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This commit is contained in:
sjplimp
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@ -71,14 +71,22 @@ All of the styles define point particles, except the {sphere},
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particles.
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For the {sphere} style, the particles are spheres and each stores a
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per-particle diameter and mass. For the {ellipsoid} style, the
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particles are ellipsoids and each stores a per-particle shape vector
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with the 3 diamters of the ellipsoid. For the {electron} style, the
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particles representing electrons are 3d Gaussians with a specified
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position and bandwidth or uncertainty in position, which is
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represented by the eradius = electron size. For the {peri} style, the
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particles are spherical and each stores a per-particle mass and
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volume.
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per-particle diameter and mass. If the diameter > 0.0, the particle
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is a finite-size sphere. If the diameter = 0.0, it is a point
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particle.
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For the {ellipsoid} style, the particles are ellipsoids and each
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stores a flag which indicates whether it is a finite-size ellipsoid or
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a point particle. If it is an ellipsoid, it also stores a shape
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vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
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with its orientation.
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For the {electron} style, the particles representing electrons are 3d
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Gaussians with a specified position and bandwidth or uncertainty in
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position, which is represented by the eradius = electron size.
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For the {peri} style, the particles are spherical and each stores a
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per-particle mass and volume.
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:line
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@ -139,7 +139,7 @@ to change these values.
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charge = 0.0
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dipole moment magnitude = 0.0
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diameter = 1.0
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shape = 1.0 1.0 1.0
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shape = 0.0 0.0 0.0
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density = 1.0
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volume = 1.0
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velocity = 0.0 0.0 0.0
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@ -148,11 +148,19 @@ angular momentum = 0.0 0.0 0.0
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quaternion = (1,0,0,0)
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bonds, angles, dihedrals, impropers = none :ul
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Note that this means the {sphere} and {ellipsoid} atom styles set the
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diameter/shape and density to 1.0 and thus calculates a mass for the
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particle, which is PI/6 * diameter^3 = 0.5236. The {peri} style sets
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the volume and density to 1.0 and thus also set the mass for the
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particle to 1.0.
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Note that the {sphere} atom style sets the default particle diameter
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to 1.0 as well as the density. This means the mass for the particle
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is not 1.0, but is PI/6 * diameter^3 = 0.5236.
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Note that the {ellipsoid} atom style sets the default particle shape
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to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
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particle, not an ellipsoid, and has a mass of 1.0.
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Note that the {peri} style sets the default volume and density to 1.0
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and thus also set the mass for the particle to 1.0.
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The "set"_set.html command can be used to override many of these
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default settings.
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[Restrictions:]
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15
doc/dump.txt
15
doc/dump.txt
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@ -41,9 +41,7 @@ args = list of arguments for a particular style :l
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vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, mu,
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radius, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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shapex,shapey, shapez,
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quatw, quati, quatj, quatk, tqx, tqy, tqz,
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angmomx, angmomy, angmomz, tqx, tqy, tqz,
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spin, eradius, ervel, erforce,
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c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
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@ -63,8 +61,6 @@ args = list of arguments for a particular style :l
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radius = radius of spherical particle
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omegax,omegay,omegaz = angular velocity of extended particle
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angmomx,angmomy,angmomz = angular momentum of extended particle
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shapex,shapey,shapez = 3 diameters of ellipsoidal particle
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quatw,quati,quatj,quatk = quaternion components for aspherical particles
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tqx,tqy,tqz = torque on extended particles
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spin = electron spin
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eradius = electron radius
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@ -415,15 +411,6 @@ The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
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extended aspherical particles that have an angular momentum. Only
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the {ellipsoid} atom style defines this quantity.
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The {shapex}, {shapey}, and {shapez} attributes are specific to
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extended ellipsoidal particles that have a finite size and shape, such
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those defined with an atom style of {ellipsoidal}.
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The {quatw}, {quati}, {quatj}, {quatk} attributes are for aspherical
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particles defined with an atom style of {ellipsoid}. They are the
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components of the quaternion that defines the orientation of the
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particle.
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The {tqx}, {tqy}, {tqz} attributes are for extended spherical or
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aspherical particles that can sustain a rotational torque due
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to interactions with other particles.
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@ -21,8 +21,7 @@ input = one or more atom attributes :l
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vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz,
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radius, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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quatw, quati, quatj, quatk, tqx, tqy, tqz
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angmomx, angmomy, angmomz, tqx, tqy, tqz
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c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
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id = atom ID
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@ -40,7 +39,6 @@ input = one or more atom attributes :l
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radius = radius of extended spherical particle
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omegax,omegay,omegaz = angular velocity of extended particle
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angmomx,angmomy,angmomz = angular momentum of extended particle
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quatw,quati,quatj,quatk = quaternion components for aspherical particles
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tqx,tqy,tqz = torque on extended particles
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c_ID = per-atom vector calculated by a compute with ID
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c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
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38
doc/set.txt
38
doc/set.txt
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@ -136,23 +136,25 @@ many processors are being used.
