From 0eeb48a7b32a458426ad0ebe160af1578d8594bf Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 4 Jun 2010 00:37:28 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4237 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 2 +- doc/Section_commands.txt | 2 +- doc/Section_howto.html | 9 +++++++++ doc/Section_howto.txt | 9 +++++++++ doc/compute_displace_atom.html | 19 +++++++++--------- doc/compute_displace_atom.txt | 17 ++++++++-------- doc/compute_msd.html | 21 ++++++++++---------- doc/compute_msd.txt | 19 +++++++++--------- doc/fix.html | 2 +- doc/fix.txt | 2 +- doc/fix_store_force.html | 2 +- doc/fix_store_force.txt | 2 +- doc/{fix_store.html => fix_store_state.html} | 12 +++++------ doc/{fix_store.txt => fix_store_state.txt} | 12 +++++------ 14 files changed, 76 insertions(+), 54 deletions(-) rename doc/{fix_store.html => fix_store_state.html} (95%) rename doc/{fix_store.txt => fix_store_state.txt} (94%) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 020d5428e8..a5e334f0f3 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -330,7 +330,7 @@ of each style or click on the style itself for a full description: nve/aspherenve/limitnve/noforcenve/spherenvtnvt/aspherenvt/sllodnvt/sphere orient/fccplaneforcepoemspourpress/berendsenprintreax/bondsrecenter rigidrigid/nverigid/nvtsetforceshakespringspring/rgspring/self -storestore/forcetemp/berendsentemp/rescalethermal/conductivitytmdttmviscosity +store/forcestore/statetemp/berendsentemp/rescalethermal/conductivitytmdttmviscosity viscouswall/colloidwall/granwall/harmonicwall/lj126wall/lj93wall/reflectwall/region diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 1f7e2a2dc4..dbf1d7f2e4 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -438,8 +438,8 @@ of each style or click on the style itself for a full description: "spring"_fix_spring.html, "spring/rg"_fix_spring_rg.html, "spring/self"_fix_spring_self.html, -"store"_fix_store.html, "store/force"_fix_store_force.html, +"store/state"_fix_store_state.html, "temp/berendsen"_fix_temp_berendsen.html, "temp/rescale"_fix_temp_rescale.html, "thermal/conductivity"_fix_thermal_conductivity.html, diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 7e9dd65087..ed57038390 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -1153,6 +1153,14 @@ quantities calculated by a compute, by a time-averaged per-atom output of this fix can be used as input to other output commands.

+

The fix store command can archive one or more +per-atom attributes at a particular time, so that the old values can +be used in a future calculation or output. The list of atom +attributes is the same as for the dump custom command, +including per-atom quantities calculated by a compute, +by a fix, or by an atom-style variable. +The output of this fix can be used as input to other output commands. +

Computes that generate values to output

Every compute in LAMMPS produces either global or @@ -1215,6 +1223,7 @@ vector input could be a column of an array. fix ave/time global scalars/vectors global scalar/vector/array, file fix ave/spatial per-atom vectors global array, file fix ave/histo global/per-atom/local scalars and vectors global array, file +fix store per-atom vectors per-atom vector/array diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index efe7620dca..9f1dc4de3e 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -1144,6 +1144,14 @@ quantities calculated by a "compute"_compute.html, by a time-averaged per-atom output of this fix can be used as input to other output commands. +The "fix store"_fix_ave_atom.html command can archive one or more +per-atom attributes at a particular time, so that the old values can +be used in a future calculation or output. The list of atom +attributes is the same as for the "dump custom"_dump.html command, +including per-atom quantities calculated by a "compute"_compute.html, +by a "fix"_fix.html, or by an atom-style "variable"_variable.html. +The output of this fix can be used as input to other output commands. + Computes that generate values to output :h5,link(compute) Every "compute"_compute.html in LAMMPS produces either global or @@ -1205,6 +1213,7 @@ Command: Input: Output: "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: "fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file: +"fix store"_fix_store.html: per-atom vectors: per-atom vector/array: :tb(s=:) :line diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html index 827547421f..e21919b5ee 100644 --- a/doc/compute_displace_atom.html +++ b/doc/compute_displace_atom.html @@ -35,19 +35,20 @@ dz*dz).

