diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index 1366ecb839..94a465e6fd 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -89,6 +89,7 @@ Packages howto Howto_drude2 Howto_peri Howto_manifold + Howto_rheo Howto_spins Tutorials howto diff --git a/doc/src/Howto_rheo.rst b/doc/src/Howto_rheo.rst new file mode 100644 index 0000000000..9dac90549c --- /dev/null +++ b/doc/src/Howto_rheo.rst @@ -0,0 +1,3 @@ +Reproducing hydrodynamics and elastic objects (RHEO) +====================== + diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index b5ee0f07ff..98d465a6f3 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -78,61 +78,65 @@ coordinates, velocities, atom IDs and types. See the :doc:`set ` commands for info on how to set these various quantities. -+--------------+-----------------------------------------------------+--------------------------------------+ -| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *angle* | bonds and angles | bead-spring polymers with stiffness | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *atomic* | only the default values | coarse-grain liquids, solids, metals | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *body* | mass, inertia moments, quaternion, angular momentum | arbitrary bodies | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *bond* | bonds | bead-spring polymers | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *charge* | charge | atomic system with charges | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *dielectric* | normx normy normz area/patch ed em epsilon curv | system with surface polarization | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *dipole* | charge and dipole moment | system with dipolar particles | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *dpd* | internal temperature and internal energies | DPD particles | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *edpd* | temperature and heat capacity | eDPD particles | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *electron* | charge and spin and eradius | electronic force field | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *full* | molecular + charge | bio-molecules | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *line* | end points, angular velocity | rigid bodies | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *mdpd* | density | mDPD particles | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *peri* | mass, volume | mesoscopic Peridynamic models | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *sph* | rho, esph, cv | SPH particles | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *sphere* | diameter, mass, angular velocity | granular models | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)| -+--------------+-----------------------------------------------------+--------------------------------------+ -| *spin* | magnetic moment | system with magnetic particles | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *tdpd* | chemical concentration | tDPD particles | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *template* | template index, template atom | small molecules with fixed topology | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *tri* | corner points, angular momentum | rigid bodies | -+--------------+-----------------------------------------------------+--------------------------------------+ -| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD | -+--------------+-----------------------------------------------------+--------------------------------------+ ++----------------+-----------------------------------------------------+--------------------------------------+ +| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *angle* | bonds and angles | bead-spring polymers with stiffness | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *atomic* | only the default values | coarse-grain liquids, solids, metals | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *body* | mass, inertia moments, quaternion, angular momentum | arbitrary bodies | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *bond* | bonds | bead-spring polymers | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *charge* | charge | atomic system with charges | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *dielectric* | normx normy normz area/patch ed em epsilon curv | system with surface polarization | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *dipole* | charge and dipole moment | system with dipolar particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *dpd* | internal temperature and internal energies | DPD particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *edpd* | temperature and heat capacity | eDPD particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *electron* | charge and spin and eradius | electronic force field | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *full* | molecular + charge | bio-molecules | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *line* | end points, angular velocity | rigid bodies | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *mdpd* | density | mDPD particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *peri* | mass, volume | mesoscopic Peridynamic models | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *rheo* | rho, status | solid and fluid RHEO particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *rheo/thermal* | rho, status, temperature | RHEO particles with temperature | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *sph* | rho, esph, cv | SPH particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *sphere* | diameter, mass, angular velocity | granular models | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)| ++----------------+-----------------------------------------------------+--------------------------------------+ +| *spin* | magnetic moment | system with magnetic particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *tdpd* | chemical concentration | tDPD particles | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *template* | template index, template atom | small molecules with fixed