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Keyword {quat} uses the specified values to create a quaternion
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(4-vector) that represents the orientation of the selected atoms.
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Note that particles defined by "atom_style ellipsoid"_atom_style.html
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have 3 shape paraeters whicha are used to specify the aspect ratios of
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an ellipsoidal particle, which is oriented by default with its x-axis
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along the simulation box's x-axis, and similarly for y and z. If this
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body is rotated (via the right-hand rule) by an angle theta around a
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unit rotation vector (a,b,c), then the quaternion that represents its
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new orientation is given by (cos(theta/2), a*sin(theta/2),
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b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c values are the
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arguments to the {quat} keyword. LAMMPS normalizes the quaternion in
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case (a,b,c) was not specified as a unit vector. For 2d systems, the
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a,b,c values are ignored, since a rotation vector of (0,0,1) is the
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only valid choice.
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have 3 shape parameters. The 3 values must be non-zero for each
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particle set by this command. They are used to specify the aspect
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ratios of an ellipsoidal particle, which is oriented by default with
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its x-axis along the simulation box's x-axis, and similarly for y and
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z. If this body is rotated (via the right-hand rule) by an angle
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theta around a unit rotation vector (a,b,c), then the quaternion that
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represents its new orientation is given by (cos(theta/2),
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a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
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values are the arguments to the {quat} keyword. LAMMPS normalizes the
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quaternion in case (a,b,c) was not specified as a unit vector. For 2d
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systems, the a,b,c values are ignored, since a rotation vector of
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(0,0,1) is the only valid choice.
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Keyword {quat/random} randomizes the orientation of the quaternion of
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the selected atoms. Random numbers are used in such a way that the
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orientation of a particular atom is the same, regardless of how many
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processors are being used. For 2d systems, only orientations in the
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xy plane are generated.
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xy plane are generated. As with keyword {quat}, the 3 shape values
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must be non-zero for each particle set by this command.
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Keyword {diameter} sets the size of the selected atoms. The particles
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must be finite-size spheres as defined by the "atom_style
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@ -167,13 +169,13 @@ particles must be aspherical ellipsoids as defined by the "atom_style
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ellipsoid"_atom_style.html command. The {Sx}, {Sy}, {Sz} settings are
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the 3 diameters of the ellipsoid in each direction. All 3 can be set
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to the same value, which means the ellipsoid is effectively a sphere.
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Or then can all be set to 0.0 which means the particle will be treated
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as a point particle. Note that this command does not adjust the
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particle mass, even if it was defined with a density, e.g. via the
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They can also all be set to 0.0 which means the particle will be
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treated as a point particle. Note that this command does not adjust
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the particle mass, even if it was defined with a density, e.g. via the
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"read_data"_read_data.html command.
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Keyword {mas} sets the mass of all selected particles. The
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particles must have a per-atom mass attribute, as defined by the
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Keyword {mass} sets the mass of all selected particles. The particles
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must have a per-atom mass attribute, as defined by the
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"atom_style"_atom_style.html command. See the "mass" command for how
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to set mass values on a per-type basis.
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@ -184,7 +186,7 @@ to set mass values on a per-type basis. If the atom has a radius
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attribute (see "atom_style sphere"_atom_style.html) and its radius is
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non-zero, its mass is set from the density and particle volume. The
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same is true if the atom has a shape attribute (see "atom_style
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ellipsoid"_atom_style.html) and its shape parameters are non-zero.
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ellipsoid"_atom_style.html) and its 3 shape parameters are non-zero.
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Otherwise the mass is set to the density value directly.
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Keyword {volume} sets the volume of all selected particles.