The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, -the compute creates its own fix of style "store", as if this command -had been issued: +the compute creates its own fix of style "store/state", as if this +command had been issued:

-
fix compute-ID_store group-ID store xu yu zu 
+
fix compute-ID_store_state group-ID store/state xu yu zu 
 

-
See the fix store command for details.  Note that the
-ID of the new fix is the compute-ID + underscore + "store", and the
-group for the new fix is the same as the compute group.
+
See the fix store/state command for details.
+Note that the ID of the new fix is the compute-ID + underscore +
+"store/state", and the group for the new fix is the same as the
+compute group.
 

 
The value of the displacement will be 0.0 for atoms not in the
 specified compute group.
 

-
IMPORTANT NOTE: Fix store stores the initial coordinates in
+
IMPORTANT NOTE: Fix store/state stores the initial coordinates in
 "unwrapped" form, by using the image flags associated with each atom.
 See the dump custom command for a discussion of
 "unwrapped" coordinates.  See the Atoms section of the
@@ -84,8 +85,8 @@ overview of LAMMPS output options.
 

 
Related commands:
 

-
compute msd, dump custom, fix
-store
+
compute msd, dump custom, fix
+store/state
 

 
Default: none
 

diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt
index ea96fb5cb4..9cd35c4a23 100644
--- a/doc/compute_displace_atom.txt
+++ b/doc/compute_displace_atom.txt
@@ -32,19 +32,20 @@ dz*dz).
 
 The displacement of an atom is from its original position at the time
 the compute command was issued.  To store the original coordinates,
-the compute creates its own fix of style "store", as if this command
-had been issued:
+the compute creates its own fix of style "store/state", as if this
+command had been issued:
 
-fix compute-ID_store group-ID store xu yu zu :pre
+fix compute-ID_store_state group-ID store/state xu yu zu :pre
 
-See the "fix store"_fix_store.html command for details.  Note that the
-ID of the new fix is the compute-ID + underscore + "store", and the
-group for the new fix is the same as the compute group.
+See the "fix store/state"_fix_store_state.html command for details.
+Note that the ID of the new fix is the compute-ID + underscore +
+"store/state", and the group for the new fix is the same as the
+compute group.
 
 The value of the displacement will be 0.0 for atoms not in the
 specified compute group.
 
-IMPORTANT NOTE: Fix store stores the initial coordinates in
+IMPORTANT NOTE: Fix store/state stores the initial coordinates in
 "unwrapped" form, by using the image flags associated with each atom.
 See the "dump custom"_dump.html command for a discussion of
 "unwrapped" coordinates.  See the Atoms section of the
@@ -82,6 +83,6 @@ The per-atom array values will be in distance "units"_units.html.
 [Related commands:]
 
 "compute msd"_compute_msd.html, "dump custom"_dump.html, "fix
-store"_fix_store.html
+store/state"_fix_store_state.html
 
 [Default:] none
diff --git a/doc/compute_msd.html b/doc/compute_msd.html
index 5b5bde6c1f..fde408b9e4 100644
--- a/doc/compute_msd.html
+++ b/doc/compute_msd.html
@@ -49,21 +49,22 @@ proportional to the diffusion coefficient of the diffusing atoms.
 

 
The displacement of an atom is from its original position at the time
 the compute command was issued.  To store the original coordinates,
-the compute creates its own fix of style "store", as if this command
-had been issued:
+the compute creates its own fix of style "store/state", as if this
+command had been issued:
 

-
fix compute-ID_store group-ID store xu yu zu 
+
fix compute-ID_store_state group-ID store/state xu yu zu 
 

-
See the fix store command for details.  Note that the
-ID of the new fix is the compute-ID + underscore + "store", and the
-group for the new fix is the same as the compute group.
+
See the fix store/state command for details.
+Note that the ID of the new fix is the compute-ID + underscore +
+"store_state", and the group for the new fix is the same as the
+compute group.
 

