reference the Howto from the rest of the manual. Spelling fixes.

doc/src/Howto_peri.rst

@@ -16,8 +16,8 @@ model is discretized within LAMMPS as described in the original article
 :ref:`(Parks) <Parks2>`.  An example problem with comments is also
 included.
 
-Quickstart
-""""""""""
+Quick Start
+"""""""""""
 
 The peridynamics styles are included in the optional :ref:`PERI package
 <PKG-PERI>`.  If your LAMMPS executable does not already include the
@@ -54,7 +54,7 @@ Some notes on this input example:
 - particles must be created on a :doc:`simple cubic lattice <lattice>`
 - using the :doc:`atom style peri <atom_style>` is required
 - an :doc:`atom map <atom_modify>` is required for indexing particles
-- The :doc:`skin distance <neighbor>` used when computing neighborlists
+- The :doc:`skin distance <neighbor>` used when computing neighbor lists
   should be defined appropriately for your choice of simulation
   parameters. The *skin* should be set to a value such that the
   peridynamic horizon plus the skin distance is larger than the maximum
@@ -254,11 +254,11 @@ extension :math:`\underline{e}^{\rm d}`.
    not change as bonds break. It is computed with respect to the bond
    family defined at the reference (initial) configuration.
 
-The nonnegative scalar state :math:`\underline{\omega}` is an *influence
-function* :ref:`(Silling 2007) <Silling2007_2>`. For more on influence
-functions, see :ref:`(Seleson 2010) <Seleson2010>`. If an influence
-function :math:`\underline{\omega}` depends only upon the scalar
-:math:`\left\Vert \boldsymbol{\xi} \right\Vert`, (i.e.,
+The non-negative scalar state :math:`\underline{\omega}` is an
+*influence function* :ref:`(Silling 2007) <Silling2007_2>`. For more on
+influence functions, see :ref:`(Seleson 2010) <Seleson2010>`. If an
+influence function :math:`\underline{\omega}` depends only upon the
+scalar :math:`\left\Vert \boldsymbol{\xi} \right\Vert`, (i.e.,
 :math:`\underline{\omega}\left<\boldsymbol{\xi}\right> =
 \underline{\omega}\left<\left\Vert \boldsymbol{\xi} \right\Vert\right>`\
 ), then :math:`\underline{\omega}` is a spherical influence function.
@@ -369,7 +369,7 @@ critical stretch defined as
 
    s_0(t,\mathbf{\eta},\mathbf{\xi}) = s_{00} - \alpha s_{\min}(t,\mathbf{\eta},\mathbf{\xi}), \qquad s_{\min}(t) = \min_{\mathbf{\xi}} s(t,\mathbf{\eta},\mathbf{\xi}),
 
-where :math:`s_{00}` and :math:`\alpha` are material-dependant
+where :math:`s_{00}` and :math:`\alpha` are material-dependent
 constants. The history function :math:`\mu` breaks bonds when the
 stretch :math:`s` exceeds the critical stretch :math:`s_0`.
 
@@ -557,7 +557,7 @@ described in the :ref:`Damage section <peridamage>`. Bonds are recorded
 as broken in a simulation by removing them from the bond family
 :math:`\mathcal{F}_i` (see \eqref{eqn:BondFamily}).
 
-A naiive implementation would have us first loop over all bonds and
+A naive implementation would have us first loop over all bonds and
 compute :math:`s_{min}` in \eqref{eqn:s0}, then loop over all bonds
 again and break bonds with a stretch :math:`s > s0` as in
 \eqref{eqn:mu}, and finally loop over all particles and compute forces
@@ -761,20 +761,20 @@ Pitfalls
 **Parallel Scalability**
 
 LAMMPS operates in parallel in a :doc:`spatial-decomposition mode
-<Developer_par_part>`, where each processor owns a spatial subdomain of
+<Developer_par_part>`, where each processor owns a spatial sub-domain of
 the overall simulation domain and communicates with its neighboring
 processors via distributed-memory message passing (MPI) to acquire ghost
 atom information to allow forces on the atoms it owns to be
 computed. LAMMPS also uses Verlet neighbor lists which are recomputed
 every few timesteps as particles move. On these timesteps, particles
 also migrate to new processors as needed. LAMMPS decomposes the overall
-simulation domain so that spatial subdomains of nearly equal volume are
-assigned to each processor. When each subdomain contains nearly the same
-number of particles, this results in a reasonable load balance among all
-processors. As is more typical with some peridynamic simulations, some
-subdomains may contain many particles while other subdomains contain few
-particles, resulting in a load imbalance that impacts parallel
-scalability.
+simulation domain so that spatial sub-domains of nearly equal volume are
+assigned to each processor. When each sub-domain contains nearly the
+same number of particles, this results in a reasonable load balance
+among all processors. As is more typical with some peridynamic
+simulations, some sub-domains may contain many particles while other
+sub-domains contain few particles, resulting in a load imbalance that
+impacts parallel scalability.
 
