From e5d19d4a9ec388fc384d39acaf9516d0244468ec Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 13 Dec 2006 00:37:25 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@188 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 12 +- doc/Section_commands.txt | 3 +- doc/Section_history.html | 2 +- doc/Section_howto.html | 2 +- doc/Section_howto.txt | 2 +- doc/fix.html | 5 +- doc/fix.txt | 5 +- doc/fix_deposit.html | 145 +++++++++++++++++++++++++ doc/fix_deposit.txt | 131 ++++++++++++++++++++++ doc/fix_indent.html | 2 +- doc/fix_indent.txt | 2 +- doc/{fix_insert.html => fix_pour.html} | 24 ++-- doc/{fix_insert.txt => fix_pour.txt} | 24 ++-- doc/temp_modify.html | 19 +++- doc/temp_modify.txt | 19 +++- doc/temperature.html | 5 +- doc/temperature.txt | 5 +- examples/pour/in.pour | 2 +- examples/pour/in.pour.2d | 2 +- 19 files changed, 361 insertions(+), 50 deletions(-) create mode 100644 doc/fix_deposit.html create mode 100644 doc/fix_deposit.txt rename doc/{fix_insert.html => fix_pour.html} (85%) rename doc/{fix_insert.txt => fix_pour.txt} (85%) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 5514643049..c3a0356f3d 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -305,14 +305,14 @@ in the command's documentation. or click on the command itself for a full description:

- - + + - - - - + + +
fix addforcefix aveforcefix comfix dragfix efieldfix enforce2d
fix freezefix gran/diagfix gravityfix gyrationfix indentfix insert
fix addforcefix aveforcefix comfix depositfix dragfix efield
fix enforce2dfix freezefix gran/diagfix gravityfix gyrationfix indent
fix langevinfix lineforcefix msdfix momentumfix nphfix npt
fix nvefix nve/granfix nvtfix orient/fccfix planeforcefix poems
fix printfix rdffix recenterfix rigidfix setforcefix shake
fix springfix spring/rgfix spring/selffix temp/rescalefix tmdfix uniaxial
fix vcmfix viscousfix volume/rescalefix wall/granfix wall/lj93fix wall/lj126
fix wall/reflectfix wiggle +
fix pourfix printfix rdffix recenterfix rigidfix setforce
fix shakefix springfix spring/rgfix spring/selffix temp/rescalefix tmd
fix uniaxialfix vcmfix viscousfix volume/rescalefix wall/granfix wall/lj93
fix wall/lj126fix wall/reflectfix wiggle

Pair styles. See the pair_style command for an diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 35b798d48b..c5041bd9c8 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -361,6 +361,7 @@ or click on the command itself for a full description: "fix addforce"_fix_addforce.html, "fix aveforce"_fix_aveforce.html, "fix com"_fix_com.html, +"fix deposit"_fix_deposit.html, "fix drag"_fix_drag.html, "fix efield"_fix_efield.html, "fix enforce2d"_fix_enforce2d.html, @@ -369,7 +370,6 @@ or click on the command itself for a full description: "fix gravity"_fix_gravity.html, "fix gyration"_fix_gyration.html, "fix indent"_fix_indent.html, -"fix insert"_fix_insert.html, "fix langevin"_fix_langevin.html, "fix lineforce"_fix_lineforce.html, "fix msd"_fix_msd.html, @@ -382,6 +382,7 @@ or click on the command itself for a full description: "fix orient/fcc"_fix_orient_fcc.html, "fix planeforce"_fix_planeforce.html, "fix poems"_fix_poems.html, +"fix pour"_fix_pour.html, "fix print"_fix_print.html, "fix rdf"_fix_rdf.html, "fix recenter"_fix_recenter.html, diff --git a/doc/Section_history.html b/doc/Section_history.html index c45f64fedf..881d419cd3 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -37,7 +37,7 @@ time or interest; others are just a lot of work!

  • point dipole force fields
  • many-body and bond-order potentials for materials like C, Si, or silica
  • modified EAM (MEAM) potentials for metals -
  • REAXX force field from Bill Goddard's group +
  • ReaxFF force field from Bill Goddard's group
  • Parinello-Rahman non-rectilinear simulation box
    diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 26d959887d..6c68d757b0 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -328,7 +328,7 @@ the following commands:

    diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index ebb89cc241..3fd05f1f75 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -324,7 +324,7 @@ These commands implement fix options specific to granular systems: "fix freeze"_fix_freeze.html "fix gran/diag"_fix_gran_diag.html -"fix insert"_fix_insert.html +"fix pour"_fix_pour.html "fix viscous"_fix_viscous.html "fix wall/gran"_fix_wall_gran.html :ul diff --git a/doc/fix.html b/doc/fix.html index e5720381e7..4188dcae41 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -62,6 +62,7 @@ integrators would be in place!

    Examples:

    -
    temp_modify mine extra 0 
+
    temp_modify mine extra 0
+temp_modify mine dynamic yes 
 
    
 
    Description:
 
    
@@ -42,6 +45,14 @@ subtracted (typically from 3N) as a normalizing factor in the
 temperature computation.  The default is 3 which is a correction
 factor for an ensemble of velocities with zero total linear momentum.
 
