From 1fa91920a2b739a42d4664d5f85830d8cec13dc9 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 21 Dec 2009 17:34:52 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3593 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_com.html | 4 +++- doc/compute_com.txt | 4 +++- doc/compute_com_molecule.html | 6 +++--- doc/compute_com_molecule.txt | 6 +++--- doc/compute_gyration.html | 8 +++++--- doc/compute_gyration.txt | 8 +++++--- doc/compute_gyration_molecule.html | 11 ++++++----- doc/compute_gyration_molecule.txt | 11 ++++++----- doc/compute_msd.html | 3 ++- doc/compute_msd.txt | 3 ++- doc/compute_msd_molecule.html | 4 ++-- doc/compute_msd_molecule.txt | 4 ++-- 12 files changed, 42 insertions(+), 30 deletions(-) diff --git a/doc/compute_com.html b/doc/compute_com.html index 865294a0d4..a5d1258eb9 100644 --- a/doc/compute_com.html +++ b/doc/compute_com.html @@ -60,7 +60,9 @@ number of atoms in the simulation.

Restrictions: none

-

Related commands: none +

Related commands: +

+

compute com/molecule

Default: none

diff --git a/doc/compute_com.txt b/doc/compute_com.txt index 57737f443b..8c0dd7c8a5 100644 --- a/doc/compute_com.txt +++ b/doc/compute_com.txt @@ -57,6 +57,8 @@ number of atoms in the simulation. [Restrictions:] none -[Related commands:] none +[Related commands:] + +"compute com/molecule"_compute_com_molecule.html [Default:] none diff --git a/doc/compute_com_molecule.html b/doc/compute_com_molecule.html index 5829b592ad..2214596c36 100644 --- a/doc/compute_com_molecule.html +++ b/doc/compute_com_molecule.html @@ -28,8 +28,8 @@ molecules. The calculation includes all effects due to atoms passing thru periodic boundaries.

-

The x,y,z coordinate of the center-of-mass for a particular molecule -is only computed if one or more of its atoms are in the specified +

The x,y,z coordinates of the center-of-mass for a particular molecule +are 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 warn you if this is not the case. Only atoms in the group contribute to the center-of-mass @@ -59,7 +59,7 @@ file containing coordinates of the atoms in the bodies.

Output info:

-

This compute calculates a global array with the number of rows = +

This compute calculates a global array where the number of rows = Nmolecules and the number of columns = 3 for the x,y,z center-of-mass coordinates of each molecule. These values can be accessed by any command that uses global array values from a compute as input. See diff --git a/doc/compute_com_molecule.txt b/doc/compute_com_molecule.txt index 034ea647c6..7c3b3d3227 100644 --- a/doc/compute_com_molecule.txt +++ b/doc/compute_com_molecule.txt @@ -25,8 +25,8 @@ Define a computation that calculates the center-of-mass of individual molecules. The calculation includes all effects due to atoms passing thru periodic boundaries. -The x,y,z coordinate of the center-of-mass for a particular molecule -is only computed if one or more of its atoms are in the specified +The x,y,z coordinates of the center-of-mass for a particular molecule +are 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 warn you if this is not the case. Only atoms in the group contribute to the center-of-mass @@ -56,7 +56,7 @@ file"_dump.html containing coordinates of the atoms in the bodies. [Output info:] -This compute calculates a global array with the number of rows = +This compute calculates a global array where the number of rows = Nmolecules and the number of columns = 3 for the x,y,z center-of-mass coordinates of each molecule. These values can be accessed by any command that uses global array values from a compute as input. See diff --git a/doc/compute_gyration.html b/doc/compute_gyration.html index b3888a3729..e4d0278499 100644 --- a/doc/compute_gyration.html +++ b/doc/compute_gyration.html @@ -33,8 +33,8 @@ this formula

-

where M is the total mass of the group and Rcm is the center-of-mass -position of the group. +

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.

IMPORTANT NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. @@ -57,7 +57,9 @@ is independent of the number of atoms in the simulation.

