Creating doc pages and links for rheo
This commit is contained in:
jtclemm
@ -89,6 +89,7 @@ Packages howto
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Howto_drude2
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Howto_peri
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Howto_manifold
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Howto_rheo
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Howto_spins
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Tutorials howto
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3
doc/src/Howto_rheo.rst
Normal file
3
doc/src/Howto_rheo.rst
Normal file
@ -0,0 +1,3 @@
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Reproducing hydrodynamics and elastic objects (RHEO)
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======================
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@ -78,61 +78,65 @@ coordinates, velocities, atom IDs and types. See the
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:doc:`set <set>` commands for info on how to set these various
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quantities.
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *angle* | bonds and angles | bead-spring polymers with stiffness |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *atomic* | only the default values | coarse-grain liquids, solids, metals |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *body* | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *bond* | bonds | bead-spring polymers |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *charge* | charge | atomic system with charges |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *dielectric* | normx normy normz area/patch ed em epsilon curv | system with surface polarization |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *dipole* | charge and dipole moment | system with dipolar particles |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *dpd* | internal temperature and internal energies | DPD particles |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *edpd* | temperature and heat capacity | eDPD particles |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *electron* | charge and spin and eradius | electronic force field |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *full* | molecular + charge | bio-molecules |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *line* | end points, angular velocity | rigid bodies |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *mdpd* | density | mDPD particles |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *peri* | mass, volume | mesoscopic Peridynamic models |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *sph* | rho, esph, cv | SPH particles |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *sphere* | diameter, mass, angular velocity | granular models |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)|
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *spin* | magnetic moment | system with magnetic particles |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *tdpd* | chemical concentration | tDPD particles |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *template* | template index, template atom | small molecules with fixed topology |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *tri* | corner points, angular momentum | rigid bodies |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD |
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+--------------+-----------------------------------------------------+--------------------------------------+
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *angle* | bonds and angles | bead-spring polymers with stiffness |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *atomic* | only the default values | coarse-grain liquids, solids, metals |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *body* | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *bond* | bonds | bead-spring polymers |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *charge* | charge | atomic system with charges |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *dielectric* | normx normy normz area/patch ed em epsilon curv | system with surface polarization |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *dipole* | charge and dipole moment | system with dipolar particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *dpd* | internal temperature and internal energies | DPD particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *edpd* | temperature and heat capacity | eDPD particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *electron* | charge and spin and eradius | electronic force field |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *full* | molecular + charge | bio-molecules |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *line* | end points, angular velocity | rigid bodies |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *mdpd* | density | mDPD particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *peri* | mass, volume | mesoscopic Peridynamic models |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *rheo* | rho, status | solid and fluid RHEO particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *rheo/thermal* | rho, status, temperature | RHEO particles with temperature |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *sph* | rho, esph, cv | SPH particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *sphere* | diameter, mass, angular velocity | granular models |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)|
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *spin* | magnetic moment | system with magnetic particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *tdpd* | chemical concentration | tDPD particles |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *template* | template index, template atom | small molecules with fixed topology |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *tri* | corner points, angular momentum | rigid bodies |
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+----------------+-----------------------------------------------------+--------------------------------------+
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| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD |
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+----------------+-----------------------------------------------------+--------------------------------------+
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.. note::
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@ -271,6 +271,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
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* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
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* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
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* :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
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* :doc:`rheo/property/atom <compute_rheo_property_atom>` - convert atom attributes in RHEO package to per-atom vectors/arrays
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* :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
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* :doc:`saed <compute_saed>` - electron diffraction intensity on a mesh of reciprocal lattice nodes
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* :doc:`slice <compute_slice>` - extract values from global vector or array
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@ -353,6 +353,10 @@ accelerated styles exist.