topology | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *tri* | corner points, angular momentum | rigid bodies | ++----------------+-----------------------------------------------------+--------------------------------------+ +| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD | ++----------------+-----------------------------------------------------+--------------------------------------+ .. note:: diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 880f60a8a6..5e90d78e83 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -271,6 +271,7 @@ The individual style names on the :doc:`Commands compute ` pag * :doc:`reduce ` - combine per-atom quantities into a single global value * :doc:`reduce/chunk ` - reduce per-atom quantities within each chunk * :doc:`reduce/region ` - same as compute reduce, within a region +* :doc:`rheo/property/atom ` - convert atom attributes in RHEO package to per-atom vectors/arrays * :doc:`rigid/local ` - extract rigid body attributes * :doc:`saed ` - electron diffraction intensity on a mesh of reciprocal lattice nodes * :doc:`slice ` - extract values from global vector or array diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 56c7cde464..8ab202ab38 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -353,6 +353,10 @@ accelerated styles exist. * :doc:`reaxff/species ` - write out ReaxFF molecule information * :doc:`recenter ` - constrain the center-of-mass position of a group of atoms * :doc:`restrain ` - constrain a bond, angle, dihedral +* :doc:`rheo ` - integrator for the RHEO package +* :doc:`rheo/thermal ` - thermal integrator for the RHEO package +* :doc:`rheo/pressure ` - pressure derivation for the RHEO package +* :doc:`rheo/viscosity ` - viscosity derivation for the RHEO package * :doc:`rhok ` - add bias potential for long-range ordered systems * :doc:`rigid ` - constrain one or more clusters of atoms to move as a rigid body with NVE integration * :doc:`rigid/meso ` - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body diff --git a/doc/src/fix_rheo.rst b/doc/src/fix_rheo.rst new file mode 100644 index 0000000000..7200d456dd --- /dev/null +++ b/doc/src/fix_rheo.rst @@ -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 ` 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 `. None of the :doc:`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 `. +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +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 ` page for more info. + +Related commands +"""""""""""""""" + +:doc:`fix rheo/viscosity `, +:doc:`fix rheo/pressure `, +:doc:`fix rheo/thermal `, +:doc:`pair rheo `, +:doc:`compute rheo/property/atom ` + +Default +""""""" + +none diff --git a/doc/src/fix_rheo_pressure.rst b/doc/src/fix_rheo_pressure.rst new file mode 100644 index 0000000000..7200d456dd --- /dev/null +++ b/doc/src/fix_rheo_pressure.rst @@ -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 ` 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 `. None of the :doc:`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 `. +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +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 ` page for more info. + +Related commands +"""""""""""""""" + +:doc:`fix rheo/viscosity `, +:doc:`fix rheo/pressure `, +:doc:`fix rheo/thermal `, +:doc:`pair rheo `, +:doc:`compute rheo/property/atom ` + +Default +""""""" + +none diff --git a/doc/src/fix_rheo_thermal.rst b/doc/src/fix_rheo_thermal.rst new file mode 100644 index 0000000000..7200d456dd --- /dev/null +++ b/doc/src/fix_rheo_thermal.rst @@ -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 ` 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 `. None of the :doc:`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 `. +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +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 ` page for more info. + +Related commands +"""""""""""""""" + +:doc:`fix rheo/viscosity `, +:doc:`fix rheo/pressure `, +:doc:`fix rheo/thermal `, +:doc:`pair rheo `, +:doc:`compute rheo/property/atom ` + +Default +""""""" + +none diff --git a/doc/src/fix_rheo_viscosity.rst b/doc/src/fix_rheo_viscosity.rst new file mode 100644 index 0000000000..7200d456dd --- /dev/null +++ b/doc/src/fix_rheo_viscosity.rst @@ -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 ` 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 `. None of the :doc:`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 `. +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +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 ` page for more info. + +Related commands +"""""""""""""""" + +:doc:`fix rheo/viscosity `, +:doc:`fix rheo/pressure `, +:doc:`fix rheo/thermal `, +:doc:`pair rheo `, +:doc:`compute rheo/property/atom ` + +Default +""""""" + +none diff --git a/doc/src/pair_rheo.rst b/doc/src/pair_rheo.rst new file mode 100644 index 0000000000..b5c02c41ff --- /dev/null +++ b/doc/src/pair_rheo.rst @@ -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) `. 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) `. + +See `this PDF guide `_ to using SPH in +LAMMPS. + +The following coefficients must be defined for each pair of atoms +types via the :doc:`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 ` +shift, table, and tail options. + +This style does not write information to :doc:`binary restart files `. 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 ` 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 ` page for more info. + +Related commands +"""""""""""""""" + +:doc:`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). diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 0ecd2b6fa2..4950d8bc25 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -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 diff --git a/doc/src/set.rst b/doc/src/set.rst index 0073e44bf8..96e48a8893 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -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 ` 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 `. + 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 `_ to using SPH in LAMMPS.