git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@632 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_deform.html

@@ -25,7 +25,7 @@
 
 <PRE>parameter = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>xz</I> or <I>yz</I>
   <I>x</I>, <I>y</I>, <I>z</I> args = style value(s)
-    style = <I>final</I> or <I>delta</I> or <I>scale</I> or <I>vel</I> or <I>rate</I> or <I>volume</I>
+    style = <I>final</I> or <I>delta</I> or <I>scale</I> or <I>vel</I> or <I>erate</I> or <I>trate</I> or <I>volume</I>
       <I>final</I> values = lo hi
         lo hi = box boundaries at end of run (distance units)
       <I>delta</I> values = dlo dhi
@@ -35,11 +35,13 @@
       <I>vel</I> value = V
         V = change box length at this velocity (distance/time units),
 	    effectively an engineering strain rate
-      <I>rate</I> value = R
+      <I>erate</I> value = R
+        R = engineering strain rate (1/time units)
+      <I>trate</I> value = R
         R = true strain rate (1/time units)
       <I>volume</I> value = none = adjust this dim to preserve volume of system
   <I>xy</I>, <I>xz</I>, <I>yz</I> args = style value
-    style = <I>final</I> or <I>delta</I> or <I>vel</I> or <I>rate</I>
+    style = <I>final</I> or <I>delta</I> or <I>vel</I> or <I>erate</I> or <I>trate</I>
       <I>final</I> value = tilt
         tilt = tilt factor at end of run (distance units)
       <I>delta</I> value = dtilt
@@ -47,7 +49,10 @@
       <I>vel</I> value = V
         V = change tilt factor at this velocity (distance/time units),
 	    effectively an engineering shear strain rate
-      <I>rate</I> value = R
+      <I>erate</I> value = R
+        R = engineering shear strain rate (1/time units) 
+</PRE>
+<PRE>      <I>trate</I> value = R
         R = true shear strain rate (1/time units) 
 </PRE>
 <LI>zero or more keyword/value pairs may be appended to the args 
@@ -67,8 +72,8 @@
 <P><B>Examples:</B>
 </P>
 <PRE>fix 1 all deform x final 0.0 9.0 z final 0.0 5.0 units box
-fix 1 all deform x rate 0.1 y volume z volume
+fix 1 all deform x trate 0.1 y volume z volume
-fix 1 all deform xy rate 0.001 remap v
+fix 1 all deform xy erate 0.001 remap v
 fix 1 all deform y delta 0.5 xz vel 1.0 
 </PRE>
 <P><B>Description:</B>
@@ -114,10 +119,11 @@ the ramping take place across multiple runs.
 <P>For the <I>x</I>, <I>y</I>, and <I>z</I> parameters, this is the meaning of their
 styles and values.
 </P>
-<P>The <I>final</I>, <I>delta</I>, <I>scale</I>, and <I>vel</I> styles all change the
+<P>The <I>final</I>, <I>delta</I>, <I>scale</I>, <I>vel</I>, and <I>erate</I> styles all change
-specified dimension of the box via "constant displacement" which is
+the specified dimension of the box via "constant displacement" which
-effectively a "constant engineering strain rate".  This means the box
+is effectively a "constant engineering strain rate".  This means the
-dimension changes linearly with time from its initial to final value.
+box dimension changes linearly with time from its initial to final
+value.
 </P>
 <P>For style <I>final</I>, the final lo and hi box boundaries of a dimension
 are specified.  The values can be in lattice or box distance units.
@@ -133,36 +139,57 @@ is 10, and the factor is 1.1, then the final box length will be 11.  A
 factor less than 1.0 means compression.
 </P>
 <P>For style <I>vel</I>, a velocity at which the box length changes is
-specified in units of distance/time.  This is effectively an
+specified in units of distance/time.  This is effectively a "constant
-"engineering strain rate", where rate = V/L0 and L0 is the initial box
+engineering strain rate", where rate = V/L0 and L0 is the initial box
 length.  The distance can be in lattice or box distance units.  See
 the discussion of the units keyword below.  For example, if the
-initial box length is 100 Angstroms, and V is 10 Angstroms/psec,
+initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
-then after 10 psec, the box length will have doubled.  After 20 psec,
+after 10 psec, the box length will have doubled.  After 20 psec, it
-it will have tripled.
+will have tripled.
 </P>
-<P>The <I>rate</I> style changes a dimension of the box at a "true constant
