From 647d4fe62666eff3b2cc136244c8d8e8a28e1f22 Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Thu, 31 Jan 2013 16:39:48 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9348
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/Section_commands.html | 74 +++++++++++++-------------
doc/Section_commands.txt | 3 ++
doc/atom_style.html | 54 +++++++++++++------
doc/atom_style.txt | 52 +++++++++++++------
doc/compute.html | 1 +
doc/compute.txt | 1 +
doc/fix.html | 5 +-
doc/fix.txt | 3 +-
doc/pair_coeff.html | 1 +
doc/pair_coeff.txt | 1 +
doc/pair_style.html | 1 +
doc/pair_style.txt | 1 +
doc/read_data.html | 106 ++++++++++++++++++++++++++++++--------
doc/read_data.txt | 97 ++++++++++++++++++++++++++--------
doc/read_restart.html | 2 +-
doc/read_restart.txt | 2 +-
16 files changed, 288 insertions(+), 116 deletions(-)
diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index e19d54733f..220a3db9a0 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -344,13 +344,13 @@ of each style or click on the style itself for a full description:
| drag | dt/reset | efield | enforce2d | evaporate | external | freeze | gcmc |
| gravity | heat | indent | langevin | lineforce | momentum | move | msst |
| neb | nph | nphug | nph/asphere | nph/sphere | npt | npt/asphere | npt/sphere |
-| nve | nve/asphere | nve/asphere/noforce | nve/limit | nve/line | nve/noforce | nve/sphere | nve/tri |
-| nvt | nvt/asphere | nvt/sllod | nvt/sphere | orient/fcc | planeforce | poems | pour |
-| press/berendsen | print | qeq/comb | reax/bonds | recenter | restrain | rigid | rigid/nph |
-| rigid/npt | rigid/nve | rigid/nvt | setforce | shake | spring | spring/rg | spring/self |
-| srd | store/force | store/state | temp/berendsen | temp/rescale | thermal/conductivity | tmd | ttm |
-| viscosity | viscous | wall/colloid | wall/gran | wall/harmonic | wall/lj126 | wall/lj93 | wall/piston |
-| wall/reflect | wall/region | wall/srd
+ |
| nve | nve/asphere | nve/asphere/noforce | nve/body | nve/limit | nve/line | nve/noforce | nve/sphere |
+| nve/tri | nvt | nvt/asphere | nvt/sllod | nvt/sphere | orient/fcc | planeforce | poems |
+| pour | press/berendsen | print | qeq/comb | reax/bonds | recenter | restrain | rigid |
+| rigid/nph | rigid/npt | rigid/nve | rigid/nvt | setforce | shake | spring | spring/rg |
+| spring/self | srd | store/force | store/state | temp/berendsen | temp/rescale | thermal/conductivity | tmd |
+| ttm | viscosity | viscous | wall/colloid | wall/gran | wall/harmonic | wall/lj126 | wall/lj93 |
+| wall/piston | wall/reflect | wall/region | wall/srd
|
These are fix styles contributed by users, which can be used if
@@ -381,15 +381,15 @@ package.
each style or click on the style itself for a full description:
These are compute styles contributed by users, which can be used if
@@ -418,27 +418,27 @@ potentials. Click on the style itself for a full description:
These are pair styles contributed by users, which can be used if
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index a313d6ca8b..d61077259b 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -446,6 +446,7 @@ of each style or click on the style itself for a full description:
"nve"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
+"nve/body"_fix_nve_body.html,
"nve/limit"_fix_nve_limit.html,
"nve/line"_fix_nve_line.html,
"nve/noforce"_fix_nve_noforce.html,
@@ -547,6 +548,7 @@ each style or click on the style itself for a full description:
"angle/local"_compute_angle_local.html,
"atom/molecule"_compute_atom_molecule.html,
+"body/local"_compute_body_local.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"cluster/atom"_compute_cluster_atom.html,
@@ -634,6 +636,7 @@ potentials. Click on the style itself for a full description:
"adp"_pair_adp.html,
"airebo"_pair_airebo.html,
"beck"_pair_beck.html,
+"body"_pair_body.html,
"bop"_pair_bop.html,
"born"_pair_born.html,
"born/coul/long"_pair_born.html,
diff --git a/doc/atom_style.html b/doc/atom_style.html
index 77ca19b72f..ff8009158f 100644
--- a/doc/atom_style.html
+++ b/doc/atom_style.html
@@ -15,17 +15,21 @@
atom_style style args
-- style = angle or atomic or bond or charge or dipole or electron or ellipsoid or full or line or meso or molecular or peri or sphere or tri or hybrid
+
- 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 sphere or tri or hybrid
- args = none for any style except hybrid
- hybrid args = list of one or more sub-styles
+ args = none for any style except body and hybrid
+ body args = Bstyle
+ Bstyle = style of body particles
+ hybrid args = list of one or more sub-styles, each with their args
Examples:
atom_style atomic
atom_style bond
atom_style full
-atom_style hybrid charge bond
+atom_style body nparticle
+atom_style hybrid charge bond
+atom_style hybrid charge body nparticle
Description:
@@ -55,11 +59,12 @@ quantities.
