Merge pull request #3462 from akohlmey/pdlammps-howto

Add peridynamics howto document

doc/src/Howto.rst

@@ -85,6 +85,7 @@ Packages howto
    Howto_coreshell
    Howto_drude
    Howto_drude2
+   Howto_peri
    Howto_manifold
    Howto_spins
 

doc/src/Packages_details.rst

@@ -2220,6 +2220,7 @@ 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

@@ -32,10 +32,9 @@ 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
-<https://download.lammps.org/pdfs/PDLAMMPS_user_guide.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.
 

doc/src/compute_dilatation_atom.rst

@@ -35,12 +35,12 @@ 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
-fraction of the particles and an influence function.  See the `PDLAMMPS
-user guide <https://download.lammps.org/pdfs/PDLAMMPS_user_guide.pdf>`_
-for a formal definition of dilatation.
+fraction of the particles and an influence function.  See the
+: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.
+: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.

doc/src/pair_peri.rst

@@ -70,25 +70,24 @@ 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
-<https://download.lammps.org/pdfs/PDLAMMPS_user_guide.pdf>`_ for more
+<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:
 
@@ -99,8 +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.
 
@@ -113,8 +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:
@@ -128,12 +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:

doc/utils/sphinx-config/_static/css/lammps.css

@@ -1,3 +1,11 @@
+.math {
+        text-align: left;
+}
+
+.eqno {
+        float: right;
+}
+
 .wy-nav-content {
     max-width: 100% !important;
 }

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
@@ -2124,6 +2126,7 @@ modelled
 modelling
 Modelling
 Modine
+moduli
 mofff
 MOFFF
 Mohd
@@ -2139,6 +2142,7 @@ Monaghan
 Monaghans
 monodisperse
 monodispersity
+monolayer
 monopole
 monovalent
 Montalenti
@@ -2414,6 +2418,7 @@ normy
 normz
 Noskov
 noslip
+notational
 noticable
 Nout
 noutcol
@@ -2774,6 +2779,7 @@ ps
 Ps
 pscreen
 pscrozi
+Pseudocode
 pseudodynamics
 pseudopotential
 pSp
@@ -3133,6 +3139,7 @@ sectoring
 sed
 segmental
 Seifert
+Seleson
 sellerio
 Sellerio
 Semaev
@@ -3211,7 +3218,7 @@ slategray
 slater
 Slepoy
 Sliozberg
-sLLG
+sLL
 sllod
 sm
 smallbig
@@ -3622,6 +3629,7 @@ unsmoothed
 unsolvated
 unsplit
 unstrained
+unstretched
 untar
 untilted
 Unwin