+<P>The <I>erate</I> style changes a dimension of the the box at a "constant
+engineering strain rate".  The units of the specified strain rate are
+1/time.  See the <A HREF = "units.html">units</A> command for the time units
+associated with different choices of simulation units,
+e.g. picoseconds for "metal" units).  Tensile strain is unitless and
+is defined as delta/length0, where length0 is the original box length
+and delta is the change relative to the original length.  Thus if the
+<I>erate</I> R is 0.1 and time units are picoseconds, this means the box
+length will increase by 10% of its original length every picosecond.
+I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc.
+R = -0.01 means the box length will shrink by 1% of its original
+length every picosecond.  Note that for an "engineering" rate the
+change is based on the original box length, so running with R = 1 for
+10 picoseconds expands the box length by a factor of 10, not 1024 as
+it would with <I>trate</I>.
+</P>
+<P>The <I>trate</I> style changes a dimension of the box at a "constant true
 strain rate".  Note that this is not an "engineering strain rate", as
 the other styles are.  Rather, for a "true" rate, the rate of change
 is constant, which means the box dimension changes non-linearly with
 time from its initial to final value.  The units of the specified
 strain rate are 1/time.  See the <A HREF = "units.html">units</A> command for the
 time units associated with different choices of simulation units,
-e.g. picoseconds for "metal" units).  Thus if the <I>rate</I> R is 0.01 and
+e.g. picoseconds for "metal" units).  Tensile strain is unitless and
-time units are picoseconds, this means the box length will increase by
+is defined as delta/length0, where length0 is the original box length
-1% every picosecond.  R = 1 or 2 means the box length will double or
+and delta is the change relative to the original length.  Thus if the
-triple every picosecond.  R = -0.1 means the box length will shrink by
+<I>trate</I> R is 0.1 and time units are picoseconds, this means the box
-10% every picosecond.  Note that for a "true" rate the change is
+length will increase by 10% of its current length every picosecond.
-continuous, so running with R = 1 for 10 picoseconds does not expand
+I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.21, etc.
-the box length by a factor of 10, but by a factor of 1024 since it
+R = 1 or 2 means the box length will double or triple every
-doubles every picosecond.
+picosecond.  R = -0.01 means the box length will shrink by 1% of its
+current length every picosecond.  Note that for a "true" rate the
+change is continuous and based on the current length, so running with
+R = 1 for 10 picoseconds does not expand the box length by a factor of
+10 as it would with <I>erate</I>, but by a factor of 1024 since it doubles
+every picosecond.
 </P>
 <P>Note that to change the volume (or cross-sectional area) of the
 simulation box at a constant rate, you can change multiple dimensions
-via <I>rate</I>.  E.g. to double the box volume every picosecond, you could
+via <I>erate</I> or <I>trate</I>.  E.g. to double the box volume every
-set "x rate M", "y rate M", "z rate M", with M = pow(2,1/3) - 1 =
+picosecond, you could set "x trate M", "y trate M", "z trate M", with
-1.26, since if each box dimension grows by 26%, the box volume
+M = pow(2,1/3) - 1 = 1.26, since if each box dimension grows by 26%,
-doubles.
+the box volume doubles.
 </P>
 <P>The <I>volume</I> style changes the specified dimension in such a way that
 the box volume remains constant while other box dimensions are changed
@@ -187,8 +214,8 @@ potentials whose Poisson ratio is not 0.5.  An alternative is to use
 <A HREF = "fix_npt.html">fix npt aniso</A> with zero applied pressure on those 2
 dimensions, so that they respond to the tensile strain dynamically.
 </P>
-<P>For the <I>scale</I>, <I>vel</I>, <I>rate</I>, and <I>volume</I> styles, the box length is
+<P>For the <I>scale</I>, <I>vel</I>, <I>erate</I>, <I>trate</I>, and <I>volume</I> styles, the box
-expanded or compressed around its mid point.
+length is expanded or compressed around its mid point.
 </P>
 <HR>
 