 
If the com option is set to yes then the effect of any drift in
 the center-of-mass of the group of atoms is subtracted out before the
 displacment of each atom is calcluated.  The com option is also
-passed to the created fix store.
+passed to the created fix store/state.
 

-
IMPORTANT NOTE: Fix store stores the initial coordinates in
+
IMPORTANT NOTE: Fix store/state stores the initial coordinates in
 "unwrapped" form, by using the image flags associated with each atom.
 See the dump custom command for a discussion of
 "unwrapped" coordinates.  See the Atoms section of the
@@ -101,8 +102,8 @@ distance^2 units.
 

 
Related commands:
 

-
compute displace_atom, fix
-store, compute
+
compute displace_atom, fix
+store/state, compute
 msd/molecule
 

 
Default:
diff --git a/doc/compute_msd.txt b/doc/compute_msd.txt
index a07591aea3..10bd9fecdc 100644
--- a/doc/compute_msd.txt
+++ b/doc/compute_msd.txt
@@ -41,21 +41,22 @@ proportional to the diffusion coefficient of the diffusing atoms.
 
 The displacement of an atom is from its original position at the time
 the compute command was issued.  To store the original coordinates,
-the compute creates its own fix of style "store", as if this command
-had been issued:
+the compute creates its own fix of style "store/state", as if this
+command had been issued:
 
-fix compute-ID_store group-ID store xu yu zu :pre
+fix compute-ID_store_state group-ID store/state xu yu zu :pre
 
-See the "fix store"_fix_store.html command for details.  Note that the
-ID of the new fix is the compute-ID + underscore + "store", and the
-group for the new fix is the same as the compute group.
+See the "fix store/state"_fix_store_state.html command for details.
+Note that the ID of the new fix is the compute-ID + underscore +
+"store_state", and the group for the new fix is the same as the
+compute group.
 
 If the {com} option is set to {yes} then the effect of any drift in
 the center-of-mass of the group of atoms is subtracted out before the
 displacment of each atom is calcluated.  The {com} option is also
-passed to the created fix store.
+passed to the created fix store/state.
 
-IMPORTANT NOTE: Fix store stores the initial coordinates in
+IMPORTANT NOTE: Fix store/state stores the initial coordinates in
 "unwrapped" form, by using the image flags associated with each atom.
 See the "dump custom"_dump.html command for a discussion of
 "unwrapped" coordinates.  See the Atoms section of the
@@ -94,7 +95,7 @@ distance^2 "units"_units.html.
 [Related commands:]
 
 "compute displace_atom"_compute_displace_atom.html, "fix
-store"_fix_store.html, "compute
+store/state"_fix_store_state.html, "compute
 msd/molecule"_compute_msd_molecule.html
 
 [Default:]
diff --git a/doc/fix.html b/doc/fix.html
index 01aada5371..a702e638f0 100644
--- a/doc/fix.html
+++ b/doc/fix.html
@@ -215,8 +215,8 @@ list of fix styles available in LAMMPS:
 
  • spring - apply harmonic spring force to group of atoms
 
  • spring/rg - spring on radius of gyration of      group of atoms
 
  • spring/self - spring from each atom to its origin
-
  • store - store attributes for each atom
 
  • store/force - store force on each atom
+
  • store/state - store attributes for each atom
 
