git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@732 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Eqs/pressure.tex

@@ -3,7 +3,7 @@
 \begin{document}
 
 $$
-   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{3V}
+   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{dV}
 $$
 
 \end{document}

doc/compute_pressure.html

@@ -36,10 +36,13 @@ in your system.
 <CENTER><IMG SRC = "Eqs/pressure.jpg">
 </CENTER>
 <P>where N is the number of atoms in the system (see discussion of DOF
-below), Kb is the Boltzmann constant, T is the temperature, V is the
-system volume, and the second term is the virial, computed within
-LAMMPS for all pairwise as well as 2-body, 3-body, 4-body bonded
-interactions.
+below), Kb is the Boltzmann constant, T is the temperature, d is the
+dimensionality of the system (2 or 3 for 2d/3d), V is the system
+volume (or area in 2d), and the second term is the virial, computed
+within LAMMPS for all pairwise as well as 2-body, 3-body, 4-body, and
+long-range interactions.  <A HREF = "fix.html">Fixes</A> that impose constraints
+(e.g. the <A HREF = "fix_shake.html">fix shake</A> command) also contribute to the
+virial term.
 </P>
 <P>A 6-component pressure tensor is also calculated by this compute which
 can be output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
@@ -55,7 +58,7 @@ temperature of all atoms for consistency with the virial term, but any
 compute style that calculates temperature can be used, e.g. one that
 excludes frozen atoms or other degrees of freedom.
 </P>
-<P>Note that the N is the above formula is really degrees-of-freedom/3
+<P>Note that the N is the above formula is really degrees-of-freedom/d
 where the DOF is specified by the temperature compute.  See the
 various <A HREF = "compute.html">compute temperature</A> styles for details.
 </P>

doc/compute_pressure.txt

@@ -33,10 +33,13 @@ The pressure is computed by the standard formula
 :c,image(Eqs/pressure.jpg)
 
 where N is the number of atoms in the system (see discussion of DOF
-below), Kb is the Boltzmann constant, T is the temperature, V is the
-system volume, and the second term is the virial, computed within
-LAMMPS for all pairwise as well as 2-body, 3-body, 4-body bonded
-interactions.
+below), Kb is the Boltzmann constant, T is the temperature, d is the
+dimensionality of the system (2 or 3 for 2d/3d), V is the system
+volume (or area in 2d), and the second term is the virial, computed
+within LAMMPS for all pairwise as well as 2-body, 3-body, 4-body, and
+long-range interactions.  "Fixes"_fix.html that impose constraints
+(e.g. the "fix shake"_fix_shake.html command) also contribute to the
+virial term.
 
 A 6-component pressure tensor is also calculated by this compute which
 can be output by the "thermo_style custom"_thermo_style.html command.
@@ -52,7 +55,7 @@ temperature of all atoms for consistency with the virial term, but any
 compute style that calculates temperature can be used, e.g. one that
 excludes frozen atoms or other degrees of freedom.
 
-Note that the N is the above formula is really degrees-of-freedom/3
+Note that the N is the above formula is really degrees-of-freedom/d
 where the DOF is specified by the temperature compute.  See the
 various "compute temperature"_compute.html styles for details.
 

doc/fix_nph.html

@@ -78,23 +78,26 @@ by the <I>p-style</I> argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
 the end value.
 </P>
-<P>Style <I>xyz</I> means couple all 3 dimensions together when pressure is
-computed (isotropic pressure), and dilate/contract the 3 dimensions
+<P>Style <I>xyz</I> means couple all dimensions together when pressure is
+computed (isotropic pressure), and dilate/contract the dimensions
 together.
 </P>
 <P>Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified dimensions are
 coupled together, both for pressure computation and for
 dilation/contraction.  The 3rd dimension dilates/contracts
 independently, using its pressure component as the driving force.
+These styles cannot be used for a 2d simulation.
 </P>
-<P>For style <I>aniso</I>, all 3 dimensions dilate/contract independently
-using their individual pressure components as the 3 driving forces.
+<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
+their individual pressure components as the driving forces.
 </P>
 <P>For any of the styles except <I>xyz</I>, any of the independent pressure
 components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>) can have
 their target pressures (both start and stop values) specified as NULL.
 This means that no pressure control is applied to that dimension so
-that the box dimension remains unchanged.
+that the box dimension remains unchanged.  For a 2d simulation the z
+pressure components must be specified as NULL when using style
+<I>aniso</I>.
 </P>
 <P>In some cases (e.g. for solids) the pressure (volume) and/or
 temperature of the system can oscillate undesirably when a Nose/Hoover

doc/fix_nph.txt

@@ -69,23 +69,26 @@ by the {p-style} argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
 the end value.
 
