git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13013 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/create_box.html

@@ -68,30 +68,41 @@ positive or negative values and are called "tilt factors" because they
 are the amount of displacement applied to faces of an originally
 orthogonal box to transform it into the parallelipiped.
 </P>
-<P>A <I>prism</I> region used with the create_box command must have tilt
-factors (xy,xz,yz) that do not skew the box more than half the
-distance of the parallel box length.  For example, if xlo = 2 and xhi
-= 12, then the x box length is 10 and the xy tilt factor must be
+<P>By default, a <I>prism</I> region used with the create_box command must
+have tilt factors (xy,xz,yz) that do not skew the box more than half
+the distance of the parallel box length.  For example, if xlo = 2 and
+xhi = 12, then the x box length is 10 and the xy tilt factor must be
 between -5 and 5.  Similarly, both xz and yz must be between
 -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a limitation,
 since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
-geometrically equivalent.
+geometrically equivalent.  If you wish to define a box with tilt
+factors that exceed these limits, you can use the <A HREF = "box.html">box tilt</A>
+command, with a setting of <I>large</I>; a setting of <I>small</I> is the
+default.
 </P>
 <P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
 for a geometric description of triclinic boxes, as defined by LAMMPS,
 and how to transform these parameters to and from other commonly used
 triclinic representations.
 </P>
-<P>When a prism region is used, the simulation domain must be periodic in
-any dimensions with a non-zero tilt factor, as defined by the
-<A HREF = "boundary.html">boundary</A> command.  I.e. if the xy tilt factor is
-non-zero, then both the x and y dimensions must be periodic.
-Similarly, x and z must be periodic if xz is non-zero and y and z must
-be periodic if yz is non-zero.  Also note that if your simulation will
-tilt the box, e.g. via the <A HREF = "fix_deform.html">fix deform</A> command, the
-simulation box must be defined as triclinic, even if the tilt factors
-are initially 0.0.
+<P>When a prism region is used, the simulation domain should normally be
+periodic in the dimension that the tilt is applied to, which is given
+by the second dimension of the tilt factor (e.g. y for xy tilt).  This
+is so that pairs of atoms interacting across that boundary will have
+one of them shifted by the tilt factor.  Periodicity is set by the
+<A HREF = "boundary.html">boundary</A> command.  For example, if the xy tilt factor
+is non-zero, then the y dimension should be periodic.  Similarly, the
+z dimension should be periodic if xz or yz is non-zero.  LAMMPS does
+not require this periodicity, but you may lose atoms if this is not
+the case.
+</P>
+<P>Also note that if your simulation will tilt the box, e.g. via the <A HREF = "fix_deform.html">fix
+deform</A> command, the simulation box must be setup to
+be triclinic, even if the tilt factors are initially 0.0.  You can
+also change an orthogonal box to a triclinic box or vice versa by
+using the <A HREF = "change_box.html">change box</A> command with its <I>ortho</I> and
+<I>triclinic</I> options.
 </P>
 <P>IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
 you should not make the lo/hi box dimensions (as defined in your

doc/create_box.txt

@@ -60,30 +60,41 @@ positive or negative values and are called "tilt factors" because they
 are the amount of displacement applied to faces of an originally
 orthogonal box to transform it into the parallelipiped.
 
-A {prism} region used with the create_box command must have tilt
-factors (xy,xz,yz) that do not skew the box more than half the
-distance of the parallel box length.  For example, if xlo = 2 and xhi
-= 12, then the x box length is 10 and the xy tilt factor must be
+By default, a {prism} region used with the create_box command must
+have tilt factors (xy,xz,yz) that do not skew the box more than half
+the distance of the parallel box length.  For example, if xlo = 2 and
+xhi = 12, then the x box length is 10 and the xy tilt factor must be
 between -5 and 5.  Similarly, both xz and yz must be between
 -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a limitation,
 since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
-geometrically equivalent.
+geometrically equivalent.  If you wish to define a box with tilt
+factors that exceed these limits, you can use the "box tilt"_box.html
+command, with a setting of {large}; a setting of {small} is the
+default.
 
