The radius and diameter attributes are specific to extended -spherical particles that have a finite size, such as those defined -with an atom style of sphere. +
The radius and diameter attributes are specific to spherical +particles that have a finite size, such as those defined with an atom +style of sphere.
The omegax, omegay, and omegaz attributes are specific to -extended spherical or aspherical particles that have an angular -velocity. Only certain atom styles, such as sphere define this -quantity. +finite-size spherical particles that have an angular velocity. Only +certain atom styles, such as sphere define this quantity.
The angmomx, angmomy, and angmomz attributes are specific to -extended aspherical particles that have an angular momentum. Only +finite-size aspherical particles that have an angular momentum. Only the ellipsoid atom style defines this quantity.
-The tqx, tqy, tqz attributes are for extended spherical or -aspherical particles that can sustain a rotational torque due -to interactions with other particles. +
The tqx, tqy, tqz attributes are for finite-size particles that +can sustain a rotational torque due to interactions with other +particles.
The spin, eradius, ervel, and erforce attributes are for particles that represent nuclei and electrons modeled with the diff --git a/doc/dump.txt b/doc/dump.txt index 7254255601..9d3538c275 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -442,22 +442,21 @@ defined with an atom style of {dipole}. They give the orientation of the atom's point dipole moment. The {mu} attribute gives the magnitude of the atom's dipole moment. -The {radius} and {diameter} attributes are specific to extended -spherical particles that have a finite size, such as those defined -with an atom style of {sphere}. +The {radius} and {diameter} attributes are specific to spherical +particles that have a finite size, such as those defined with an atom +style of {sphere}. The {omegax}, {omegay}, and {omegaz} attributes are specific to -extended spherical or aspherical particles that have an angular -velocity. Only certain atom styles, such as {sphere} define this -quantity. +finite-size spherical particles that have an angular velocity. Only +certain atom styles, such as {sphere} define this quantity. The {angmomx}, {angmomy}, and {angmomz} attributes are specific to -extended aspherical particles that have an angular momentum. Only +finite-size aspherical particles that have an angular momentum. Only the {ellipsoid} atom style defines this quantity. -The {tqx}, {tqy}, {tqz} attributes are for extended spherical or -aspherical particles that can sustain a rotational torque due -to interactions with other particles. +The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that +can sustain a rotational torque due to interactions with other +particles. The {spin}, {eradius}, {ervel}, and {erforce} attributes are for particles that represent nuclei and electrons modeled with the diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index 45e444e5a4..4774eb007c 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -93,11 +93,10 @@ a Gaussian random number) for speed.
Note that unless you use the omega or angmom keywords, the thermostat effect of this fix is applied to only the translational degrees of freedom for the particles, which is an important -consideration if extended spherical or aspherical particles, which -have rotational degrees of freedom, are being thermostatted. The -translational degrees of freedom can also have a bias velocity removed -from them before thermostatting takes place; see the description -below. +consideration for finite-size particles, which have rotational degrees +of freedom, are being thermostatted. The translational degrees of +freedom can also have a bias velocity removed from them before +thermostatting takes place; see the description below.
IMPORTANT NOTE: Unlike the fix nvt command which performs Nose/Hoover thermostatting AND time integration, this fix diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt index 09e382ee1b..3e3a092d57 100644 --- a/doc/fix_langevin.txt +++ b/doc/fix_langevin.txt @@ -81,11 +81,10 @@ a Gaussian random number) for speed. Note that unless you use the {omega} or {angmom} keywords, the thermostat effect of this fix is applied to only the translational degrees of freedom for the particles, which is an important -consideration if extended spherical or aspherical particles, which -have rotational degrees of freedom, are being thermostatted. The -translational degrees of freedom can also have a bias velocity removed -from them before thermostatting takes place; see the description -below. +consideration for finite-size particles, which have rotational degrees +of freedom, are being thermostatted. The translational degrees of +freedom can also have a bias velocity removed from them before +thermostatting takes place; see the description below. IMPORTANT NOTE: Unlike the "fix nvt"_fix_nh.html command which performs Nose/Hoover thermostatting AND time integration, this fix diff --git a/doc/fix_nph_sphere.html b/doc/fix_nph_sphere.html index c2cb52a285..77d202ca2a 100644 --- a/doc/fix_nph_sphere.html +++ b/doc/fix_nph_sphere.html @@ -29,8 +29,8 @@ fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial
Description:
Perform constant NPH integration to update position, velocity, and -angular velocity each timestep for extended spherical particles in the -group using a Nose/Hoover pressure barostat. P is pressure; H is +angular velocity each timestep for finite-size spherical particles in +the group using a Nose/Hoover pressure barostat. P is pressure; H is enthalpy. This creates a system trajectory consistent with the isenthalpic ensemble.
