From 13a3a1d17410d3ce24ca8bd9b9cc45fa23ae7e91 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 21 Dec 2009 23:01:36 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3603 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 8 ++++---- doc/Section_commands.txt | 1 + doc/compute.html | 1 + doc/compute.txt | 1 + doc/compute_property_local.html | 23 +++++++++++++++++------ doc/compute_property_local.txt | 21 ++++++++++++++++----- 6 files changed, 40 insertions(+), 15 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 5a06d5c52c..fac74d61bc 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -349,10 +349,10 @@ each style or click on the style itself for a full description: angle/localbond/localcna/atomcomcom/moleculecoord/atom damage/atomdihedral/localdisplace/atomerotate/asphereerotate/sphereevent/displace group/groupgyrationgyration/moleculeheat/fluximproper/localke -ke/atommsdmsd/moleculepepe/atompressure -property/atomproperty/localproperty/moleculerdfreducereduce/region -stress/atomtemptemp/aspheretemp/comtemp/deformtemp/partial -temp/profiletemp/ramptemp/regiontemp/sphere +ke/atommsdmsd/moleculepair/localpepe/atom +pressureproperty/atomproperty/localproperty/moleculerdfreduce +reduce/regionstress/atomtemptemp/aspheretemp/comtemp/deform +temp/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 a7618b2b1c..74af2e5a0e 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -480,6 +480,7 @@ each style or click on the style itself for a full description: "ke/atom"_compute_ke_atom.html, "msd"_compute_msd.html, "msd/molecule"_compute_msd_molecule.html, +"pair/local"_compute_pair_local.html, "pe"_compute_pe.html, "pe/atom"_compute_pe_atom.html, "pressure"_compute_pressure.html, diff --git a/doc/compute.html b/doc/compute.html index 4680194fa2..f4a1784dcb 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -188,6 +188,7 @@ available in LAMMPS:

  • ke/atom - kinetic energy for each atom
  • msd - mean-squared displacement of group of atoms
  • msd/molecule - mean-squared displacement for each molecule +
  • pair/local - distance/energy/force of each pairwise interaction
  • pe - potential energy
  • pe/atom - potential energy for each atom
  • pressure - total pressure and pressure tensor diff --git a/doc/compute.txt b/doc/compute.txt index 7f1db9050a..48571da2c2 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -183,6 +183,7 @@ available in LAMMPS: "ke/atom"_compute_ke_atom.html - kinetic energy for each atom "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/molecule"_compute_msd_molecule.html - mean-squared displacement for each molecule +"pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction "pe"_compute_pe.html - potential energy "pe/atom"_compute_pe_atom.html - potential energy for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor diff --git a/doc/compute_property_local.html b/doc/compute_property_local.html index 22250039b7..8a1d8cec92 100644 --- a/doc/compute_property_local.html +++ b/doc/compute_property_local.html @@ -21,12 +21,14 @@
  • input = one or more attributes -
      possible attributes = batom1 batom2 btype
+
      possible attributes = patom1 patom2
+                        batom1 batom2 btype
                         aatom1 aatom2 aatom3 atype
                         datom1 datom2 datom3 dtype
                         iatom1 iatom2 iatom3 itype 
 
    
-
         batom1, batom2 = IDs of 2 atoms in each bond
+
         patom1, patom2 = IDs of 2 atoms in each pair
+     batom1, batom2 = IDs of 2 atoms in each bond
      btype = bond type of each bond
      aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
      atype = angle type of each angle
@@ -49,6 +51,7 @@ data so it can be accessed by other output
 commands.  If the input attributes refer to
 bond information, then the number of datums generated, aggregated
 across all processors, equals the number of bonds in the system.
+Ditto for pairs, angles, etc.
 
    
 
    If multiple input attributes are specified then they must all generate
 the same amount of information, so that the resulting local array has
@@ -62,6 +65,14 @@ processor and extracting bond, angle, etc info.  For bonds, info about
 an individual bond will only be included if both atoms in the bond are
 in the specified compute group.  Likewise for angles, dihedrals, etc.
 