| 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 |
| dipole | charge and dipole moment | system with dipolar particles |
| electron | charge and spin and eradius | electronic force field |
-| ellipsoid | shape, quaternion for particle orientation, angular momentum | extended aspherical particles |
+| ellipsoid | shape, quaternion, angular momentum | extended aspherical particles |
| full | molecular + charge | bio-molecules |
| line | end points, angular velocity | rigid bodies |
| meso | rho, e, cv | SPH particles |
@@ -70,13 +75,14 @@ quantities.
| wavepacket | charge, spin, eradius, etag, cs_re, cs_im | AWPMD
|
+All of the styles define point particles, except the sphere,
+ellipsoid, electron, peri, wavepacket, line, tri, and
+body styles, which define finite-size particles.
+
All of the styles assign mass to particles on a per-type basis, using
the mass command, except for the finite-size particle
-styles discussed below. They assign mass on a per-atom basis.
-
-All of the styles define point particles, except the sphere,
-ellipsoid, electron, peri, wavepacket, line, and tri
-styles, which define finite-size particles.
+styles. They assign mass to individual particles on a per-particle
+basis.
For the sphere style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
@@ -114,6 +120,23 @@ end points of the line segment).
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
+For the body style, the particles are arbitrary bodies with internal
+attributes defined by the "style" of the bodies, which is specified by
+the Bstyle argument. Each body particle stores moments of inertia
+and a quaternion 4-vector, so that its orientation can be time
+integrated. This atom style enables LAMMPS to work with particles
+that represent complex entities, such as surface meshes of discrete
+points, collections of sub-particles, deformable objects, etc. Of
+course, the interactions between pairs of bodies will need to be
+encoded in an appropriate pair style.
+
+These are the body styles that LAMMPS currently supports. The name in
+the first column is used as the Bstyle argument for atom_style body:
+
+
+| nparticle | body with N sub-particles
+ |
+
Typically, simulations require only a single (non-hybrid) atom style.
@@ -125,13 +148,13 @@ If some atoms have bonds, but others do not, use the bond style.
The only scenario where the hybrid style is needed is if there is no
single style which defines all needed properties of all atoms. For
-example, if you want dipolar particles which will be torqued and
-rotate, you would need to use "atom_style hybrid sphere dipole". When
+example, if you want dipolar particles which will rotate due to
+torque, you would need to use "atom_style hybrid sphere dipole". When
a hybrid style is used, atoms store and communicate the union of all
quantities implied by the individual styles.
-LAMMPS can be extended with new atom styles; see this
-section.
+
LAMMPS can be extended with new atom styles as well as new body
+styles; see this section.
Restrictions:
@@ -139,7 +162,8 @@ section.
read_data or create_box command.
