For the sphere style, the particles are spheres and each stores a -per-particle diameter and mass. For the ellipsoid style, the -particles are ellipsoids and each stores a per-particle shape vector -with the 3 diamters of the ellipsoid. For the electron style, the -particles representing electrons are 3d 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. +per-particle diameter and mass. If the diameter > 0.0, the particle +is a finite-size sphere. If the diameter = 0.0, it is a point +particle. +
+For the ellipsoid style, the particles are ellipsoids and each +stores a flag which indicates whether it is a finite-size ellipsoid or +a point particle. If it is an ellipsoid, it also stores a shape +vector with the 3 diamters of the ellipsoid and a quaternion 4-vector +with its orientation. +
+For the electron style, the particles representing electrons are 3d +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.
Note that this means the sphere and ellipsoid atom styles set the -diameter/shape and density to 1.0 and thus calculates a mass for the -particle, which is PI/6 * diameter^3 = 0.5236. The peri style sets -the volume and density to 1.0 and thus also set the mass for the -particle to 1.0. +
Note that the sphere atom style sets the default particle diameter +to 1.0 as well as the density. This means the mass for the particle +is not 1.0, but is PI/6 * diameter^3 = 0.5236. +
+Note that the ellipsoid atom style sets the default particle shape +to (0.0 0.0 0.0) and the density to 1.0 which means it is a point +particle, not an ellipsoid, and has a mass of 1.0. +
+Note that the peri style sets the default volume and density to 1.0 +and thus also set the mass for the particle to 1.0. +
+The set command can be used to override many of these +default settings.
Restrictions:
diff --git a/doc/dump.html b/doc/dump.html index 0b155e3514..418f4996b5 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -51,9 +51,7 @@ vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, radius, omegax, omegay, omegaz, - angmomx, angmomy, angmomz, - shapex,shapey, shapez, - quatw, quati, quatj, quatk, tqx, tqy, tqz, + angmomx, angmomy, angmomz, tqx, tqy, tqz, spin, eradius, ervel, erforce, c_ID, c_ID[N], f_ID, f_ID[N], v_name @@ -73,8 +71,6 @@ radius = radius of spherical particle omegax,omegay,omegaz = angular velocity of extended particle angmomx,angmomy,angmomz = angular momentum of extended particle - shapex,shapey,shapez = 3 diameters of ellipsoidal particle - quatw,quati,quatj,quatk = quaternion components for aspherical particles tqx,tqy,tqz = torque on extended particles spin = electron spin eradius = electron radius @@ -426,15 +422,6 @@ quantity. extended aspherical particles that have an angular momentum. Only the ellipsoid atom style defines this quantity. -The shapex, shapey, and shapez attributes are specific to -extended ellipsoidal particles that have a finite size and shape, such -those defined with an atom style of ellipsoidal. -
-The quatw, quati, quatj, quatk attributes are for aspherical -particles defined with an atom style of ellipsoid. They are the -components of the quaternion that defines the orientation of the -particle. -
The tqx, tqy, tqz attributes are for extended spherical or aspherical particles that can sustain a rotational torque due to interactions with other particles. diff --git a/doc/dump_image.html b/doc/dump_image.html index 82826a4fd6..a700b3e8e0 100644 --- a/doc/dump_image.html +++ b/doc/dump_image.html @@ -11,6 +11,9 @@
NOTE: The dump image command has not yet been released as part of +LAMMPS. +
Syntax:
dump ID group-ID image N file keyword value ... diff --git a/doc/dump_image.txt b/doc/dump_image.txt index 324ba2d7a7..80153f265b 100644 --- a/doc/dump_image.txt +++ b/doc/dump_image.txt @@ -8,6 +8,9 @@ dump image command :h3 +NOTE: The dump image command has not yet been released as part of +LAMMPS. + [Syntax:] dump ID group-ID image N file keyword value ... :pre diff --git a/doc/dump_modify.html b/doc/dump_modify.html index aad55efb16..c4a2f9c46b 100644 --- a/doc/dump_modify.html +++ b/doc/dump_modify.html @@ -11,6 +11,9 @@dump_modify command
