git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3621 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_reduce.html

@@ -15,7 +15,7 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>compute ID group-ID style arg mode input1 input2 ... 
+<PRE>compute ID group-ID style arg mode input1 input2 ... keyword args ... 
 </PRE>
 <UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command 
 
@@ -38,13 +38,22 @@
   f_ID[I] = Ith column of array calculated by a fix with ID
   v_name = per-atom vector calculated by an atom-style variable with name 
 </PRE>
+<LI>zero or more keyword/args pairs may be appended 
+
+<LI>keyword = <I>replace</I> 
+
+<PRE>  <I>replace</I> args = vec1 vec2
+    vec1 = reduced value from this input vector will be replaced
+    vec2 = replace it with vec1[N] where N is index of max/min value from vec2 
+</PRE>
 
 </UL>
 <P><B>Examples:</B>
 </P>
 <PRE>compute 1 all reduce sum c_force
 compute 1 all reduce/region subbox sum c_force
-compute 2 all reduce min c_press<B>2</B> f_ave v_myKE 
+compute 2 all reduce min c_press<B>2</B> f_ave v_myKE
+compute 3 fluid reduce max c_index<B>1</B> c_index<B>2</B> c_dist replace 1 3 replace 2 3 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -110,6 +119,36 @@ invoke other computes, fixes, or variables when they are evaluated, so
 this is a very general means of generating per-atom quantities to
 reduce.
 </P>
+<HR>
+
+<P>If the <I>replace</I> keyword is used, two indices <I>vec1</I> and <I>vec2</I> are
+specified, where each index ranges from 1 to the # of input values.
+The replace keyword can only be used if the <I>mode</I> is <I>min</I> or <I>max</I>.
+It works as follows.  A min/max is computed as usual on the <I>vec2</I>
+input vector.  The index N of that value within <I>vec2</I> is also stored.
+Then, instead of performing a min/max on the <I>vec1</I> input vector, the
+stored index is used to select the Nth element of the <I>vec1</I> vector.
+</P>
+<P>Thus, for example, if you wish to use this compute to find the bond
+with maximum stretch, you can do it as follows:
+</P>
+<PRE>compute 1 all property/local batom1 batom2
+compute	2 all bond/local dist
+compute	3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
+thermo_style custom step temp c_3[1] c_3[2] c_3[3] 
+</PRE>
+<P>The first two input values in the compute reduce command are vectors
+with the IDs of the 2 atoms in each bond, using the <A HREF = "compute_property_local.html">compute
+property/local</A> command.  The last input
+value is bond distance, using the <A HREF = "compute_bond_local.html">compute
+bond/local</A> command.  Instead of taking the
+max of the two atom ID vectors, which does not yield useful
+information in this context, the <I>replace</I> keywords will extract the
+atom IDs for the two atoms in the bond of maximum stretch.  These atom
+IDs and the bond stretch will be printed with thermodynamic output.
+</P>
+<HR>
+
 <P>If a single input is specified this compute produces a global scalar
 value.  If multiple inputs are specified, this compute produces a
 vector of global values, the length of which is equal to the number of

doc/compute_reduce.txt

@@ -11,7 +11,7 @@ compute reduce/region command :h3
 
 [Syntax:]
 
-compute ID group-ID style arg mode input1 input2 ... :pre
+compute ID group-ID style arg mode input1 input2 ... keyword args ... :pre
 
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 style = {reduce} or {reduce/region} :l
@@ -27,13 +27,20 @@ input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_nam
   f_ID = vector calculated by a fix with ID
   f_ID\[I\] = Ith column of array calculated by a fix with ID
   v_name = per-atom vector calculated by an atom-style variable with name :pre
+
+zero or more keyword/args pairs may be appended :l
+keyword = {replace} :l
+  {replace} args = vec1 vec2
+    vec1 = reduced value from this input vector will be replaced
+    vec2 = replace it with vec1\[N\] where N is index of max/min value from vec2 :pre
 :ule
 
 [Examples:]
 
 compute 1 all reduce sum c_force
 compute 1 all reduce/region subbox sum c_force
-compute 2 all reduce min c_press[2] f_ave v_myKE :pre
+compute 2 all reduce min c_press[2] f_ave v_myKE
+compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3 :pre
 
 [Description:]
 
@@ -99,6 +106,36 @@ invoke other computes, fixes, or variables when they are evaluated, so
 this is a very general means of generating per-atom quantities to
 reduce.
 