The angle, bond, full, and molecular styles are part of the
-MOLECULAR package. The dipole style is part of the "dipole"
+MOLECULAR package. The line, tri, and body styles are part of
+the ASPHERE pacakge. 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
diff --git a/doc/atom_style.txt b/doc/atom_style.txt
index ee0375927f..8301968f77 100644
--- a/doc/atom_style.txt
+++ b/doc/atom_style.txt
@@ -12,18 +12,22 @@ atom_style command :h3
atom_style style args :pre
-style = {angle} or {atomic} or {bond} or {charge} or {dipole} or \
+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 {sphere} or {tri} or {hybrid} :ul
- args = none for any style except {hybrid}
- {hybrid} args = list of one or more sub-styles :pre
+ args = none for any style except {body} and {hybrid}
+ {body} args = Bstyle
+ Bstyle = style of body particles
+ {hybrid} args = list of one or more sub-styles, each with their args :pre
[Examples:]
atom_style atomic
atom_style bond
atom_style full
-atom_style hybrid charge bond :pre
+atom_style body nparticle
+atom_style hybrid charge bond
+atom_style hybrid charge body nparticle :pre
[Description:]
@@ -52,11 +56,12 @@ quantities.
{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 |
{dipole} | charge and dipole moment | system with dipolar particles |
{electron} | charge and spin and eradius | electronic force field |
-{ellipsoid} | shape, quaternion for particle orientation, angular momentum | extended aspherical particles |
+{ellipsoid} | shape, quaternion, angular momentum | extended aspherical particles |
{full} | molecular + charge | bio-molecules |
{line} | end points, angular velocity | rigid bodies |
{meso} | rho, e, cv | SPH particles |
@@ -66,13 +71,14 @@ quantities.
{tri} | corner points, angular momentum | rigid bodies |
{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
+All of the styles define point particles, except the {sphere},
+{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
+{body} styles, which define finite-size particles.
+
All of the styles assign mass to particles on a per-type basis, using
the "mass"_mass.html command, except for the finite-size particle
-styles discussed below. They assign mass on a per-atom basis.
-
-All of the styles define point particles, except the {sphere},
-{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, and {tri}
-styles, which define finite-size particles.
+styles. They assign mass to individual particles on a per-particle
+basis.
For the {sphere} style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
@@ -110,6 +116,21 @@ For the {tri} style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
+For the {body} style, the particles are arbitrary bodies with internal
+attributes defined by the "style" of the bodies, which is specified by
+the {Bstyle} argument. Each body particle stores moments of inertia
+and a quaternion 4-vector, so that its orientation can be time
+integrated. This atom style enables LAMMPS to work with particles
+that represent complex entities, such as surface meshes of discrete
+points, collections of sub-particles, deformable objects, etc. Of
+course, the interactions between pairs of bodies will need to be
+encoded in an appropriate pair style.
+
+These are the body styles that LAMMPS currently supports. The name in
+the first column is used as the {Bstyle} argument for atom_style body:
+
+{nparticle} | body with N sub-particles :tb(c=2,s=|)
+
:line
Typically, simulations require only a single (non-hybrid) atom style.
@@ -121,13 +142,13 @@ If some atoms have bonds, but others do not, use the {bond} style.
The only scenario where the {hybrid} style is needed is if there is no
single style which defines all needed properties of all atoms. For
-example, if you want dipolar particles which will be torqued and
-rotate, you would need to use "atom_style hybrid sphere dipole". When
+example, if you want dipolar particles which will rotate due to
+torque, you would need to use "atom_style hybrid sphere dipole". When
a hybrid style is used, atoms store and communicate the union of all
quantities implied by the individual styles.
-LAMMPS can be extended with new atom styles; see "this
-section"_Section_modify.html.
+LAMMPS can be extended with new atom styles as well as new body
+styles; see "this section"_Section_modify.html.
