From e247ee0edc09c739cb4c2ab43354ed8ab7585e4c Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 19 Dec 2014 22:44:45 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12840 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_gyration.html | 24 +++++++++++++----------- doc/compute_gyration.txt | 24 +++++++++++++----------- doc/compute_gyration_molecule.html | 22 ++++++++++++---------- doc/compute_gyration_molecule.txt | 22 ++++++++++++---------- doc/fix_nvt_sllod.html | 19 +++++++++++++------ 5 files changed, 63 insertions(+), 48 deletions(-) diff --git a/doc/compute_gyration.html b/doc/compute_gyration.html index fb340c4719..e5633840da 100644 --- a/doc/compute_gyration.html +++ b/doc/compute_gyration.html @@ -28,19 +28,22 @@ group of atoms, including all effects due to atoms passing thru periodic boundaries.

-

Rg is a measure of the size of the group of atoms, and is computed by -this formula +

Rg is a measure of the size of the group of atoms, and is computed as +the square root of the Rg^2 value in 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. +

A Rg^2 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. Note +that unlike the scalar Rg, each of the 6 values of the tensor is +effectively a "squared" value, since the cross-terms may be negative +and taking a sqrt() would be invalid.

IMPORTANT NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. @@ -54,16 +57,15 @@ image command.

Output info:

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 +length 6 (Rg^2 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 and vector values calculated by this compute are -"intensive". The scalar and vector values will be in distance -units, since they are the square root of values -represented by the formula above. +"intensive". The scalar and vector values will be in distance and +distance^2 units respectively.

Restrictions: none

diff --git a/doc/compute_gyration.txt b/doc/compute_gyration.txt index c704bbdf3d..7eb56a1584 100644 --- a/doc/compute_gyration.txt +++ b/doc/compute_gyration.txt @@ -25,19 +25,22 @@ Define a computation that calculates the radius of gyration Rg of the group of atoms, including all effects due to atoms passing thru periodic boundaries. -Rg is a measure of the size of the group of atoms, and is computed by -this formula +Rg is a measure of the size of the group of atoms, and is computed as +the square root of the Rg^2 value in this formula :c,image(Eqs/compute_gyration.jpg) 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. +A Rg^2 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. Note +that unlike the scalar Rg, each of the 6 values of the tensor is +effectively a "squared" value, since the cross-terms may be negative +and taking a sqrt() would be invalid. IMPORTANT NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. @@ -51,16 +54,15 @@ image"_set.html command. [Output info:] 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 +length 6 (Rg^2 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 and vector values calculated by this compute are -"intensive". The scalar and vector values will be in distance -"units"_units.html, since they are the square root of values -represented by the formula above. +"intensive". The scalar and vector values will be in distance and +distance^2 "units"_units.html respectively. [Restrictions:] none diff --git a/doc/compute_gyration_molecule.html b/doc/compute_gyration_molecule.html index e8b1e52e30..d5c0f6e784 100644 --- a/doc/compute_gyration_molecule.html +++ b/doc/compute_gyration_molecule.html @@ -38,8 +38,8 @@ compute 2 molecule gyration/molecule tensor individual molecules. The calculation includes all effects due to atoms passing thru periodic boundaries.

-

Rg is a measure of the size of a molecule, and is computed by this -formula +

Rg is a measure of the size of a molecule, and is computed as the +square root of the Rg^2 value in this formula

@@ -48,11 +48,14 @@ 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. +calculated, but a 6-element Rg^2 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. Note +that unlike the scalar Rg, each of the 6 values of the tensor is +effectively a "squared" value, since the cross-terms may be negative +and taking a sqrt() would be invalid.

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 @@ -87,9 +90,8 @@ section for an overview of LAMMPS output options.

All the vector or array values calculated by this compute are -"intensive". The vector or array values will be in distance -units, since they are the square root of values -represented by the formula above. +"intensive". The vector and aray values will be in distance and +distance^2 units respectively.

Restrictions: none

diff --git a/doc/compute_gyration_molecule.txt b/doc/compute_gyration_molecule.txt index 82647137ab..60a31c77ad 100644 --- a/doc/compute_gyration_molecule.txt +++ b/doc/compute_gyration_molecule.txt @@ -30,8 +30,8 @@ Define a computation that calculates the radius of gyration Rg of individual molecules. The calculation includes all effects due to atoms passing thru periodic boundaries. -Rg is a measure of the size of a molecule, and is computed by this -formula +Rg is a measure of the size of a molecule, and is computed as the +square root of the Rg^2 value in this formula :c,image(Eqs/compute_gyration.jpg) @@ -40,11 +40,14 @@ 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. +calculated, but a 6-element Rg^2 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. Note +that unlike the scalar Rg, each of the 6 values of the tensor is +effectively a "squared" value, since the cross-terms may be negative +and taking a sqrt() would be invalid. 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 @@ -79,9 +82,8 @@ section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. All the vector or array values calculated by this compute are -"intensive". The vector or array values will be in distance -"units"_units.html, since they are the square root of values -represented by the formula above. +"intensive". The vector and aray values will be in distance and +distance^2 "units"_units.html respectively. [Restrictions:] none diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html index 1a9846f936..941350a272 100644 --- a/doc/fix_nvt_sllod.html +++ b/doc/fix_nvt_sllod.html @@ -56,9 +56,13 @@ periodic boundaries since that is consistent with maintaining the velocity profile created by fix nvt/sllod. LAMMPS will give an error if this setting is not consistent.

-

The SLLOD equations of motion coupled to a Nose/Hoover thermostat are -discussed in (Tuckerman) (eqs 4 and 5), which is what is -implemented in LAMMPS in a velocity Verlet formulation. +

The SLLOD equations of motion, originally proposed by Hoover and Ladd +(see (Evans and Morriss)), were proven to be identical to +Newton's equations of motion for all forms of homogeneous flow by +(Daivis and Todd). As implemented in LAMMPS, they are +coupled to a Nose/Hoover chain thermostat in a velocity Verlet +formulation, closely following the implementation used for the fix +nvt command.

Additional parameters affecting the thermostat are specified by keywords and values documented with the fix nvt @@ -170,9 +174,12 @@ temp/deform

- + -

(Tuckerman) Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, -106, 5615 (1997). +

(Evans and Morriss) Evans and Morriss, Phys Rev A, 30, 1528 (1984). +

+ + +

(Daivis and Todd) Daivis and Todd, J Chem Phys, 124, 194103 (2006).