From 2b3965902b8c96c820914811e44ee4ad205c5c39 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 17 Dec 2009 17:28:42 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3560 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 6 +++--- doc/Section_commands.txt | 1 + doc/Section_howto.html | 35 ++++++++++++++++++++++++++-------- doc/Section_howto.txt | 35 ++++++++++++++++++++++++++-------- doc/compute.html | 6 ++++-- doc/compute.txt | 6 ++++-- doc/compute_property_atom.html | 5 +++-- doc/compute_property_atom.txt | 3 ++- doc/dump.html | 5 +++-- doc/dump.txt | 3 ++- 10 files changed, 76 insertions(+), 29 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 25f812863f..3ff51d15c9 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -349,9 +349,9 @@ each style or click on the style itself for a full description: centro/atomcna/atomcomcoord/atomdamage/atomdisplace/atom erotate/asphereerotate/sphereevent/displacegroup/groupgyrationheat/flux keke/atommsdpepe/atompressure -property/atomrdfreducereduce/regionstress/atomtemp -temp/aspheretemp/comtemp/deformtemp/partialtemp/profiletemp/ramp -temp/regiontemp/sphere +property/atomproperty/localrdfreducereduce/regionstress/atom +temptemp/aspheretemp/comtemp/deformtemp/partialtemp/profile +temp/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 96d49dacc5..06b465408e 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -478,6 +478,7 @@ each style or click on the style itself for a full description: "pe/atom"_compute_pe_atom.html, "pressure"_compute_pressure.html, "property/atom"_compute_property_atom.html, +"property/local"_compute_property_local.html, "rdf"_compute_rdf.html, "reduce"_compute_reduce.html, "reduce/region"_compute_reduce.html, diff --git a/doc/Section_howto.html b/doc/Section_howto.html index b5596aefca..aee85ecc25 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -1053,14 +1053,25 @@ command.

Dump file output is specified by the dump and dump_modify commands. There are several -pre-defined formats (dump atom, dump xtc, etc). There is also a dump -custom format where the user specifies what values are -output with each atom. Pre-defined atom attributes can be specified -(id, x, fx, etc). Three additional kinds of keywords can also be -specified (c_ID, f_ID, v_name), where a compute or -fix or variable provides the values to be -output. In each case, the compute, fix, or variable must generate -per-atom values for input to the dump custom command. +pre-defined formats (dump atom, dump xtc, etc). +

+

There is also a dump custom format where the user +specifies what values are output with each atom. Pre-defined atom +attributes can be specified (id, x, fx, etc). Three additional kinds +of keywords can also be specified (c_ID, f_ID, v_name), where a +compute or fix or variable +provides the values to be output. In each case, the compute, fix, or +variable must generate per-atom values for input to the dump +custom command. +

+

There is also a dump local format where the user specifies +what local values to output. A pre-defined index keyword can be +specified to enumuerate the local values. Two additional kinds of +keywords can also be specified (c_ID, f_ID), where a +compute or fix or variable +provides the values to be output. In each case, the compute or fix +must generate local values for input to the dump local +command.

Fixes that write output files
@@ -1124,6 +1135,12 @@ as output values which can be used as input to other output commands. The list of atom attributes is the same as for the dump custom command.

+

The compute property/local command takes +a list of one or more pre-defined local attributes (bond info, angle +info, etc) and stores the values in a local vector or array. These +are produced as output values which can be used as input to other +output commands. +

