diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index d8dd0a0531..aa41f2d488 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -87,7 +87,7 @@ commands) * water potentials: TIP3P, TIP4P, SPC * implicit solvent potentials: hydrodynamic lubrication, Debye * force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options -* access to the `OpenKIM Repository `_ of potentials via :doc:`kim\_init, kim\_interactions, and kim\_query ` commands +* access to the `OpenKIM Repository `_ of potentials via :doc:`kim_init, kim_interactions, and kim_query ` commands * hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation * overlaid potentials: superposition of multiple pair potentials diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index efdd222cf1..fc0175433b 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -927,7 +927,7 @@ Also several computes which calculate properties of rigid bodies. * src/RIGID: filenames -> commands * :doc:`compute erotate/rigid ` -* fix shake"_fix\_shake.html +* :doc:`fix shake ` * :doc:`fix rattle ` * :doc:`fix rigid/\* ` * examples/ASPHERE diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index 61e598948e..d122fceea1 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -54,19 +54,22 @@ effects, smaller timestep inaccuracy, faster equilibration and shorter decorrelation time. HMA should not be used if atoms are expected to diffuse. It is also -restricted to simulations in the NVT ensemble. While this compute may be -used with any potential in LAMMPS, it will provide inaccurate results +restricted to simulations in the NVT ensemble. While this compute may +be used with any potential in LAMMPS, it will provide inaccurate results for potentials that do not go to 0 at the truncation distance; -:doc:`pair\_lj\_smooth\_linear ` and Ewald summation should -work fine, while :doc:`pair_lj ` will perform poorly unless -the potential is shifted (via :doc:`pair_modify ` shift) or the cutoff is large. Furthermore, computation of the heat capacity with -this compute is restricted to those that implement the single\_hessian method -in Pair. Implementing single\_hessian in additional pair styles is simple. -Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at -buffalo.edu) if your desired pair style does not have this method. This is -the list of pair styles that currently implement pair\_hessian: +:doc:`pair_style lj/smooth/linear ` and Ewald +summation should work fine, while :doc:`pair_style lj/cut ` +will perform poorly unless the potential is shifted (via +:doc:`pair_modify ` shift) or the cutoff is large. +Furthermore, computation of the heat capacity with this compute is +restricted to those that implement the *single\_hessian* method in Pair. +Implementing *single\_hessian* in additional pair styles is simple. +Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke +(kofke at buffalo.edu) if your desired pair style does not have this +method. This is the list of pair styles that currently implement +*single\_hessian*: -* :doc:`lj\_smooth\_linear ` +* :doc:`pair_style lj/smooth/linear ` In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index 2a9aadc99e..b0e6b0f8f6 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -92,7 +92,7 @@ Related commands """""""""""""""" :doc:`dihedral_coeff `, -:doc:`angle\_cosine\_shift\_exp ` +:doc:`angle_style cosine/shift/exp ` **Default:** none diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 2cc3a59191..76dcfadda1 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -319,7 +319,7 @@ Restrictions Related commands """""""""""""""" -:doc:`compute fep `, :doc:`fix adapt `, :doc:`compute ti `, :doc:`pair\_fep\_soft ` +:doc:`compute fep `, :doc:`fix adapt `, :doc:`compute ti `, :doc:`pair_style \*/soft ` Default """"""" diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index ec9533788e..f066eb8e45 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -390,7 +390,7 @@ the activation energy (:doc:`units ` of energy), and *seed* is a random number seed. The temperature is defined as the instantaneous temperature averaged over all atoms in the reaction site, and is calculated in the same manner as for example -:doc:`compute\_temp\_chunk `. Currently, there are no +:doc:`compute temp/chunk `. Currently, there are no options for additional temperature averaging or velocity-biased temperature calculations. A uniform random number between 0 and 1 is generated using *seed*\ ; if this number is less than the result of the diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 7c15f5ffcb..99660ac672 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -89,14 +89,14 @@ in the LAMMPS frame. Only when the positions and velocities are updated is the system rotated to the flow frame, and it is rotated back to the LAMMPS frame immediately afterwards. For this reason, all vector-valued quantities (except for the tensors from -:doc:`compute\_pressure/uef ` and -:doc:`compute\_temp/uef `) will be computed in the +:doc:`compute pressure/uef ` and +:doc:`compute temp/uef `) will be computed in the LAMMPS frame. Rotationally invariant scalar quantities like the temperature and hydrostatic pressure are frame-invariant and will be computed correctly. Additionally, the system is in the LAMMPS frame during all of the output steps, and therefore trajectory files made using the dump command will be in the LAMMPS frame unless the -:doc:`dump\_cfg/uef ` command is used. +:doc:`dump cfg/uef ` command is used. ---------- diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index b81d0a8bf8..9cd15119bd 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -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_wall_gran.rst b/doc/src/fix_wall_gran.rst index 0db5a3e5ac..bb06aec0f6 