Merge branch release-5-1 into release-2016

Change-Id: I4195829e82c50f3d0aa04644a99ae53beb2e24c3

diff --git a/cmake/TestFileOffsetBits.c b/cmake/TestFileOffsetBits.c
index df671cf73fd598acd992426aa08de055899bac40..e7efc0e6342a4b3af28a6f821b5309281eb9788b 100644 (file)
--- a/cmake/TestFileOffsetBits.c
+++ b/cmake/TestFileOffsetBits.c
@@ -3,8 +3,7 @@
 int main()
 {
   /* Cause a compile-time error if off_t is smaller than 64 bits */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
-  int off_t_is_large[ (LARGE_OFF_T % 2147483629 == 721 && LARGE_OFF_T % 2147483647 == 1) ? 1 : -1 ];  
+  int off_t_is_large[sizeof(off_t)-7];
   return off_t_is_large[0];
 }
 

diff --git a/docs/manual/defunits.tex b/docs/manual/defunits.tex
index 7138acc06330fe9ce207628cb0394f7b70906511..13f8bb8b5e354c2a9868ea06c5cf6ffecdd95723 100644 (file)
--- a/docs/manual/defunits.tex
+++ b/docs/manual/defunits.tex
@@ -78,16 +78,16 @@ Quantity    & Symbol&  Unit                                         \\
 \hline                 
 length         &  r    &  nm $= 10^{-9}$ m                             \\
 mass           &  m    &  u (unified atomic mass unit) $=$ 
-                               $1.660\,538\,921(73) \times 10^{-27}$ kg        \\
+                               $1.660\,538\,921 \times 10^{-27}$ kg    \\
 time           &  t    &  ps $= 10^{-12}$ s                            \\
 charge         &  q    &  {\it e} $=$ elementary charge $=
-                               1.602\,176\,565(35)\times 10^{-19}$ C   \\
+                               1.602\,176\,565(\times 10^{-19}$ C      \\
 temperature    &  T    &  K                                            \\
 \dline
 \end{tabular}
 }
 \caption[Basic units used in {\gromacs}.]{Basic units used in
-{\gromacs}. Numbers in parentheses give accuracy.}
+{\gromacs}.}
 \label{tab:basicunits}
 \end{table}
 
@@ -101,20 +101,19 @@ Quantity  & Symbol   & Unit                               \\
 \hline
 energy         & $E,V$    & kJ~mol$^{-1}$                      \\
 Force          & $\ve{F}$ & kJ~mol$^{-1}$~nm$^{-1}$            \\
-pressure       & $p$      & kJ~mol$^{-1}$~nm$^{-3} =
-                               10^{30}/N_{AV}$~Pa              \\
-               &          & $1.660\,538\,921\times 10^6$~Pa $= 
-                               16.605\,389\,21$~bar                    \\
+pressure       & $p$      & bar                               \\
 velocity       & $v$      & nm~ps$^{-1} = 1000$ m s$^{-1}$             \\
 dipole moment   & $\mu$           & \emph{e}~nm                                \\ 
 electric potential& $\Phi$ & kJ~mol$^{-1}$~\emph{e}$^{-1} = 
-                               0.010\,364\,269\,19(32)$ Volt           \\
+                               0.010\,364\,269\,19$ Volt       \\
 electric field & $E$      & kJ~mol$^{-1}$~nm$^{-1}$~\emph{e}$^{-1} =
-                               1.036\,426\,919(32) \times 10^7$~V m$^{-1}$     \\
+                               1.036\,426\,919 \times 10^7$~V m$^{-1}$ \\
 \dline
 \end{tabular}
 }
-\caption{Derived units}
+\caption{Derived units. Note that an additional conversion factor of 10$^{28}$ a.m.u ($\approx$16.6)
+is applied to get bar instead of internal MD units in the energy and
+log files.}
 \label{tab:derivedunits}
 \end{table}
 
@@ -163,11 +162,11 @@ $0.008\,314\,462\,1$~kJ~mol$^{-1}$~K$^{-1}$.
 \dline
 Symbol & Name                  & Value                                 \\
 \hline
-$N_{AV}$& Avogadro's number    & $6.022\,141\,29(27)\times 10^{23}$  mol$^{-1}$        \\
-$R$    & gas constant  & $8.314\,462\,1(75)\times 10^{-3}$~kJ~mol$^{-1}$~K$^{-1}$      \\
+$N_{AV}$& Avogadro's number    & $6.022\,141\,29\times 10^{23}$  mol$^{-1}$    \\
+$R$    & gas constant  & $8.314\,462\,1\times 10^{-3}$~kJ~mol$^{-1}$~K$^{-1}$  \\
 $k_B$          & Boltzmann's constant  & \emph{idem}   \\
-$h$    & Planck's constant     & $0.399\,031\,271(17)$~kJ~mol$^{-1}$~ps \\
-$\hbar$        & Dirac's constant      & $0.063\,507\,799\,3(28)$~kJ~mol$^{-1}$~ps \\
+$h$    & Planck's constant     & $0.399\,031\,271$~kJ~mol$^{-1}$~ps \\
+$\hbar$        & Dirac's constant      & $0.063\,507\,799\,3$~kJ~mol$^{-1}$~ps \\
 $c$    & velocity of light     & $299\,792.458$~nm~ps$^{-1}$ \\
 \dline
 \end{tabular}

diff --git a/docs/manual/macros.tex b/docs/manual/macros.tex
index 8a9c2d7f4db707231d00375f42772dda7230994b..5d317f8673e0913a92e97932456c9d196cbc9d46 100644 (file)
--- a/docs/manual/macros.tex
+++ b/docs/manual/macros.tex
@@ -64,7 +64,7 @@
 \newcommand{\Fvij}{\ve{F}_{ij}}
 \newcommand{\Fvji}{\ve{F}_{ji}}
 \newcommand{\vvi}{\ve{v}_i}
-\newcommand{\electricConvFactorValue}{138.935\,458(9)}  % Electric conversion factor in kJ*nm/(mol*e^2)
+\newcommand{\electricConvFactorValue}{138.935\,458}  % Electric conversion factor in kJ*nm/(mol*e^2)
 \newcommand{\al}{\alpha}
 \newcommand{\be}{\beta}
 \newcommand{\ab}{\alpha\beta}