[Restrictions:]
@@ -135,7 +156,8 @@ This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
The {angle}, {bond}, {full}, and {molecular} styles are part of the
-MOLECULAR package. The {dipole} style is part of the "dipole"
+MOLECULAR package. The {line}, {tri}, and {body} styles are part of
+the ASPHERE pacakge. 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"_pair_eff.html. The {meso} style is part
diff --git a/doc/compute.html b/doc/compute.html
index c25364fa3c..a7272cdfb7 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -169,6 +169,7 @@ available in LAMMPS:
- angle/local - theta and energy of each angle
- atom/molecule - sum per-atom properties for each molecule
+
- body/local - attributes of body sub-particles
- bond/local - distance and energy of each bond
- centro/atom - centro-symmetry parameter for each atom
- cluster/atom - cluster ID for each atom
diff --git a/doc/compute.txt b/doc/compute.txt
index 3621654682..cc64d107ce 100644
--- a/doc/compute.txt
+++ b/doc/compute.txt
@@ -164,6 +164,7 @@ available in LAMMPS:
"angle/local"_compute_bond_local.html - theta and energy of each angle
"atom/molecule"_compute_atom_molecule.html - sum per-atom properties for each molecule
+"body/local"_compute_body_local.html - attributes of body sub-particles
"bond/local"_compute_bond_local.html - distance and energy of each bond
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
diff --git a/doc/fix.html b/doc/fix.html
index 1833706066..a621c3eb2e 100644
--- a/doc/fix.html
+++ b/doc/fix.html
@@ -200,8 +200,9 @@ list of fix styles available in LAMMPS:
- npt/sphere - NPT for spherical particles
- nve - constant NVE time integration
- nve/asphere - NVE for aspherical particles
-
- nve/asphere/noforce - NVE for aspherical particles without forces
-
- nve/limit
- NVE with limited step length
+ - nve/asphere/noforce - NVE for aspherical particles without forces"
+
- nve/body - NVE for body particles
+
- nve/limit - NVE with limited step length
- nve/line - NVE for line segments
- nve/noforce - NVE without forces (v only)
- nve/sphere - NVE for spherical particles
diff --git a/doc/fix.txt b/doc/fix.txt
index de5e5e63c5..a077122c72 100644
--- a/doc/fix.txt
+++ b/doc/fix.txt
@@ -196,7 +196,8 @@ list of fix styles available in LAMMPS:
"nve"_fix_nve.html - constant NVE time integration
"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces"
-nve/limit"_fix_nve_limit.html - NVE with limited step length
+"nve/body"_fix_nve_body.html - NVE for body particles
+"nve/limit"_fix_nve_limit.html - NVE with limited step length
"nve/line"_fix_nve_line.html - NVE for line segments
"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
"nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html
index 6147eaf049..7cbff10352 100644
--- a/doc/pair_coeff.html
+++ b/doc/pair_coeff.html
@@ -99,6 +99,7 @@ section of this page.
- pair_style adp - angular dependent potential (ADP) of Mishin
- pair_style airebo - AIREBO potential of Stuart
+
- pair_style body - interactions between body particles
- pair_style bop - BOP potential of Pettifor
- pair_style born - Born-Mayer-Huggins potential
- pair_style born/coul/long - Born-Mayer-Huggins with long-range Coulombics
diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt
index 3ee89a8d6a..14a00f882e 100644
--- a/doc/pair_coeff.txt
+++ b/doc/pair_coeff.txt
@@ -96,6 +96,7 @@ section of "this page"_Section_commands.html#cmd_5.
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
+"pair_style body"_pair_body.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics
diff --git a/doc/pair_style.html b/doc/pair_style.html
index 1024ac5e5d..1931c695dd 100644
--- a/doc/pair_style.html
+++ b/doc/pair_style.html
@@ -101,6 +101,7 @@ section of this page.
- pair_style adp - angular dependent potential (ADP) of Mishin
- pair_style airebo - AIREBO potential of Stuart
+
- pair_style body - interactions between body particles
- pair_style bop - BOP potential of Pettifor
- pair_style born - Born-Mayer-Huggins potential
- pair_style born/coul/long - Born-Mayer-Huggins with long-range Coulombics
diff --git a/doc/pair_style.txt b/doc/pair_style.txt
index d9fe32df97..3e9de618b4 100644
--- a/doc/pair_style.txt
+++ b/doc/pair_style.txt
@@ -98,6 +98,7 @@ section of "this page"_Section_commands.html#cmd_5.
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
+"pair_style body"_pair_body.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics
diff --git a/doc/read_data.html b/doc/read_data.html
index 28e7148e8a..e06f2c731c 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -102,6 +102,7 @@ is different than the default.