 **Setting the "skin" distance**
 
@@ -937,7 +937,7 @@ In line 2 we specify that SI units are to be used. We specify the
 dimension (3) and boundary conditions ("shrink-wrapped") for the
 computational domain in lines 3 and 4. In line 5 we specify that
 peridynamic particles are to be used for this simulation. In line 7, we
-set the "skin" distance used in building the LAMMPS neighborlist. In
+set the "skin" distance used in building the LAMMPS neighbor list. In
 line 8 we set the lattice constant (in meters) and in line 10 we define
 the spatial region where the target will be placed. In line 12 we
 specify a rectangular box enclosing the target region that defines the

doc/src/Packages_details.rst

@@ -2200,6 +2200,7 @@ Foster (UTSA).
 **Supporting info:**
 
 * src/PERI: filenames -> commands
+* :doc:`Peridynamics Howto <Howto_peri>`
 * `doc/PDF/PDLammps_overview.pdf <PDF/PDLammps_overview.pdf>`_
 * `doc/PDF/PDLammps_EPS.pdf <PDF/PDLammps_EPS.pdf>`_
 * `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_

doc/src/compute_damage_atom.rst

@@ -24,16 +24,17 @@ Description
 """""""""""
 
 Define a computation that calculates the per-atom damage for each atom
-in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
-for an overview of LAMMPS commands for Peridynamics modeling.
+in a group.  This is a quantity relevant for :doc:`Peridynamics models
+<pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_ for an
+overview of LAMMPS commands for Peridynamics modeling.
 
 The "damage" of a Peridynamics particles is based on the bond breakage
 between the particle and its neighbors.  If all the bonds are broken
 the particle is considered to be fully damaged.
 
-See the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal
-definition of "damage" and more details about Peridynamics as it is
-implemented in LAMMPS.
+See the :doc:`Peridynamics Howto <Howto_peri>` for a formal definition
+of "damage" and more details about Peridynamics as it is implemented in
+LAMMPS.
 
 This command can be used with all the Peridynamic pair styles.
 
@@ -53,8 +54,9 @@ The per-atom vector values are unitless numbers (damage) :math:`\ge 0.0`.
 Restrictions
 """"""""""""
 
-This compute is part of the PERI package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+This compute is part of the PERI package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_dilatation_atom.rst

@@ -24,7 +24,8 @@ Description
 """""""""""
 
 Define a computation that calculates the per-atom dilatation for each
-atom in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
+atom in a group.  This is a quantity relevant for :doc:`Peridynamics
+models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
 for an overview of LAMMPS commands for Peridynamics modeling.
 
 For small deformation, dilatation of is the measure of the volumetric
@@ -32,13 +33,14 @@ strain.
 
 The dilatation :math:`\theta` for each peridynamic particle :math:`i` is
 calculated as a sum over its neighbors with unbroken bonds, where the
-contribution of the :math:`ij` pair is a function of the change in bond length
-(versus the initial length in the reference state), the volume
+contribution of the :math:`ij` pair is a function of the change in bond
+length (versus the initial length in the reference state), the volume
 fraction of the particles and an influence function.  See the
-`PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
-a formal definition of dilatation.
+:doc:`Peridynamics Howto <Howto_peri>` for a formal definition of
+dilatation.
 
-This command can only be used with a subset of the Peridynamic :doc:`pair styles <pair_peri>`: peri/lps, peri/ves and peri/eps.
+This command can only be used with a subset of the Peridynamic
+:doc:`pair styles <pair_peri>`: *peri/lps*, *peri/ves*, and *peri/eps*.
 
 The dilatation value will be 0.0 for atoms not in the specified
 compute group.
@@ -56,9 +58,9 @@ The per-atom vector values are unitless numbers :math:`(\theta \ge 0.0)`.
 Restrictions
 """"""""""""
 
-This compute is part of the PERI package.  It is only enabled if
-LAMMPS was built with that package.  See the
-:doc:`Build package <Build_package>` page for more info.
+This compute is part of the PERI package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/pair_peri.rst

@@ -51,8 +51,9 @@ Description
 """""""""""
 
 The peridynamic pair styles implement material models that can be used
-at the mesoscopic and macroscopic scales.  See `this document <PDF/PDLammps_overview.pdf>`_ for an overview of LAMMPS commands
-for Peridynamics modeling.
+at the mesoscopic and macroscopic scales.  See `this document
+<PDF/PDLammps_overview.pdf>`_ for an overview of LAMMPS commands for
+Peridynamics modeling.
 
 Style *peri/pmb* implements the Peridynamic bond-based prototype
 microelastic brittle (PMB) model.
@@ -66,26 +67,27 @@ peridynamic viscoelastic solid (VES) model.
 Style *peri/eps* implements the Peridynamic state-based elastic-plastic
 solid (EPS) model.
 
-The canonical papers on Peridynamics are :ref:`(Silling 2000) <Silling2000>`
-and :ref:`(Silling 2007) <Silling2007>`.  The implementation of Peridynamics
-in LAMMPS is described in :ref:`(Parks) <Parks>`.  Also see the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
-more details about its implementation.
+The canonical papers on Peridynamics are :ref:`(Silling 2000)
+<Silling2000>` and :ref:`(Silling 2007) <Silling2007>`.  The
+implementation of Peridynamics in LAMMPS is described in :ref:`(Parks)
+<Parks>`.  Also see the :doc:`Peridynamics Howto <Howto_peri>` for more
+details about its implementation.
 