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* :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information
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* :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
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* :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
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* :doc:`rheo <fix_rheo>` - integrator for the RHEO package
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* :doc:`rheo/thermal <fix_rheo_thermal>` - thermal integrator for the RHEO package
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* :doc:`rheo/pressure <fix_rheo_pressure>` - pressure derivation for the RHEO package
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* :doc:`rheo/viscosity <fix_rheo_pressure>` - viscosity derivation for the RHEO package
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* :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems
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* :doc:`rigid <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVE integration
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* :doc:`rigid/meso <fix_rigid_meso>` - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
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59
doc/src/fix_rheo.rst
Normal file
59
doc/src/fix_rheo.rst
Normal file
@ -0,0 +1,59 @@
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.. index:: fix rheo
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fix rheo command
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===============
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID rheo
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* rheo = style name of this fix command
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all rheo 1.0 CRK1 shift
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Description
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"""""""""""
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Perform time integration to update position, velocity, internal energy
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and local density for atoms in the group each timestep. This fix is
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needed to time-integrate SPH systems where particles carry internal
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variables such as internal energy. SPH stands for Smoothed Particle
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Hydrodynamics.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix is part of the RHEO package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
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Related commands
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""""""""""""""""
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:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
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:doc:`fix rheo/pressure <fix_rheo_pressure>`,
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:doc:`fix rheo/thermal <fix_rheo_thermal>`,
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:doc:`pair rheo <pair_rheo>`,
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:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
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Default
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"""""""
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none
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59
doc/src/fix_rheo_pressure.rst
Normal file
59
doc/src/fix_rheo_pressure.rst
Normal file
@ -0,0 +1,59 @@
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.. index:: fix rheo
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fix rheo command
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===============
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID rheo
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* rheo = style name of this fix command
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all rheo 1.0 CRK1 shift
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Description
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"""""""""""
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||||
|
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Perform time integration to update position, velocity, internal energy
|
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and local density for atoms in the group each timestep. This fix is
|
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needed to time-integrate SPH systems where particles carry internal
|
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variables such as internal energy. SPH stands for Smoothed Particle
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Hydrodynamics.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
|
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are relevant to this fix. No global or per-atom quantities are stored
|
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by this fix for access by various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix is part of the RHEO package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
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|
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Related commands
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""""""""""""""""
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:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
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:doc:`fix rheo/pressure <fix_rheo_pressure>`,
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:doc:`fix rheo/thermal <fix_rheo_thermal>`,
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:doc:`pair rheo <pair_rheo>`,
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:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
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Default
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"""""""
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none
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59
doc/src/fix_rheo_thermal.rst
Normal file
59
doc/src/fix_rheo_thermal.rst
Normal file
@ -0,0 +1,59 @@
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.. index:: fix rheo
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fix rheo command
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===============
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID rheo
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* rheo = style name of this fix command
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Examples
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""""""""
|
||||
|
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.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all rheo 1.0 CRK1 shift
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Perform time integration to update position, velocity, internal energy
|
||||
and local density for atoms in the group each timestep. This fix is
|
||||
needed to time-integrate SPH systems where particles carry internal
|
||||
variables such as internal energy. SPH stands for Smoothed Particle
|
||||
Hydrodynamics.
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various :doc:`output commands <Howto_output>`.
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix is part of the RHEO 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:`fix rheo/viscosity <fix_rheo_viscosity>`,
|
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:doc:`fix rheo/pressure <fix_rheo_pressure>`,
|
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:doc:`fix rheo/thermal <fix_rheo_thermal>`,
|
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:doc:`pair rheo <pair_rheo>`,
|
||||
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
|
||||
|
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Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
59
doc/src/fix_rheo_viscosity.rst
Normal file
59
doc/src/fix_rheo_viscosity.rst
Normal file
@ -0,0 +1,59 @@
|
||||
.. index:: fix rheo
|
||||
|
||||
fix rheo command
|
||||
===============
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID rheo
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* rheo = style name of this fix command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all rheo 1.0 CRK1 shift
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Perform time integration to update position, velocity, internal energy
|
||||
and local density for atoms in the group each timestep. This fix is
|
||||
needed to time-integrate SPH systems where particles carry internal
|
||||
variables such as internal energy. SPH stands for Smoothed Particle
|
||||
Hydrodynamics.
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various :doc:`output commands <Howto_output>`.
