From c7292cdb37792b74cf8c19f01870699815eff37b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 18 Dec 2009 21:24:44 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3582 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 10 ++--- doc/Section_commands.txt | 2 + doc/compute.html | 2 + doc/compute.txt | 2 + doc/compute_angle_local.html | 18 +++++--- doc/compute_angle_local.txt | 18 +++++--- doc/compute_bond_local.html | 19 +++++--- doc/compute_bond_local.txt | 19 +++++--- doc/compute_dihedral_local.html | 78 +++++++++++++++++++++++++++++++++ doc/compute_dihedral_local.txt | 68 ++++++++++++++++++++++++++++ doc/compute_improper_local.html | 78 +++++++++++++++++++++++++++++++++ doc/compute_improper_local.txt | 68 ++++++++++++++++++++++++++++ 12 files changed, 351 insertions(+), 31 deletions(-) create mode 100644 doc/compute_dihedral_local.html create mode 100644 doc/compute_dihedral_local.txt create mode 100644 doc/compute_improper_local.html create mode 100644 doc/compute_improper_local.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 83f4cd86e0..f61c9c082f 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -347,11 +347,11 @@ each style or click on the style itself for a full description:

- - - - - + + + +
angle/localbond/localcna/atomcomcoord/atomdamage/atom
displace/atomerotate/asphereerotate/sphereevent/displacegroup/groupgyration
heat/fluxkeke/atommsdpepe/atom
pressureproperty/atomproperty/localrdfreducereduce/region
stress/atomtemptemp/aspheretemp/comtemp/deformtemp/partial
temp/profiletemp/ramptemp/regiontemp/sphere +
dihedral/localdisplace/atomerotate/asphereerotate/sphereevent/displacegroup/group
gyrationheat/fluximproper/localkeke/atommsd
pepe/atompressureproperty/atomproperty/localrdf
reducereduce/regionstress/atomtemptemp/aspheretemp/com
temp/deformtemp/partialtemp/profiletemp/ramptemp/regiontemp/sphere

These are compute styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 014589fb7e..9d827c06bc 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -465,6 +465,7 @@ each style or click on the style itself for a full description: "com"_compute_com.html, "coord/atom"_compute_coord_atom.html, "damage/atom"_compute_damage_atom.html, +"dihedral/local"_compute_dihedral_local.html, "displace/atom"_compute_displace_atom.html, "erotate/asphere"_compute_erotate_asphere.html, "erotate/sphere"_compute_erotate_sphere.html, @@ -472,6 +473,7 @@ each style or click on the style itself for a full description: "group/group"_compute_group_group.html, "gyration"_compute_gyration.html, "heat/flux"_compute_heat_flux.html, +"improper/local"_compute_improper_local.html, "ke"_compute_ke.html, "ke/atom"_compute_ke_atom.html, "msd"_compute_msd.html, diff --git a/doc/compute.html b/doc/compute.html index 044ca7a5f7..611fdc8c35 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -173,6 +173,7 @@ available in LAMMPS:

  • com - center-of-mass of group of atoms
  • coord/atom - coordination number for each atom
  • damage/atom - Peridynamic damage for each atom +
  • dihedral/local - angle of each dihedral
  • displace/atom - displacement of each atom
  • erotate/asphere - rotational energy of aspherical particles
  • erotate/sphere - rotational energy of spherical particles @@ -180,6 +181,7 @@ available in LAMMPS:
  • group/group - energy/force between two groups of atoms
  • gyration - radius of gyration of group of atoms
  • heat/flux - heat flux through a group of atoms +
  • improper/local - angle of each improper
  • ke - translational kinetic energy
  • ke/atom - kinetic energy for each atom
  • msd - mean-squared displacement of group of atoms diff --git a/doc/compute.txt b/doc/compute.txt index b27f6224bc..a6149ca35e 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -168,6 +168,7 @@ available in LAMMPS: "com"_compute_com.html - center-of-mass of group of atoms "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom +"dihedral/local"_compute_dihedral_local.html - angle of each dihedral "displace/atom"_compute_displace_atom.html - displacement of each atom "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles @@ -175,6 +176,7 @@ available in LAMMPS: "group/group"_compute_group_group.html - energy/force between two groups of atoms "gyration"_compute_gyration.html - radius of gyration of group of atoms "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms +"improper/local"_compute_improper_local.html - angle of each improper "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom "msd"_compute_msd.html - mean-squared displacement of group of atoms diff --git a/doc/compute_angle_local.html b/doc/compute_angle_local.html index 0cbf91c904..730d548c28 100644 --- a/doc/compute_angle_local.html +++ b/doc/compute_angle_local.html @@ -21,17 +21,17 @@
  • zero or more keywords may be appended -
  • keyword = theta or energy +
  • keyword = theta or eng 
      theta = tabulate angles
-  energy = tabulate angle energies 
+  eng = tabulate angle energies