 The peridynamic VES and EPS models in PDLAMMPS were implemented by
 R. Rahman and J. T. Foster at University of Texas at San Antonio.  The
 original VES formulation is described in "(Mitchell2011)" and the
 original EPS formulation is in "(Mitchell2011a)".  Additional PDF docs
-that describe the VES and EPS implementations are include in the
-LAMMPS distribution in `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_ and
+that describe the VES and EPS implementations are include in the LAMMPS
+distribution in `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_ and
 `doc/PDF/PDLammps_EPS.pdf <PDF/PDLammps_EPS.pdf>`_.  For questions
 regarding the VES and EPS models in LAMMPS you can contact R. Rahman
 (rezwanur.rahman at utsa.edu).
 
 The following coefficients must be defined for each pair of atom types
 via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
-or in the data file or restart files read by the
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
-commands, or by mixing as described below.
+or in the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands, or by
+mixing as described below.
 
 For the *peri/pmb* style:
 
@@ -96,8 +98,8 @@ For the *peri/pmb* style:
 
 C is the effectively a spring constant for Peridynamic bonds, the
 horizon is a cutoff distance for truncating interactions, and s00 and
-:math:`\alpha` are used as a bond breaking criteria.  The units of c are such
-that c/distance = stiffness/volume\^2, where stiffness is
+:math:`\alpha` are used as a bond breaking criteria.  The units of c are
+such that c/distance = stiffness/volume\^2, where stiffness is
 energy/distance\^2 and volume is distance\^3.  See the users guide for
 more details.
 
@@ -110,8 +112,8 @@ For the *peri/lps* style:
 * :math:`\alpha` (unitless)
 
 K is the bulk modulus and G is the shear modulus.  The horizon is a
-cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
-used as a bond breaking criteria. See the users guide for more
+cutoff distance for truncating interactions, and s00 and :math:`\alpha`
+are used as a bond breaking criteria. See the users guide for more
 details.
 
 For the *peri/ves* style:
@@ -125,12 +127,12 @@ For the *peri/ves* style:
 * m_taubi (unitless)
 
 K is the bulk modulus and G is the shear modulus. The horizon is a
-cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
-used as a bond breaking criteria. m_lambdai and m_taubi are the
+cutoff distance for truncating interactions, and s00 and :math:`\alpha`
+are used as a bond breaking criteria. m_lambdai and m_taubi are the
 viscoelastic relaxation parameter and time constant,
-respectively. m_lambdai varies within zero to one. For very small
-values of m_lambdai the viscoelastic model responds very similar to a
-linear elastic model. For details please see the description in
+respectively. m_lambdai varies within zero to one. For very small values
+of m_lambdai the viscoelastic model responds very similar to a linear
+elastic model. For details please see the description in
 "(Mitchell2011)".
 
 For the *peri/eps* style:
@@ -165,8 +167,9 @@ shift option.
 The :doc:`pair_modify <pair_modify>` table and tail options are not
 relevant for these pair styles.
 
-These pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
-to be specified in an input script that reads a restart file.
+These pair styles write their information to :doc:`binary restart files
+<restart>`, so pair_style and pair_coeff commands do not need to be
+specified in an input script that reads a restart file.
 
 These pair styles can only be used via the *pair* keyword of the
 :doc:`run_style respa <run_style>` command.  They do not support the
@@ -177,8 +180,9 @@ These pair styles can only be used via the *pair* keyword of the
 Restrictions
 """"""""""""
 
-All of these styles are part of the PERI package. They are only
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+All of these styles are part of the PERI package. They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/utils/sphinx-config/false_positives.txt

@@ -747,6 +747,7 @@ dirname
 discoverable
 discretization
 discretized
+discretizing
 disp
 dissipative
 Dissipative
@@ -915,6 +916,7 @@ emax
 Emax
 Embt
 emi
+Emmrich
 emol
 eN
 endian
@@ -2125,6 +2127,7 @@ modelled
 modelling
 Modelling
 Modine
+moduli
 mofff
 MOFFF
 Mohd
@@ -2140,6 +2143,7 @@ Monaghan
 Monaghans
 monodisperse
 monodispersity
+monolayer
 monopole
 monovalent
 Montalenti
@@ -2415,6 +2419,7 @@ normy
 normz
 Noskov
 noslip
+notational
 noticable
 Nout
 noutcol
@@ -2775,6 +2780,7 @@ ps
 Ps
 pscreen
 pscrozi
+Pseudocode
 pseudodynamics
 pseudopotential
 pSp
@@ -3134,6 +3140,7 @@ sectoring
 sed
 segmental
 Seifert
+Seleson
 sellerio
 Sellerio
 Semaev
@@ -3212,7 +3219,7 @@ slategray
 slater
 Slepoy
 Sliozberg
-sLLG
+sLL
 sllod
 sm
 smallbig
@@ -3623,6 +3630,7 @@ unsmoothed
 unsolvated
 unsplit
 unstrained
+unstretched
 untar
 untilted
 Unwin