diff --git a/doc/fix_nph_sphere.txt b/doc/fix_nph_sphere.txt index 153a5cf535..24038971df 100755 --- a/doc/fix_nph_sphere.txt +++ b/doc/fix_nph_sphere.txt @@ -26,8 +26,8 @@ fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial :pre [Description:] Perform constant NPH integration to update position, velocity, and -angular velocity each timestep for extended spherical particles in the -group using a Nose/Hoover pressure barostat. P is pressure; H is +angular velocity each timestep for finite-size spherical particles in +the group using a Nose/Hoover pressure barostat. P is pressure; H is enthalpy. This creates a system trajectory consistent with the isenthalpic ensemble. diff --git a/doc/fix_npt_sphere.html b/doc/fix_npt_sphere.html index 03948a35ff..65995962f2 100644 --- a/doc/fix_npt_sphere.html +++ b/doc/fix_npt_sphere.html @@ -29,8 +29,8 @@ fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partiaDescription:
Perform constant NPT integration to update position, velocity, and -angular velocity each timestep for extended spherical particles in the -group using a Nose/Hoover temperature thermostat and Nose/Hoover +angular velocity each timestep for finite-sizex spherical particles in +the group using a Nose/Hoover temperature thermostat and Nose/Hoover pressure barostat. P is pressure; T is temperature. This creates a system trajectory consistent with the isothermal-isobaric ensemble.
diff --git a/doc/fix_npt_sphere.txt b/doc/fix_npt_sphere.txt index 945af23ef4..435acbbd2a 100755 --- a/doc/fix_npt_sphere.txt +++ b/doc/fix_npt_sphere.txt @@ -26,8 +26,8 @@ fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partia [Description:] Perform constant NPT integration to update position, velocity, and -angular velocity each timestep for extended spherical particles in the -group using a Nose/Hoover temperature thermostat and Nose/Hoover +angular velocity each timestep for finite-sizex spherical particles in +the group using a Nose/Hoover temperature thermostat and Nose/Hoover pressure barostat. P is pressure; T is temperature. This creates a system trajectory consistent with the isothermal-isobaric ensemble. diff --git a/doc/fix_nve_sphere.html b/doc/fix_nve_sphere.html index 0134e8ff68..1d50b251b2 100644 --- a/doc/fix_nve_sphere.html +++ b/doc/fix_nve_sphere.html @@ -38,7 +38,7 @@ fix 1 all nve/sphere update dipoleDescription:
Perform constant NVE integration to update position, velocity, and -angular velocity for extended spherical particles in the group each +angular velocity for finite-size spherical particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble.
diff --git a/doc/fix_nve_sphere.txt b/doc/fix_nve_sphere.txt index 2577be82ad..5bca308d66 100755 --- a/doc/fix_nve_sphere.txt +++ b/doc/fix_nve_sphere.txt @@ -29,7 +29,7 @@ fix 1 all nve/sphere update dipole :pre [Description:] Perform constant NVE integration to update position, velocity, and -angular velocity for extended spherical particles in the group each +angular velocity for finite-size spherical particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. diff --git a/doc/fix_nvt_sphere.html b/doc/fix_nvt_sphere.html index e1c2fa1ce2..c4a494bdef 100644 --- a/doc/fix_nvt_sphere.html +++ b/doc/fix_nvt_sphere.html @@ -27,9 +27,9 @@ fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2Description:
Perform constant NVT integration to update position, velocity, and -angular velocity each timestep for extended spherical particles in the -group using a Nose/Hoover temperature thermostat. V is volume; T is -temperature. This creates a system trajectory consistent with the +angular velocity each timestep for finite-size spherical particles in +the group using a Nose/Hoover temperature thermostat. V is volume; T +is temperature. This creates a system trajectory consistent with the canonical ensemble.
This fix differs from the fix nvt command, which diff --git a/doc/fix_nvt_sphere.txt b/doc/fix_nvt_sphere.txt index 7c9ddc99a7..9cc8d1e089 100755 --- a/doc/fix_nvt_sphere.txt +++ b/doc/fix_nvt_sphere.txt @@ -24,9 +24,9 @@ fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2 :pre [Description:] Perform constant NVT integration to update position, velocity, and -angular velocity each timestep for extended spherical particles in the -group using a Nose/Hoover temperature thermostat. V is volume; T is -temperature. This creates a system trajectory consistent with the +angular velocity each timestep for finite-size spherical particles in +the group using a Nose/Hoover temperature thermostat. V is volume; T +is temperature. This creates a system trajectory consistent with the canonical ensemble. This fix differs from the "fix nvt"_fix_nh.html command, which diff --git a/doc/fix_store_state.html b/doc/fix_store_state.html index 067ad38aea..81a4882730 100644 --- a/doc/fix_store_state.html +++ b/doc/fix_store_state.html @@ -43,10 +43,10 @@ fx,fy,fz = forces on atoms q = atom charge mux,muy,muz = orientation of dipolar atom - radius = radius of extended spherical particle - omegax,omegay,omegaz = angular velocity of extended particle - angmomx,angmomy,angmomz = angular momentum of extended particle - tqx,tqy,tqz = torque on extended particles + radius = radius of spherical particle + omegax,omegay,omegaz = angular velocity of spherical particle + angmomx,angmomy,angmomz = angular momentum of aspherical particle + tqx,tqy,tqz = torque on finite-size 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 f_ID = per-atom vector calculated by a fix with ID diff --git a/doc/fix_store_state.txt b/doc/fix_store_state.txt index 05b6d8878b..bc3e9d2d8d 100644 --- a/doc/fix_store_state.txt +++ b/doc/fix_store_state.txt @@ -36,10 +36,10 @@ input = one or more atom attributes :l fx,fy,fz = forces on atoms q = atom charge mux,muy,muz = orientation of dipolar atom - radius = radius of extended spherical particle - omegax,omegay,omegaz = angular velocity of extended particle - angmomx,angmomy,angmomz = angular momentum of extended particle - tqx,tqy,tqz = torque on extended particles + radius = radius of spherical particle + omegax,omegay,omegaz = angular velocity of spherical particle + angmomx,angmomy,angmomz = angular momentum of aspherical particle + tqx,tqy,tqz = torque on finite-size 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 f_ID = per-atom vector calculated by a fix with ID diff --git a/doc/fix_temp_berendsen.html b/doc/fix_temp_berendsen.html index dfd2bc88c8..443f491a6d 100644 --- a/doc/fix_temp_berendsen.html +++ b/doc/fix_temp_berendsen.html @@ -38,11 +38,11 @@ thermostat (Berendsen), which rescales their velociti every timestep.