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@ -10,12 +10,11 @@ create_box 2 box
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create_atoms 1 box
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set group all type/fraction 2 0.1 95392
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set group all quat/random 18238
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set type 1 mass 1.0
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set type 2 mass 1.5
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set type 1 shape 1 1 1
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set type 2 shape 3 1 1
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set group all quat/random 18238
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compute rot all temp/asphere
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group spheroid type 1
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@ -41,11 +40,13 @@ thermo 100
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timestep 0.002
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compute q all property/atom quatw quati quatj quatk
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dump 1 all custom 100 dump.ellipse.gayberne &
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id type x y z quatw quati quatj quatk
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id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
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#dump 1 all custom 100 dump.ellipse.resquared &
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# id type x y z quatw quati quatj quatk
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# id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
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fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
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mtk no pchain 0 tchain 1
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@ -10,12 +10,11 @@ create_box 2 box
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create_atoms 1 box
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set group all type/fraction 2 0.1 95392
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set group all quat/random 18238
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set type 1 mass 1.0
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set type 2 mass 1.5
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set type 1 shape 1 1 1
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set type 2 shape 3 1 1
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set group all quat/random 18238
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compute rot all temp/asphere
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group spheroid type 1
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@ -41,11 +40,13 @@ thermo 100
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timestep 0.002
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compute q all property/atom quatw quati quatj quatk
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#dump 1 all custom 100 dump.ellipse.gayberne &
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# id type x y z quatw quati quatj quatk
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# id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
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dump 1 all custom 100 dump.ellipse.resquared &
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id type x y z quatw quati quatj quatk
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id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
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fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
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mtk no pchain 0 tchain 1
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@ -92,6 +92,7 @@ class Data {
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int style_hybrid,style_molecular,style_peri,style_sphere;
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bigint natoms;
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bigint nellipsoids;
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bigint nbonds,nangles,ndihedrals,nimpropers;
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int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
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int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
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@ -202,6 +203,7 @@ class Data {
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double *s0,*x0x,*x0y,*x0z;
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double *shapex,*shapey,*shapez;
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double *quatw,*quati,*quatj,*quatk,*angmomx,*angmomy,*angmomz;
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int *ellipsoid;
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int *bond_type,*angle_type,*dihedral_type,*improper_type;
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int *bond_atom1,*bond_atom2;
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int *angle_atom1,*angle_atom2,*angle_atom3;
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@ -916,22 +918,25 @@ int atom_ellipsoid(double *buf, Data &data, int iatoms)
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data.vy[iatoms] = buf[m++];
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data.vz[iatoms] = buf[m++];
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data.rmass[iatoms] = buf[m++];
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data.angmomx[iatoms] = buf[m++];
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data.angmomy[iatoms] = buf[m++];
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data.angmomz[iatoms] = buf[m++];
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data.ellipsoid[iatoms] = static_cast<int> (buf[m++]);
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if (data.ellipsoid[iatoms]) {
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data.nellipsoids++;
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data.shapex[iatoms] = buf[m++];
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data.shapey[iatoms] = buf[m++];
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data.shapez[iatoms] = buf[m++];
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data.rmass[iatoms] = buf[m++];
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if (data.shapex[iatoms] == 0.0) data.density[iatoms] = data.rmass[iatoms];
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else
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data.density[iatoms] = data.rmass[iatoms] /
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(4.0*PI/3.0 *
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data.shapex[iatoms]*data.shapey[iatoms]*data.shapez[iatoms]);
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data.quatw[iatoms] = buf[m++];
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data.quati[iatoms] = buf[m++];
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data.quatj[iatoms] = buf[m++];
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data.quatk[iatoms] = buf[m++];
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data.angmomx[iatoms] = buf[m++];
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data.angmomy[iatoms] = buf[m++];
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data.angmomz[iatoms] = buf[m++];
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data.density[iatoms] = data.rmass[iatoms] /
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(4.0*PI/3.0 *