@@ -196,6 +223,11 @@ expanded or compressed around its mid point.
 styles and values.  Note that changing the tilt factors of a triclinic
 box does not change its volume.
 </P>
+<P>The <I>final</I>, <I>delta</I>, <I>vel</I>, and <I>erate</I> styles all change the shear
+strain at a "constant engineering shear strain rate".  This means the
+tilt factor changes linearly with time from its initial to final
+value.
+</P>
 <P>For style <I>final</I>, the final tilt factor is specified.  The value
 can be in lattice or box distance units.  See the discussion of the
 units keyword below.
@@ -214,28 +246,53 @@ is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
 tilt factor will be 15 Angstroms.  After 2 psec, it will be 25
 Angstroms.
 </P>
-<P>The <I>rate</I> style changes a tilt factor at a "true constant shear
+<P>The <I>erate</I> style changes a tilt factor at a "constant engineering
+shear strain rate".  The units of the specified shear strain rate are
+1/time.  See the <A HREF = "units.html">units</A> command for the time units
+associated with different choices of simulation units,
+e.g. picoseconds for "metal" units).  Shear strain is unitless and is
+defined as offset/length, where length is the box length perpendicular
+to the shear direction (e.g. y box length for xy deformation) and
+offset is the displacement distance in the shear direction (e.g. x
+direction for xy deformation) from the unstrained orientation.  Thus
+if the <I>erate</I> R is 0.1 and time units are picoseconds, this means the
+shear strain will increase by 0.1 every picosecond.  I.e. if the xy
+shear strain was initially 0.0, then strain after 1 psec = 0.1, strain
+after 2 psec = 0.2, etc.  Thus the tilt factor would be 0.0 at time 0,
+0.1*ybox at 1 psec, 0.2*ybox at 2 psec, etc, where ybox is the
+original y box length.  R = 1 or 2 means the tilt factor will increase
+by 1 or 2 every picosecond.  R = -0.01 means a decrease in shear
+strain by 0.01 every picosecond.
+</P>
+<P>The <I>trate</I> style changes a tilt factor at a "constant true shear
 strain rate".  Note that this is not an "engineering shear strain
 rate", as the other styles are.  Rather, for a "true" rate, the rate
 of change is constant, which means the tilt factor changes
 non-linearly with time from its initial to final value.  The units of
-shear strain rate are 1/time.  See the <A HREF = "units.html">units</A> command for
+the specified shear strain rate are 1/time.  See the
-the time units associated with different choices of simulation units,
+<A HREF = "units.html">units</A> command for the time units associated with
-e.g. picoseconds for "metal" units).  Thus if the <I>rate</I> R is 0.01 and
+different choices of simulation units, e.g. picoseconds for "metal"
-time units are picoseconds, this means the tilt factor will increase
+units).  Shear strain is unitless and is defined as offset/length,
-by 1% every picosecond.  R = 1 or 2 means the tilt factor will double
+where length is the box length perpendicular to the shear direction
-or triple every picosecond.  R = -0.1 means the tilt factor will
+(e.g. y box length for xy deformation) and offset is the displacement
-shrink by 10% every picosecond.  Note that the change is continuous,
+distance in the shear direction (e.g. x direction for xy deformation)
-so running with R = 1 for 10 picoseconds does not change the tilt
+from the unstrained orientation.  Thus if the <I>trate</I> R is 0.1 and
-factor by a factor of 10, but by a factor of 1024 since it doubles
+time units are picoseconds, this means the shear strain or tilt factor
-every picosecond.  Also note, that the initial tilt factor must be
+will increase by 10% every picosecond.  I.e. if the xy shear strain
-non-zero to use the <I>rate</I> option.
+was initially 0.1, then strain after 1 psec = 0.11, strain after 2
+psec = 0.121, etc.  R = 1 or 2 means the tilt factor will double or
+triple every picosecond.  R = -0.01 means the tilt factor will shrink
+by 1% every picosecond.  Note that the change is continuous, so
+running with R = 1 for 10 picoseconds does not change the tilt factor
+by a factor of 10, but by a factor of 1024 since it doubles every
+picosecond.  Also note that the initial tilt factor must be non-zero
+to use the <I>trate</I> option.
 </P>
 <P>Note that shear strain is defined as the tilt factor divided by the
-perpendicular box length.  The <I>rate</I> style controls the tilt factor,
+perpendicular box length.  The <I>erate</I> and <I>trate</I> styles control the
-but assumes the perpendicular box length remains constant.  If this is
+tilt factor, but assume the perpendicular box length remains constant.
-not the case (e.g. it changes due to another fix deform parameter),
+If this is not the case (e.g. it changes due to another fix deform
-then this effect on the shear strain is ignored.
+parameter), then this effect on the shear strain is ignored.
 </P>
 <P>All of these styles change the xy, xz, yz tilt factors during a
 simulation.  In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes

doc/fix_deform.txt

@@ -18,7 +18,7 @@ N = perform box deformation every this many timesteps :l
 one or more parameter/arg pairs may be appended :l
 parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
   {x}, {y}, {z} args = style value(s)
-    style = {final} or {delta} or {scale} or {vel} or {rate} or {volume}
+    style = {final} or {delta} or {scale} or {vel} or {erate} or {trate} or {volume}
       {final} values = lo hi
         lo hi = box boundaries at end of run (distance units)
       {delta} values = dlo dhi
@@ -28,11 +28,13 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
       {vel} value = V
         V = change box length at this velocity (distance/time units),
 	    effectively an engineering strain rate
-      {rate} value = R
+      {erate} value = R
+        R = engineering strain rate (1/time units)
+      {trate} value = R
         R = true strain rate (1/time units)
       {volume} value = none = adjust this dim to preserve volume of system
   {xy}, {xz}, {yz} args = style value
-    style = {final} or {delta} or {vel} or {rate}
+    style = {final} or {delta} or {vel} or {erate} or {trate}
       {final} value = tilt
         tilt = tilt factor at end of run (distance units)
       {delta} value = dtilt
@@ -40,7 +42,9 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
       {vel} value = V
         V = change tilt factor at this velocity (distance/time units),
 	    effectively an engineering shear strain rate
-      {rate} value = R
+      {erate} value = R
+        R = engineering shear strain rate (1/time units) :pre
+      {trate} value = R
         R = true shear strain rate (1/time units) :pre
 
 zero or more keyword/value pairs may be appended to the args :l
@@ -57,8 +61,8 @@ keyword = {remap} or {units} :l
 [Examples:]
 
 fix 1 all deform x final 0.0 9.0 z final 0.0 5.0 units box
-fix 1 all deform x rate 0.1 y volume z volume
+fix 1 all deform x trate 0.1 y volume z volume
-fix 1 all deform xy rate 0.001 remap v
+fix 1 all deform xy erate 0.001 remap v
 fix 1 all deform y delta 0.5 xz vel 1.0 :pre
 
 [Description:]
@@ -104,10 +108,11 @@ the ramping take place across multiple runs.
 For the {x}, {y}, and {z} parameters, this is the meaning of their
 styles and values.
 
-The {final}, {delta}, {scale}, and {vel} styles all change the
+The {final}, {delta}, {scale}, {vel}, and {erate} styles all change
-specified dimension of the box via "constant displacement" which is
+the specified dimension of the box via "constant displacement" which
-effectively a "constant engineering strain rate".  This means the box
+is effectively a "constant engineering strain rate".  This means the
-dimension changes linearly with time from its initial to final value.
+box dimension changes linearly with time from its initial to final
+value.
 
 For style {final}, the final lo and hi box boundaries of a dimension
 are specified.  The values can be in lattice or box distance units.
@@ -123,36 +128,57 @@ is 10, and the factor is 1.1, then the final box length will be 11.  A
 factor less than 1.0 means compression.
 
 For style {vel}, a velocity at which the box length changes is
-specified in units of distance/time.  This is effectively an
+specified in units of distance/time.  This is effectively a "constant
-"engineering strain rate", where rate = V/L0 and L0 is the initial box
+engineering strain rate", where rate = V/L0 and L0 is the initial box
 length.  The distance can be in lattice or box distance units.  See
 the discussion of the units keyword below.  For example, if the
-initial box length is 100 Angstroms, and V is 10 Angstroms/psec,
+initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
-then after 10 psec, the box length will have doubled.  After 20 psec,
+after 10 psec, the box length will have doubled.  After 20 psec, it
-it will have tripled.
+will have tripled.
 
-The {rate} style changes a dimension of the box at a "true constant
+The {erate} style changes a dimension of the the box at a "constant
+engineering strain rate".  The units of the specified strain rate are
+1/time.  See the "units"_units.html command for the time units
+associated with different choices of simulation units,
+e.g. picoseconds for "metal" units).  Tensile strain is unitless and
+is defined as delta/length0, where length0 is the original box length
+and delta is the change relative to the original length.  Thus if the
+{erate} R is 0.1 and time units are picoseconds, this means the box
+length will increase by 10% of its original length every picosecond.
+I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc.
+R = -0.01 means the box length will shrink by 1% of its original
+length every picosecond.  Note that for an "engineering" rate the
+change is based on the original box length, so running with R = 1 for
+10 picoseconds expands the box length by a factor of 10, not 1024 as
+it would with {trate}.
+
+The {trate} style changes a dimension of the box at a "constant true
 strain rate".  Note that this is not an "engineering strain rate", as
 the other styles are.  Rather, for a "true" rate, the rate of change
 is constant, which means the box dimension changes non-linearly with
 time from its initial to final value.  The units of the specified
 strain rate are 1/time.  See the "units"_units.html command for the
 time units associated with different choices of simulation units,
-e.g. picoseconds for "metal" units).  Thus if the {rate} R is 0.01 and
+e.g. picoseconds for "metal" units).  Tensile strain is unitless and
-time units are picoseconds, this means the box length will increase by
+is defined as delta/length0, where length0 is the original box length
-1% every picosecond.  R = 1 or 2 means the box length will double or
+and delta is the change relative to the original length.  Thus if the
-triple every picosecond.  R = -0.1 means the box length will shrink by
+{trate} R is 0.1 and time units are picoseconds, this means the box
-10% every picosecond.  Note that for a "true" rate the change is
+length will increase by 10% of its current length every picosecond.
-continuous, so running with R = 1 for 10 picoseconds does not expand
+I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.21, etc.
-the box length by a factor of 10, but by a factor of 1024 since it
+R = 1 or 2 means the box length will double or triple every
-doubles every picosecond.
+picosecond.  R = -0.01 means the box length will shrink by 1% of its
+current length every picosecond.  Note that for a "true" rate the
+change is continuous and based on the current length, so running with
+R = 1 for 10 picoseconds does not expand the box length by a factor of
+10 as it would with {erate}, but by a factor of 1024 since it doubles
+every picosecond.
 