- ellipsoids = # of ellipsoids in system
- lines = # of line segments in system
- triangles = # of triangles in system
+
- bodies = # of bodies in system
- xlo xhi = simulation box boundaries in x dimension
- ylo yhi = simulation box boundaries in y dimension
- zlo zhi = simulation box boundaries in z dimension
@@ -178,19 +179,21 @@ added to the system when a simulation runs, e.g. by using the atom_style ellipsoid or line or tri and
-specifies how many of the atoms are finite-size ellipsoids or lines or
-triangles; the remainder are point particles. See the discussion of
-ellipsoidflag and the Ellipsoids section below. See the discussion
-of lineflag and the Lines section below. See the discussion of
-triangleflag and the Triangles section below.
+
The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
+only used with atom_style ellipsoid or line or tri or
+body and specify how many of the atoms are
+finite-size ellipsoids or lines or triangles or bodies; the remainder
+are point particles. See the discussion of ellipsoidflag and the
+Ellipsoids section below. See the discussion of lineflag and the
+Lines section below. See the discussion of triangleflag and the
+Triangles section below. See the discussion of bodyflag and the
+Bodies section below.
These are the section keywords for the body of the file.
-- Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles = atom-property sections
+
- Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies = atom-property sections
- Bonds, Angles, Dihedrals, Impropers = molecular topology sections
- Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs = force field sections
- BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs = class 2 force field sections
@@ -309,6 +312,7 @@ of analysis.
| angle | atom-ID molecule-ID atom-type x y z |
| atomic | atom-ID atom-type x y z |
+| body | atom-ID atom-type bodyflag mass x y z |
| bond | atom-ID molecule-ID atom-type x y z |
| charge | atom-ID atom-type q x y z |
| dipole | atom-ID atom-type q x y z mux muy muz |
@@ -335,8 +339,10 @@ of analysis.
- 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
- density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
-
- volume = volume of atom (distance^3 units)
+
- 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
@@ -371,24 +377,28 @@ keep track of molecule assignments.
The diameter specifies the size of a finite-size spherical particle.
It can be set to 0.0, which means that atom is a point particle.
-The ellipsoidflag, lineflag, and triangleflag determine whether the
-particle is a finite-size ellipsoid or line or triangle of finite
-size, or a point particle. Additional attributes must be defined for
-each ellipsoid in the Ellipsoids section. Additional attributes
-must be defined for each line in the Lines section. Additional
-attributes must be defined for each triangle in the Triangles
-section.
+
The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
+whether the particle is a finite-size ellipsoid or line or triangle or
+body of finite size, or a point particle. Additional attributes must
+be defined for each ellipsoid in the Ellipsoids section. Additional
+attributes must be defined for each line in the Lines section.
+Additional attributes must be defined for each triangle in the
+Triangles section. Additional attributes must be defined for each
+body in the Bodies section.
Some pair styles and fixes and computes that operate on finite-size
particles allow for a mixture of finite-size and point particles. See
the doc pages of individual commands for details.
-The density is used in conjunction with the particle volume for
-finite-size particles to set the mass of the particle as mass =
-density * volume. In this context, volume can be a 3d quantity (for
-spheres or ellipsoids), a 2d quantity (for triangles), or a 1d
-quantity (for line segments). If the volume is 0.0, meaning a point
-particle, then the density value is used as the mass.
+
For finite-size particles, the density is used in conjunction with the
+particle volume to set the mass of each particle as mass = density *
+volume. In this context, volume can be a 3d quantity (for spheres or
+ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line
+segments). If the volume is 0.0, meaning a point particle, then the
+density value is used as the mass. One exception is for the body
+style, in which case the mass of each particle (body or point
+particle) is specified explicitly. This is because the volume of the
+body is not known.
For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
specific values for each sub-style must be listed. The order of the
@@ -437,6 +447,58 @@ script.
+Bodies section:
+
+- one or more lines per body
+
+
- first line syntax: atom-ID ninteger ndouble
+
+
ninteger = # of integer quantities for this particle
+ ndouble = # of floating-point quantities for this particle
+
+ - 0 or more integer lines: one line for every 10 integer quantities
+
+
- 0 or more double lines: one line for every 10 double quantities
+
+
- example:
+
+
12 3 6
+ 2 3 2
+ 1.0 2.0 3.0 1.0 2.0 4.0
+
+ - example:
+
+
12 0 14
+ 1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0
+ 2.0 4.0 4.0 2.0
+
+
+
+The Bodies section must appear if atom_style body
+is used and any atoms are listed in the Atoms section with a
+bodyflag = 1. The number of bodies should be specified in the header
+section via the "bodies" keyword.