    Examples: 

    compute 1 all angle/local theta
-compute 1 all angle/local theta energy 
+compute 1 all angle/local eng theta

    Description:

    @@ -40,10 +40,16 @@ The number of datums generated, aggregated across all processors, equals the number of angles in the system.

    The local data stored by this command is generated by looping over all -the atoms owned on a processor and their angles. An angle will only be -included if all 3 atoms in the angle are in the specified compute group. +the atoms owned on a processor and their angles. An angle will only +be included if all 3 atoms in the angle are in the specified compute +group. Any angles that have been broken (see the +angle_style command) by setting their angle type to +0 are not included. Angles that have been turned off (see the fix +shake or delete_bonds commands) by +setting their angle type negative are written into the file, but their +energy will be 0.0.

    -

    The output theta will be in degrees. The output energy will be in +

    The output theta will be in degrees. The output eng will be in energy units.

    Note that as atoms migrate from processor to processor, there will be diff --git a/doc/compute_angle_local.txt b/doc/compute_angle_local.txt index 368f55d4d2..e439a1b37e 100644 --- a/doc/compute_angle_local.txt +++ b/doc/compute_angle_local.txt @@ -15,15 +15,15 @@ compute ID group-ID angle/local input1 input2 ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l angle/local = style name of this compute command :l zero or more keywords may be appended :l -keyword = {theta} or {energy} :l +keyword = {theta} or {eng} :l {theta} = tabulate angles - {energy} = tabulate angle energies :pre + {eng} = tabulate angle energies :pre :ule [Examples:] compute 1 all angle/local theta -compute 1 all angle/local theta energy :pre +compute 1 all angle/local eng theta :pre [Description:] @@ -32,10 +32,16 @@ The number of datums generated, aggregated across all processors, equals the number of angles in the system. The local data stored by this command is generated by looping over all -the atoms owned on a processor and their angles. An angle will only be -included if all 3 atoms in the angle are in the specified compute group. +the atoms owned on a processor and their angles. An angle will only +be included if all 3 atoms in the angle are in the specified compute +group. Any angles that have been broken (see the +"angle_style"_angle_style.html command) by setting their angle type to +0 are not included. Angles that have been turned off (see the "fix +shake"_fix_shake.html or "delete_bonds"_delete_bonds.html commands) by +setting their angle type negative are written into the file, but their +energy will be 0.0. -The output {theta} will be in degrees. The output {energy} will be in +The output {theta} will be in degrees. The output {eng} will be in energy "units"_units.html. Note that as atoms migrate from processor to processor, there will be diff --git a/doc/compute_bond_local.html b/doc/compute_bond_local.html index 658ba084a1..04d8621134 100644 --- a/doc/compute_bond_local.html +++ b/doc/compute_bond_local.html @@ -21,17 +21,17 @@

  • zero or more keywords may be appended -
  • keyword = distance or energy +
  • keyword = dist or eng -
      distance = tabulate bond distances
-  energy = tablutate bond energies 
+
      dist = tabulate bond distances
+  eng = tablutate bond energies 
 
    
 
 
 
    Examples:
 
    
-
    compute 1 all bond/local energy
-compute 1 all bond/local distance energy 
+
    compute 1 all bond/local eng
+compute 1 all bond/local dist eng 
 
    
 
    Description:
 
    
@@ -42,9 +42,14 @@ equals the number of bonds in the system.
 
    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.
+Any bonds that have been broken (see the bond_style
+command) by setting their bond type to 0 are not included.  Bonds that
+have been turned off (see the fix shake or
+delete_bonds commands) by setting their bond type
+negative are written into the file, but their energy will be 0.0.
 
    
-
    The output distance will be in distance units.  The
-output energy will be in energy units.
+
    The output dist will be in distance units.  The output
+eng will be in energy units.
 
