \left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right]\left[\frac{1}{r^3} - (\vec{p_i} \bullet \vec{p_j}) - \frac{3}{r^5} + 3\left(\frac{r}{r_c}\right)^{\!4}\right]\left[\frac{1}{r^3} + (\vec{p_i} \bullet \vec{p_j}) - \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})\right] \\ & \\ - - F_{LJ} = & \left\{\left[48\epsilon \left(\frac{\sigma}{r}\right)^{\!12} - - 24\epsilon \left(\frac{\sigma}{r}\right)^{\!6} \right]\frac{1}{r^2} - - \left[48\epsilon \left(\frac{\sigma}{r_c}\right)^{\!12} - 24\epsilon + + F_{LJ} = & \left\{\left[48\epsilon \left(\frac{\sigma}{r}\right)^{\!12} - + 24\epsilon \left(\frac{\sigma}{r}\right)^{\!6} \right]\frac{1}{r^2} - + \left[48\epsilon \left(\frac{\sigma}{r_c}\right)^{\!12} - 24\epsilon \left(\frac{\sigma}{r_c}\right)^{\!6} \right]\frac{1}{r_c^2}\right\}\vec{r}\\ F_{qq} = & \frac{q_i q_j}{r}\left(\frac{1}{r^2} - \frac{1}{r_c^2}\right)\vec{r} \\ @@ -178,22 +178,22 @@ potentials are computed by these formulas for the energy (E), force \left(\frac{r}{r_c}\right)^{\!2}\right](\vec{p}\bullet\vec{r})\vec{r} + \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} + 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\ - F_{qp} = & F_{ij} = \frac{3q}{r^5} \left[ 1 - + F_{qp} = & F_{ij} = \frac{3q}{r^5} \left[ 1 - \left(\frac{r}{r_c}\right)^{\!2}\right] (\vec{p}\bullet\vec{r})\vec{r} - \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} + 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\ F_{pp} = &\frac{3}{r^5}\Bigg\{\left[1-\left(\frac{r}{r_c}\right)^{\!4}\right] - \left[(\vec{p_i}\bullet\vec{p_j}) - \frac{3}{r^2} (\vec{p_i}\bullet\vec{r}) + \left[(\vec{p_i}\bullet\vec{p_j}) - \frac{3}{r^2} (\vec{p_i}\bullet\vec{r}) (\vec{p_j} \bullet \vec{r})\right] \vec{r} + \\ & \left[1 - 4\left(\frac{r}{r_c}\right)^{\!3}+3\left(\frac{r}{r_c}\right)^{\!4}\right] - \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + (\vec{p_i} \bullet \vec{r}) + \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + (\vec{p_i} \bullet \vec{r}) \vec{p_j} -\frac{2}{r^2} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})\vec{r}\right] \Bigg\} .. math:: - T_{pq} = T_{ij} = & \frac{q_j}{r^3} \left[ 1 - + T_{pq} = T_{ij} = & \frac{q_j}{r^3} \left[ 1 - 3\left(\frac{r}{r_c}\right)^{\!2} + 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p_i}\times\vec{r}) \\ T_{qp} = T_{ji} = & - \frac{q_i}{r^3} \left[ 1 - @@ -207,8 +207,8 @@ potentials are computed by these formulas for the energy (E), force T_{pp} = T_{ji} = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + 3\left(\frac{r}{r_c}\right)^{\!4}\right](\vec{p_j} \times \vec{p_i}) + \\ & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} + - 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \bullet \vec{r}) - (\vec{p_j} \times \vec{r}) + 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \bullet \vec{r}) + (\vec{p_j} \times \vec{r}) where :math:`\epsilon` and :math:`\sigma` are the standard LJ diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index fecd602c50..c66350b46d 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -107,9 +107,9 @@ energies are computed within style *dpd/fdt/energy* as: .. math:: du_{i}^{cond} = & \kappa_{ij}(\frac{1}{\theta_{i}}-\frac{1}{\theta_{j}})\omega_{ij}^{2} + \alpha_{ij}\omega_{ij}\zeta_{ij}^{q}(\Delta{t})^{-1/2} \\ - du_{i}^{mech} = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} - - \frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} - - \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2} + du_{i}^{mech} = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} - + \frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} - + \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2} where diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index 82da121a79..c428141b89 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -104,7 +104,7 @@ energy Ei of an atom I is given by .. math:: - E_i = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) + + E_i = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) + \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij}) @@ -376,8 +376,8 @@ given by .. math:: - E_i = F_\alpha \left(\sum_{j \neq i}\ - \rho_{\alpha\beta} (r_{ij})\right) + + E_i = F_\alpha \left(\sum_{j \neq i}\ + \rho_{\alpha\beta} (r_{ij})\right) + \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij}) diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index 24f1aebd74..13f0ef7fa9 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -45,7 +45,7 @@ In EDIP, the energy E of a system of atoms is \phi_{2}(r, Z) = & A\left[\left(\frac{B}{r}\right)^{\rho} - e^{-\beta Z^2}\right]exp{\left(\frac{\sigma}{r-a}\right)} \\ \phi_{3}(R_{ij}, R_{ik}, Z_i) = & exp{\left(\frac{\gamma}{R_{ij}-a}\right)}exp{\left(\frac{\gamma}{R_{ik}-a}\right)}h(cos\theta_{ijk},Z_i) \\ Z_i = & \sum_{m \ne i} f(R_{im}) \qquad - f(r) = \begin{cases} + f(r) = \begin{cases} 1 & \quad ra diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index 9a902054da..b873e9d6e4 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -13,9 +13,9 @@ Syntax * cutoff = global cutoff for Coulombic interactions * zero or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *limit/eradius* or *pressure/evirials* or *ecp* *limit/eradius* args = none *pressure/evirials* args = none @@ -226,7 +226,7 @@ representations, after the "ecp" keyword. .. math:: E_{Pauli(ECP_s)} = & p_1\exp\left(-\frac{p_2r^2}{p_3+s^2} \right) \\ - E_{Pauli(ECP_p)} = & p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right] + E_{Pauli(ECP_p)} = & p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right] Where the 1st form correspond to core interactions with s-type valence electrons and the 2nd to core interactions with p-type valence diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index 453f6f9aa8..44ba319566 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -155,7 +155,7 @@ where .. math:: \epsilon_{ab} = & \sqrt{\epsilon_{a}\epsilon_{b}} \\ - R_{m,ab} = & \frac{R_{m,a}+R_{m,b}}{2} \\ + R_{m,ab} = & \frac{R_{m,a}+R_{m,b}}{2} \\ \alpha_{ab} = & \sqrt{\alpha_{a}\alpha_{b}} diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 3a75a410b1..3548b5528a 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -72,8 +72,8 @@ The two Hookean styles use this formula: .. math:: - F_{hk} = (k_n \delta \mathbf{n}_{ij} - - m_{eff} \gamma_n\mathbf{ v}_n) - + F_{hk} = (k_n \delta \mathbf{n}_{ij} - + m_{eff} \gamma_n\mathbf{ v}_n) - (k_t \mathbf{ \Delta s}_t + m_{eff} \gamma_t \mathbf{v}_t) @@ -82,9 +82,9 @@ The Hertzian style uses this formula: .. math:: - F_{hz} = \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}} F_{hk} = - \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}} - \Big[ (k_n \delta \mathbf{n}_{ij} - + F_{hz} = \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}} F_{hk} = + \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}} + \Big[ (k_n \delta \mathbf{n}_{ij} - m_{eff} \: \gamma_n \mathbf{ v}_n) - (k_t \mathbf{ \Delta s}_t + m_{eff} \: \gamma_t \mathbf{v}_t) \Big] diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index fd309c25a0..4a4d482282 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -66,7 +66,7 @@ the coarse-grained models of :ref:`(Marrink) `. .. math:: - E_{LJ} = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + E_{LJ} = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + S_{LJ}(r) \qquad r < r_c \\ E_C = & \frac{C q_i q_j}{\epsilon r} + S_C(r) \qquad r < r_c \\ diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 1deaf35c39..1f4f179623 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -55,10 +55,10 @@ force field, given by: \epsilon\left\lbrace 5\left[ \frac{\sigma}{r}\right]^{12}- 6\left[ \frac{\sigma}{r}\right]^{10} \right\rbrace cos^n\theta\\ Morse(r) = & D_0\left\lbrace \chi^2 - 2\chi\right\rbrace cos^n\theta= - D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} + D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right\rbrace cos^n\theta \\ - S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 - \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} + S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 + \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index a727d87eb6..ef1207fffe 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -43,8 +43,8 @@ in :ref:`(Kolmogorov) `. .. math:: E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} - \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - + V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\ \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ @@ -96,7 +96,7 @@ list for calculating the normals for each atom pair. .. note:: - Four new sets of parameters of ILP for 2D layered Materials with bilayer and + Four new sets of parameters of ILP for 2D layered Materials with bilayer and bulk configurations are presented in :ref:`(Ouyang1) ` and :ref:`(Ouyang2) `, respectively. These parameters provide a good description in both short- and long-range interaction regimes. While the old ILP parameters published in :ref:`(Leven2) ` and diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst index 2dd5ec44de..f70c2f76b1 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -50,9 +50,9 @@ The format of the list file is as follows: * empty lines will be ignored * comment text starts with a '#' character * line syntax: *ID1 ID2 style coeffs cutoff* - + .. parsed-literal:: - + ID1 = atom ID of first atom ID2 = atom ID of second atom style = style of interaction diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 7f97913be6..e2bffb4531 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -213,7 +213,7 @@ given by .. math:: - E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c @@ -250,9 +250,9 @@ shifted force model described in :ref:`Fennell `, given by: .. math:: - E = - q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + - \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c + E = + q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + + \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c where :math:`\alpha` is the damping parameter and erfc() is the complementary @@ -281,9 +281,9 @@ summation method, described in :ref:`Wolf `, given by: .. math:: - E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + - \frac{1}{2} \sum_{j \neq i} + E_i = \frac{1}{2} \sum_{j \neq i} + \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{1}{2} \sum_{j \neq i} \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 2f2dcc76e4..2bb914c0b2 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -37,7 +37,7 @@ of the standard 12/6 potential, given by .. math:: - E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} - + E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index f975a65524..5ef497cf6e 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -43,7 +43,7 @@ the energy and force are zero. E & = u_{LJ}(r) \qquad r \leq r_s \\ & = u_{LJ}(r_s) + (r-r_s) u'_{LJ}(r_s) - \frac{1}{6} A_3 (r-r_s)^3 \qquad r_s < r \leq r_c \\ - & = 0 \qquad r > r_c + & = 0 \qquad r > r_c The location of the inflection point :math:`r_s` is defined diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 8d69c760ad..113080ea1e 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -53,7 +53,7 @@ formula: .. math:: - E = 4 \epsilon \left[ \left(\frac{\sigma}{r - \Delta}\right)^{12} - + E = 4 \epsilon \left[ \left(\frac{\sigma}{r - \Delta}\right)^{12} - \left(\frac{\sigma}{r - \Delta}\right)^6 \right] \qquad r < r_c + \Delta diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index 628eb40664..ac7b6c4c50 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -79,7 +79,7 @@ Style *lj/long/coul/long* computes the standard 12/6 Lennard-Jones potential: .. math:: - E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c \\ diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index d4be64fcc1..681425acc0 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -35,10 +35,10 @@ applied between the inner and outer cutoff. .. math:: - E & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + E & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_{in} \\ - F & = C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3 + F & = C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3 \qquad r_{in} < r < r_c diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index 42da051b57..bf15205fad 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -37,9 +37,9 @@ continuously to zero at the cutoff Rc :ref:`(Toxvaerd) `: .. math:: - \phi\left(r\right) & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + \phi\left(r\right) & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \\ - E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c + E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c The following coefficients must be defined for each pair of atoms diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst index af317ac99c..7aa570925a 100644 --- a/doc/src/pair_local_density.rst +++ b/doc/src/pair_local_density.rst @@ -22,34 +22,34 @@ Examples pair_style local/density benzene_water.localdensity.table - pair_style hybrid/overlay table spline 500 local/density + pair_style hybrid/overlay table spline 500 local/density pair_coeff * * local/density benzene_water.localdensity.table Description """"""""""" -The local density (LD) potential is a mean-field manybody potential, and, in some -sense,a generalization of embedded atom models (EAM). The name "local density -potential" arises from the fact that it assigns an energy to an atom depending -on the number of neighboring atoms of given type around it within a predefined +The local density (LD) potential is a mean-field manybody potential, and, in some +sense,a generalization of embedded atom models (EAM). The name "local density +potential" arises from the fact that it assigns an energy to an atom depending +on the number of neighboring atoms of given type around it within a predefined spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG) -literature suggests that such potentials can be widely useful in capturing -effective multibody forces in a computationally efficient manner so as to -improve the quality of CG models of implicit solvation:ref:`(Sanyal1) ` and -phase-segregation in liquid mixtures:ref:`(Sanyal2) `, and provide guidelines -to determine the extent of manybody correlations present in a CG -model.:ref:`(Rosenberger) ` The LD potential in LAMMPS is primarily -intended to be used as a corrective potential over traditional pair potentials -in bottom-up CG models, i.e., as a hybrid pair style with -other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.). -Because the LD potential is not a pair potential per se, it is implemented -simply as a single auxiliary file with all specifications that will be read +literature suggests that such potentials can be widely useful in capturing +effective multibody forces in a computationally efficient manner so as to +improve the quality of CG models of implicit solvation:ref:`(Sanyal1) ` and +phase-segregation in liquid mixtures:ref:`(Sanyal2) `, and provide guidelines +to determine the extent of manybody correlations present in a CG +model.:ref:`(Rosenberger) ` The LD potential in LAMMPS is primarily +intended to be used as a corrective potential over traditional pair potentials +in bottom-up CG models, i.e., as a hybrid pair style with +other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.). +Because the LD potential is not a pair potential per se, it is implemented +simply as a single auxiliary file with all specifications that will be read upon initialization. .. note:: - Thus when used as the only interaction in the system, there is no - corresponding pair\_coeff command and when used with other pair styles using the + Thus when used as the only interaction in the system, there is no + corresponding pair\_coeff command and when used with other pair styles using the hybrid/overlay option, the corresponding pair\_coeff command must be supplied \* \* as placeholders for the atom types. @@ -84,24 +84,24 @@ function has proven sufficiently general: :ref:`(Sanyal1) `, .. math:: - \varphi(r) = + \varphi(r) = \begin{cases} 1 & r \le R_1 \\ c_0 + c_2r^2 + c_4r^4 + c_6r^6 & r \in (R_1, R_2) \\ 0 & r \ge R_2 \end{cases} -The constants *c* are chosen so that the indicator function smoothly -interpolates between 1 and 0 between the distances R1 and R2, which are -called the inner and outer cutoffs, respectively. Thus phi satisfies -phi(R1) = 1, phi(R2) = dphi/dr @ (r=R1) = dphi/dr @ (r=R2) = 0. The embedding -function F(rho) may or may not have a closed-form expression. To maintain -generality, it is practically represented with a spline-interpolated table -over a predetermined range of rho. Outside of that range it simply adopts zero +The constants *c* are chosen so that the indicator function smoothly +interpolates between 1 and 0 between the distances R1 and R2, which are +called the inner and outer cutoffs, respectively. Thus phi satisfies +phi(R1) = 1, phi(R2) = dphi/dr @ (r=R1) = dphi/dr @ (r=R2) = 0. The embedding +function F(rho) may or may not have a closed-form expression. To maintain +generality, it is practically represented with a spline-interpolated table +over a predetermined range of rho. Outside of that range it simply adopts zero values at the endpoints. -It can be shown that the total force between two atoms due to the LD potential -takes the form of a pair force, which motivates its designation as a LAMMPS +It can be shown that the total force between two atoms due to the LD potential +takes the form of a pair force, which motivates its designation as a LAMMPS pair style. Please see :ref:`(Sanyal1) ` for details of the derivation. @@ -146,14 +146,14 @@ which atom types to use in the calculation of the LD; :math:`b_{\beta} = **General form for implementation in LAMMPS:** -Of course, a system with many atom types may have many different possible LD -potentials, each with their own atom type filters, cutoffs, and embedding -functions. The most general form of this potential as implemented in the +Of course, a system with many atom types may have many different possible LD +potentials, each with their own atom type filters, cutoffs, and embedding +functions. The most general form of this potential as implemented in the pair\_style local/density is: .. math:: - U_{LD} = \sum_k U_{LD}^{(k)} = \sum_i \left[ \sum_k a_\alpha^{(k)} F^{(k)} \left(\rho_i^{(k)}\right) \right] + U_{LD} = \sum_k U_{LD}^{(k)} = \sum_i \left[ \sum_k a_\alpha^{(k)} F^{(k)} \left(\rho_i^{(k)}\right) \right] where, *k* is an index that spans the (arbitrary) number of applied LD @@ -164,9 +164,9 @@ potentials N\_LD. Each LD is calculated as before with: \rho_i^{(k)} = \sum_j b_\beta^{(k)} \varphi^{(k)} (r_{ij}) -The superscript on the indicator function phi simply indicates that it is -associated with specific values of the cutoff distances R1(k) and R2(k). In -summary, there may be N\_LD distinct LD potentials. With each potential type (k), +The superscript on the indicator function phi simply indicates that it is +associated with specific values of the cutoff distances R1(k) and R2(k). In +summary, there may be N\_LD distinct LD potentials. With each potential type (k), one must specify: * the inner and outer cutoffs as R1 and R2 @@ -202,9 +202,9 @@ one must specify: Block N_LD -Lines 5 to 9+N\_rho constitute the first block. Thus the input file is separated -(by blank lines) into N\_LD blocks each representing a separate LD potential and -each specifying its own upper and lower cutoffs, central and neighbor atoms, +Lines 5 to 9+N\_rho constitute the first block. Thus the input file is separated +(by blank lines) into N\_LD blocks each representing a separate LD potential and +each specifying its own upper and lower cutoffs, central and neighbor atoms, and potential. In general, blank lines anywhere are ignored. ---------- diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index 6e2cefd091..d97ba80fe9 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -53,8 +53,8 @@ Ball-Melrose lubrication terms via the formulas in :ref:`(Ball and Melrose) ` and +and implementation details, the reader is referred to the +original papers :ref:`(Volkov1) ` and :ref:`(Volkov2) `. -The potential requires tabulated data provided in a single ASCII -text file specified in the :doc:`pair_coeff ` command. +The potential requires tabulated data provided in a single ASCII +text file specified in the :doc:`pair_coeff ` command. The first line of the file provides a time stamp and general information. The second line lists four integers giving the number of data points provided in the subsequent four -data tables. The third line lists four floating point numbers: -the CNT radius R, the LJ parameter sigma and two numerical +data tables. The third line lists four floating point numbers: +the CNT radius R, the LJ parameter sigma and two numerical parameters delta1 and delta2. These four parameters are given in Angstroms. This is followed by four data tables each separated by a single empty line. The first two tables have two columns @@ -66,11 +66,11 @@ array and list the parameters Phi and uSemiParallel respectively. uInfParallel and uSemiParallel are given in eV/Angstrom, Phi is given in eV and Gamma is unitless. -Potential files for CNTs can be readily generated using the freely +Potential files for CNTs can be readily generated using the freely available code provided on .. parsed-literal:: - + https://github.com/phankl/cntpot Using the same approach, it should also be possible to @@ -89,7 +89,7 @@ boron nitride nanotubes. The *mesocnt* style requires CNTs to be represented as a chain of atoms connected by bonds. Atoms need - to be numbered consecutively within one chain. + to be numbered consecutively within one chain. Atoms belonging to different CNTs need to be assigned different molecule IDs. @@ -108,7 +108,7 @@ This pair style does not support mixing. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. -The *mesocnt* pair style do not write their information to :doc:`binary restart files `, +The *mesocnt* pair style do not write their information to :doc:`binary restart files `, since it is stored in tabulated potential files. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. @@ -152,5 +152,5 @@ Related commands -**(Volkov2)** Volkov, Simov and Zhigilei, APS Meeting Abstracts, +**(Volkov2)** Volkov, Simov and Zhigilei, APS Meeting Abstracts, Q31.013 (2008). diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index f51b1b4a2c..c5cf52330d 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -22,9 +22,9 @@ Syntax * style = *edpd* or *mdpd* or *mdpd/rhosum* or *tdpd* * args = list of arguments for a particular style - + .. parsed-literal:: - + *edpd* args = cutoff seed cutoff = global cutoff for eDPD interactions (distance units) seed = random # seed (integer) (if <= 0, eDPD will use current time as the seed) diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 3d33d7da26..67078252da 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -35,9 +35,9 @@ elemental bulk material in the form .. math:: - E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega ) - + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega ) - + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega ) + E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega ) + + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega ) + + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega ) + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega ) diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index 2b294574b1..ab683f321c 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -43,7 +43,7 @@ vdW potential :ref:`(Allinger) ` .. math:: E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\ - r_{v,ij} & = r_{v,i} + r_{v,j} \\ + r_{v,ij} & = r_{v,i} + r_{v,j} \\ \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j} diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index 5c78b93716..63622623cf 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -13,11 +13,11 @@ Syntax * one or more