+
+Each body can have a variable number of integer and/or floating-point
+values. The number and meaning of the values is defined by the Body
+style which will process and store them for each body. This style is
+given as an argument to the atom_style body command.
+
+The ninteger and ndouble values determine how many integer and
+floating-point values are specified for this particle. Ninteger and
+ndouble can be as large as needed and can be different for every body.
+Integer values are then listed on subsequent lines, 10 values per
+line. Floating-point values follow on subsequent lines, again 10 per
+line. If the number of lines is not evenly divisible by 10, the last
+line in that group contains the remaining values, e.g. 4 values out of
+14 in the last example above, for floating-point values. If there are
+no values of a particular type, no lines appear for that type,
+e.g. there are no integer lines in the last example above.
+
+The Bodies section must appear after the Atoms section.
+
+
+
Bond Coeffs section:
- one line per bond type
diff --git a/doc/read_data.txt b/doc/read_data.txt
index 17f627c1eb..827b67620c 100644
--- a/doc/read_data.txt
+++ b/doc/read_data.txt
@@ -96,6 +96,7 @@ is different than the default.
{ellipsoids} = # of ellipsoids in system
{lines} = # of line segments in system
{triangles} = # of triangles in system
+{bodies} = # of bodies in system
{xlo xhi} = simulation box boundaries in x dimension
{ylo yhi} = simulation box boundaries in y dimension
{zlo zhi} = simulation box boundaries in z dimension
@@ -172,19 +173,21 @@ added to the system when a simulation runs, e.g. by using the "fix
bond/create"_fix_bond_create.html command. This will pre-allocate
space in LAMMPS data structures for storing the new bonds.
-The "ellipsoids" and "lines" and "triangles" settings are only used
-with "atom_style ellipsoid or line or tri"_atom_style.html and
-specifies how many of the atoms are finite-size ellipsoids or lines or
-triangles; the remainder are point particles. See the discussion of
-ellipsoidflag and the {Ellipsoids} section below. See the discussion
-of lineflag and the {Lines} section below. See the discussion of
-triangleflag and the {Triangles} section below.
+The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
+only used with "atom_style ellipsoid or line or tri or
+body"_atom_style.html and specify how many of the atoms are
+finite-size ellipsoids or lines or triangles or bodies; the remainder
+are point particles. See the discussion of ellipsoidflag and the
+{Ellipsoids} section below. See the discussion of lineflag and the
+{Lines} section below. See the discussion of triangleflag and the
+{Triangles} section below. See the discussion of bodyflag and the
+{Bodies} section below.
:line
These are the section keywords for the body of the file.
-{Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles} = atom-property sections
+{Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies} = atom-property sections
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
{Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
Improper Coeffs} = force field sections
@@ -286,6 +289,7 @@ of analysis.
angle: atom-ID molecule-ID atom-type x y z
atomic: atom-ID atom-type x y z
+body: atom-ID atom-type bodyflag mass x y z
bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
dipole: atom-ID atom-type q x y z mux muy muz
@@ -311,8 +315,10 @@ 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
density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
-volume = volume of atom (distance^3 units)
+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
@@ -347,24 +353,28 @@ keep track of molecule assignments.
The diameter specifies the size of a finite-size spherical particle.
It can be set to 0.0, which means that atom is a point particle.
-The ellipsoidflag, lineflag, and triangleflag determine whether the
-particle is a finite-size ellipsoid or line or triangle of finite
-size, or a point particle. Additional attributes must be defined for
-each ellipsoid in the {Ellipsoids} section. Additional attributes
-must be defined for each line in the {Lines} section. Additional
-attributes must be defined for each triangle in the {Triangles}
-section.
+The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
+whether the particle is a finite-size ellipsoid or line or triangle or
+body of finite size, or a point particle. Additional attributes must
+be defined for each ellipsoid in the {Ellipsoids} section. Additional
+attributes must be defined for each line in the {Lines} section.
