From 9d0e8539255507734dc24f13036f34db385ecde0 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 13 Sep 2016 22:58:33 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15571 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/comm_modify.html | 22 +++++----- doc/html/compute_bond_local.html | 68 +++++++++++++++++++++++------ doc/html/genindex.html | 2 +- doc/src/compute_bond_local.txt | 74 ++++++++++++++++++++++++++------ 4 files changed, 126 insertions(+), 40 deletions(-) diff --git a/doc/html/comm_modify.html b/doc/html/comm_modify.html index 81645ca56b..5bc228cc68 100644 --- a/doc/html/comm_modify.html +++ b/doc/html/comm_modify.html @@ -128,9 +128,9 @@

comm_modify command

Syntax

-
comm_modify keyword value ...
-
-
+
+comm_modify keyword value ...
+

Examples

-
comm_modify mode multi
-comm_modify mode multi group solvent
-comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
-comm_modify vel yes
-comm_modify mode single cutoff 5.0 vel yes
-comm_modify cutoff/multi * 0.0
-
-
+
+comm_modify mode multi
+comm_modify mode multi group solvent
+comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
+comm_modify vel yes
+comm_modify mode single cutoff 5.0 vel yes
+comm_modify cutoff/multi * 0.0
+

Description

diff --git a/doc/html/compute_bond_local.html b/doc/html/compute_bond_local.html index 79f34ad60f..515cfd5484 100644 --- a/doc/html/compute_bond_local.html +++ b/doc/html/compute_bond_local.html @@ -135,18 +135,25 @@
  • ID, group-ID are documented in compute command
  • bond/local = style name of this compute command
  • one or more values may be appended
    • -
  • value = dist or eng or force
    • +
  • value = dist or engpot or force or engvib or engrot or engtrans or omega or velvib
    •  dist = bond distance
-eng = bond energy
+engpot = bond potential energy
 force = bond force
    +
    +engvib = bond kinetic energy of vibration
+engrot = bond kinetic energy of rotation
+engtrans = bond kinetic energy of translation
+omega = magnitude of bond angular velocity
+velvib = vibrational velocity along the bond length
+

    Examples

    -
    compute 1 all bond/local eng
-compute 1 all bond/local dist eng force
+
    compute 1 all bond/local engpot
+compute 1 all bond/local dist engpot force
    @@ -154,12 +161,42 @@

    Description

    Define a computation that calculates properties of individual bond interactions. The number of datums generated, aggregated across all -processors, equals the number of bonds in the system, modified -by the group parameter as explained below.

    -

    The value dist is the length of the bond.

    -

    The value eng is the interaction energy for the bond.

    -

    The value force is the force acting between the pair of atoms in the +processors, equals the number of bonds in the system, modified by the +group parameter as explained below.

    +

    The value dist is the current length of the bond.

    +

    The value engpot is the potential energy for the bond, +based on the current separation of the pair of atoms in the bond.

    +

    The value force is the magnitude of the force acting between the +pair of atoms in the bond.

    +

    The remaining properties are all computed for motion of the two atoms +relative to the center of mass (COM) velocity of the 2 atoms in the bond.

    +

    The value engvib is the vibrational kinetic energy of the two atoms +in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and +v2 are the magnitude of the velocity of the 2 atoms along the bond +direction, after the COM velocity has been subtracted from each.

    +

    The value engrot is the rotationsl kinetic energy of the two atoms +in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and +v2 are the magnitude of the velocity of the 2 atoms perpendicular to +the bond direction, after the COM velocity has been subtracted from +each.

    +

    The value engtrans is the translational kinetic energy associated +with the motion of the COM of the system itself, namely 1/2 (m1+m2) +Vcm^2 where Vcm = magnitude of the velocity of the COM.

    +

    Note that these 3 kinetic energy terms are simply a partitioning of +the summed kinetic energy of the 2 atoms themselves. I.e. total KE = +1/2 m1 v1^2 + 1/2 m2 v3^2 = engvib + engrot + engtrans, where v1,v2 +are the magnitude of the velocities of the 2 atoms, without any +adjustment for the COM velocity.

    +

    The value omega is the magnitude of the angular velocity of the +two atoms around their COM position.

    +

    The value velvib is the magnitude of the relative velocity of the +two atoms in the bond towards each other. A negative value means the +2 atoms are moving toward each other; a positive value means they are +moving apart.

    +

    Note that all these properties are computed for the pair of atoms in a +bond, whether the 2 atoms represent a simple diatomic molecule, or are +part of some larger molecule.

    The local data stored by this command is generated by looping over all the atoms owned on a processor and their bonds. A bond will only be included if both atoms in the bond are in the specified compute group. @@ -179,8 +216,8 @@ command in a consistent way.