keyword/value pairs may be listed * keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner* - or *tabinner/disp* or *tail* or *compute* or *nofdotr* or *special* or + or *tabinner/disp* or *tail* or *compute* or *nofdotr* or *special* or *compute/tally* - + .. parsed-literal:: - + *pair* value = sub-style N sub-style = sub-style of :doc:`pair hybrid ` N = which instance of sub-style (1 to M), only specify if sub-style is used multiple times diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 121d4fbc76..a9abebc982 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -89,7 +89,7 @@ so that both, potential energy and force, go to zero at the cut-off: .. math:: \phi\left(r\right) & = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c \\ - E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c + E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c The syntax of the pair\_style and pair\_coeff commands are the same for diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index 39b641361e..26b681e08b 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -32,8 +32,8 @@ the many-body form described in :ref:`(Moore) ` and .. math:: - F_{i}^{DD}(\rho_i,\rho_j,r_{ij}) = \frac{1}{2} \omega_{DD}\left(r_{ij}\right) - \left[A\left(\rho_i\right) + A\left(\rho_j\right)\right]e_{ij} + F_{i}^{DD}(\rho_i,\rho_j,r_{ij}) = \frac{1}{2} \omega_{DD}\left(r_{ij}\right) + \left[A\left(\rho_i\right) + A\left(\rho_j\right)\right]e_{ij} which consists of a density-dependent function, :math:`A(\rho)`, and a diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index e057b184f7..a197fc1ec1 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -45,8 +45,8 @@ following from the many-body form described in :ref:`(Moore) ` and .. math:: - F_{i}^{DD}(\rho_i,\rho_j,r_{ij}) = \frac{1}{2} \omega_{DD}\left(r_{ij}\right) - \left[A\left(\rho_i\right) + A\left(\rho_j\right)\right]e_{ij} + F_{i}^{DD}(\rho_i,\rho_j,r_{ij}) = \frac{1}{2} \omega_{DD}\left(r_{ij}\right) + \left[A\left(\rho_i\right) + A\left(\rho_j\right)\right]e_{ij} which consists of a density-dependent function, :math:`A(\rho)`, and a diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index 48a7038fb2..b1c3e5c077 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -28,7 +28,7 @@ energy E of a system of atoms as .. math:: - E = K (\theta - \theta_0)^2 + E = K (\theta - \theta_0)^2 where :math:`\theta_0` is the equilibrium value of the angle and *K* is a diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index 27bb11fe65..49761afc6b 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -28,9 +28,9 @@ Syntax * style = *nm/cut* or *nm/cut/coul/cut* or *nm/cut/coul/long* * args = list of arguments for a particular style - + .. parsed-literal:: - + *nm/cut* args = cutoff cutoff = global cutoff for Pair interactions (distance units) *nm/cut/coul/cut* args = cutoff (cutoff2) diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index f24520f473..b34515868c 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -66,9 +66,9 @@ excluded volume interaction *oxdna/excv*\ , the stacking *oxdna/stk*\ , cross-st 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 -are supported :ref:`(Sulc) `. Quasi-unique base-pairing between nucleotides can be achieved by using -more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. -This prevents the hybridization of in principle complementary bases within Ntypes/4 bases +are supported :ref:`(Sulc) `. Quasi-unique base-pairing between nucleotides can be achieved by using +more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. +This prevents the hybridization of in principle complementary bases within Ntypes/4 bases up and down along the backbone. The exact functional form of the pair styles is rather complex. @@ -100,7 +100,7 @@ on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found `here `_. Please cite also the relevant oxDNA publications -:ref:`(Ouldridge) `, +:ref:`(Ouldridge) `, :ref:`(Ouldridge-DPhil) ` and :ref:`(Sulc) `. @@ -122,7 +122,7 @@ Related commands :doc:`bond_style oxdna2/fene `, :doc:`pair_style oxdna2/excv `, :doc:`bond_style oxrna2/fene `, :doc:`pair_style oxrna2/excv `, :doc:`fix nve/dotc/langevin ` - + **Default:** none diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 368a203b8a..6897eb859f 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -74,9 +74,9 @@ excluded volume interaction *oxdna2/excv*\ , the stacking *oxdna2/stk*\ , cross- 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 -more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. -This prevents the hybridization of in principle complementary bases within Ntypes/4 bases +are supported :ref:`(Sulc) `. Quasi-unique base-pairing between nucleotides can be achieved by using +more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. +This prevents the hybridization of in principle complementary bases within Ntypes/4 bases up and down along the backbone. The exact functional form of the pair styles is rather complex. diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 38e77e3368..ebaf085341 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -41,7 +41,7 @@ Syntax T = temperature (oxDNA units, 0.1 = 300 K) xi = 1.40206 (temperature-independent coefficient in stacking strength) kappa = 2.77 (coefficient of linear temperature dependence in stacking strength) - *oxrna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + *oxrna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) eps = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs) *oxrna2/dh* args = T rhos qeff @@ -75,9 +75,9 @@ excluded volume interaction *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross- 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 -more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. -This prevents the hybridization of in principle complementary bases within Ntypes/4 bases +are supported :ref:`(Sulc2) `. Quasi-unique base-pairing between nucleotides can be achieved by using +more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. +This prevents the hybridization of in principle complementary bases within Ntypes/4 bases up and down along the backbone. The exact functional form of the pair styles is rather complex. diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index b19f3b9f3b..22d262e288 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -64,9 +64,9 @@ Stillinger-Weber potential (:ref:`SW `) if we set \left\{\begin{array}{l} \eta_{ij} = \delta_{ij},\xi_{IJ}=0 \\ U_{IJ}\left(r\right)=A_{IJ}\cdot\epsilon_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^q\cdot \left[B_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^{p-q}-1\right]\cdot exp\left(\frac{\sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ - V_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ + V_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ F_{IJ}\left(X\right)=-X \\ - P_{IJ}\left(\Delta r\right)=1 \\ + P_{IJ}\left(\Delta r\right)=1 \\ W_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ G_{JIK}\left(\theta\right)=\left(cos\theta+\frac{1}{3}\right)^2 \end{array}\right. @@ -82,7 +82,7 @@ The potential reduces to Tersoff types of potential U_{IJ}\left(r\right)=\frac{D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{2S_{IJ}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\ V_{IJ}\left(r\right)=\frac{S_{IJ}\cdot D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{\frac{2}{S_{IJ}}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\ F_{IJ}\left(X\right)=\left(1+X\right)^{-\frac{1}{2}} \\ - P_{IJ}\left(\Delta r\right)=exp\left(2\mu_{IK}\cdot \Delta r\right) \\ + P_{IJ}\left(\Delta r\right)=exp\left(2\mu_{IK}\cdot \Delta r\right) \\ W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\ G_{JIK}\left(\theta\right)=\gamma_{IK}\left[1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}\right] \end{array}\right. @@ -114,7 +114,7 @@ The potential reduces to Rockett-Tersoff (:ref:`Wang `) type if we set B_{IJ} \cdot exp\left(-\lambda_{2,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right)+A_{IJ}\cdot