The thermostat is applied to only the translational degrees of freedom -for the particles, which is an important consideration if extended -spherical or aspherical particles which have rotational degrees of -freedom are being thermostatted with this fix. The translational -degrees of freedom can also have a bias velocity removed from them -before thermostatting takes place; see the description below. +for the particles, which is an important consideration for finite-size +particles which have rotational degrees of freedom are being +thermostatted with this fix. The translational degrees of freedom can +also have a bias velocity removed from them before thermostatting +takes place; see the description below.
The desired temperature at each timestep is a ramped value during the run from Tstart to Tstop. The Tdamp parameter is specified in diff --git a/doc/fix_temp_berendsen.txt b/doc/fix_temp_berendsen.txt index 94fca057ee..4412481aee 100644 --- a/doc/fix_temp_berendsen.txt +++ b/doc/fix_temp_berendsen.txt @@ -30,11 +30,11 @@ thermostat "(Berendsen)"_#Berendsen, which rescales their velocities every timestep. The thermostat is applied to only the translational degrees of freedom -for the particles, which is an important consideration if extended -spherical or aspherical particles which have rotational degrees of -freedom are being thermostatted with this fix. The translational -degrees of freedom can also have a bias velocity removed from them -before thermostatting takes place; see the description below. +for the particles, which is an important consideration for finite-size +particles which have rotational degrees of freedom are being +thermostatted with this fix. The translational degrees of freedom can +also have a bias velocity removed from them before thermostatting +takes place; see the description below. The desired temperature at each timestep is a ramped value during the run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in diff --git a/doc/pair_gayberne.html b/doc/pair_gayberne.html index b41efdc59d..91172da3ff 100644 --- a/doc/pair_gayberne.html +++ b/doc/pair_gayberne.html @@ -200,7 +200,7 @@ diameter.
This pair style requires that atoms be ellipsoids as defined by the atom_style ellipsoid command.
-Particles acted on by the potential can be extended aspherical or +
Particles acted on by the potential can be finite-size aspherical or spherical particles, or point particles. Spherical particles have all 3 of their shape parameters equal to each other. Point particles have all 3 of their shape parameters equal to 0.0. diff --git a/doc/pair_gayberne.txt b/doc/pair_gayberne.txt index d7403df468..dea23d4d75 100755 --- a/doc/pair_gayberne.txt +++ b/doc/pair_gayberne.txt @@ -195,7 +195,7 @@ diameter. This pair style requires that atoms be ellipsoids as defined by the "atom_style ellipsoid"_atom_style.html command. -Particles acted on by the potential can be extended aspherical or +Particles acted on by the potential can be finite-size aspherical or spherical particles, or point particles. Spherical particles have all 3 of their shape parameters equal to each other. Point particles have all 3 of their shape parameters equal to 0.0. diff --git a/doc/pair_resquared.html b/doc/pair_resquared.html index 2cd51731b4..b2ed70ded0 100644 --- a/doc/pair_resquared.html +++ b/doc/pair_resquared.html @@ -214,7 +214,7 @@ LAMMPS section for more info.
This pair style requires that atoms be ellipsoids as defined by the atom_style ellipsoid command.
-Particles acted on by the potential can be extended aspherical or +
Particles acted on by the potential can be finite-size aspherical or spherical particles, or point particles. Spherical particles have all 3 of their shape parameters equal to each other. Point particles have all 3 of their shape parameters equal to 0.0. diff --git a/doc/pair_resquared.txt b/doc/pair_resquared.txt index 1a4c76650d..be201fa405 100755 --- a/doc/pair_resquared.txt +++ b/doc/pair_resquared.txt @@ -209,7 +209,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. This pair style requires that atoms be ellipsoids as defined by the "atom_style ellipsoid"_atom_style.html command. -Particles acted on by the potential can be extended aspherical or +Particles acted on by the potential can be finite-size aspherical or spherical particles, or point particles. Spherical particles have all 3 of their shape parameters equal to each other. Point particles have all 3 of their shape parameters equal to 0.0.