 Note that to change the volume (or cross-sectional area) of the
 simulation box at a constant rate, you can change multiple dimensions
-via {rate}.  E.g. to double the box volume every picosecond, you could
+via {erate} or {trate}.  E.g. to double the box volume every
-set "x rate M", "y rate M", "z rate M", with M = pow(2,1/3) - 1 =
+picosecond, you could set "x trate M", "y trate M", "z trate M", with
-1.26, since if each box dimension grows by 26%, the box volume
+M = pow(2,1/3) - 1 = 1.26, since if each box dimension grows by 26%,
-doubles.
+the box volume doubles.
 
 The {volume} style changes the specified dimension in such a way that
 the box volume remains constant while other box dimensions are changed
@@ -177,8 +203,8 @@ potentials whose Poisson ratio is not 0.5.  An alternative is to use
 "fix npt aniso"_fix_npt.html with zero applied pressure on those 2
 dimensions, so that they respond to the tensile strain dynamically.
 
-For the {scale}, {vel}, {rate}, and {volume} styles, the box length is
+For the {scale}, {vel}, {erate}, {trate}, and {volume} styles, the box
-expanded or compressed around its mid point.
+length is expanded or compressed around its mid point.
 
 :line
 
@@ -186,6 +212,11 @@ For the {xy}, {xz}, and {yz} parameters, this is the meaning of their
 styles and values.  Note that changing the tilt factors of a triclinic
 box does not change its volume.
 
+The {final}, {delta}, {vel}, and {erate} styles all change the shear
+strain at a "constant engineering shear strain rate".  This means the
+tilt factor changes linearly with time from its initial to final
+value.
+
 For style {final}, the final tilt factor is specified.  The value
 can be in lattice or box distance units.  See the discussion of the
 units keyword below.
@@ -204,28 +235,53 @@ is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
 tilt factor will be 15 Angstroms.  After 2 psec, it will be 25
 Angstroms.
 