exp\left(-\lambda_{1,IJ}\cdot r\right)\cdot & \\ ~~~~~~ f_{c,IJ}\left(r\right) & r \ge r_{c,1,IJ} \end{array}\right. \\ F_{IJ}\left(X\right)=\left[1+\left(\beta_{IJ}\cdot X\right)^{n_{IJ}}\right]^{-\frac{1}{2n_{IJ}}} \\ - P_{IJ}\left(\Delta r\right)=exp\left(\lambda_{3,IK}\cdot \Delta r^3\right) \\ + P_{IJ}\left(\Delta r\right)=exp\left(\lambda_{3,IK}\cdot \Delta r^3\right) \\ W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\ G_{JIK}\left(\theta\right)=1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2} \end{array}\right. @@ -147,7 +147,7 @@ The potential becomes embedded atom method (:ref:`Daw `) if we set U_{IJ}\left(r\right)=\phi_{IJ}\left(r\right) \\ V_{IJ}\left(r\right)=1 \\ F_{II}\left(X\right)=-2F_I\left(X\right) \\ - P_{IJ}\left(\Delta r\right)=1 \\ + P_{IJ}\left(\Delta r\right)=1 \\ W_{IJ}\left(r\right)=f_{K}\left(r\right) \\ G_{JIK}\left(\theta\right)=1 \end{array}\right. diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index 23c83ed52e..f848cba6dc 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -86,7 +86,7 @@ The python potential file has to start with the following code: .. code-block:: python from __future__ import print_function - + class LAMMPSPairPotential(object): def __init__(self): self.pmap=dict() diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index ee5eb878c8..e9196fc4b3 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -19,9 +19,9 @@ Syntax * cfile = NULL or name of a control file * zero or more keyword/value pairs may be appended - + .. parsed-literal:: - + keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* *checkqeq* value = *yes* or *no* = whether or not to require qeq/reax fix *enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index ba28262813..9c17abb862 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -72,14 +72,14 @@ given by .. math:: - E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} - - \left(\frac{\sigma}{r}\right)^6 \right] + E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} - + \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c \\ - E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^4 \right] + E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + \left(\frac{\sigma}{r}\right)^4 \right] \qquad r < r_c \\ - E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] + E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index b3ce8d7c5d..bccf53344a 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -62,7 +62,7 @@ pair\_coeff command should then be used: pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti -The electrostatic part of the energy consists of two components +The electrostatic part of the energy consists of two components self-energy of atom *i* in the form of a second order charge dependent polynomial and a long-range Coulombic electrostatic interaction. The @@ -94,7 +94,7 @@ ffield.SMTBQ.Syst. The energy band term is given by: .. math:: E_{cov}^{i(i=M,O)} & = - \biggl\{\eta_i(\mu \xi^{0})^2 f_{cut}^{r_{c1}r_{c2}}(r_{ij}) - \biggl( \sum_{j(j=O,M)}{ exp[ -2q(\frac{r_{ij}}{r_0} - 1)] } \biggr) + \biggl( \sum_{j(j=O,M)}{ exp[ -2q(\frac{r_{ij}}{r_0} - 1)] } \biggr) \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 | @@ -162,7 +162,7 @@ quotation marks (''). 2) Atomic parameters -For the anion (oxygen) +For the anion (oxygen) * Name of element (char) and stoichiometry in oxide * Formal charge and mass of element @@ -240,7 +240,7 @@ For each cations (metal): * Parameter if necessary * Divider line -9) Verbose +9) Verbose * If you want the code to work in verbose mode or not : 'true' or 'false' * If you want to print or not in the file 'Energy\_component.txt' the diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 32c092ee69..815b1614be 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -153,7 +153,7 @@ The default values for these keywords are * *chunksize* = 2000 The keyword *chunksize* is only applicable when using the -pair style *snap* with the KOKKOS package and is ignored otherwise. +pair style *snap* with the KOKKOS package and is ignored otherwise. This keyword controls the number of atoms in each pass used to compute the bispectrum components and is used to avoid running out of memory. For example @@ -161,8 +161,8 @@ if there are 4000 atoms in the simulation and the *chunksize* is set to 2000, the bispectrum calculation will be broken up into two passes. -Detailed definitions for all the other keywords -are given on the :doc:`compute sna/atom ` doc page. +Detailed definitions for all the other keywords +are given on the :doc:`compute sna/atom ` doc page. If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term, 0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix. The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index d1d35f9b8d..ddd678a860 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -44,15 +44,15 @@ vector omega and mechanical force between particles I and J. .. math:: - \mathcal{H}_{\rm long} & = - -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi} + \mathcal{H}_{\rm long} & = + -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi} \sum_{i,j,i\neq j}^{N} \frac{g_i g_j}{r_{ij}^3} - \biggl(3 - \left(\vec{e}_{ij}\cdot \vec{s}_{i}\right) - \left(\vec{e}_{ij}\cdot \vec{s}_{j}\right) + \biggl(3 + \left(\vec{e}_{ij}\cdot \vec{s}_{i}\right) + \left(\vec{e}_{ij}\cdot \vec{s}_{j}\right) -\vec{s}_i\cdot\vec{s}_j \biggr) \\ - \mathbf{\omega}_i & = + \mathbf{\omega}_i & = \frac{\mu_0 (\mu_B)^2}{4\pi\hbar}\sum_{j} \frac{g_i g_j}{r_{ij}^3} \, \biggl( @@ -61,7 +61,7 @@ vector omega and mechanical force between particles I and J. \mathbf{F}_i & = \frac{3\, \mu_0 (\mu_B)^2}{4\pi} \sum_j \frac{g_i g_j}{r_{ij}^4} - \biggl[\bigl( (\vec{s}_i\cdot\vec{s}_j) + \biggl[\bigl( (\vec{s}_i\cdot\vec{s}_j) -5(\vec{e}_{ij}\cdot\vec{s}_i) (\vec{e}_{ij}\cdot\vec{s}_j)\bigr) \vec{e}_{ij}+ \bigl( diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 6ef65dfa93..26df9a86ed 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -32,9 +32,9 @@ the following DM energy: .. math:: - \mathbf{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N} + \mathbf{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N} \left( \vec{e}_{ij} \times \vec{D} \right) - \cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right), + \cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right), where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two neighboring magnetic spins of two particles, :math:`\vec{e}_ij = \frac{r_i - r_j}{\left| r_i - r_j \right|}` @@ -52,9 +52,9 @@ particle i: .. math:: - \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right) + \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right) ~~{\rm and}~~ - \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right) + \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right) More details about the derivation of these torques/forces are reported in :ref:`(Tranchida) `. diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index b2ad9a8f69..bd3a811f7f 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -32,11 +32,11 @@ pairs of magnetic spins: .. math:: - H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j + H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two neighboring magnetic spins of two particles, :math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance between the two -particles. The summation is over pairs of nearest neighbors. +particles. The summation is over pairs of nearest neighbors. :math:`J(r_{ij})` is a function defining the intensity and the sign of the exchange interaction for different neighboring shells. This function is defined as: @@ -60,10 +60,10 @@ such as: .. math:: - \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} - \left(r_{ij} \right)\,\vec{s}_{j} - ~~{\rm and}~~ - \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij} + \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} + \left(r_{ij} \right)\,\vec{s}_{j} + ~~{\rm and}~~ + \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij} with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij} = \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit vector between sites :math:`i` and :math:`j`. diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index 39ece6ea97..52f68da9f7 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -40,13 +40,13 @@ potential for the energy E of a system of atoms as .. math:: - E & = \sum_i \sum_{j > i} \phi_2 (r_{ij}) + - \sum_i \sum_{j \neq i} \sum_{k > j} + E & = \sum_i \sum_{j > i} \phi_2 (r_{ij}) + + \sum_i \sum_{j \neq i} \sum_{k > j} \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) \\ - \phi_2(r_{ij}) & = A_{ij} \epsilon_{ij} \left[ B_{ij} (\frac{\sigma_{ij}}{r_{ij}})^{p_{ij}} - - (\frac{\sigma_{ij}}{r_{ij}})^{q_{ij}} \right] + \phi_2(r_{ij}) & = A_{ij} \epsilon_{ij} \left[ B_{ij} (\frac{\sigma_{ij}}{r_{ij}})^{p_{ij}} - + (\frac{\sigma_{ij}}{r_{ij}})^{q_{ij}} \right] \exp \left( \frac{\sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) \\ - \phi_3(r_{ij},r_{ik},\theta_{ijk}) & = \lambda_{ijk} \epsilon_{ijk} \left[ \cos \theta_{ijk} - + \phi_3(r_{ij},r_{ik},\theta_{ijk}) & = \lambda_{ijk} \epsilon_{ijk} \left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2 \exp \left( \frac{\gamma_{ij} \sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) \exp \left( \frac{\gamma_{ik} \sigma_{ik}}{r_{ik} - a_{ik} \sigma_{ik}} \right) diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 655a4bb47a..183c149a11 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -64,7 +64,7 @@ The *tersoff* style computes a 3-body Tersoff potential b_{ij} & = \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\ \zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk}) \exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\ - g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} - + g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} - \frac{c^2}{\left[ d^2 + (\cos \theta - \cos \theta_0)^2\right]} \right) diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index 19cbafa192..be7cfcc331 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -62,7 +62,7 @@ system of atoms as b_{ij} & = \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\ \zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk}) \exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\ - g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} - + g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} - \frac{c^2}{\left[ d^2 + (\cos \theta - \cos \theta_0)^2\right]} \right) diff --git a/doc/src/prd.rst b/doc/src/prd.rst index 212439ddce..d6cda1ac28 100644 --- a/doc/src/prd.rst +++ b/doc/src/prd.rst @@ -20,9 +20,9 @@ Syntax * random\_seed = random # seed (positive integer) * zero or more keyword/value pairs may be appended * keyword = *min* or *temp* or *vel* - + .. parsed-literal:: - + *min* values = etol ftol maxiter maxeval etol = stopping tolerance for energy, used in quenching ftol = stopping tolerance for force, used in quenching diff --git a/doc/src/print.rst b/doc/src/print.rst index 93534ba9b5..cbb042b7d9 100644 --- a/doc/src/print.rst +++ b/doc/src/print.rst @@ -14,9 +14,9 @@ Syntax * string = text string to print, which may contain variables * zero or more keyword/value pairs may be appended * keyword = *file* or *append* or *screen* or *universe* - + .. parsed-literal:: - + *file* value = filename *append* value = filename *screen* value = *yes* or *no* diff --git a/doc/src/processors.rst b/doc/src/processors.rst index 2b30653167..e9c3175df6 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -14,9 +14,9 @@ Syntax * Px,Py,Pz = # of processors in each dimension of 3d grid overlaying the simulation domain * zero or more keyword/arg pairs may be appended * keyword = *grid* or *map* or *part* or *file* - + .. parsed-literal:: - + *grid* arg = gstyle params ... gstyle = *onelevel* or *twolevel* or *numa* or *custom* onelevel params = none diff --git a/doc/src/python.rst b/doc/src/python.rst index a92b2d8446..64d0c8e459 100644 --- a/doc/src/python.rst +++ b/doc/src/python.rst @@ -13,9 +13,9 @@ Syntax * func = name of Python function * one or more keyword/args pairs must be appended - + .. parsed-literal:: - + keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists* or *source* *invoke* arg = none = invoke the previously defined Python function *input* args = N i1 i2 ... iN diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index ea36675bc6..abdb838c57 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -6,7 +6,7 @@ read_data command Syntax """""" - + .. code-block:: LAMMPS read_data file keyword args ... @@ -14,9 +14,9 @@ Syntax * file = name of data file to read in * zero or more keyword/arg pairs may be appended * keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *group* or *nocoeff* or *fix* - + .. parsed-literal:: - + *add* arg = *append* or *IDoffset* or *IDoffset MOLoffset* or *merge* append = add new atoms with atom IDs appended to current IDs IDoffset = add new atoms with atom IDs having IDoffset added @@ -493,16 +493,16 @@ Atoms section: * one line per angle type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = angle type (1-N) coeffs = list of coeffs * example: - + .. parsed-literal:: - + 6 70 108.5 0 0 @@ -521,9 +521,9 @@ input script. * one line per improper type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = improper type (1-N) coeffs = list of coeffs (see :doc:`improper_coeff `) @@ -537,9 +537,9 @@ input script. * one line per dihedral type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = dihedral type (1-N) coeffs = list of coeffs (see :doc:`dihedral_coeff `) @@ -553,17 +553,17 @@ input script. * one line per angle * line syntax: ID type atom1 atom2 atom3 - + .. parsed-literal:: - + ID = number of angle (1-Nangles) type = angle type (1-Nangletype) atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle example: - + .. parsed-literal:: - + 2 2 17 29 430 @@ -582,9 +582,9 @@ integers (1, not 1.0). * one line per dihedral type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = dihedral type (1-N) coeffs = list of coeffs (see :doc:`dihedral_coeff `) @@ -849,26 +849,26 @@ script. * one or more lines per body * first line syntax: atom-ID Ninteger Ndouble - + .. parsed-literal:: - + Ninteger = # of integer quantities for this particle Ndouble = # of floating-point quantities for this particle * 0 or more integer lines with total of Ninteger values * 0 or more double lines with total of Ndouble values * example: - + .. parsed-literal:: - + 12 3 6 2 3 2 1.0 2.0 3.0 1.0 2.0 4.0 * example: - + .. parsed-literal:: - + 12 0 14 1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0 2.0 4.0 4.0 2.0 @@ -904,16 +904,16 @@ The *Bodies* section must appear after the *Atoms* section. * one line per bond type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = bond type (1-N) coeffs = list of coeffs * example: - + .. parsed-literal:: - + 4 250 1.49 @@ -932,9 +932,9 @@ script. * one line per angle type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = angle type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`angle_coeff `) @@ -948,9 +948,9 @@ script. * one line per angle type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = angle type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`angle_coeff `) @@ -964,9 +964,9 @@ script. * one line per dihedral type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = dihedral type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`dihedral_coeff `) @@ -980,17 +980,17 @@ script. * one line per bond * line syntax: ID type atom1 atom2 - + .. parsed-literal:: - + ID = bond number (1-Nbonds) type = bond type (1-Nbondtype) atom1,atom2 = IDs of 1st,2nd atoms in bond * example: - + .. parsed-literal:: - + 12 3 17 29 @@ -1006,16 +1006,16 @@ in this section must be integers (1, not 1.0). * one line per dihedral type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = dihedral type (1-N) coeffs = list of coeffs * example: - + .. parsed-literal:: - + 3 0.6 1 0 1 @@ -1034,17 +1034,17 @@ Coefficients can also be set via the * one line per dihedral * line syntax: ID type atom1 atom2 atom3 atom4 - + .. parsed-literal:: - + ID = number of dihedral (1-Ndihedrals) type = dihedral type (1-Ndihedraltype) atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral * example: - + .. parsed-literal:: - + 12 4 17 29 30 21 @@ -1061,17 +1061,17 @@ section must be integers (1, not 1.0). * one line per ellipsoid * line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk - + .. parsed-literal:: - + atom-ID = ID of atom which is an ellipsoid shapex,shapey,shapez = 3 diameters of ellipsoid (distance units) quatw,quati,quatj,quatk = quaternion components for orientation of atom * example: - + .. parsed-literal:: - + 12 1 2 1 1 0 0 0 @@ -1107,9 +1107,9 @@ The *Ellipsoids* section must appear after the *Atoms* section. * one line per dihedral type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = dihedral type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`dihedral_coeff `) @@ -1123,16 +1123,16 @@ The *Ellipsoids* section must appear after the *Atoms* section. * one line per improper type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = improper type (1-N) coeffs = list of coeffs * example: - + .. parsed-literal:: - + 2 20 0.0548311 @@ -1151,17 +1151,17 @@ Coefficients can also be set via the * one line per improper * line syntax: ID type atom1 atom2 atom3 atom4 - + .. parsed-literal:: - + ID = number of improper (1-Nimpropers) type = improper type (1-Nimpropertype) atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper * example: - + .. parsed-literal:: - + 12 3 17 29 13 100 @@ -1181,17 +1181,17 @@ values in this section must be integers (1, not 1.0). * one line per line segment * line syntax: atom-ID x1 y1 x2 y2 - + .. parsed-literal:: - + atom-ID = ID of atom which is a line segment x1,y1 = 1st end point x2,y2 = 2nd end point * example: - + .. parsed-literal:: - + 12 1.0 0.0 2.0 0.0 @@ -1218,16 +1218,16 @@ The *Lines* section must appear after the *Atoms* section. * one line per atom type * line syntax: ID mass - + .. parsed-literal:: - + ID = atom type (1-N) mass = mass value * example: - + .. parsed-literal:: - + 3 1.01 @@ -1245,9 +1245,9 @@ e.g. :doc:`atom_style sphere `. * one line per dihedral type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = dihedral type (1-N) coeffs = list of coeffs (see class 2 section of :doc:`dihedral_coeff `) @@ -1261,16 +1261,16 @@ e.g. :doc:`atom_style sphere `. * one line per atom type * line syntax: ID coeffs - + .. parsed-literal:: - + ID = atom type (1-N) coeffs = list of coeffs * example: - + .. parsed-literal:: - + 3 0.022 2.35197 0.022 2.35197 @@ -1292,17 +1292,17 @@ script. * one line per pair of atom types for all I,J with I <= J * line syntax: ID1 ID2 coeffs - + .. parsed-literal:: - + ID1 = atom type I = 1-N ID2 = atom type J = I-N, with I <= J coeffs = list of coeffs * examples: - + .. parsed-literal:: - + 3 3 0.022 2.35197 0.022 2.35197 3 5 0.022 2.35197 0.022 2.35197 @@ -1326,18 +1326,18 @@ script. * one line per triangle * line syntax: atom-ID x1 y1 z1 x2 y2 z2 x3 y3 z3 - + .. parsed-literal:: - + atom-ID = ID of atom which is a line segment x1,y1,z1 = 1st corner point x2,y2,z2 = 2nd corner point x3,y3,z3 = 3rd corner point * example: - + .. parsed-literal:: - + 12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0 diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index 5de1e8f25d..8e35030666 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -14,9 +14,9 @@ Syntax * file = name of dump file to read * Nstep = snapshot timestep to read from file * one or more fields may be appended - + .. 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 @@ -26,9 +26,9 @@ Syntax * 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* - + .. parsed-literal:: - + *nfile* value = Nfiles = how many parallel dump files exist *box* value = *yes* or *no* = replace simulation box with dump box *replace* value = *yes* or *no* = overwrite atoms with dump atoms @@ -141,16 +141,16 @@ contain multiple directories separated by a colon (or semi-colon on windows). The *path* keyword is optional and defaults to ".", i.e. the current directory. -The *adios* format supports reading data that was written by the -:doc:`dump adios ` command. The +The *adios* format supports reading data that was written by the +:doc:`dump adios ` command. The entire dump is read in parallel across all the processes, dividing the atoms evenly among the processes. The number of writers that has written the dump file does not matter. Using the adios style for -dump and read_dump is a convenient way to dump all atoms from *N* -writers and read it back by *M* readers. If one is running two -LAMMPS instances concurrently where one dumps data and the other is -reading it with the rerun command, the timeout option can be specified -to wait on the reader side for the arrival of the requested step. +dump and read_dump is a convenient way to dump all atoms from *N* +writers and read it back by *M* readers. If one is running two +LAMMPS instances concurrently where one dumps data and the other is +reading it with the rerun command, the timeout option can be specified +to wait on the reader side for the arrival of the requested step. Support for other dump format readers may be added in the future. @@ -163,16 +163,16 @@ and box information. The dump file is scanned for a snapshot with a timestamp that matches the specified *Nstep*\ . This means the LAMMPS timestep the dump file -snapshot was written on for the *native* or *adios* formats. +snapshot was written on for the *native* or *adios* formats. -The list of timestamps available in an adios .bp file is stored in the +The list of timestamps available in an adios .bp file is stored in the variable *ntimestep*: .. parsed-literal:: $ bpls dump.bp -d ntimestep - uint64_t ntimestep 5*scalar - (0) 0 50 100 150 200 + uint64_t ntimestep 5*scalar + (0) 0 50 100 150 200 Note that the *xyz* @@ -261,7 +261,7 @@ See the :doc:`dump_modify sort ` command if the dump file was written by LAMMPS. The *adios* format supports all fields that the *native* format supports -except for the *q* charge field. +except for the *q* charge field. The list of fields stored in an adios .bp file is recorded in the attributes *columns* (array of short strings) and *columnstr* (space-separated single string). diff --git a/doc/src/region.rst b/doc/src/region.rst index f1d008cbd3..2dcbd76628 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -13,9 +13,9 @@ Syntax * ID = user-assigned name for the region * style = *delete* or *block* or *cone* or *cylinder* or *plane* or *prism* or *sphere* or *union* or *intersect* - + .. parsed-literal:: - + *delete* = no args *block* args = xlo xhi ylo yhi zlo zhi xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units) @@ -51,9 +51,9 @@ Syntax * zero or more keyword/arg pairs may be appended * keyword = *side* or *units* or *move* or *rotate* or *open* - + .. parsed-literal:: - + *side* value = *in* or *out* *in* = the region is inside the specified geometry *out* = the region is outside the specified geometry diff --git a/doc/src/replicate.rst b/doc/src/replicate.rst index 94d899a459..0ae37c1415 100644 --- a/doc/src/replicate.rst +++ b/doc/src/replicate.rst @@ -11,12 +11,12 @@ Syntax replicate nx ny nz *keyword* -nx,ny,nz = replication factors in each dimension +nx,ny,nz = replication factors in each dimension * optional *keyword* = *bbox* - + .. parsed-literal:: - + *bbox* = only check atoms in replicas that overlap with a processor's sub-domain diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index aa244e7d72..9637b30c95 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -13,9 +13,9 @@ Syntax * file1,file2,... = dump file(s) to read * one or more keywords may be appended, keyword *dump* must appear and be last - + .. parsed-literal:: - + keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *dump* *first* args = Nfirst Nfirst = dump timestep to start on @@ -44,7 +44,7 @@ Examples rerun dump.vels dump x y z vx vy vz box yes format molfile lammpstrj