    Here is an example of how to do this:

     compute 1 all property/local btype batom1 batom2
-compute 2 all bond/local dist eng
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+compute 2 all bond/local dist engpot
+dump 1 all local 1000 tmp.dump index c_1[*] c_2[*]

    Output info:

    This compute calculates a local vector or local array depending on the @@ -191,9 +228,12 @@ local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See this section for an overview of LAMMPS output options.

    -

    The output for dist will be in distance units. The -output for eng will be in energy units. The output for -force will be in force units.

    +

    The output for dist will be in distance units. The +output for velvib will be in velocity units. The output +for omega will be in velocity/distance units. The +output for engtrans, engvib, engrot, and engpot will be in +energy units. The output for force will be in force +units.

    Restrictions

    diff --git a/doc/html/genindex.html b/doc/html/genindex.html index 6a3c85472b..b625eb13f3 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -344,7 +344,7 @@ -
    comm_modify +
    comm\_modify
    diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt index 4b48405c58..642b0e9cca 100644 --- a/doc/src/compute_bond_local.txt +++ b/doc/src/compute_bond_local.txt @@ -15,31 +15,74 @@ compute ID group-ID bond/local value1 value2 ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l bond/local = style name of this compute command :l one or more values may be appended :l -value = {dist} or {eng} or {force} :l +value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} :l {dist} = bond distance - {eng} = bond energy + {engpot} = bond potential energy {force} = bond force :pre + {engvib} = bond kinetic energy of vibration + {engrot} = bond kinetic energy of rotation + {engtrans} = bond kinetic energy of translation + {omega} = magnitude of bond angular velocity + {velvib} = vibrational velocity along the bond length :pre :ule [Examples:] -compute 1 all bond/local eng -compute 1 all bond/local dist eng force :pre +compute 1 all bond/local engpot +compute 1 all bond/local dist engpot force :pre [Description:] Define a computation that calculates properties of individual bond interactions. The number of datums generated, aggregated across all -processors, equals the number of bonds in the system, modified -by the group parameter as explained below. +processors, equals the number of bonds in the system, modified by the +group parameter as explained below. -The value {dist} is the length of the bond. +The value {dist} is the current length of the bond. -The value {eng} is the interaction energy for the bond. +The value {engpot} is the potential energy for the bond, +based on the current separation of the pair of atoms in the bond. -The value {force} is the force acting between the pair of atoms in the +The value {force} is the magnitude of the force acting between the +pair of atoms in the bond. + +The remaining properties are all computed for motion of the two atoms +relative to the center of mass (COM) velocity of the 2 atoms in the bond. +The value {engvib} is the vibrational kinetic energy of the two atoms +in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and +v2 are the magnitude of the velocity of the 2 atoms along the bond +direction, after the COM velocity has been subtracted from each. + +The value {engrot} is the rotationsl kinetic energy of the two atoms +in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and +v2 are the magnitude of the velocity of the 2 atoms perpendicular to +the bond direction, after the COM velocity has been subtracted from +each. + +The value {engtrans} is the translational kinetic energy associated +with the motion of the COM of the system itself, namely 1/2 (m1+m2) +Vcm^2 where Vcm = magnitude of the velocity of the COM. + +Note that these 3 kinetic energy terms are simply a partitioning of +the summed kinetic energy of the 2 atoms themselves. I.e. total KE = +1/2 m1 v1^2 + 1/2 m2 v3^2 = engvib + engrot + engtrans, where v1,v2 +are the magnitude of the velocities of the 2 atoms, without any +adjustment for the COM velocity. + +The value {omega} is the magnitude of the angular velocity of the +two atoms around their COM position. + +The value {velvib} is the magnitude of the relative velocity of the +two atoms in the bond towards each other. A negative value means the +2 atoms are moving toward each other; a positive value means they are +moving apart. + +Note that all these properties are computed for the pair of atoms in a +bond, whether the 2 atoms represent a simple diatomic molecule, or are +part of some larger molecule. + The local data stored by this command is generated by looping over all the atoms owned on a processor and their bonds. A bond will only be included if both atoms in the bond are in the specified compute group. @@ -62,8 +105,8 @@ command in a consistent way. Here is an example of how to do this: compute 1 all property/local btype batom1 batom2 -compute 2 all bond/local dist eng -dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_2\[1\] c_2\[2\] :pre +compute 2 all bond/local dist engpot +dump 1 all local 1000 tmp.dump index c_1\[*\] c_2\[*\] :pre [Output info:] @@ -77,9 +120,12 @@ uses local values from a compute as input. See "this section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The output for {dist} will be in distance "units"_units.html. The -output for {eng} will be in energy "units"_units.html. The output for -{force} will be in force "units"_units.html. +The output for {dist} will be in distance "units"_units.html. The +output for {velvib} will be in velocity "units"_units.html. The output +for {omega} will be in velocity/distance "units"_units.html. The +output for {engtrans}, {engvib}, {engrot}, and {engpot} will be in +energy "units"_units.html. The output for {force} will be in force +"units"_units.html. [Restrictions:] none