Restrictions: none

-

Related commands: none +

Related commands: +

+

compute gyration/molecule

Default: none

diff --git a/doc/compute_gyration.txt b/doc/compute_gyration.txt index 8cd5b445e1..83bf3a33ce 100644 --- a/doc/compute_gyration.txt +++ b/doc/compute_gyration.txt @@ -30,8 +30,8 @@ this formula :c,image(Eqs/compute_gyration.jpg) -where M is the total mass of the group and Rcm is the center-of-mass -position of the group. +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. IMPORTANT NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. @@ -54,6 +54,8 @@ is independent of the number of atoms in the simulation. [Restrictions:] none -[Related commands:] none +[Related commands:] + +"compute gyration/molecule"_compute_gyration_molecule.html [Default:] none diff --git a/doc/compute_gyration_molecule.html b/doc/compute_gyration_molecule.html index 4fb804f87a..4b380daabf 100644 --- a/doc/compute_gyration_molecule.html +++ b/doc/compute_gyration_molecule.html @@ -33,8 +33,9 @@ formula

-

where M is the total mass of the molecule and Rcm is the center-of-mass -position of the molecule. +

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.

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 @@ -58,9 +59,9 @@ image command.

Output info:

-

This compute calculates a global vector of Rg values with the number -of elements = Nmolecules. These values can be used by any command -that uses a global vector values from a compute as input. See this +

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 section for an overview of LAMMPS output options.

diff --git a/doc/compute_gyration_molecule.txt b/doc/compute_gyration_molecule.txt index ef30b48b12..cd84533de5 100644 --- a/doc/compute_gyration_molecule.txt +++ b/doc/compute_gyration_molecule.txt @@ -30,8 +30,9 @@ formula :c,image(Eqs/compute_gyration.jpg) -where M is the total mass of the molecule and Rcm is the center-of-mass -position of the molecule. +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. 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 @@ -55,9 +56,9 @@ image"_set.html command. [Output info:] -This compute calculates a global vector of Rg values with the number -of elements = Nmolecules. These values can be used by any command -that uses a global vector values from a compute as input. See "this +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 section"_Section_howto.html#4_15 for an overview of LAMMPS output options. diff --git a/doc/compute_msd.html b/doc/compute_msd.html index 4af1d6a1d2..57c549c89d 100644 --- a/doc/compute_msd.html +++ b/doc/compute_msd.html @@ -103,7 +103,8 @@ number of atoms in the simulation.

Related commands:

compute displace_atom, fix -coord/original +coord/original, compute +msd/molecule

Default:

diff --git a/doc/compute_msd.txt b/doc/compute_msd.txt index 523b224801..796d0cca8f 100644 --- a/doc/compute_msd.txt +++ b/doc/compute_msd.txt @@ -95,7 +95,8 @@ number of atoms in the simulation. [Related commands:] "compute displace_atom"_compute_displace_atom.html, "fix -coord/original"_fix_coord_original.html +coord/original"_fix_coord_original.html, "compute +msd/molecule"_compute_msd_molecule.html [Default:] diff --git a/doc/compute_msd_molecule.html b/doc/compute_msd_molecule.html index 9c75944e14..d84824bba9 100644 --- a/doc/compute_msd_molecule.html +++ b/doc/compute_msd_molecule.html @@ -72,12 +72,12 @@ coordinates of the atoms in the bodies.

IMPORTANT NOTE: Unlike the compute msd command, this compute does not store the initial center-of-mass coorindates of its molecules in a restart file. Thus you cannot continue the MSD per -molecule calculation when running from a restart +molecule calculation of this compute when running from a restart file.

Output info:

-

This compute calculates a global array with the number of rows = +

This compute calculates a global array where the number of rows = Nmolecules and the number of columns = 4 for dx,dy,dz and the total displacement. These values can be accessed by any command that uses global array values from a compute as input. See this diff --git a/doc/compute_msd_molecule.txt b/doc/compute_msd_molecule.txt index 4869d8c5a7..b69ee25dbd 100644 --- a/doc/compute_msd_molecule.txt +++ b/doc/compute_msd_molecule.txt @@ -69,12 +69,12 @@ coordinates of the atoms in the bodies. IMPORTANT NOTE: Unlike the "compute msd"_compute_msd.html command, this compute does not store the initial center-of-mass coorindates of its molecules in a restart file. Thus you cannot continue the MSD per -molecule calculation when running from a "restart +molecule calculation of this compute when running from a "restart file"_read_restart.html. [Output info:] -This compute calculates a global array with the number of rows = +This compute calculates a global array where the number of rows = Nmolecules and the number of columns = 4 for dx,dy,dz and the total displacement. These values can be accessed by any command that uses global array values from a compute as input. See "this