+NOTE: This options relevant for the dump image command have not yet +been released as part of LAMMPS. +
Syntax:
dump_modify dump-ID keyword values ... @@ -99,8 +102,6 @@ dump_modify xtcdump precision 10000 dump_modify 1 every 1000 dump_modify 1 every v_myVar-NOTE: add some image examples -
Description:
Modify the parameters of a previously defined dump command. Not all diff --git a/doc/dump_modify.txt b/doc/dump_modify.txt index 081a252ec6..715775d416 100644 --- a/doc/dump_modify.txt +++ b/doc/dump_modify.txt @@ -8,6 +8,9 @@ dump_modify command :h3 +NOTE: This options relevant for the dump image command have not yet +been released as part of LAMMPS. + [Syntax:] dump_modify dump-ID keyword values ... :pre @@ -92,8 +95,6 @@ dump_modify xtcdump precision 10000 dump_modify 1 every 1000 dump_modify 1 every v_myVar :pre -NOTE: add some image examples - [Description:] Modify the parameters of a previously defined dump command. Not all diff --git a/doc/fix_store_state.html b/doc/fix_store_state.html index 0d1ad87faf..210a552d28 100644 --- a/doc/fix_store_state.html +++ b/doc/fix_store_state.html @@ -28,8 +28,7 @@ vx, vy, vz, fx, fy, fz, q, mux, muy, muz, radius, omegax, omegay, omegaz, - angmomx, angmomy, angmomz, - quatw, quati, quatj, quatk, tqx, tqy, tqz + angmomx, angmomy, angmomz, tqx, tqy, tqz c_ID, c_ID[N], f_ID, f_ID[N], v_name
id = atom ID
@@ -47,7 +46,6 @@
radius = radius of extended spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
- quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
diff --git a/doc/read_data.html b/doc/read_data.html
index 136b3b0398..af3d2c5700 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -79,6 +79,7 @@ is different than the default.
These are the section keywords for the body of the file.
-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 3 shape values specify the 3 diameters or aspect ratios of a -finite-size ellipsoidal particle, when it is oriented along the 3 -coordinate axes. They can all be set to 0.0, which means that atom is -a point particle. +
The ellipseflag determines whether the particle is a finite-size +ellipsoid of finite size, or a point particle. Additional attributes +must be defined for each ellipsoid in the Ellipsoids 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 @@ -344,18 +348,6 @@ finite-size particles to set the mass of the particle as mass = density * volume. If the volume is 0.0, meaning a point particle, then the density value is used as the mass.
-The values quatw, quati, quatj, and quatk set the orientation -of the atom as a quaternion (4-vector). Note that the shape -attributes specify the aspect ratios of an ellipsoidal particle, which -is oriented by default with its x-axis along the simulation box's -x-axis, and similarly for y and z. If this body is rotated (via the -right-hand rule) by an angle theta around a unit vector (a,b,c), then -the quaternion that represents its new orientation is given by -(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These -4 components are quatw, quati, quatj, and quatk as specified above. -LAMMPS normalizes each atom's quaternion in case (a,b,c) was not -specified as a unit vector. -
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 sub-styles is the same as they were listed in the @@ -363,9 +355,7 @@ sub-styles is the same as they were listed in the are those that are not the 5 standard ones (ID,type,x,y,z). For example, for the "charge" sub-style, a "q" value would appear. For the "full" sub-style, a "molecule-ID" and "q" would appear. These are -listed in the same order they appear as listed above. -
-Thus if +listed in the same order they appear as listed above. Thus if
atom_style hybrid charge sphere@@ -527,6 +517,50 @@ section must be integers (1, not 1.0).