+Additional attributes must be defined for each triangle in the
+{Triangles} section. Additional attributes must be defined for each
+body in the {Bodies} section.
Some pair styles and fixes and computes that operate on finite-size
particles allow for a mixture of finite-size and point particles. See
the doc pages of individual commands for details.
-The density is used in conjunction with the particle volume for
-finite-size particles to set the mass of the particle as mass =
-density * volume. In this context, volume can be a 3d quantity (for
-spheres or ellipsoids), a 2d quantity (for triangles), or a 1d
-quantity (for line segments). If the volume is 0.0, meaning a point
-particle, then the density value is used as the mass.
+For finite-size particles, the density is used in conjunction with the
+particle volume to set the mass of each particle as mass = density *
+volume. In this context, volume can be a 3d quantity (for spheres or
+ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line
+segments). If the volume is 0.0, meaning a point particle, then the
+density value is used as the mass. One exception is for the body
+style, in which case the mass of each particle (body or point
+particle) is specified explicitly. This is because the volume of the
+body is not known.
For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
specific values for each sub-style must be listed. The order of the
@@ -413,6 +423,49 @@ script.
:line
+{Bodies} section:
+
+one or more lines per body :ulb,l
+first line syntax: atom-ID ninteger ndouble :l
+ ninteger = # of integer quantities for this particle
+ ndouble = # of floating-point quantities for this particle :pre
+0 or more integer lines: one line for every 10 integer quantities :l
+0 or more double lines: one line for every 10 double quantities :l
+example: :l
+ 12 3 6
+ 2 3 2
+ 1.0 2.0 3.0 1.0 2.0 4.0 :pre
+example: :l
+ 12 0 14
+ 1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0
+ 2.0 4.0 4.0 2.0 :pre
+:ule
+
+The {Bodies} section must appear if "atom_style body"_atom_style.html
+is used and any atoms are listed in the {Atoms} section with a
+bodyflag = 1. The number of bodies should be specified in the header
+section via the "bodies" keyword.
+
+Each body can have a variable number of integer and/or floating-point
+values. The number and meaning of the values is defined by the Body
+style which will process and store them for each body. This style is
+given as an argument to the "atom_style body"_atom_style.html command.
+
+The ninteger and ndouble values determine how many integer and
+floating-point values are specified for this particle. Ninteger and
+ndouble can be as large as needed and can be different for every body.
+Integer values are then listed on subsequent lines, 10 values per
+line. Floating-point values follow on subsequent lines, again 10 per
+line. If the number of lines is not evenly divisible by 10, the last
+line in that group contains the remaining values, e.g. 4 values out of
+14 in the last example above, for floating-point values. If there are
+no values of a particular type, no lines appear for that type,
+e.g. there are no integer lines in the last example above.
+
+The {Bodies} section must appear after the {Atoms} section.
+
+:line
+
{Bond Coeffs} section:
one line per bond type :ulb,l
diff --git a/doc/read_restart.html b/doc/read_restart.html
index 4bddba300e..0b012647c0 100644
--- a/doc/read_restart.html
+++ b/doc/read_restart.html
@@ -50,7 +50,7 @@ shake and fix langevin.
provide statistically similar results. This is because the forces
they compute depend on atom velocities, which are used at half-step
values every timestep when forces are computed. When a run restarts,
-forces are initiall evaluated with a full-step velocity, which is
+forces are initially evaluated with a full-step velocity, which is
different than if the run had continued. These pair styles include
granular pair styles, pair dpd, and
pair lubricate.
diff --git a/doc/read_restart.txt b/doc/read_restart.txt
index 4626c12275..5431855eb4 100644
--- a/doc/read_restart.txt
+++ b/doc/read_restart.txt
@@ -47,7 +47,7 @@ Certain pair styles will not restart exactly, though they should
provide statistically similar results. This is because the forces
they compute depend on atom velocities, which are used at half-step
values every timestep when forces are computed. When a run restarts,
-forces are initiall evaluated with a full-step velocity, which is
+forces are initially evaluated with a full-step velocity, which is
different than if the run had continued. These pair styles include
"granular pair styles"_pair_gran.html, "pair dpd"_pair_dpd.html, and
"pair lubricate"_pair_lubricate.html.