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -89,7 +89,7 @@ The nature of the wall/particle interactions are determined by the *pair\_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the corresponding equation on the :doc:`pair_style gran/\* ` and -:doc:`pair\_style\_granular ` doc pages, in the limit of +:doc:`pair_style granular ` doc pages, in the limit of one of the two particles going to infinite radius and mass (flat wall). Specifically, delta = radius - r = overlap of particle with wall, m\_eff = mass of particle, and the effective radius of contact = diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 3ca17aa440..c2ecff8119 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -160,7 +160,7 @@ The nature of the wall/particle interactions are determined by the *pair\_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the corresponding equation on the :doc:`pair_style gran/\* ` and -:doc:`pair\_style\_granular ` doc pages, but the effective +:doc:`pair_style granular ` doc pages, but the effective radius is calculated using the radius of the particle and the radius of curvature of the wall at the contact point. diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index b90354deb0..b9426020af 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -106,34 +106,31 @@ all atoms in the system: For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force norm is replaced by the spin-torque norm. -Keywords *alpha\_damp* and *discrete\_factor* only make sense when -a :doc:`min_spin ` command is declared. -Keyword *alpha\_damp* defines an analog of a magnetic Gilbert -damping. It defines a relaxation rate toward an equilibrium for -a given magnetic system. -Keyword *discrete\_factor* defines a discretization factor for the -adaptive timestep used in the *spin* minimization. -See :doc:`min_spin ` for more information about those -quantities. +Keywords *alpha\_damp* and *discrete\_factor* only make sense when a +:doc:`min_spin ` command is declared. Keyword *alpha\_damp* +defines an analog of a magnetic Gilbert damping. It defines a relaxation +rate toward an equilibrium for a given magnetic system. Keyword +*discrete\_factor* defines a discretization factor for the adaptive +timestep used in the *spin* minimization. See :doc:`min_spin +` for more information about those quantities. -The choice of a line search algorithm for the *spin/cg* and -*spin/lbfgs* styles can be specified via the *line* keyword. -The *spin\_cubic* and *spin\_none* only make sense when one of those -two minimization styles is declared. -The *spin\_cubic* performs the line search based on a cubic interpolation -of the energy along the search direction. The *spin\_none* keyword -deactivates the line search procedure. -The *spin\_none* is a default value for *line* keyword for both *spin/lbfgs* -and *spin/cg*\ . Convergence of *spin/lbfgs* can be more robust if -*spin\_cubic* line search is used. +The choice of a line search algorithm for the *spin/cg* and *spin/lbfgs* +styles can be specified via the *line* keyword. The *spin\_cubic* and +*spin\_none* options only make sense when one of those two minimization +styles is declared. The *spin\_cubic* option performs the line search +based on a cubic interpolation of the energy along the search +direction. The *spin\_none* option deactivates the line search +procedure. The *spin\_none* option is a default value for *line* +keyword for both *spin/lbfgs* and *spin/cg*\ . Convergence of +*spin/lbfgs* can be more robust if *spin\_cubic* line search is used. Restrictions """""""""""" -For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used -when styles *spin/cg* and *spin/lbfgs* are employed. -See :doc:`neb/spin ` for more explanation. +For magnetic GNEB calculations, only the *spin\_none* value for *line* keyword can be used +when minimization styles *spin/cg* and *spin/lbfgs* are employed. +See :doc:`neb/spin ` for more explanations. Related commands """""""""""""""" diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 96053fda98..57416ec826 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -70,14 +70,13 @@ discretization factor *discrete\_factor*. 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) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno -(L-BFGS) algorithm. -By default, style *spin/lbfgs* does not employ line search procedure. -If the line search procedure is not used then the discrete factor defines -the maximum root mean squared rotation angle of spins by equation *pi/(5\*Kappa)*. -The default value for Kappa is 10. -The *spin\_cubic* line search can improve the convergence of the +Style *spin/lbfgs* defines an orthogonal spin optimization (OSO) +combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) +algorithm. By default, style *spin/lbfgs* does not employ line search +procedure. If the line search procedure is not used then the discrete +factor defines the maximum root mean squared rotation angle of spins by +equation *pi/(5\*Kappa)*. The default value for Kappa is 10. The +*spin\_cubic* line search option can improve the convergence of the *spin/lbfgs* algorithm. The :doc:`min_modify ` command can be used to diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 74c46ff58e..9d7e2ba17f 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -389,8 +389,9 @@ This command can only be used if LAMMPS was built with the SPIN package. See the :doc:`Build package ` doc page for more info. -For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used -when styles *spin/cg* and *spin/lbfgs* are employed. +For magnetic GNEB calculations, only the *spin\_none* value for the +*line* keyword can be used when minimization styles *spin/cg* and +*spin/lbfgs* are employed. ---------- diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 01c442176f..b45dd32bac 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -133,7 +133,7 @@ cutoff distance. A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in free energy calculations, is part of the USER-FEP package and is documented with -the :doc:`pair\_fep\_soft ` styles. The version with soft core is +the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -203,7 +203,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair\_fep\_soft ` +:doc:`pair_coeff `, :doc:`pair_style */soft ` **Default:** none diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 735b52cb6e..d85df6ad6a 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -392,7 +392,7 @@ info. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair\_style, hybrid/overlay `, :doc:`kspace_style ` +:doc:`pair_coeff `, :doc:`pair_style, hybrid/overlay `, :doc:`kspace_style ` **Default:** none diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index d1e64ae5df..8e706f77df 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -193,7 +193,7 @@ and Coulomb potentials modified by a soft core, with the functional form The *lj/class2/soft* style is a 9-6 potential with the exponent of the denominator of the first term in brackets taking the value 1.5 instead of 2 (other details differ, see the form of the potential in -:doc:`pair\_class2 `). +:doc:`pair_style lj/class2 `). Coulomb interactions can also be damped with a soft core at short distance, @@ -255,14 +255,14 @@ optional cutoffs. Style *lj/charmm/coul/long/soft* implements a soft-core version of the modified 12-6 LJ potential used in CHARMM and documented in the -:doc:`pair\_lj\_charmm ` style. In the soft version the parameters n, +:doc:`pair_style lj/charmm/coul/long ` style. In the soft version the parameters n, alpha\_LJ and alpha\_C are set in the :doc:`pair_style ` command, before the global cutoffs. The activation parameter lambda is introduced as an argument of the :doc:`pair_coeff ` command, after epsilon and sigma and before the optional eps14 and sigma14. Style *lj/class2/soft* implements a soft-core version of the 9-6 potential in -:doc:`pair\_class2 `. In the soft version the parameters n, alpha\_LJ +:doc:`pair_style lj/class2 `. In the soft version the parameters n, alpha\_LJ and alpha\_C are set in the :doc:`pair_style ` command, before the global cutoffs. The activation parameter lambda is introduced as an argument of the the :doc:`pair_coeff ` command, after epsilon and sigma and before diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 3fa1cb0bca..cdcb481e5f 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -348,7 +348,7 @@ pair\_style command. A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in free energy calculations, is part of the USER-FEP package and is documented with -the :doc:`pair\_fep\_soft ` styles. The version with soft core is +the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index 40d5688a33..3a0afbd674 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -180,7 +180,7 @@ specified in the pair\_style command. A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in free energy calculations, is part of the USER-FEP package and is documented with -the :doc:`pair\_fep\_soft ` styles. The version with soft core is +the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index ac1c106b06..f5d95f3f85 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -95,7 +95,7 @@ the *morse* and *morse/smooth/linear* styles. A version of the *morse* style with a soft core, *morse/soft*\ , suitable for use in free energy calculations, is part of the USER-FEP package and is documented with -the :doc:`pair\_fep\_soft ` styles. The version with soft core is only +the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -160,7 +160,7 @@ built with the USER-MISC package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair\_fep\_soft ` +:doc:`pair_coeff `, :doc:`pair_style */soft ` **Default:** none diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index b232649f95..1393e47cdd 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -55,7 +55,7 @@ in :ref:`(Tranchida) `. From this exchange interaction, each spin :math:`i` will be submitted to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a -force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix\_nve\_spin `), +force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix nve/spin `), such as: .. math:: diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index bd5ff51650..66bb82dafc 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -41,7 +41,7 @@ direction of a screened dielectric atomic polarization (in eV). From this magneto-electric interaction, each spin i will be submitted to a magnetic torque omega, and its associated atom can be submitted to a -force F for spin-lattice calculations (see :doc:`fix\_nve\_spin `), +force F for spin-lattice calculations (see :doc:`fix nve/spin `), such as: .. image:: Eqs/pair_spin_me_forces.jpg @@ -68,7 +68,7 @@ Related commands """""""""""""""" :doc:`atom_style spin `, :doc:`pair_coeff `, -:doc:`pair\_spin\_exchange `, :doc:`pair_eam `, +:doc:`pair_style spin/exchange `, :doc:`pair_eam `, **Default:** none diff --git a/doc/src/temper_grem.rst b/doc/src/temper_grem.rst index e686ef23a4..2e19592879 100644 --- a/doc/src/temper_grem.rst +++ b/doc/src/temper_grem.rst @@ -14,7 +14,7 @@ Syntax * N = total # of timesteps to run * M = attempt a tempering swap every this many steps * lambda = initial lambda for this ensemble -* fix-ID = ID of fix\_grem +* fix-ID = ID of *fix grem* * thermostat-ID = ID of the thermostat that controls kinetic temperature * seed1 = random # seed used to decide on adjacent temperature to partner with * seed2 = random # seed for Boltzmann factor in Metropolis swap