-The {rate} style changes a tilt factor at a "true constant shear
+The {erate} style changes a tilt factor at a "constant engineering
+shear strain rate".  The units of the specified shear strain rate are
+1/time.  See the "units"_units.html command for the time units
+associated with different choices of simulation units,
+e.g. picoseconds for "metal" units).  Shear strain is unitless and is
+defined as offset/length, where length is the box length perpendicular
+to the shear direction (e.g. y box length for xy deformation) and
+offset is the displacement distance in the shear direction (e.g. x
+direction for xy deformation) from the unstrained orientation.  Thus
+if the {erate} R is 0.1 and time units are picoseconds, this means the
+shear strain will increase by 0.1 every picosecond.  I.e. if the xy
+shear strain was initially 0.0, then strain after 1 psec = 0.1, strain
+after 2 psec = 0.2, etc.  Thus the tilt factor would be 0.0 at time 0,
+0.1*ybox at 1 psec, 0.2*ybox at 2 psec, etc, where ybox is the
+original y box length.  R = 1 or 2 means the tilt factor will increase
+by 1 or 2 every picosecond.  R = -0.01 means a decrease in shear
+strain by 0.01 every picosecond.
+
+The {trate} style changes a tilt factor at a "constant true shear
 strain rate".  Note that this is not an "engineering shear strain
 rate", as the other styles are.  Rather, for a "true" rate, the rate
 of change is constant, which means the tilt factor changes
 non-linearly with time from its initial to final value.  The units of
-shear strain rate are 1/time.  See the "units"_units.html command for
+the specified shear strain rate are 1/time.  See the
-the time units associated with different choices of simulation units,
+"units"_units.html command for the time units associated with
-e.g. picoseconds for "metal" units).  Thus if the {rate} R is 0.01 and
+different choices of simulation units, e.g. picoseconds for "metal"
-time units are picoseconds, this means the tilt factor will increase
+units).  Shear strain is unitless and is defined as offset/length,
-by 1% every picosecond.  R = 1 or 2 means the tilt factor will double
+where length is the box length perpendicular to the shear direction
-or triple every picosecond.  R = -0.1 means the tilt factor will
+(e.g. y box length for xy deformation) and offset is the displacement
-shrink by 10% every picosecond.  Note that the change is continuous,
+distance in the shear direction (e.g. x direction for xy deformation)
-so running with R = 1 for 10 picoseconds does not change the tilt
+from the unstrained orientation.  Thus if the {trate} R is 0.1 and
-factor by a factor of 10, but by a factor of 1024 since it doubles
+time units are picoseconds, this means the shear strain or tilt factor
-every picosecond.  Also note, that the initial tilt factor must be
+will increase by 10% every picosecond.  I.e. if the xy shear strain
-non-zero to use the {rate} option.
+was initially 0.1, then strain after 1 psec = 0.11, strain after 2
+psec = 0.121, etc.  R = 1 or 2 means the tilt factor will double or
+triple every picosecond.  R = -0.01 means the tilt factor will shrink
+by 1% every picosecond.  Note that the change is continuous, so
+running with R = 1 for 10 picoseconds does not change the tilt factor
+by a factor of 10, but by a factor of 1024 since it doubles every
+picosecond.  Also note that the initial tilt factor must be non-zero
+to use the {trate} option.
 
 Note that shear strain is defined as the tilt factor divided by the
-perpendicular box length.  The {rate} style controls the tilt factor,
+perpendicular box length.  The {erate} and {trate} styles control the
-but assumes the perpendicular box length remains constant.  If this is
+tilt factor, but assume the perpendicular box length remains constant.
-not the case (e.g. it changes due to another fix deform parameter),
+If this is not the case (e.g. it changes due to another fix deform
-then this effect on the shear strain is ignored.
+parameter), then this effect on the shear strain is ignored.
 
 All of these styles change the xy, xz, yz tilt factors during a
 simulation.  In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes

doc/pair_gayberne.html

@@ -28,8 +28,8 @@ pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
 <P><B>Description:</B>
 </P>
 <P>Style <I>gayberne</I> computes a Gay-Berne anisotropic LJ interaction
-<A HREF = "#Beradi">(Beradi)</A> between pairs of ellipsoidal particles via the
+<A HREF = "#Beradi">(Beradi)</A> between pairs of ellipsoidal particles or an
-formulas
+ellipsoidal and spherical particle via the formulas
 </P>
 <CENTER><IMG SRC = "Eqs/pair_gayberne.jpg">
 </CENTER>
@@ -37,7 +37,10 @@ formulas
 box frame to the body frame and r12 is the center to center vector
 between the particles.  Ur controls the shifted distance dependent
 interaction based on the distance of closest approach of the two
-particles (h12) and the user-specified shift parameter gamma.
+particles (h12) and the user-specified shift parameter gamma.  When
+both particles are spherical, the formula reduces to the usual
+Lennard-Jones interaction (see details below for when Gay-Berne treats
+a particle as "spherical").
 </P>
 <P>For large uniform molecules it has been shown that the energy
 parameters are approximately representable in terms of local contact
@@ -68,12 +71,12 @@ commands:
 </P>
 <UL><LI>epsilon = well depth (energy units)
 <LI>sigma = minimum effective particle radii (distance units)
-<LI>epsilon_i_a = relative well depth of I for side-to-side interactions
+<LI>epsilon_i_a = relative well depth of type I for side-to-side interactions
-<LI>epsilon_i_b = relative well depth of I for face-to-face interactions
+<LI>epsilon_i_b = relative well depth of type I for face-to-face interactions
-<LI>epsilon_i_c = relative well depth of I for end-to-end interactions
+<LI>epsilon_i_c = relative well depth of type I for end-to-end interactions
-<LI>epsilon_j_a = relative well depth of J for side-to-side interactions
+<LI>epsilon_j_a = relative well depth of type J for side-to-side interactions
-<LI>epsilon_j_b = relative well depth of J for face-to-face interactions
+<LI>epsilon_j_b = relative well depth of type J for face-to-face interactions
-<LI>epsilon_j_c = relative well depth of J for end-to-end interactions
+<LI>epsilon_j_c = relative well depth of type J for end-to-end interactions
 <LI>cutoff (distance units) 
 </UL>
 <P>The last coefficient is optional.  If not specified, the global
@@ -81,22 +84,52 @@ cutoff specified in the pair_style command is used.
 </P>
 <P>The epsilon and sigma parameters are mixed for I != J atom pairings
 the same as Lennard-Jones parameters; see the <A HREF = "pair_modify.html">pair_modify
-mix</A> documentation for details.  The other parameters
+mix</A> documentation for details. 
-(except cutoff) are really specific to a single atom type, and not a
+</P>
-pair of atoms.  Thus they are applied to atom type I only.
+<P>The epsilon_i and epsilon_j coefficients are actually defined for atom
+types, not for pairs of atom types.  Thus, in a series of pair_coeff
+commands, they only need to be specified once for each atom type.
+</P>
+<P>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
+non-zero, the three values are assigned to atom type I.  If all the
+epsilon_i values are zero, they are ignored.  If any of epsilon_j_a,
+epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
+to atom type J.  If all three epsilon_i values are zero, they are
+ignored.  Thus the typical way to define the epsilon_i and epsilon_j
+coefficients is to list their values in "pair_coeff I J" commands when
+I = J, but set them to 0.0 when I != J.  If you do list them when I !=
+J, you should insure they are consistent with their values in other
+pair_coeff commands.
+</P>
+<P>Note that if this potential is being used as a sub-style of
+<A HREF = "pair_hybrid.html">pair_style hybrid</A>, and there is no "pair_coeff I I"
+setting made for Gay-Berne for a particular type I (because I-I
+interactions are computed by another hybrid pair potential), then you
+still need to insure the epsilon a,b,c coefficients are assigned to
+that type in a "pair_coeff I J" command.
+</P>
+<P>IMPORTANT NOTE: If the epsilon a,b,c for an atom type are all 1.0, and
+if the shape of the particle is spherical (see the <A HREF = "shape.html">shape</A>
+command), meaning the 3 diameters are all the same, then the particle
+is treated as "spherical" by the Gay-Berne potential.  This is
+significant because if two "spherical" particles interact, then the
+simple Lennard-Jones formula is used to compute their interaction
+energy/force using epsilon and sigma, which is much cheaper to compute
+than the full Gay-Berne formula.  Thus you should insure epsilon a,b,c
+are set to 1.0 for spherical particle types and use epsilon and sigma
+to specify its interaction with other spherical particles.
 </P>
 <P><B>Restrictions:</B>
 </P>
 <P>Can only be used if LAMMPS was built with the "asphere" package.
 </P>
-<P>The use of this potential requires additional fixes as described
+<P>The "shift yes" option in <A HREF = "pair_modify.html">pair_modify</A> only applies
-above.  The "shift yes" option currently cannot be used with this
+to sphere-sphere interactions for this potential; there is no shifting
-potential to shift energies to 0 at the cutoff due to the anisotropic
+performed for ellipsoidal interactions due to the anisotropic
-dependence of the interaction.  Angular velocities are all set to zero
+dependence of the interaction.  The Gay-Berne potential does not
-initially.  The Gay-Berne potential does not become isotropic as r
+become isotropic as r increases <A HREF = "#Everaers">(Everaers)</A>.  The
-increases <A HREF = "#Everaers">(Everaers)</A>.  The distance-of-closest-approach
+distance-of-closest-approach approximation used by LAMMPS becomes less
-approximation used by the code becomes less accurate as the shape of
+accurate when high-aspect ratio ellipsoids are used.
-ellipsoids becomes more dissimilar (high-aspect-ratio particles).
 </P>
 <P><B>Related commands:</B>
 </P>

doc/pair_gayberne.txt

@@ -25,8 +25,8 @@ pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 :pre
 [Description:]
 
 Style {gayberne} computes a Gay-Berne anisotropic LJ interaction
-"(Beradi)"_#Beradi between pairs of ellipsoidal particles via the
+"(Beradi)"_#Beradi between pairs of ellipsoidal particles or an
-formulas
+ellipsoidal and spherical particle via the formulas
 
 :c,image(Eqs/pair_gayberne.jpg)
 
@@ -34,7 +34,10 @@ where A1 and A2 are the transformation matrices from the simulation
 box frame to the body frame and r12 is the center to center vector
 between the particles.  Ur controls the shifted distance dependent
 interaction based on the distance of closest approach of the two
-particles (h12) and the user-specified shift parameter gamma.
+particles (h12) and the user-specified shift parameter gamma.  When
+both particles are spherical, the formula reduces to the usual
+Lennard-Jones interaction (see details below for when Gay-Berne treats
+a particle as "spherical").
 