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix is part of the RHEO 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:`fix rheo/viscosity <fix_rheo_viscosity>`,
|
||||
:doc:`fix rheo/pressure <fix_rheo_pressure>`,
|
||||
:doc:`fix rheo/thermal <fix_rheo_thermal>`,
|
||||
:doc:`pair rheo <pair_rheo>`,
|
||||
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
86
doc/src/pair_rheo.rst
Normal file
86
doc/src/pair_rheo.rst
Normal file
@ -0,0 +1,86 @@
|
||||
.. index:: pair_style sph/lj
|
||||
|
||||
pair_style sph/lj command
|
||||
=========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style sph/lj
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style sph/lj
|
||||
pair_coeff * * 1.0 2.4
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The sph/lj style computes pressure forces between particles according
|
||||
to the Lennard-Jones equation of state, which is computed according to
|
||||
Ree's 1980 polynomial fit :ref:`(Ree) <Ree>`. The Lennard-Jones parameters
|
||||
epsilon and sigma are set to unity. This pair style also computes
|
||||
Monaghan's artificial viscosity to prevent particles from
|
||||
interpenetrating :ref:`(Monaghan) <Monoghan>`.
|
||||
|
||||
See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
|
||||
LAMMPS.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||
above.
|
||||
|
||||
* :math:`\nu` artificial viscosity (no units)
|
||||
* h kernel function cutoff (distance units)
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
This style does not support mixing. Thus, coefficients for all
|
||||
I,J pairs must be specified explicitly.
|
||||
|
||||
This style does not support the :doc:`pair_modify <pair_modify>`
|
||||
shift, table, and tail options.
|
||||
|
||||
This style does not write information to :doc:`binary restart files <restart>`. Thus, you need to re-specify the pair_style and
|
||||
pair_coeff commands in an input script that reads a restart file.
|
||||
|
||||
This style can only be used via the *pair* keyword of the :doc:`run_style respa <run_style>` command. It does not support the *inner*,
|
||||
*middle*, *outer* keywords.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
As noted above, the Lennard-Jones parameters epsilon and sigma are set
|
||||
to unity.
|
||||
|
||||
This pair style is part of the SPH package. It is only enabled
|
||||
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`, pair_sph/rhosum
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
.. _Ree:
|
||||
|
||||
**(Ree)** Ree, Journal of Chemical Physics, 73, 5401 (1980).
|
||||
|
||||
.. _Monoghan:
|
||||
|
||||
**(Monaghan)** Monaghan and Gingold, Journal of Computational Physics,
|
||||
52, 374-389 (1983).
|
||||
@ -714,6 +714,10 @@ of analysis.
|
||||
- atom-ID molecule-ID atom-type x y z
|
||||
* - peri
|
||||
- atom-ID atom-type volume density x y z
|
||||
* - rheo
|
||||
- atom-ID atom-type status rho x y z
|
||||
* - rheo/thermal
|
||||
- atom-ID atom-type status rho temperature x y z
|
||||
* - smd
|
||||
- atom-ID atom-type molecule volume mass kradius cradius x0 y0 z0 x y z
|
||||
* - sph
|
||||
|
||||
@ -111,6 +111,8 @@ Syntax
|
||||
*angle* value = angle type for all angles between selected atoms
|
||||
*dihedral* value = dihedral type for all dihedrals between selected atoms
|
||||
*improper* value = improper type for all impropers between selected atoms
|
||||
*rheo/rho* value = density of RHEO particles (mass/distance\^3)
|
||||
*rheo/status* value = status or phase of RHEO particles (unitless)
|
||||
*sph/e* value = energy of SPH particles (need units)
|
||||
value can be an atom-style variable (see below)
|
||||
*sph/cv* value = heat capacity of SPH particles (need units)
|
||||
@ -472,6 +474,10 @@ the *bond types* (\ *angle types*, etc) field in the header of the data
|
||||
file read by the :doc:`read_data <read_data>` command. These keywords
|
||||
do not allow use of an atom-style variable.
|
||||
|
||||
Keywords *rheo/rho* and *rheo/status* set the density and the status of
|
||||
rheo particles. In particular, one can only set the phase in the status
|
||||
as described by the :doc:`RHEO howto page <Howto_rheo>`.
|
||||
|
||||
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
|
||||
and density of smoothed particle hydrodynamics (SPH) particles. See
|
||||
`this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
|
||||
|
||||
Reference in New Issue
Block a user