    
 
    Note that as atoms migrate from processor to processor, there will be
 no consistent ordering of the entries within the local vector or array
diff --git a/doc/compute_bond_local.txt b/doc/compute_bond_local.txt
index 376e6e5144..ceb336e275 100644
--- a/doc/compute_bond_local.txt
+++ b/doc/compute_bond_local.txt
@@ -15,15 +15,15 @@ compute ID group-ID bond/local input1 input2 ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 bond/local = style name of this compute command :l
 zero or more keywords may be appended :l
-keyword = {distance} or {energy} :l
-  {distance} = tabulate bond distances
-  {energy} = tablutate bond energies :pre
+keyword = {dist} or {eng} :l
+  {dist} = tabulate bond distances
+  {eng} = tablutate bond energies :pre
 :ule
 
 [Examples:]
 
-compute 1 all bond/local energy
-compute 1 all bond/local distance energy :pre
+compute 1 all bond/local eng
+compute 1 all bond/local dist eng :pre
 
 [Description:]
 
@@ -34,9 +34,14 @@ equals the number of bonds in the system.
 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.
+Any bonds that have been broken (see the "bond_style"_bond_style.html
+command) by setting their bond type to 0 are not included.  Bonds that
+have been turned off (see the "fix shake"_fix_shake.html or
+"delete_bonds"_delete_bonds.html commands) by setting their bond type
+negative are written into the file, but their energy will be 0.0.
 
-The output {distance} will be in distance "units"_units.html.  The
-output {energy} will be in energy "units"_units.html.
+The output {dist} will be in distance "units"_units.html.  The output
+{eng} will be in energy "units"_units.html.
 
 Note that as atoms migrate from processor to processor, there will be
 no consistent ordering of the entries within the local vector or array
diff --git a/doc/compute_dihedral_local.html b/doc/compute_dihedral_local.html
new file mode 100644
index 0000000000..a8a440f8cc
--- /dev/null
+++ b/doc/compute_dihedral_local.html
@@ -0,0 +1,78 @@
+
+
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands 
+
    
+
+
+
+
+
+
+
    
+
+
    compute dihedral/local command 
+
    
+
    Syntax:
+
    
+
    compute ID group-ID dihedral/local input1 input2 ... 
+
    
+
    • ID, group-ID are documented in compute command 
+
+
    • dihedral/local = style name of this compute command 
+
+
    • zero or more keywords may be appended 
+
+
    • keyword = phi 
+
+
        phi = tabulate dihedral angles 
+
      
+
+
    
+
    Examples:
+
    
+
    compute 1 all dihedral/local phi 
+
    
+
    Description:
+
    
+
    Define a computation that calculates properties of individual
+dihedrals.  The number of datums generated, aggregated across all
+processors, equals the number of angles in the system.
+
    
+
    The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their dihedrals.  A dihedral will
+only be included if all 4 atoms in the dihedral are in the specified
+compute group.
+
    
+
    The output phi will be in degrees.
+
    
+
    Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, dihedral output from the compute
+property/local command can be combined
+with data from this command and output by the dump local
+command in a consistent way.
+
    
+
    Output info:
+
    
+
    This compute calculates a local vector or local array depending on the
+number of keywords.  The length of the vector or number of rows in the
+array is the number of dihedrals.  If a single keyword is specified, a
+local vector is produced.  If two or more keywords are specified, a
+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.
+
    