 See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
 for a geometric description of triclinic boxes, as defined by LAMMPS,
 and how to transform these parameters to and from other commonly used
 triclinic representations.
 
-When a prism region is used, the simulation domain must be periodic in
-any dimensions with a non-zero tilt factor, as defined by the
-"boundary"_boundary.html command.  I.e. if the xy tilt factor is
-non-zero, then both the x and y dimensions must be periodic.
-Similarly, x and z must be periodic if xz is non-zero and y and z must
-be periodic if yz is non-zero.  Also note that if your simulation will
-tilt the box, e.g. via the "fix deform"_fix_deform.html command, the
-simulation box must be defined as triclinic, even if the tilt factors
-are initially 0.0.
+When a prism region is used, the simulation domain should normally be
+periodic in the dimension that the tilt is applied to, which is given
+by the second dimension of the tilt factor (e.g. y for xy tilt).  This
+is so that pairs of atoms interacting across that boundary will have
+one of them shifted by the tilt factor.  Periodicity is set by the
+"boundary"_boundary.html command.  For example, if the xy tilt factor
+is non-zero, then the y dimension should be periodic.  Similarly, the
+z dimension should be periodic if xz or yz is non-zero.  LAMMPS does
+not require this periodicity, but you may lose atoms if this is not
+the case.
+
+Also note that if your simulation will tilt the box, e.g. via the "fix
+deform"_fix_deform.html command, the simulation box must be setup to
+be triclinic, even if the tilt factors are initially 0.0.  You can
+also change an orthogonal box to a triclinic box or vice versa by
+using the "change box"_change_box.html command with its {ortho} and
+{triclinic} options.
 
 IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
 you should not make the lo/hi box dimensions (as defined in your

doc/read_data.html

@@ -141,29 +141,40 @@ and are called "tilt factors" because they are the amount of
 displacement applied to faces of an originally orthogonal box to
 transform it into the parallelepiped.
 </P>
-<P>The tilt factors (xy,xz,yz) can not skew the box more than half the
-distance of the corresponding parallel box length.  For example, if
-xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
-factor must be between -5 and 5.  Similarly, both xz and yz must be
-between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a
-limitation, since if the maximum tilt factor is 5 (as in this
+<P>By default, the tilt factors (xy,xz,yz) can not skew the box more than
+half the distance of the corresponding parallel box length.  For
+example, if xlo = 2 and xhi = 12, then the x box length is 10 and the
+xy tilt factor must be between -5 and 5.  Similarly, both xz and yz
+must be between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not
+a limitation, since if the maximum tilt factor is 5 (as in this
 example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
-... are all geometrically equivalent.
+... are all geometrically equivalent.  If you wish to define a box
+with tilt factors that exceed these limits, you can use the <A HREF = "box.html">box
+tilt</A> command, with a setting of <I>large</I>; a setting of
+<I>small</I> is the default.
 </P>
 <P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
 for a geometric description of triclinic boxes, as defined by LAMMPS,
 and how to transform these parameters to and from other commonly used
 triclinic representations.
 </P>
-<P>When a triclinic system is used, the simulation domain must be
-periodic in any dimensions with a non-zero tilt factor, as defined by
-the <A HREF = "boundary.html">boundary</A> command.  I.e. if the xy tilt factor is
-non-zero, then both the x and y dimensions must be periodic.
-Similarly, x and z must be periodic if xz is non-zero and y and z must
-be periodic if yz is non-zero.  Also note that if your simulation will
-tilt the box, e.g. via the <A HREF = "fix_deform.html">fix deform</A> command, the
-simulation box must be defined as triclinic, even if the tilt factors
-are initially 0.0.
+<P>When a triclinic system is used, the simulation domain should normally
+be periodic in the dimension that the tilt is applied to, which is
+given by the second dimension of the tilt factor (e.g. y for xy tilt).
+This is so that pairs of atoms interacting across that boundary will
+have one of them shifted by the tilt factor.  Periodicity is set by
+the <A HREF = "boundary.html">boundary</A> command.  For example, if the xy tilt
+factor is non-zero, then the y dimension should be periodic.
+Similarly, the z dimension should be periodic if xz or yz is non-zero.
+LAMMPS does not require this periodicity, but you may lose atoms if
+this is not the case.
+</P>
+<P>Also note that if your simulation will tilt the box, e.g. via the <A HREF = "fix_deform.html">fix
+deform</A> command, the simulation box must be setup to
+be triclinic, even if the tilt factors are initially 0.0.  You can
+also change an orthogonal box to a triclinic box or vice versa by
+using the <A HREF = "change_box.html">change box</A> command with its <I>ortho</I> and
+<I>triclinic</I> options.
 </P>
 <P>For 2d simulations, the <I>zlo zhi</I> values should be set to bound the z
 coords for atoms that appear in the file; the default of -0.5 0.5 is

