diff --git a/doc/_sources/atom_style.txt b/doc/_sources/atom_style.txt index 18d888243a..b875001298 100644 --- a/doc/_sources/atom_style.txt +++ b/doc/_sources/atom_style.txt @@ -10,10 +10,10 @@ Syntax atom_style style args -* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *tri* or *template* or *hybrid* +* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *tri* or *template* or *hybrid* .. parsed-literal:: - args = none for any style except *body* and *hybrid* + args = none for any style except the following *body* args = bstyle bstyle-args bstyle = style of body particles bstyle-args = additional arguments specific to the bstyle @@ -48,6 +48,12 @@ used before a simulation is setup via a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. +.. note:: + + Many of the atom styles discussed here are only enabled if + LAMMPS was built with a specific package, as listed below in the + Restrictions section. + Once a style is assigned, it cannot be changed, so use a style general enough to encompass all attributes. E.g. with style *bond*, angular terms cannot be used or added later to the model. It is OK to use a @@ -78,6 +84,8 @@ quantities. +--------------+-----------------------------------------------------+--------------------------------------+ | *dipole* | charge and dipole moment | system with dipolar particles | +--------------+-----------------------------------------------------+--------------------------------------+ +| *dpd* | internal temperature and internal energies | DPD particles | ++--------------+-----------------------------------------------------+--------------------------------------+ | *electron* | charge and spin and eradius | electronic force field | +--------------+-----------------------------------------------------+--------------------------------------+ | *ellipsoid* | shape, quaternion, angular momentum | aspherical particles | @@ -147,6 +155,10 @@ position, which is represented by the eradius = electron size. For the *peri* style, the particles are spherical and each stores a per-particle mass and volume. +The *dpd* style is for dissipative particle dynamics (DPD) particles +which store the particle internal temperature (dpdTheta), internal +conductive energy (uCond) and internal mechanical energy (uMech). + The *meso* style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity (cv). @@ -272,16 +284,30 @@ Restrictions This command cannot be used after the simulation box is defined by a :doc:`read_data ` or :doc:`create_box ` command. +Many of the styles listed above are only enabled if LAMMPS was built +with a specific package, as listed below. See the :ref:`Making LAMMPS ` section for more info. + The *angle*, *bond*, *full*, *molecular*, and *template* styles are -part of the MOLECULE package. The *line* and *tri* styles are part -of the ASPHERE pacakge. The *body* style is part of the BODY package. -The *dipole* style is part of the DIPOLE package. The *peri* style is -part of the PERI package for Peridynamics. The *electron* style is -part of the USER-EFF package for :doc:`electronic force fields `. The *meso* style is part of the USER-SPH -package for smoothed particle hydrodyanmics (SPH). See `this PDF guide `_ to using SPH in LAMMPS. The -*wavepacket* style is part of the USER-AWPMD package for the -:doc:`antisymmetrized wave packet MD method `. They are -only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. +part of the MOLECULE package. + +The *line* and *tri* styles are part of the ASPHERE pacakge. + +The *body* style is part of the BODY package. + +The *dipole* style is part of the DIPOLE package. + +The *peri* style is part of the PERI package for Peridynamics. + +The *electron* style is part of the USER-EFF package for :doc:`electronic force fields `. + +The *dpd* style is part of the USER-DPD package for dissipative +particle dynamics (DPD). + +The *meso* style is part of the USER-SPH package for smoothed particle +hydrodyanmics (SPH). See `this PDF guide `_ to using SPH in LAMMPS. + +The *wavepacket* style is part of the USER-AWPMD package for the +:doc:`antisymmetrized wave packet MD method `. Related commands """""""""""""""" diff --git a/doc/_sources/read_data.txt b/doc/_sources/read_data.txt index 5c1ff4b4f1..a2b051d92c 100644 --- a/doc/_sources/read_data.txt +++ b/doc/_sources/read_data.txt @@ -582,6 +582,8 @@ of analysis. +------------+---------------------------------------------------------------------------+ | dipole | atom-ID atom-type q x y z mux muy muz | +------------+---------------------------------------------------------------------------+ +| dpd | atom-ID atom-type theta x y z | ++------------+---------------------------------------------------------------------------+ | electron | atom-ID atom-type q spin eradius x y z | +------------+---------------------------------------------------------------------------+ | ellipsoid | atom-ID atom-type ellipsoidflag density x y z | @@ -596,7 +598,7 @@ of analysis. +------------+---------------------------------------------------------------------------+ | peri | atom-ID atom-type volume density x y z | +------------+---------------------------------------------------------------------------+ -| smd | atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z | +| smd | atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z | +------------+---------------------------------------------------------------------------+ | sphere | atom-ID atom-type diameter density x y z | +------------+---------------------------------------------------------------------------+ @@ -609,33 +611,34 @@ of analysis. | hybrid | atom-ID atom-type x y z sub-style1 sub-style2 ... | +------------+---------------------------------------------------------------------------+ -The keywords have these meanings: +The per-atom values have these meanings and units, listed alphabetically: * atom-ID = integer ID of atom -* molecule-ID = integer ID of molecule the atom belongs to * atom-type = type of atom (1-Ntype) -* q = charge on atom (charge units) -* diameter = diameter of spherical atom (distance units) -* ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles -* lineflag = 1 for line segment particles, 0 for point particles -* triangleflag = 1 for triangular particles, 0 for point particles * bodyflag = 1 for body particles, 0 for point particles -* template-index = which molecule within the molecule template the atom is part of -* template-atom = which atom within a template molecule the atom is -* density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) -* mass = mass of particle (mass units) -* volume = volume of particle (distance^3 units) -* x,y,z = coordinates of atom -* mux,muy,muz = components of dipole moment of atom (dipole units) -* rho = density (need units) for SPH particles -* e = energy (need units) for SPH particles +* contact-radius = ??? (distance units) +* cs_re,cs_im = real/imaginary parts of wavepacket coefficients * cv = heat capacity (need units) for SPH particles -* spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) +* density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) +* diameter = diameter of spherical atom (distance units) +* e = energy (need units) for SPH particles +* ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles * eradius = electron radius (or fixed-core radius) * etag = integer ID of electron that each wavepacket belongs to -* cs_re,cs_im = real/imaginary parts of wavepacket coefficients -* kernel_radius = ??? (distance units) -* contact_radius = ??? (distance units) +* kernel-radius = ??? (distance units) +* lineflag = 1 for line segment particles, 0 for point or spherical particles +* mass = mass of particle (mass units) +* molecule-ID = integer ID of molecule the atom belongs to +* mux,muy,muz = components of dipole moment of atom (dipole units) +* q = charge on atom (charge units) +* rho = density (need units) for SPH particles +* spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) +* template-atom = which atom within a template molecule the atom is +* template-index = which molecule within the molecule template the atom is part of +* theta = internal temperature of a DPD particle +* triangleflag = 1 for triangular particles, 0 for point or sperhical particles +* volume = volume of Peridynamic particle (distance^3 units) +* x,y,z = coordinates of atom (distance units) The units for these quantities depend on the unit style; see the :doc:`units ` command for details. diff --git a/doc/_sources/set.txt b/doc/_sources/set.txt index 9f7b4f6b6c..8b914bbb28 100644 --- a/doc/_sources/set.txt +++ b/doc/_sources/set.txt @@ -13,7 +13,7 @@ Syntax * style = *atom* or *type* or *mol* or *group* or *region* * ID = atom ID range or type range or mol ID range or group ID or region ID * one or more keyword/value pairs may be appended -* keyword = *type* or *type/fraction* or *mol* or *x* or *y* or *z* or *charge* or *dipole* or *dipole/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or *omega* or *mass* or *density* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *meso/e* or *meso/cv* or *meso/rho* or *smd/contact/radius* or *smd/mass/density* or *i_name* or *d_name* +* keyword = *type* or *type/fraction* or *mol* or *x* or *y* or *z* or *charge* or *dipole* or *dipole/random* or *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or *theta* or *theta/random* or *angmom* or *omega* or *mass* or *density* or *volume* or *image* or *bond* or *angle* or *dihedral* or *improper* or *meso/e* or *meso/cv* or *meso/rho* or *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or *i_name* or *d_name* .. parsed-literal:: *type* value = atom type @@ -83,6 +83,7 @@ Syntax value can be an atom-style variable (see below) *smd/mass/density* = set particle mass based on volume by providing a mass density value can be an atom-style variable (see below) + *dpd/theta* value = internal temperature of DPD particles (temperature units) *i_name* value = value for custom integer vector with name *d_name* value = value for custom floating-point vector with name @@ -382,6 +383,9 @@ other. Note that the SPH smoothing kernel diameter used for computing long range, nonlocal interactions, is set using the *diameter* keyword. +Keyword *dpd/theta* sets the internal temperature of a DPD particle +as defined by the USER-DPD package. + Keywords *i_name* and *d_name* refer to custom integer and floating-point properties that have been added to each atom via the :doc:`fix property/atom ` command. When that command diff --git a/doc/atom_style.html b/doc/atom_style.html index f0b9b35de2..c3ec18c68f 100644 --- a/doc/atom_style.html +++ b/doc/atom_style.html @@ -132,10 +132,10 @@
    -
  • style = angle or atomic or body or bond or charge or dipole or electron or ellipsoid or full or line or meso or molecular or peri or smd or sphere or tri or template or hybrid
    • +
  • style = angle or atomic or body or bond or charge or dipole or dpd or electron or ellipsoid or full or line or meso or molecular or peri or smd or sphere or tri or template or hybrid
-args = none for any style except body and hybrid
+args = none for any style except the following
 body args = bstyle bstyle-args
   bstyle = style of body particles
   bstyle-args = additional arguments specific to the bstyle
@@ -168,6 +168,12 @@ what attributes are associated with the atoms.  This command must be
 used before a simulation is setup via a read_data,
 read_restart, or create_box
 command.