Ellipsoids section: +
+atom-ID = ID of atom which is an ellipsoid + shapex,shapey,shapez = 3 diameters of ellipsoid (distance units) + quatw,quati,quatj,quatk = quaternion components for orientation of atom +type = bond type (1-Nbondtype) + atom1,atom2 = IDs of 1st,2nd atoms in bond ++
12 3 17 29 ++ +
The Ellipsoids section must appear if atom_style +ellipsoid is used and any atoms are listed in the +Atoms section with an ellipsoidflag = 1. The number of ellipsoids +should be specified in the header section via the "ellipsoids" +keyword. +
+The 3 shape values specify the 3 diameters or aspect ratios of a +finite-size ellipsoidal particle, when it is oriented along the 3 +coordinate axes. They must all be non-zero values. +
+The values quatw, quati, quatj, and quatk set the orientation +of the atom as a quaternion (4-vector). Note that the shape +attributes specify the aspect ratios of an ellipsoidal particle, which +is oriented by default with its x-axis along the simulation box's +x-axis, and similarly for y and z. If this body is rotated (via the +right-hand rule) by an angle theta around a unit vector (a,b,c), then +the quaternion that represents its new orientation is given by +(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These +4 components are quatw, quati, quatj, and quatk as specified above. +LAMMPS normalizes each atom's quaternion in case (a,b,c) is not +specified as a unit vector. +
+The Ellipsoids section must appear after the Atoms section. +
+EndBondTorsion Coeffs section:
Keyword quat uses the specified values to create a quaternion (4-vector) that represents the orientation of the selected atoms. Note that particles defined by atom_style ellipsoid -have 3 shape paraeters whicha are used to specify the aspect ratios of -an ellipsoidal particle, which is oriented by default with its x-axis -along the simulation box's x-axis, and similarly for y and z. If this -body is rotated (via the right-hand rule) by an angle theta around a -unit rotation vector (a,b,c), then the quaternion that represents its -new orientation is given by (cos(theta/2), a*sin(theta/2), -b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c values are the -arguments to the quat keyword. LAMMPS normalizes the quaternion in -case (a,b,c) was not specified as a unit vector. For 2d systems, the -a,b,c values are ignored, since a rotation vector of (0,0,1) is the -only valid choice. +have 3 shape parameters. The 3 values must be non-zero for each +particle set by this command. They are used to specify the aspect +ratios of an ellipsoidal particle, which is oriented by default with +its x-axis along the simulation box's x-axis, and similarly for y and +z. If this body is rotated (via the right-hand rule) by an angle +theta around a unit rotation vector (a,b,c), then the quaternion that +represents its new orientation is given by (cos(theta/2), +a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c +values are the arguments to the quat keyword. LAMMPS normalizes the +quaternion in case (a,b,c) was not specified as a unit vector. For 2d +systems, the a,b,c values are ignored, since a rotation vector of +(0,0,1) is the only valid choice.
Keyword quat/random randomizes the orientation of the quaternion of the selected atoms. Random numbers are used in such a way that the orientation of a particular atom is the same, regardless of how many processors are being used. For 2d systems, only orientations in the -xy plane are generated. +xy plane are generated. As with keyword quat, the 3 shape values +must be non-zero for each particle set by this command.
Keyword diameter sets the size of the selected atoms. The particles must be finite-size spheres as defined by the atom_style @@ -172,13 +174,13 @@ particles must be aspherical ellipsoids as defined by the read_data command.
-Keyword mas sets the mass of all selected particles. The -particles must have a per-atom mass attribute, as defined by the +
Keyword mass sets the mass of all selected particles. The particles +must have a per-atom mass attribute, as defined by the atom_style command. See the "mass" command for how to set mass values on a per-type basis.
@@ -189,7 +191,7 @@ to set mass values on a per-type basis. If the atom has a radius attribute (see atom_style sphere) and its radius is non-zero, its mass is set from the density and particle volume. The same is true if the atom has a shape attribute (see atom_style -ellipsoid) and its shape parameters are non-zero. +ellipsoid) and its 3 shape parameters are non-zero. Otherwise the mass is set to the density value directly.Keyword volume sets the volume of all selected particles.