Fixes that process output quantities

The fix ave/atom command performs time-averaging @@ -1181,6 +1198,7 @@ vector input could be a column of an array. Command Input Output thermo_style custom global scalars screen, log file dump custom per-atom vectors dump file +dump local local vectors dump file fix print global scalar from variable screen, file print global scalar from variable screen computes N/A global/per-atom/local scalar/vector/array @@ -1188,6 +1206,7 @@ vector input could be a column of an array. variables global scalars, per-atom vectors global scalar, per-atom vector compute reduce global/per-atom/local vectors global scalar/vector compute property/atom per-atom vectors per-atom vector/array +compute property/local local vectors local vector/array fix ave/atom per-atom vectors per-atom vector/array fix ave/time global scalars/vectors global scalar/vector/array, file fix ave/spatial per-atom vectors global array, file diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 373282b5b8..0f93550a51 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -1044,14 +1044,25 @@ Dump file output :h5,link(dump) Dump file output is specified by the "dump"_dump.html and "dump_modify"_dump_modify.html commands. There are several -pre-defined formats (dump atom, dump xtc, etc). There is also a "dump -custom"_dump.html format where the user specifies what values are -output with each atom. Pre-defined atom attributes can be specified -(id, x, fx, etc). Three additional kinds of keywords can also be -specified (c_ID, f_ID, v_name), where a "compute"_compute.html or -"fix"_fix.html or "variable"_variable.html provides the values to be -output. In each case, the compute, fix, or variable must generate -per-atom values for input to the "dump custom"_dump.html command. +pre-defined formats (dump atom, dump xtc, etc). + +There is also a "dump custom"_dump.html format where the user +specifies what values are output with each atom. Pre-defined atom +attributes can be specified (id, x, fx, etc). Three additional kinds +of keywords can also be specified (c_ID, f_ID, v_name), where a +"compute"_compute.html or "fix"_fix.html or "variable"_variable.html +provides the values to be output. In each case, the compute, fix, or +variable must generate per-atom values for input to the "dump +custom"_dump.html command. + +There is also a "dump local"_dump.html format where the user specifies +what local values to output. A pre-defined index keyword can be +specified to enumuerate the local values. Two additional kinds of +keywords can also be specified (c_ID, f_ID), where a +"compute"_compute.html or "fix"_fix.html or "variable"_variable.html +provides the values to be output. In each case, the compute or fix +must generate local values for input to the "dump local"_dump.html +command. Fixes that write output files :h5,link(fixoutput) @@ -1115,6 +1126,12 @@ as output values which can be used as input to other output commands. The list of atom attributes is the same as for the "dump custom"_dump.html command. +The "compute property/local"_compute_property_local.html command takes +a list of one or more pre-defined local attributes (bond info, angle +info, etc) and stores the values in a local vector or array. These +are produced as output values which can be used as input to other +output commands. + Fixes that process output quantities :h5,link(fixoutput) The "fix ave/atom"_fix_ave_atom.html command performs time-averaging @@ -1171,6 +1188,7 @@ vector input could be a column of an array. Command: Input: Output: "thermo_style custom"_thermo_style.html: global scalars: screen, log file: "dump custom"_dump.html: per-atom vectors: dump file: +"dump local"_dump.html: local vectors: dump file: "fix print"_fix_print.html: global scalar from variable: screen, file: "print"_print.html: global scalar from variable: screen: "computes"_compute.html: N/A: global/per-atom/local scalar/vector/array: @@ -1178,6 +1196,7 @@ Command: Input: Output: "variables"_variable.html: global scalars, per-atom vectors: global scalar, per-atom vector: "compute reduce"_compute_reduce.html: global/per-atom/local vectors: global scalar/vector: "compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array: +"compute property/local"_compute_local_atom.html: local vectors: local vector/array: "fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array: "fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file: "fix ave/spatial"_fix_ave_spatial.html: per-atom vectors: global array, file: diff --git a/doc/compute.html b/doc/compute.html index 5dd4c5f248..ee1daa948a 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -112,7 +112,8 @@ variable.

  • Local values can be reduced by the compute reduce command, or histogrammed by the fix -ave/histo command. +ave/histo command, or output by the dump +local command.