+
    Restrictions: none
+
    
+
    Related commands:
+
    
+
    dump local, compute
+property/local
+
    
+
    Default: none
+
    
+
diff --git a/doc/compute_dihedral_local.txt b/doc/compute_dihedral_local.txt
new file mode 100644
index 0000000000..b46df1f3cd
--- /dev/null
+++ b/doc/compute_dihedral_local.txt
@@ -0,0 +1,68 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute dihedral/local command :h3
+
+[Syntax:]
+
+compute ID group-ID dihedral/local input1 input2 ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+dihedral/local = style name of this compute command :l
+zero or more keywords may be appended :l
+keyword = {phi} :l
+  {phi} = tabulate dihedral angles :pre
+:ule
+
+[Examples:]
+
+compute 1 all dihedral/local phi :pre
+
+[Description:]
+
+Define a computation that calculates properties of individual
+dihedrals.  The number of datums generated, aggregated across all
+processors, equals the number of angles in the system.
+
+The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their dihedrals.  A dihedral will
+only be included if all 4 atoms in the dihedral are in the specified
+compute group.
+
+The output {phi} will be in degrees.
+
+Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, dihedral output from the "compute
+property/local"_compute_property_local.html command can be combined
+with data from this command and output by the "dump local"_dump.html
+command in a consistent way.
+
+[Output info:]
+
+This compute calculates a local vector or local array depending on the
+number of keywords.  The length of the vector or number of rows in the
+array is the number of dihedrals.  If a single keyword is specified, a
+local vector is produced.  If two or more keywords are specified, a
+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"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"dump local"_dump.html, "compute
+property/local"_compute_property_local.html
+
+[Default:] none
diff --git a/doc/compute_improper_local.html b/doc/compute_improper_local.html
new file mode 100644
index 0000000000..0a498fdc9c
--- /dev/null
+++ b/doc/compute_improper_local.html
@@ -0,0 +1,78 @@
+
+
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands 
+
    
+
+
+
+
+
+
+
    
+
+
    compute improper/local command 
+
    
+
    Syntax:
+
    
+
    compute ID group-ID improper/local input1 input2 ... 
+
    
+
    • ID, group-ID are documented in compute command 
+
+
    • improper/local = style name of this compute command 
+
+
    • zero or more keywords may be appended 
+
+
    • keyword = chi 
+
+
        chi = tabulate improper angles 
+
      
+
+
    
+
    Examples:
+
    
+
    compute 1 all improper/local chi 
+
    
+
    Description:
+
    
+
    Define a computation that calculates properties of individual improper
+interactions.  The number of datums generated, aggregated across all
+processors, equals the number of impropers in the system.
+
    
+
    The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their impropers.  An improper will
+only be included if all 4 atoms in the improper are in the specified
+compute group.
+
    
+
    The output chi will be in degrees.
+
    
+
    Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, improper output from the compute
+property/local command can be combined
+with data from this command and output by the dump local
+command in a consistent way.
+
    
+
    Output info:
+
    
+
    This compute calculates a local vector or local array depending on the
+number of keywords.  The length of the vector or number of rows in the
+array is the number of impropers.  If a single keyword is specified, a
+local vector is produced.  If two or more keywords are specified, a
+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.
+
    
+
    Restrictions: none
+
    
+
    Related commands:
+
    
+
    dump local, compute
+property/local
+
    
+
    Default: none
+
    
+
diff --git a/doc/compute_improper_local.txt b/doc/compute_improper_local.txt
new file mode 100644
index 0000000000..8970657544
--- /dev/null
+++ b/doc/compute_improper_local.txt
@@ -0,0 +1,68 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute improper/local command :h3
+
+[Syntax:]
+
+compute ID group-ID improper/local input1 input2 ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+improper/local = style name of this compute command :l
+zero or more keywords may be appended :l
+keyword = {chi} :l
+  {chi} = tabulate improper angles :pre
+:ule
+
+[Examples:]
+
+compute 1 all improper/local chi :pre
+
+[Description:]
+
+Define a computation that calculates properties of individual improper
+interactions.  The number of datums generated, aggregated across all
+processors, equals the number of impropers in the system.
+
+The local data stored by this command is generated by looping over all
+the atoms owned on a processor and their impropers.  An improper will
+only be included if all 4 atoms in the improper are in the specified
+compute group.
+
+The output {chi} will be in degrees.
+
+Note that as atoms migrate from processor to processor, there will be
+no consistent ordering of the entries within the local vector or array
+from one timestep to the next.  The only consistency that is
+guaranteed is that the ordering on a particular timestep will be the
+same for local vectors or arrays generated by other compute commands.
+For example, improper output from the "compute
+property/local"_compute_property_local.html command can be combined
+with data from this command and output by the "dump local"_dump.html
+command in a consistent way.
+
+[Output info:]
+
+This compute calculates a local vector or local array depending on the
+number of keywords.  The length of the vector or number of rows in the
+array is the number of impropers.  If a single keyword is specified, a
+local vector is produced.  If two or more keywords are specified, a
+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"_Section_howto.html#4_15 for an overview of LAMMPS output
+options.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"dump local"_dump.html, "compute
+property/local"_compute_property_local.html
+
+[Default:] none