    
+
    The dynamic keyword determines whether the number of atoms N in the
+temperature group is re-computed each time the temperature is
+computed.  By default, N is assumed to be constant.  If you are adding
+atoms to the system (see the fix pour or fix
+deposit commands) or expect atoms to be lost
+(e.g. due to evaporation), then this option can be used to insure the
+temperature is correctly normalized.
+
    
 
    Restrictions: none
 
    
 
    Related commands:
@@ -50,6 +61,6 @@ factor for an ensemble of velocities with zero total linear momentum.
 
    
 
    Default:
 
    
-
    The option defaults are extra = 3.
+
    The option defaults are extra = 3 and dynamic = no.
 
    
 
diff --git a/doc/temp_modify.txt b/doc/temp_modify.txt
index faf772b410..ec13f9403d 100644
--- a/doc/temp_modify.txt
+++ b/doc/temp_modify.txt
@@ -14,14 +14,17 @@ temp_modify temp-ID keyword value ... :pre
 
 temp-ID = ID of temperature to modify :ulb,l
 one or more keyword/value pairs may be listed :l
-keyword = {extra} :l
+keyword = {extra} or {dynamic} :l
   {extra} value = N
-    N = # of extra degrees of freedom to subtract :pre
+    N = # of extra degrees of freedom to subtract
+  {dynamic} value = {yes} or {no}
+    yes/no = do or do not recompute the number of atoms contributing to the temperature :pre
 :ule
 
 [Examples:]
 
-temp_modify mine extra 0 :pre
+temp_modify mine extra 0
+temp_modify mine dynamic yes :pre
 
 [Description:]
 
@@ -35,6 +38,14 @@ subtracted (typically from 3N) as a normalizing factor in the
 temperature computation.  The default is 3 which is a correction
 factor for an ensemble of velocities with zero total linear momentum.
 
+The {dynamic} keyword determines whether the number of atoms N in the
+temperature group is re-computed each time the temperature is
+computed.  By default, N is assumed to be constant.  If you are adding
+atoms to the system (see the "fix pour"_fix_pour.html or "fix
+deposit"_fix_deposit.html commands) or expect atoms to be lost
+(e.g. due to evaporation), then this option can be used to insure the
+temperature is correctly normalized.
+
 [Restrictions:] none
 
 [Related commands:]
@@ -43,4 +54,4 @@ factor for an ensemble of velocities with zero total linear momentum.
 
 [Default:]
 
-The option defaults are extra = 3.
+The option defaults are extra = 3 and dynamic = no.
diff --git a/doc/temperature.html b/doc/temperature.html
index 61d2dc6dde..35d995042d 100644
--- a/doc/temperature.html
+++ b/doc/temperature.html
@@ -63,7 +63,10 @@ nvt, fix npt, etc.
 style means KE = dim/2 N k T, where KE = total kinetic energy of the
 group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of
 the simulation, N = number of atoms in the group, k = Boltzmann
-constant, and T = temperature.
+constant, and T = temperature.  The number of atoms contributing to
+the temperature is assumed to be constant for the duration of the run;
+use the dynamic option of the temp_modify command
+if this is not the case.
 
    
 
    The partial style uses the same formula as full, except entire
 dimensions can be eliminated from the kinetic energy computation.
diff --git a/doc/temperature.txt b/doc/temperature.txt
index b6f8cd44a4..80d5aade25 100644
--- a/doc/temperature.txt
+++ b/doc/temperature.txt
@@ -53,7 +53,10 @@ The style determines how the temperature is computed.  The {full}
 style means KE = dim/2 N k T, where KE = total kinetic energy of the
 group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of
 the simulation, N = number of atoms in the group, k = Boltzmann
-constant, and T = temperature.
+constant, and T = temperature.  The number of atoms contributing to
+the temperature is assumed to be constant for the duration of the run;
+use the {dynamic} option of the "temp_modify"_temp_modify.html command
+if this is not the case.
 
 The {partial} style uses the same formula as {full}, except entire
 dimensions can be eliminated from the kinetic energy computation.
diff --git a/examples/pour/in.pour b/examples/pour/in.pour
index 9b8e123c90..708aa6d875 100644
--- a/examples/pour/in.pour
+++ b/examples/pour/in.pour
@@ -23,7 +23,7 @@ fix		2 all gravity spherical 0.0 -180.0
 fix		zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
 
 region		slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
-fix		ins all insert 3000 1 300719 vol 0.13 50 region slab
+fix		ins all pour 3000 1 300719 vol 0.13 50 region slab
 
 thermo_style	granular
 thermo		1000
diff --git a/examples/pour/in.pour.2d b/examples/pour/in.pour.2d
index 561c8509d5..ba5574e0f7 100644
--- a/examples/pour/in.pour.2d
+++ b/examples/pour/in.pour.2d
@@ -25,7 +25,7 @@ fix		xwalls all wall/gran xplane 0 100 50 0
 fix		ywalls all wall/gran yplane 0 NULL 50 0
  
 region          slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
-fix             ins all insert 1000 1 4767548 vol 0.4 10 &
+fix             ins all pour 1000 1 4767548 vol 0.4 10 &
 	        diam 0.5 1.0 region slab
 
 fix             3 all enforce2d