+

+
Note

+
Many of the atom styles discussed here are only enabled if
+LAMMPS was built with a specific package, as listed below in the
+Restrictions section.

+

 
Once a style is assigned, it cannot be changed, so use a style general
 enough to encompass all attributes.  E.g. with style bond, angular
 terms cannot be used or added later to the model.  It is OK to use a
@@ -213,51 +219,55 @@ quantities.

 charge and dipole moment
 system with dipolar particles
 
-electron
+dpd
+internal temperature and internal energies
+DPD particles
+
+electron
 charge and spin and eradius
 electronic force field
 
-ellipsoid
+ellipsoid
 shape, quaternion, angular momentum
 aspherical particles
 
-full
+full
 molecular + charge
 bio-molecules
 
-line
+line
 end points, angular velocity
 rigid bodies
 
-meso
+meso
 rho, e, cv
 SPH particles
 
-molecular
+molecular
 bonds, angles, dihedrals, impropers
 uncharged molecules
 
-peri
+peri
 mass, volume
 mesocopic Peridynamic models
 
-smd
+smd
 volume, kernel diameter, contact radius, mass
 solid and fluid SPH particles
 
-sphere
+sphere
 diameter, mass, angular velocity
 granular models
 
-template
+template
 template index, template atom
 small molecules with fixed topology
 
-tri
+tri
 corner points, angular momentum
 rigid bodies
 
-wavepacket
+wavepacket
 charge, spin, eradius, etag, cs_re, cs_im
 AWPMD
 
@@ -300,6 +310,9 @@ Gaussians with a specified position and bandwidth or uncertainty in
 position, which is represented by the eradius = electron size.

 
For the peri style, the particles are spherical and each stores a
 per-particle mass and volume.

+
The dpd style is for dissipative particle dynamics (DPD) particles
+which store the particle internal temperature (dpdTheta), internal
+conductive energy (uCond) and internal mechanical energy (uMech).

 
The meso style is for smoothed particle hydrodynamics (SPH)
 particles which store a density (rho), energy (e), and heat capacity
 (cv).

@@ -399,16 +412,21 @@ more instructions on how to use the accelerated styles effectively.

 
Restrictions

 
This command cannot be used after the simulation box is defined by a
 read_data or create_box command.

+
Many of the styles listed above are only enabled if LAMMPS was built
+with a specific package, as listed below.  See the Making LAMMPS section for more info.

 
The angle, bond, full, molecular, and template styles are
-part of the MOLECULE package.  The line and tri styles are part
-of the ASPHERE pacakge.  The body style is part of the BODY package.
-The dipole style is part of the DIPOLE package.  The peri style is
-part of the PERI package for Peridynamics.  The electron style is
-part of the USER-EFF package for electronic force fields.  The meso style is part of the USER-SPH
-package for smoothed particle hydrodyanmics (SPH).  See this PDF guide to using SPH in LAMMPS.  The
-wavepacket style is part of the USER-AWPMD package for the
-antisymmetrized wave packet MD method.  They are
-only enabled if LAMMPS was built with that package.  See the Making LAMMPS section for more info.

+part of the MOLECULE package.

+
The line and tri styles are part of the ASPHERE pacakge.

+
The body style is part of the BODY package.

+
The dipole style is part of the DIPOLE package.

+
The peri style is part of the PERI package for Peridynamics.

+
The electron style is part of the USER-EFF package for electronic force fields.

+
The dpd style is part of the USER-DPD package for dissipative
+particle dynamics (DPD).

+
The meso style is part of the USER-SPH package for smoothed particle
+hydrodyanmics (SPH).  See this PDF guide to using SPH in LAMMPS.

+
The wavepacket style is part of the USER-AWPMD package for the
+antisymmetrized wave packet MD method.