-Style {xyz} means couple all 3 dimensions together when pressure is
-computed (isotropic pressure), and dilate/contract the 3 dimensions
+Style {xyz} means couple all dimensions together when pressure is
+computed (isotropic pressure), and dilate/contract the dimensions
 together.
 
 Styles {xy} or {yz} or {xz} means that the 2 specified dimensions are
 coupled together, both for pressure computation and for
 dilation/contraction.  The 3rd dimension dilates/contracts
 independently, using its pressure component as the driving force.
+These styles cannot be used for a 2d simulation.
 
-For style {aniso}, all 3 dimensions dilate/contract independently
-using their individual pressure components as the 3 driving forces.
+For style {aniso}, all dimensions dilate/contract independently using
+their individual pressure components as the driving forces.
 
 For any of the styles except {xyz}, any of the independent pressure
 components (e.g. z in {xy}, or any dimension in {aniso}) can have
 their target pressures (both start and stop values) specified as NULL.
 This means that no pressure control is applied to that dimension so
-that the box dimension remains unchanged.
+that the box dimension remains unchanged.  For a 2d simulation the z
+pressure components must be specified as NULL when using style
+{aniso}.
 
 In some cases (e.g. for solids) the pressure (volume) and/or
 temperature of the system can oscillate undesirably when a Nose/Hoover

doc/fix_npt.html

@@ -82,23 +82,26 @@ by the <I>p-style</I> argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
 the end value.
 </P>
-<P>Style <I>xyz</I> means couple all 3 dimensions together when pressure is
-computed (isotropic pressure), and dilate/contract the 3 dimensions
+<P>Style <I>xyz</I> means couple all dimensions together when pressure is
+computed (isotropic pressure), and dilate/contract the dimensions
 together.
 </P>
 <P>Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified dimensions are
 coupled together, both for pressure computation and for
 dilation/contraction.  The 3rd dimension dilates/contracts
 independently, using its pressure component as the driving force.
+These styles cannot be used for a 2d simulation.
 </P>
-<P>For style <I>aniso</I>, all 3 dimensions dilate/contract independently
-using their individual pressure components as the 3 driving forces.
+<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
+their individual pressure components as the driving forces.
 </P>
 <P>For any of the styles except <I>xyz</I>, any of the independent pressure
 components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>) can have
 their target pressures (both start and stop values) specified as NULL.
 This means that no pressure control is applied to that dimension so
-that the box dimension remains unchanged.
+that the box dimension remains unchanged.  For a 2d simulation the z
+pressure components must be specified as NULL when using style
+<I>aniso</I>.
 </P>
 <P>In some cases (e.g. for solids) the pressure (volume) and/or
 temperature of the system can oscillate undesirably when a Nose/Hoover

doc/fix_npt.txt

@@ -71,23 +71,26 @@ by the {p-style} argument.  In each case, the desired pressure at each
 timestep is a ramped value during the run from the starting value to
 the end value.
 
-Style {xyz} means couple all 3 dimensions together when pressure is
-computed (isotropic pressure), and dilate/contract the 3 dimensions
+Style {xyz} means couple all dimensions together when pressure is
+computed (isotropic pressure), and dilate/contract the dimensions
 together.
 
 Styles {xy} or {yz} or {xz} means that the 2 specified dimensions are
 coupled together, both for pressure computation and for
 dilation/contraction.  The 3rd dimension dilates/contracts
 independently, using its pressure component as the driving force.
+These styles cannot be used for a 2d simulation.
 
-For style {aniso}, all 3 dimensions dilate/contract independently
-using their individual pressure components as the 3 driving forces.
+For style {aniso}, all dimensions dilate/contract independently using
+their individual pressure components as the driving forces.
 
 For any of the styles except {xyz}, any of the independent pressure
 components (e.g. z in {xy}, or any dimension in {aniso}) can have
 their target pressures (both start and stop values) specified as NULL.
 This means that no pressure control is applied to that dimension so
-that the box dimension remains unchanged.
+that the box dimension remains unchanged.  For a 2d simulation the z
+pressure components must be specified as NULL when using style
+{aniso}.
 
 In some cases (e.g. for solids) the pressure (volume) and/or
 temperature of the system can oscillate undesirably when a Nose/Hoover