where M is the total mass of the group, Rcm is the center-of-mass position of the group, and the sum is over all atoms in the group.
+A Rg tensor, stored as a 6-element vector, is also calculated by this +compute. The formula for the components of the tensor is the same as +the above formula, except that (Ri - Rcm)^2 is replaced by (Rix - +Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6 components of +the vector are ordered xx, yy, zz, xy, xz, yz. +
IMPORTANT NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. See the dump custom command for a discussion of @@ -47,13 +53,16 @@ image command.
Output info:
-This compute calculates a global scalar (Rg). This value can be used -by any command that uses a global scalar value from a compute as -input. See Section_howto 15 for an -overview of LAMMPS output options. +
This compute calculates a global scalar (Rg) and a global vector of +length 6 (Rg tensor), which can be accessed by indices 1-6. These +values can be used by any command that uses a global scalar value or +vector values from a compute as input. See Section_howto +15 for an overview of LAMMPS output +options.
-The scalar value calculated by this compute is "intensive". The -scalar value will be in distance units. +
The scalar and vector values calculated by this compute are +"intensive". The scalar and vector values will be in distance +units.
Restrictions: none
diff --git a/doc/compute_gyration.txt b/doc/compute_gyration.txt index 2cc818c5f5..6661fb439a 100644 --- a/doc/compute_gyration.txt +++ b/doc/compute_gyration.txt @@ -33,6 +33,12 @@ this formula where M is the total mass of the group, Rcm is the center-of-mass position of the group, and the sum is over all atoms in the group. +A Rg tensor, stored as a 6-element vector, is also calculated by this +compute. The formula for the components of the tensor is the same as +the above formula, except that (Ri - Rcm)^2 is replaced by (Rix - +Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6 components of +the vector are ordered xx, yy, zz, xy, xz, yz. + IMPORTANT NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. See the "dump custom"_dump.html command for a discussion of @@ -44,13 +50,16 @@ image"_set.html command. [Output info:] -This compute calculates a global scalar (Rg). This value can be used -by any command that uses a global scalar value from a compute as -input. See "Section_howto 15"_Section_howto.html#howto_15 for an -overview of LAMMPS output options. +This compute calculates a global scalar (Rg) and a global vector of +length 6 (Rg tensor), which can be accessed by indices 1-6. These +values can be used by any command that uses a global scalar value or +vector values from a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. -The scalar value calculated by this compute is "intensive". The -scalar value will be in distance "units"_units.html. +The scalar and vector values calculated by this compute are +"intensive". The scalar and vector values will be in distance +"units"_units.html. [Restrictions:] none diff --git a/doc/compute_gyration_molecule.html b/doc/compute_gyration_molecule.html index f74218009f..e3d49358cb 100644 --- a/doc/compute_gyration_molecule.html +++ b/doc/compute_gyration_molecule.html @@ -13,14 +13,23 @@Syntax:
-compute ID group-ID gyration/molecule +compute ID group-ID gyration/molecule keyword value ...-
Examples:
-compute 1 molecule gyration/molecule +compute 1 molecule gyration/molecule +compute 2 molecule gyration/molecule tensorDescription:
@@ -37,6 +46,13 @@ formula position of the molecule, and the sum is over all atoms in the molecule and in the group. +If the tensor keyword is specified, then the scalar Rg value is not +calculated, but an Rg tensor is instead calculated for each molecule. +The formula for the components of the tensor is the same as the above +formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy - +Rcmy) for the xy component, etc. The 6 components of the tensor are +ordered xx, yy, zz, xy, xz, yz. +
Rg for a particular molecule is only computed if one or more of its atoms are in the specified group. Normally all atoms in the molecule should be in the group, however this is not required. LAMMPS will @@ -60,14 +76,18 @@ image command.
Output info:
-This compute calculates a global vector of Rg values where the length -of the vector = Nmolecules. These values can be used by any command -that uses global vector values from a compute as input. See this +
This compute calculates a global vector if the tensor keyword is not +specified and a global array if it is. The length of the vector or +number of rows in the array is the number of molecules. If the +tensor keyword is specified, the global array has 6 columns. The +vector or array can be accessed by any command that uses global values +from a compute as input. See this section for an overview of LAMMPS output options.
-The vector values calculated by this compute are "intensive". The -vector values will be in distance units. +
All the vector or array values calculated by this compute are +"intensive". The vector or array values will be in distance +units.
Restrictions: none
diff --git a/doc/compute_gyration_molecule.txt b/doc/compute_gyration_molecule.txt index 375e109326..a9c2d5a79f 100644 --- a/doc/compute_gyration_molecule.txt +++ b/doc/compute_gyration_molecule.txt @@ -10,14 +10,19 @@ compute gyration/molecule command :h3 [Syntax:] -compute ID group-ID gyration/molecule :pre +compute ID group-ID gyration/molecule keyword value ... :pre -ID, group-ID are documented in "compute"_compute.html command -gyration/molecule = style name of this compute command :ul +ID, group-ID are documented in "compute"_compute.html command :ulb,l +gyration/molecule = style name of this compute command :l +zero or more keyword/value pairs may be appended :l +keyword = {tensor} :l + {tensor} value = none +:ule [Examples:] -compute 1 molecule gyration/molecule :pre +compute 1 molecule gyration/molecule +compute 2 molecule gyration/molecule tensor :pre [Description:] @@ -34,6 +39,13 @@ where M is the total mass of the molecule, Rcm is the center-of-mass position of the molecule, and the sum is over all atoms in the molecule and in the group. +If the {tensor} keyword is specified, then the scalar Rg value is not +calculated, but an Rg tensor is instead calculated for each molecule. +The formula for the components of the tensor is the same as the above +formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy - +Rcmy) for the xy component, etc. The 6 components of the tensor are +ordered xx, yy, zz, xy, xz, yz. + Rg for a particular molecule is only computed if one or more of its atoms are in the specified group. Normally all atoms in the molecule should be in the group, however this is not required. LAMMPS will @@ -57,14 +69,18 @@ image"_set.html command. [Output info:] -This compute calculates a global vector of Rg values where the length -of the vector = Nmolecules. These values can be used by any command -that uses global vector values from a compute as input. See "this +This compute calculates a global vector if the {tensor} keyword is not +specified and a global array if it is. The length of the vector or +number of rows in the array is the number of molecules. If the +{tensor} keyword is specified, the global array has 6 columns. The +vector or array can be accessed by any command that uses global values +from a compute as input. See "this section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The vector values calculated by this compute are "intensive". The -vector values will be in distance "units"_units.html. +All the vector or array values calculated by this compute are +"intensive". The vector or array values will be in distance +"units"_units.html. [Restrictions:] none