  • temp/berendsen - temperature control by      Berendsen thermostat
 
  • temp/rescale - temperature control by      velocity rescaling
 
  • thermal/conductivity - Muller-Plathe kinetic energy exchange for      thermal conductivity calculation
diff --git a/doc/fix.txt b/doc/fix.txt
index b4290d9ed8..041f46df6e 100644
--- a/doc/fix.txt
+++ b/doc/fix.txt
@@ -218,8 +218,8 @@ list of fix styles available in LAMMPS:
 "spring/rg"_fix_spring_rg.html - spring on radius of gyration of \
      group of atoms
 "spring/self"_fix_spring_self.html - spring from each atom to its origin
-"store"_fix_store.html - store attributes for each atom
 "store/force"_fix_store_force.html - store force on each atom
+"store/state"_fix_store_state.html - store attributes for each atom
 "temp/berendsen"_fix_temp_berendsen.html - temperature control by \
      Berendsen thermostat
 "temp/rescale"_fix_temp_rescale.html - temperature control by \
diff --git a/doc/fix_store_force.html b/doc/fix_store_force.html
index 782697cb05..8fcd4f8cd1 100644
--- a/doc/fix_store_force.html
+++ b/doc/fix_store_force.html
@@ -70,7 +70,7 @@ minimization.
 
    
 
    Related commands:
 
    
-
    fix store
+
    fix store_state
 
    
 
    Default: none
 
    
diff --git a/doc/fix_store_force.txt b/doc/fix_store_force.txt
index 4057393572..12a810db61 100644
--- a/doc/fix_store_force.txt
+++ b/doc/fix_store_force.txt
@@ -67,6 +67,6 @@ minimization"_minimize.html.
 
 [Related commands:]
 
-"fix store"_fix_store.html
+"fix store_state"_fix_store_state.html
 
 [Default:] none
diff --git a/doc/fix_store.html b/doc/fix_store_state.html
similarity index 95%
rename from doc/fix_store.html
rename to doc/fix_store_state.html
index ef6ec187b5..0d1ad87faf 100644
--- a/doc/fix_store.html
+++ b/doc/fix_store_state.html
@@ -9,15 +9,15 @@
 
 
    
 
-
    fix store command 
+
    fix store/state command 
 
    
 
    Syntax:
 
    
-
    fix ID group-ID store N input1 input2 ... keyword value ... 
+
    fix ID group-ID store/state N input1 input2 ... keyword value ... 
 
    
 
    • ID, group-ID are documented in fix command 
 
-
    • store= style name of this fix command 
+
    • store/state = style name of this fix command 
 
 
    • N = store atom attributes every N steps, N = 0 for initial store only 
 
@@ -65,9 +65,9 @@
 
    
 
    Examples:
 
    
-
    fix 1 all store 0 x y z
-fix 1 all store 0 xu yu zu com yes
-fix 2 all store 1000 vx vy vz 
+
    fix 1 all store/state 0 x y z
+fix 1 all store/state 0 xu yu zu com yes
+fix 2 all store/state 1000 vx vy vz 
 
    
 
    Description:
 
    
diff --git a/doc/fix_store.txt b/doc/fix_store_state.txt
similarity index 94%
rename from doc/fix_store.txt
rename to doc/fix_store_state.txt
index 7f1db79578..ea98d36fd9 100644
--- a/doc/fix_store.txt
+++ b/doc/fix_store_state.txt
@@ -6,14 +6,14 @@
 
 :line
 
-fix store command :h3
+fix store/state command :h3
 
 [Syntax:]
 
-fix ID group-ID store N input1 input2 ... keyword value ... :pre
+fix ID group-ID store/state N input1 input2 ... keyword value ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
-store= style name of this fix command :l
+store/state = style name of this fix command :l
 N = store atom attributes every N steps, N = 0 for initial store only :l
 input = one or more atom attributes :l
   possible attributes = id, mol, type, mass,
@@ -55,9 +55,9 @@ keyword = {com} :l
 
 [Examples:]
 
-fix 1 all store 0 x y z
-fix 1 all store 0 xu yu zu com yes
-fix 2 all store 1000 vx vy vz :pre
+fix 1 all store/state 0 x y z
+fix 1 all store/state 0 xu yu zu com yes
+fix 2 all store/state 1000 vx vy vz :pre
 
 [Description:]