+:line
+
+If the {replace} keyword is used, two indices {vec1} and {vec2} are
+specified, where each index ranges from 1 to the # of input values.
+The replace keyword can only be used if the {mode} is {min} or {max}.
+It works as follows.  A min/max is computed as usual on the {vec2}
+input vector.  The index N of that value within {vec2} is also stored.
+Then, instead of performing a min/max on the {vec1} input vector, the
+stored index is used to select the Nth element of the {vec1} vector.
+
+Thus, for example, if you wish to use this compute to find the bond
+with maximum stretch, you can do it as follows:
+
+compute 1 all property/local batom1 batom2
+compute	2 all bond/local dist
+compute	3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
+thermo_style custom step temp c_3\[1\] c_3\[2\] c_3\[3\] :pre
+
+The first two input values in the compute reduce command are vectors
+with the IDs of the 2 atoms in each bond, using the "compute
+property/local"_compute_property_local.html command.  The last input
+value is bond distance, using the "compute
+bond/local"_compute_bond_local.html command.  Instead of taking the
+max of the two atom ID vectors, which does not yield useful
+information in this context, the {replace} keywords will extract the
+atom IDs for the two atoms in the bond of maximum stretch.  These atom
+IDs and the bond stretch will be printed with thermodynamic output.
+
+:line
+
 If a single input is specified this compute produces a global scalar
 value.  If multiple inputs are specified, this compute produces a
 vector of global values, the length of which is equal to the number of

doc/region.html

@@ -17,7 +17,7 @@
 </PRE>
 <UL><LI>ID = user-assigned name for the region 
 
-<LI>style = <I>block</I> or <I>cone</I> or <I>cylinder</I> or <I>prism</I> or <I>sphere</I> or <I>union</I> or <I>intersect</I> 
+<LI>style = <I>block</I> or <I>cone</I> or <I>cylinder</I> or <I>plane</I> or <I>prism</I> or <I>sphere</I> or <I>union</I> or <I>intersect</I> 
 
 <PRE>  <I>block</I> args = xlo xhi ylo yhi zlo zhi
     xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
@@ -31,6 +31,9 @@
     c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
     radius = cylinder radius (distance units)
     lo,hi = bounds of cylinder in dim (distance units)
+  <I>plane</I> args = px py pz nx ny nz
+    px,py,pz = point on the plane
+    nx,ny,nz = direction normal to plane (distance units)
   <I>prism</I> args = xlo xhi ylo yhi zlo zhi xy xz yz
     xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
     xy = distance to tilt y in x direction (distance units)
@@ -88,7 +91,7 @@ parameter cannot be used.
 </P>
 <P>For style <I>cone</I>, an axis-aligned cone is defined which is like a
 <I>cylinder</I> except that two different radii (one at each end) can be
-defined.
+defined.  Either of the radii can be 0.0.
 </P>
 <P>For style <I>cone</I> and <I>cylinder</I>, the c1,c2 params are coordinates in
 the 2 other dimensions besides the cylinder axis dimension.  For dim =

doc/region.txt

@@ -13,7 +13,7 @@ region command :h3
 region ID style args keyword value ... :pre
 
 ID = user-assigned name for the region :ulb,l
-style = {block} or {cone} or {cylinder} or {prism} or {sphere} or {union} or {intersect} :l
+style = {block} or {cone} or {cylinder} or {plane} or {prism} or {sphere} or {union} or {intersect} :l
   {block} args = xlo xhi ylo yhi zlo zhi
     xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
   {cone} args = dim c1 c2 radlo radhi lo hi
@@ -26,6 +26,9 @@ style = {block} or {cone} or {cylinder} or {prism} or {sphere} or {union} or {in
     c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
     radius = cylinder radius (distance units)
     lo,hi = bounds of cylinder in dim (distance units)
+  {plane} args = px py pz nx ny nz
+    px,py,pz = point on the plane
+    nx,ny,nz = direction normal to plane (distance units)
   {prism} args = xlo xhi ylo yhi zlo zhi xy xz yz
     xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
     xy = distance to tilt y in x direction (distance units)
@@ -79,7 +82,7 @@ parameter cannot be used.
 
 For style {cone}, an axis-aligned cone is defined which is like a
 {cylinder} except that two different radii (one at each end) can be
-defined.
+defined.  Either of the radii can be 0.0.
 
 For style {cone} and {cylinder}, the c1,c2 params are coordinates in
 the 2 other dimensions besides the cylinder axis dimension.  For dim =