rerun dump.dcd dump x y z box no format molfile dcd rerun ../run7/dump.file.gz skip 2 dump x y z box yes - rerun dump.bp dump x y z box no format adios + rerun dump.bp dump x y z box no format adios rerun dump.bp dump x y z vx vy vz format adios timeout 10.0 Description diff --git a/doc/src/restart.rst b/doc/src/restart.rst index 6ff78d2f97..9000b7e9c6 100644 --- a/doc/src/restart.rst +++ b/doc/src/restart.rst @@ -19,9 +19,9 @@ Syntax * file1,file2 = two full filenames, toggle between them when writing file * zero or more keyword/value pairs may be appended * keyword = *fileper* or *nfile* - + .. parsed-literal:: - + *fileper* arg = Np Np = write one file for every this many processors *nfile* arg = Nf diff --git a/doc/src/run.rst b/doc/src/run.rst index 440d21d959..46eca78d35 100644 --- a/doc/src/run.rst +++ b/doc/src/run.rst @@ -14,9 +14,9 @@ Syntax * N = # of timesteps * zero or more keyword/value pairs may be appended * keyword = *upto* or *start* or *stop* or *pre* or *post* or *every* - + .. parsed-literal:: - + *upto* value = none *start* value = N1 N1 = timestep at which 1st run started diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index 7008f6f6bf..b0d3aae553 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -12,9 +12,9 @@ Syntax run_style style args * style = *verlet* or *verlet/split* or *respa* or *respa/omp* - + .. parsed-literal:: - + *verlet* args = none *verlet/split* args = none *respa* args = N n1 n2 ... keyword values ... diff --git a/doc/src/set.rst b/doc/src/set.rst index e7f3620b0f..0cadf9d8ef 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -15,9 +15,9 @@ Syntax * ID = atom ID range or type range or mol ID range or group ID or region ID * one or more keyword/value pairs may be appended * keyword = *type* or *type/fraction* or *type/ratio* or *type/subset* or *mol* or *x* or *y* or *z* or *charge* or *dipole* or *dipole/random* or *quat* or *spin* or *spin/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or *omega* or *mass* or *density* or *density/disc* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *meso/e* or *meso/cv* or *meso/rho* or *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or *edpd/temp* or *edpd/cv* or *cc* or *i\_name* or *d\_name* - + .. parsed-literal:: - + *type* value = atom type value can be an atom-style variable (see below) *type/fraction* values = type fraction seed diff --git a/doc/src/shell.rst b/doc/src/shell.rst index 9cb94dd93f..94cc52b8bb 100644 --- a/doc/src/shell.rst +++ b/doc/src/shell.rst @@ -12,9 +12,9 @@ Syntax shell cmd args * cmd = *cd* or *mkdir* or *mv* or *rm* or *rmdir* or *putenv* or arbitrary command - + .. parsed-literal:: - + *cd* arg = dir dir = directory to change to *mkdir* args = dir1 dir2 ... diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index 8c9a082c28..536da208d3 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -13,9 +13,9 @@ Syntax * one or more keyword/value pairs may be appended * keyword = *amber* or *charmm* or *dreiding* or *fene* or *lj/coul* or *lj* or *coul* or *angle* or *dihedral* - + .. parsed-literal:: - + *amber* values = none *charmm* values = none *dreiding* values = none diff --git a/doc/src/tad.rst b/doc/src/tad.rst index 206c915e3f..ee311ef49c 100644 --- a/doc/src/tad.rst +++ b/doc/src/tad.rst @@ -20,9 +20,9 @@ Syntax * compute-ID = ID of the compute used for event detection * zero or more keyword/value pairs may be appended * keyword = *min* or *neb* or *min\_style* or *neb\_style* or *neb\_log* - + .. parsed-literal:: - + *min* values = etol ftol maxiter maxeval etol = stopping tolerance for energy (energy units) ftol = stopping tolerance for force (force units) diff --git a/doc/src/temper.rst b/doc/src/temper.rst index 018d8b9b7a..0329c069b1 100644 --- a/doc/src/temper.rst +++ b/doc/src/temper.rst @@ -123,9 +123,9 @@ manner: dump file with snapshots at 300K (from all replicas), another with snapshots at 310K, etc. Note that these new dump files will not contain "continuous trajectories" for individual atoms, because two - successive snapshots (in time) may be from different replicas. The - reorder\_remd\_traj python script can do the reordering for you - (and additionally also calculated configurational log-weights of + successive snapshots (in time) may be from different replicas. The + reorder\_remd\_traj python script can do the reordering for you + (and additionally also calculated configurational log-weights of trajectory snapshots in the canonical ensemble). The script can be found in the tools/replica directory while instructions on how to use it is available in doc/Tools (in brief) and as a README file in tools/replica diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 1fa84a40f4..163aa2c6f3 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -6,15 +6,15 @@ thermo_modify command Syntax """""" - + .. code-block:: LAMMPS thermo_modify keyword value ... * one or more keyword/value pairs may be listed - + .. parsed-literal:: - + keyword = *lost* or *lost/bond* or *norm* or *flush* or *line* or *format* or *temp* or *press*\ :l *lost* value = *error* or *warn* or *ignore* *lost/bond* value = *error* or *warn* or *ignore* diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index b093160611..ebbf98a742 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -12,9 +12,9 @@ Syntax * style = *one* or *multi* or *custom* * args = list of arguments for a particular style - + .. parsed-literal:: - + *one* args = none *multi* args = none *custom* args = list of keywords diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index 3356bd007f..ad8512d9f7 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -15,9 +15,9 @@ Syntax * style = *regular* or *eskm* * delta = finite different displacement length (distance units) * one or more keyword/arg pairs may be appended - + .. parsed-literal:: - + keyword = *file* or *binary* *file* name = name of output file for the third order tensor *binary* arg = *yes* or *no* or *gzip* diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 9aeb9dc4ba..572ae757db 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -13,9 +13,9 @@ Syntax * name = name of variable to define * style = *delete* or *index* or *loop* or *world* or *universe* or *uloop* or *string* or *format* or *getenv* or *file* or *atomfile* or *python* or *internal* or *equal* or *vector* or *atom* - + .. parsed-literal:: - + *delete* = no args *index* args = one or more strings *loop* args = N diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index 631ef80263..d111a194f1 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -13,9 +13,9 @@ Syntax * group-ID = ID of group of atoms whose velocity will be changed * style = *create* or *set* or *scale* or *ramp* or *zero* - + .. parsed-literal:: - + *create* args = temp seed temp = temperature value (temperature units) seed = random # seed (positive integer) @@ -35,9 +35,9 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *dist* or *sum* or *mom* or *rot* or *temp* or *bias* or *loop* or *units* - + .. parsed-literal:: - + *dist* value = *uniform* or *gaussian* *sum* value = *no* or *yes* *mom* value = *no* or *yes* diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index 31f4bb64ac..40c7370c2e 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -14,9 +14,9 @@ Syntax * file = name of data file to write out * zero or more keyword/value pairs may be appended * keyword = *pair* or *nocoeff* - + .. parsed-literal:: - + *nocoeff* = do not write out force field info *nofix* = do not write out extra sections read by fixes *pair* value = *ii* or *ij* diff --git a/doc/src/write_restart.rst b/doc/src/write_restart.rst index cade19c0dc..0aa036aaba 100644 --- a/doc/src/write_restart.rst +++ b/doc/src/write_restart.rst @@ -14,9 +14,9 @@ Syntax * file = name of file to write restart information to * zero or more keyword/value pairs may be appended * keyword = *fileper* or *nfile* - + .. parsed-literal:: - + *fileper* arg = Np Np = write one file for every this many processors *nfile* arg = Nf