    The results of computes that calculate global quantities can be either "intensive" or "extensive" values. Intensive means the value is @@ -184,6 +185,7 @@ available in LAMMPS:

  • pe/atom - potential energy for each atom
  • pressure - total pressure and pressure tensor
  • property/atom - convert atom attributes to per-atom vectors/arrays +
  • property/local - convert local attributes to localvectors/arrays
  • rdf - radial distribution function g(r) histogram of group of atoms
  • reduce - combine per-atom quantities into a single global value
  • reduce/region - same as compute reduce, within a region @@ -209,7 +211,7 @@ page.

    uncompute, compute_modify, fix ave/atom, fix ave/spatial, -fix ave/time +fix ave/time, fix ave/histo

    Default: none

    diff --git a/doc/compute.txt b/doc/compute.txt index 2f4629a963..6066a89817 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -107,7 +107,8 @@ variable"_variable.html. :l Local values can be reduced by the "compute reduce"_compute_reduce.html command, or histogrammed by the "fix -ave/histo"_fix_ave_histo.html command. :l,ule +ave/histo"_fix_ave_histo.html command, or output by the "dump +local"_dump.html command. :l,ule The results of computes that calculate global quantities can be either "intensive" or "extensive" values. Intensive means the value is @@ -179,6 +180,7 @@ available in LAMMPS: "pe/atom"_compute_pe_atom.html - potential energy for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays +"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/region"_compute_reduce.html - same as compute reduce, within a region @@ -204,6 +206,6 @@ page"_Section_commands.html#3_5. "uncompute"_uncompute.html, "compute_modify"_compute_modify.html, "fix ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html, -"fix ave/time"_fix_ave_time.html +"fix ave/time"_fix_ave_time.html, "fix ave/histo"_fix_ave_histo.html [Default:] none diff --git a/doc/compute_property_atom.html b/doc/compute_property_atom.html index 981cc2368f..a8e82bffbe 100644 --- a/doc/compute_property_atom.html +++ b/doc/compute_property_atom.html @@ -27,8 +27,9 @@ q, mux, muy, muz, radius, omegax, omegay, omegaz, angmomx, angmomy, angmomz, - quatw, quati, quatj, quatk, tqx, tqy, tqz - id = atom ID + quatw, quati, quatj, quatk, tqx, tqy, tqz + +
          id = atom ID
       mol = molecule ID
       type = atom type
       mass = atom mass
diff --git a/doc/compute_property_atom.txt b/doc/compute_property_atom.txt
index 80137d33ac..203b67c646 100644
--- a/doc/compute_property_atom.txt
+++ b/doc/compute_property_atom.txt
@@ -21,7 +21,8 @@ input = one or more atom attributes :l
                         q, mux, muy, muz,
                         radius, omegax, omegay, omegaz,
                         angmomx, angmomy, angmomz,
-		        quatw, quati, quatj, quatk, tqx, tqy, tqz
+		        quatw, quati, quatj, quatk, tqx, tqy, tqz :pre
+
       id = atom ID
       mol = molecule ID
       type = atom type
diff --git a/doc/dump.html b/doc/dump.html
index 29a77f9cfb..955bd5f59b 100644
--- a/doc/dump.html
+++ b/doc/dump.html
@@ -41,8 +41,9 @@
                           radius, omegax, omegay, omegaz,
                           angmomx, angmomy, angmomz,
 			  quatw, quati, quatj, quatk, tqx, tqy, tqz,
-			  c_ID, c_ID[N], f_ID, f_ID[N], v_name
-      id = atom ID
+			  c_ID, c_ID[N], f_ID, f_ID[N], v_name 
+
    +
          id = atom ID
       mol = molecule ID
       type = atom type
       mass = atom mass
diff --git a/doc/dump.txt b/doc/dump.txt
index 29dd3480e4..f8a1cd173f 100644
--- a/doc/dump.txt
+++ b/doc/dump.txt
@@ -32,7 +32,8 @@ args = list of arguments for a particular style :l
                           radius, omegax, omegay, omegaz,
                           angmomx, angmomy, angmomz,
 			  quatw, quati, quatj, quatk, tqx, tqy, tqz,
-			  c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name
+			  c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
+
       id = atom ID
       mol = molecule ID
       type = atom type