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data.shapex[iatoms]*data.shapey[iatoms]*data.shapez[iatoms]);
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} else data.density[iatoms] = data.rmass[iatoms];
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return m;
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}
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@ -1218,18 +1223,19 @@ void allocate_full(Data &data)
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void allocate_ellipsoid(Data &data)
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{
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data.shapex = new double[data.natoms];
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data.shapey = new double[data.natoms];
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data.shapez = new double[data.natoms];
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data.rmass = new double[data.natoms];
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data.density = new double[data.natoms];
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data.quatw = new double[data.natoms];
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data.quati = new double[data.natoms];
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data.quatj = new double[data.natoms];
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data.quatk = new double[data.natoms];
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data.angmomx = new double[data.natoms];
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data.angmomy = new double[data.natoms];
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data.angmomz = new double[data.natoms];
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data.ellipsoid = new int[data.natoms];
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data.quatw = new double[data.natoms];
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data.shapex = new double[data.natoms];
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data.shapey = new double[data.natoms];
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data.shapez = new double[data.natoms];
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data.quati = new double[data.natoms];
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data.quatj = new double[data.natoms];
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data.quatk = new double[data.natoms];
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}
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void allocate_sphere(Data &data)
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@ -2625,7 +2631,10 @@ void improper(FILE *fp, Data &data)
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// initialize Data
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// ---------------------------------------------------------------------
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Data::Data() {}
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Data::Data()
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{
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nellipsoids = 0;
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}
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// ---------------------------------------------------------------------
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// print out stats on problem
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@ -2639,6 +2648,9 @@ void Data::stats()
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printf(" Ntimestep = " BIGINT_FORMAT "\n",ntimestep);
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printf(" Nprocs = %d\n",nprocs);
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printf(" Natoms = " BIGINT_FORMAT "\n",natoms);
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if (nellipsoids) printf(" Nellipsoids = " BIGINT_FORMAT "\n",nellipsoids);
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printf(" Nbonds = " BIGINT_FORMAT "\n",nbonds);
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printf(" Nangles = " BIGINT_FORMAT "\n",nangles);
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printf(" Ndihedrals = " BIGINT_FORMAT "\n",ndihedrals);
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@ -2651,6 +2663,7 @@ void Data::stats()
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printf(" Angle style = %s\n",angle_style);
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printf(" Dihedral style = %s\n",dihedral_style);
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printf(" Improper style = %s\n",improper_style);
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printf(" Xlo xhi = %g %g\n",xlo,xhi);
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printf(" Ylo yhi = %g %g\n",ylo,yhi);
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printf(" Zlo zhi = %g %g\n",zlo,zhi);
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@ -2670,6 +2683,7 @@ void Data::write(FILE *fp, FILE *fp2)
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BIGINT_FORMAT ", procs = %d\n\n",ntimestep,nprocs);
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fprintf(fp,BIGINT_FORMAT " atoms\n",natoms);
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if (nellipsoids) fprintf(fp,BIGINT_FORMAT " ellipsoids\n",nellipsoids);
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if (nbonds) fprintf(fp,BIGINT_FORMAT " bonds\n",nbonds);
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if (nangles) fprintf(fp,BIGINT_FORMAT " angles\n",nangles);
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if (ndihedrals) fprintf(fp,BIGINT_FORMAT " dihedrals\n",ndihedrals);
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@ -3240,6 +3254,17 @@ void Data::write(FILE *fp, FILE *fp2)
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}
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}
|
||||
|
||||
if (nellipsoids) {
|
||||
fprintf(fp,"\nEllipsoids\n\n");
|
||||
for (uint64_t i = 0; i < natoms; i++) {
|
||||
if (ellipsoid[i])
|
||||
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e "
|
||||
"%-1.16e %-1.16e %-1.16e %-1.16e \n",
|
||||
tag[i],2.0*shapex[i],2.0*shapey[i],2.0*shapez[i],
|
||||
quatw[i],quati[i],quatj[i],quatk[i]);
|
||||
}
|
||||
}
|
||||
|
||||
if (nbonds) {
|
||||
fprintf(fp,"\nBonds\n\n");
|
||||
for (uint64_t i = 0; i < nbonds; i++)
|
||||
|
|
@ -3302,16 +3327,16 @@ void Data::write_atom_charge(FILE *fp, int i, int ix, int iy, int iz)
|
|||
|
||||
void Data::write_atom_dipole(FILE *fp, int i, int ix, int iy, int iz)
|
||||
{
|
||||
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
|
||||
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
|
||||
"%-1.16e %-1.16e %d %d %d",
|
||||
tag[i],type[i],q[i],x[i],y[i],z[i],
|
||||
mux[i],muy[i],muz[i],ix,iy,iz);
|
||||
}
|
||||
|
||||
void Data::write_atom_ellipsoid(FILE *fp, int i, int ix, int iy, int iz)
|
||||
{
|
||||
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
|
||||
tag[i],type[i],shapex[i],shapey[i],shapez[i],density[i],
|
||||
x[i],y[i],z[i],quatw[i],quati[i],quatj[i],quatk[i],ix,iy,iz);
|
||||
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
|
||||
tag[i],type[i],ellipsoid[i],density[i],x[i],y[i],z[i],ix,iy,iz);
|
||||
}
|
||||
|
||||
void Data::write_atom_full(FILE *fp, int i, int ix, int iy, int iz)
|
||||
|
|
@ -3367,9 +3392,7 @@ void Data::write_atom_dipole_extra(FILE *fp, int i)
|
|||
|
||||
void Data::write_atom_ellipsoid_extra(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
|
||||
shapex[i],shapey[i],shapez[i],density[i],
|
||||
quatw[i],quati[i],quatj[i],quatk[i]);
|
||||
fprintf(fp," %d %-1.16e",ellipsoid[i],density[i]);
|
||||
}
|
||||
|
||||
void Data::write_atom_full_extra(FILE *fp, int i)
|
||||
|
|
|
|||
Loading…
Reference in New Issue