From 16dc820a58b4907b4fe00ac9bb9576f6320f7faa Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 28 Jul 2014 18:46:39 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12199 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/create_atoms.html | 46 ++++++++++++++++++++++++++++++++++++++++- doc/create_atoms.txt | 48 +++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 91 insertions(+), 3 deletions(-) diff --git a/doc/create_atoms.html b/doc/create_atoms.html index 6f06935377..eff378a418 100644 --- a/doc/create_atoms.html +++ b/doc/create_atoms.html @@ -31,7 +31,7 @@
  • zero or more keyword/value pairs may be appended -
  • keyword = mol or basis or remap or units +
  • keyword = mol or basis or remap or var or set or units 
      mol value = template-ID seed
     template-ID = ID of molecule template specified in a separate molecule command
@@ -40,6 +40,10 @@
     M = which basis atom
     itype = atom type (1-N) to assign to this basis atom
   remap value = yes or no
+  var value = name = variable name to evaluate for test of atom creation
+  set values = dim vname
+    dim = x or y or z
+    name = name of variable to set with x,y,z atom position
   units value = lattice or box
     lattice = the geometry is defined in lattice units
     box = the geometry is defined in simulation box units 
@@ -51,6 +55,7 @@
 
    create_atoms 1 box
 create_atoms 3 region regsphere basis 2 3
 create_atoms 3 single 0 0 5 
+create_atoms 1 box var v set x xpos set y ypos 
 
    
 
    Description:
 
    
@@ -189,6 +194,45 @@ box, it will mapped back into the box, assuming the relevant
 dimensions are periodic.  If it is set to no, no remapping is done
 and no particle is created if its position is outside the box.
 
    
+
    The var and set keywords can be used to provide a criterion for
+accepting or rejecting the addition of an individual atom, based on
+its coordinates.  The vname specified for the var keyword is the
+name of an equal-style variable which should evaluate
+to a zero or non-zero value based on one or two or three variables
+which will store the x, y, or z coordinates of an atom (one variable
+per coordinate).  These other variables must be equal-style
+variables defined in the input script, but their
+formula can by anything.  The set keyword is used to identify the
+names of these other variables, one variable for the x-coordinate of a
+created atom, one for y, and one for z.
+
    
+
    When an atom is created, its x, y, or z coordinates override the
+formula for any set variable that is defined.  The var variable is
+then evaluated.  If the returned value is 0.0, the atom is not
+created.  If it is non-zero, the atom is created.
+
    
+
    As an example, these commands can be used in a 2d simulation, to
+create a sinusoidal surface.  Note that the surface is "rough" due to
+individual lattice points being "above" or "below" the mathematical
+expression for the sinusoidal curve.  If a finer lattice were used,
+the sinusoid would appear to be "smoother".  Also note the use of the
+"xlat" and "ylat" thermo_style keywords which
+converts lattice spacings to distance.  Click on the image for a
+larger version.
+
    
+
    variable        x equal 100
+variable        y equal 25
+lattice		hex 0.8442
+region		box block 0 $x 0 $y -0.5 0.5
+create_box	1 box 
+
    
+
    variable        xx equal 0.0
+variable        yy equal 0.0
+variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
+create_atoms	1 box var v set x xx set y yy 
+
    
+
    
+
    
 
    The units keyword determines the meaning of the distance units used
 to specify the coordinates of the one particle created by the single
 style.  A box value selects standard distance units as defined by
diff --git a/doc/create_atoms.txt b/doc/create_atoms.txt
index 4552d43e9a..f395b87b32 100644
--- a/doc/create_atoms.txt
+++ b/doc/create_atoms.txt
@@ -24,7 +24,7 @@ style = {box} or {region} or {single} or {random} :l
     seed = random # seed (positive integer)
     region-ID = create atoms within this region, use NULL for entire simulation box :pre
 zero or more keyword/value pairs may be appended :l
-keyword = {mol} or {basis} or {remap} or {units} :l
+keyword = {mol} or {basis} or {remap} or {var} or {set} or {units} :l
   {mol} value = template-ID seed
     template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
     seed = random # seed (positive integer)
@@ -32,6 +32,10 @@ keyword = {mol} or {basis} or {remap} or {units} :l
     M = which basis atom
     itype = atom type (1-N) to assign to this basis atom
   {remap} value = {yes} or {no}
+  {var} value = name = variable name to evaluate for test of atom creation
+  {set} values = dim vname
+    dim = {x} or {y} or {z}
+    name = name of variable to set with x,y,z atom position
   {units} value = {lattice} or {box}
     {lattice} = the geometry is defined in lattice units
     {box} = the geometry is defined in simulation box units :pre
@@ -41,7 +45,8 @@ keyword = {mol} or {basis} or {remap} or {units} :l
 
 create_atoms 1 box
 create_atoms 3 region regsphere basis 2 3
-create_atoms 3 single 0 0 5 :pre
+create_atoms 3 single 0 0 5 
+create_atoms 1 box var v set x xpos set y ypos :pre
 
 [Description:]
 
@@ -180,6 +185,45 @@ box, it will mapped back into the box, assuming the relevant
 dimensions are periodic.  If it is set to {no}, no remapping is done
 and no particle is created if its position is outside the box.
 
+The {var} and {set} keywords can be used to provide a criterion for
+accepting or rejecting the addition of an individual atom, based on
+its coordinates.  The {vname} specified for the {var} keyword is the
+name of an "equal-style variable"_variable.html which should evaluate
+to a zero or non-zero value based on one or two or three variables
+which will store the x, y, or z coordinates of an atom (one variable
+per coordinate).  These other variables must be "equal-style
+variables"_variable.html defined in the input script, but their
+formula can by anything.  The {set} keyword is used to identify the
+names of these other variables, one variable for the x-coordinate of a
+created atom, one for y, and one for z.
+
+When an atom is created, its x, y, or z coordinates override the
+formula for any {set} variable that is defined.  The {var} variable is
+then evaluated.  If the returned value is 0.0, the atom is not
+created.  If it is non-zero, the atom is created.
+
+As an example, these commands can be used in a 2d simulation, to
+create a sinusoidal surface.  Note that the surface is "rough" due to
+individual lattice points being "above" or "below" the mathematical
+expression for the sinusoidal curve.  If a finer lattice were used,
+the sinusoid would appear to be "smoother".  Also note the use of the
+"xlat" and "ylat" "thermo_style"_thermo_style.html keywords which
+converts lattice spacings to distance.  Click on the image for a
+larger version.
+
+variable        x equal 100
+variable        y equal 25
+lattice		hex 0.8442
+region		box block 0 $x 0 $y -0.5 0.5
+create_box	1 box :pre
+
+variable        xx equal 0.0
+variable        yy equal 0.0
+variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
+create_atoms	1 box var v set x xx set y yy :pre
+
+:c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
+
 The {units} keyword determines the meaning of the distance units used
 to specify the coordinates of the one particle created by the {single}
 style.  A {box} value selects standard distance units as defined by