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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3593 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-12-21 17:34:52 +00:00
parent 94fcde12ac
commit 1fa91920a2
12 changed files with 42 additions and 30 deletions
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4
doc/compute_com.html
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@ -60,7 +60,9 @@ number of atoms in the simulation.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_com_molecule.html">compute com/molecule</A>
</P>
<P><B>Default:</B> none
</P>

4
doc/compute_com.txt
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@ -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

6
doc/compute_com_molecule.html
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@ -28,8 +28,8 @@
molecules. The calculation includes all effects due to atoms passing
thru periodic boundaries.
</P>
<P>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
<P>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</A> containing coordinates of the atoms in the bodies.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global array with the number of rows =
<P>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

6
doc/compute_com_molecule.txt
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@ -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

8
doc/compute_gyration.html
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@ -33,8 +33,8 @@ this formula
</P>
<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
</CENTER>
<P>where M is the total mass of the group and Rcm is the center-of-mass
position of the group.
<P>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.
</P>
<P>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.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_gyration_molecule.html">compute gyration/molecule</A>
</P>
<P><B>Default:</B> none
</P>

8
doc/compute_gyration.txt
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@ -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

11
doc/compute_gyration_molecule.html
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@ -33,8 +33,9 @@ formula
</P>
<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
</CENTER>
<P>where M is the total mass of the molecule and Rcm is the center-of-mass
position of the molecule.
<P>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.
</P>
<P>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</A> command.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>

11
doc/compute_gyration_molecule.txt
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@ -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.

3
doc/compute_msd.html
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@ -103,7 +103,8 @@ number of atoms in the simulation.
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_coord_original.html">fix
coord/original</A>
coord/original</A>, <A HREF = "compute_msd_molecule.html">compute
msd/molecule</A>
</P>
<P><B>Default:</B>
</P>

3
doc/compute_msd.txt
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@ -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:]

4
doc/compute_msd_molecule.html
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@ -72,12 +72,12 @@ coordinates of the atoms in the bodies.
<P>IMPORTANT NOTE: Unlike the <A HREF = "compute_msd.html">compute msd</A> 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 <A HREF = "read_restart.html">restart
molecule calculation of this compute when running from a <A HREF = "read_restart.html">restart
file</A>.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global array with the number of rows =
<P>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 <A HREF = "Section_howto.html#4_15">this

4
doc/compute_msd_molecule.txt
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@ -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