doc/read_data.txt

@@ -135,29 +135,40 @@ and are called "tilt factors" because they are the amount of
 displacement applied to faces of an originally orthogonal box to
 transform it into the parallelepiped.
 
-The tilt factors (xy,xz,yz) can not skew the box more than half the
-distance of the corresponding parallel box length.  For example, if
-xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
-factor must be between -5 and 5.  Similarly, both xz and yz must be
-between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not a
-limitation, since if the maximum tilt factor is 5 (as in this
+By default, the tilt factors (xy,xz,yz) can not skew the box more than
+half the distance of the corresponding parallel box length.  For
+example, if xlo = 2 and xhi = 12, then the x box length is 10 and the
+xy tilt factor must be between -5 and 5.  Similarly, both xz and yz
+must be between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is not
+a limitation, since if the maximum tilt factor is 5 (as in this
 example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
-... are all geometrically equivalent.
+... are all geometrically equivalent.  If you wish to define a box
+with tilt factors that exceed these limits, you can use the "box
+tilt"_box.html command, with a setting of {large}; a setting of
+{small} is the default.
 
 See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
 for a geometric description of triclinic boxes, as defined by LAMMPS,
 and how to transform these parameters to and from other commonly used
 triclinic representations.
 
-When a triclinic system is used, the simulation domain must be
-periodic in any dimensions with a non-zero tilt factor, as defined by
-the "boundary"_boundary.html command.  I.e. if the xy tilt factor is
-non-zero, then both the x and y dimensions must be periodic.
-Similarly, x and z must be periodic if xz is non-zero and y and z must
-be periodic if yz is non-zero.  Also note that if your simulation will
-tilt the box, e.g. via the "fix deform"_fix_deform.html command, the
-simulation box must be defined as triclinic, even if the tilt factors
-are initially 0.0.
+When a triclinic system is used, the simulation domain should normally
+be periodic in the dimension that the tilt is applied to, which is
+given by the second dimension of the tilt factor (e.g. y for xy tilt).
+This is so that pairs of atoms interacting across that boundary will
+have one of them shifted by the tilt factor.  Periodicity is set by
+the "boundary"_boundary.html command.  For example, if the xy tilt
+factor is non-zero, then the y dimension should be periodic.
+Similarly, the z dimension should be periodic if xz or yz is non-zero.
+LAMMPS does not require this periodicity, but you may lose atoms if
+this is not the case.
+
+Also note that if your simulation will tilt the box, e.g. via the "fix
+deform"_fix_deform.html command, the simulation box must be setup to
+be triclinic, even if the tilt factors are initially 0.0.  You can
+also change an orthogonal box to a triclinic box or vice versa by
+using the "change box"_change_box.html command with its {ortho} and
+{triclinic} options.
 
 For 2d simulations, the {zlo zhi} values should be set to bound the z
 coords for atoms that appear in the file; the default of -0.5 0.5 is