 For large uniform molecules it has been shown that the energy
 parameters are approximately representable in terms of local contact
@@ -65,12 +68,12 @@ commands:
 
 epsilon = well depth (energy units)
 sigma = minimum effective particle radii (distance units)
-epsilon_i_a = relative well depth of I for side-to-side interactions
+epsilon_i_a = relative well depth of type I for side-to-side interactions
-epsilon_i_b = relative well depth of I for face-to-face interactions
+epsilon_i_b = relative well depth of type I for face-to-face interactions
-epsilon_i_c = relative well depth of I for end-to-end interactions
+epsilon_i_c = relative well depth of type I for end-to-end interactions
-epsilon_j_a = relative well depth of J for side-to-side interactions
+epsilon_j_a = relative well depth of type J for side-to-side interactions
-epsilon_j_b = relative well depth of J for face-to-face interactions
+epsilon_j_b = relative well depth of type J for face-to-face interactions
-epsilon_j_c = relative well depth of J for end-to-end interactions
+epsilon_j_c = relative well depth of type J for end-to-end interactions
 cutoff (distance units) :ul
 
 The last coefficient is optional.  If not specified, the global
@@ -78,22 +81,52 @@ cutoff specified in the pair_style command is used.
 
 The epsilon and sigma parameters are mixed for I != J atom pairings
 the same as Lennard-Jones parameters; see the "pair_modify
-mix"_pair_modify.html documentation for details.  The other parameters
+mix"_pair_modify.html documentation for details. 
-(except cutoff) are really specific to a single atom type, and not a
+
-pair of atoms.  Thus they are applied to atom type I only.
+The epsilon_i and epsilon_j coefficients are actually defined for atom
+types, not for pairs of atom types.  Thus, in a series of pair_coeff
+commands, they only need to be specified once for each atom type.
+
+Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
+non-zero, the three values are assigned to atom type I.  If all the
+epsilon_i values are zero, they are ignored.  If any of epsilon_j_a,
+epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
+to atom type J.  If all three epsilon_i values are zero, they are
+ignored.  Thus the typical way to define the epsilon_i and epsilon_j
+coefficients is to list their values in "pair_coeff I J" commands when
+I = J, but set them to 0.0 when I != J.  If you do list them when I !=
+J, you should insure they are consistent with their values in other
+pair_coeff commands.
+
+Note that if this potential is being used as a sub-style of
+"pair_style hybrid"_pair_hybrid.html, and there is no "pair_coeff I I"
+setting made for Gay-Berne for a particular type I (because I-I
+interactions are computed by another hybrid pair potential), then you
+still need to insure the epsilon a,b,c coefficients are assigned to
+that type in a "pair_coeff I J" command.
+
+IMPORTANT NOTE: If the epsilon a,b,c for an atom type are all 1.0, and
+if the shape of the particle is spherical (see the "shape"_shape.html
+command), meaning the 3 diameters are all the same, then the particle
+is treated as "spherical" by the Gay-Berne potential.  This is
+significant because if two "spherical" particles interact, then the
+simple Lennard-Jones formula is used to compute their interaction
+energy/force using epsilon and sigma, which is much cheaper to compute
+than the full Gay-Berne formula.  Thus you should insure epsilon a,b,c
+are set to 1.0 for spherical particle types and use epsilon and sigma
+to specify its interaction with other spherical particles.
 
 [Restrictions:]
 
 Can only be used if LAMMPS was built with the "asphere" package.
 
-The use of this potential requires additional fixes as described
+The "shift yes" option in "pair_modify"_pair_modify.html only applies
-above.  The "shift yes" option currently cannot be used with this
+to sphere-sphere interactions for this potential; there is no shifting
-potential to shift energies to 0 at the cutoff due to the anisotropic
+performed for ellipsoidal interactions due to the anisotropic
-dependence of the interaction.  Angular velocities are all set to zero
+dependence of the interaction.  The Gay-Berne potential does not
-initially.  The Gay-Berne potential does not become isotropic as r
+become isotropic as r increases "(Everaers)"_#Everaers.  The
-increases "(Everaers)"_#Everaers.  The distance-of-closest-approach
+distance-of-closest-approach approximation used by LAMMPS becomes less
-approximation used by the code becomes less accurate as the shape of
+accurate when high-aspect ratio ellipsoids are used.
-ellipsoids becomes more dissimilar (high-aspect-ratio particles).
 
 [Related commands:]