    
+
    In the case of pairs, the local data is generated by looping over the
+pairwise neighbor list.  Info about an individual pairwise interaction
+will only be included if both atoms in the pair are in the specified
+compute group, and if the current pairwise distance is less than the
+force cutoff distance for that interaction, as defined by the
+pair_style and pair_coeff
+commands.  
+
    
 
    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
@@ -72,10 +83,10 @@ bond/local command can be combined with bond
 atom indices from this command and output by the dump
 local command in a consistent way.
 
    
-
    The batom1 and batom2 attributes refer the atom IDs of the 2 atoms
-in each bond.  The btype attribute refers to the
-type of the bond, from 1 to Nbtypes = # of bond types.  The number of
-bond types is defined in the data file read by the
+
    The batom1 and batom2 attributes refer to the atom IDs of the 2
+atoms in each bond.  The btype attribute refers to
+the type of the bond, from 1 to Nbtypes = # of bond types.  The number
+of bond types is defined in the data file read by the
 read_data command.  The attributes that start with
 "a", "d", "i", refer to similar values for angles,
 dihedrals, and impropers.
diff --git a/doc/compute_property_local.txt b/doc/compute_property_local.txt
index 8fb4a51afa..64b8a29c2c 100644
--- a/doc/compute_property_local.txt
+++ b/doc/compute_property_local.txt
@@ -15,11 +15,13 @@ compute ID group-ID property/local input1 input2 ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 property/local = style name of this compute command :l
 input = one or more attributes :l
-  possible attributes = batom1 batom2 btype
+  possible attributes = patom1 patom2
+                        batom1 batom2 btype
                         aatom1 aatom2 aatom3 atype
                         datom1 datom2 datom3 dtype
                         iatom1 iatom2 iatom3 itype :pre
 
+     patom1, patom2 = IDs of 2 atoms in each pair
      batom1, batom2 = IDs of 2 atoms in each bond
      btype = bond type of each bond
      aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
@@ -42,6 +44,7 @@ data so it can be accessed by other "output
 commands"_Section_howto.html#4_15.  If the input attributes refer to
 bond information, then the number of datums generated, aggregated
 across all processors, equals the number of bonds in the system.
+Ditto for pairs, angles, etc.
 
 If multiple input attributes are specified then they must all generate
 the same amount of information, so that the resulting local array has
@@ -55,6 +58,14 @@ processor and extracting bond, angle, etc info.  For bonds, info about
 an individual bond will only be included if both atoms in the bond are
 in the specified compute group.  Likewise for angles, dihedrals, etc.
 
+In the case of pairs, the local data is generated by looping over the
+pairwise neighbor list.  Info about an individual pairwise interaction
+will only be included if both atoms in the pair are in the specified
+compute group, and if the current pairwise distance is less than the
+force cutoff distance for that interaction, as defined by the
+"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html
+commands.  
+
 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
@@ -65,10 +76,10 @@ bond/local"_compute_bond_local.html command can be combined with bond
 atom indices from this command and output by the "dump
 local"_dump.html command in a consistent way.
 
-The {batom1} and {batom2} attributes refer the atom IDs of the 2 atoms
-in each "bond"_bond_style.html.  The {btype} attribute refers to the
-type of the bond, from 1 to Nbtypes = # of bond types.  The number of
-bond types is defined in the data file read by the
+The {batom1} and {batom2} attributes refer to the atom IDs of the 2
+atoms in each "bond"_bond_style.html.  The {btype} attribute refers to
+the type of the bond, from 1 to Nbtypes = # of bond types.  The number
+of bond types is defined in the data file read by the
 "read_data"_read_data.html command.  The attributes that start with
 "a", "d", "i", refer to similar values for "angles"_angle_style.html,
 "dihedrals"_dihedral_style.html, and "impropers"_improper_style.html.