Merge branch 'master' of git://github.com/espressomd/espresso

doc/ug/analysis.tex

@@ -640,7 +640,7 @@ \section{Analyze groups of particles (molecules)}
 length \var{chain\_length} which start with the particle with particle
 number \var{chain\_start} and are consecutively numbered (\ie the last
 particle in that topology has number $\var{chain\_start} +
-\var{n\_chains}*\var{chain\_length}$). 
+\var{n\_chains}*\var{chain\_length} - 1$). 
 
 Variant \variant{2} synchronizes topology and particle data, assigning \var{mol\_id} values to particles.
 

doc/ug/inter.tex

@@ -1018,6 +1018,11 @@ \section{Coulomb interaction}
 \end{equation}
 where $l_B = e_o^2 / (4 \pi \epsilon k_B T)$ denotes the Bjerrum
 length, which measures the strength of the electrostatic interaction.
+As a special case, when the internal variable \var{temperature} 
+is set to zero, the value of bjerrum length you enter 
+is treated as $l_B k_B T$ rather than $l_B$. This occurs when the
+thermostat is switched off and \es performs an NVE integration
+(see also Section~\ref{sec:thermostat}).
 
 Computing electrostatic interactions is computationally very
 expensive.  \es{} features some state-of-the-art algorithms to deal

doc/ug/setup.tex

@@ -134,6 +134,7 @@ \section{\texttt{setmd}: Setting global variables.}
 \end{globvar}
 
 \section{\texttt{thermostat}: Setting up the thermostat}
+\label{sec:thermostat}
 \newescommand{thermostat}
 
 The \keyword{thermostat} command is used to change settings of the
@@ -149,6 +150,23 @@ \section{\texttt{thermostat}: Setting up the thermostat}
 on one by one. Note that there is only one temperature for all
 thermostats.
 
+\begin{essyntax}
+  \variant{1} thermostat
+  \variant{2} thermostat off
+  \variant{3} thermostat \var{parameters}
+\end{essyntax}
+
+Variant \variant{1} returns the thermostat parameters. A TCL list is given containing all
+the parameters needed to set the specific thermostat. (exactly the
+same as the input command line, without the preceding
+\texttt{thermostat}).
+
+Variant \variant{2} turns off all thermostats and sets all thermostat 
+variables to zero. Setting temperature to zero also affects the way in which 
+electrostatics are handled (see also Section~\ref{sec:inter-electrostatics}).
+
+Variant \variant{3} sets up one of the thermostats described below.
+
 \subsection{Langevin thermostat}
 \begin{essyntax}
   thermostat langevin \var{temperature} \var{gamma}
@@ -326,23 +344,6 @@ \subsection{Isotropic NPT thermostat}
 systems nor is it maintained regularly. If you use it and notice
 strange behaviour, please contribute to solving the problem.
 
-\subsection{Turning off all thermostats}
-\begin{essyntax}
-  thermostat off
-\end{essyntax}
-
-Turns off all thermostats and sets all thermostat variables to zero.
-
-\subsection{Getting the parameters}
-\begin{essyntax}
-  thermostat
-\end{essyntax}
-
-Returns the thermostat parameters. A TCL list is given containing all
-the parameters needed to set the specific thermostat. (exactly the
-same as the input command line, without the preceding
-\texttt{thermostat}).
-
 \section{\texttt{nemd}: Setting up non-equilibrium MD}
 \newescommand{nemd}
 \label{sec:NEMD}

scripts/vtf.tcl

@@ -1,11 +1,3 @@
-#############################################################
-#                                                           #
-# vtf.tcl                                                   #
-# =======                                                   #
-#                                                           #
-# Functions that allow writing VTF files.                   #
-#                                                           #
-#############################################################
 #
 # Copyright (C) 2006,2007,2008,2009,2010,2011 Olaf Lenz
 #  
@@ -24,6 +16,14 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>. 
 #  
+#############################################################
+#                                                           #
+# vtf.tcl                                                   #
+# =======                                                   #
+#                                                           #
+# Functions that allow writing VTF files.                   #
+#                                                           #
+#############################################################
 
 # Write the structure information of the current system to the given file
 # OPTIONS:
@@ -149,6 +149,7 @@ proc writevsf { file args } {
     set to 0
     set prev_type "na"
 
+    # Output the type
     for { set pid 0 } { $pid <= $max_pid } { incr pid } {
 	if { [part $pid] != "na" } then {
 	    # look for the type
@@ -169,6 +170,15 @@ proc writevsf { file args } {
     }
     puts $file [get_atom_record $from $to $prev_type]
 
+    if { [has_feature "ELECTROSTATICS"] } {
+    # Output the charge
+	for { set pid 0 } { $pid <= $max_pid } { incr pid } {
+	    if { [part $pid] != "na" } then {
+		puts $file "atom [vtfpid $pid] q [part $pid print q]"
+	    }
+	}
+    }
+
     # Print bond data
     for { set from 0 } { $from <= $max_pid } { incr from } {
 	if { [part $from] != "na" } then {

src/energy.c

@@ -260,18 +260,14 @@ static void tclcommand_analyze_print_all(Tcl_Interp *interp)
 
 #if defined(ELECTROSTATICS) || defined(DIPOLES)
   if(
-#ifdef ELECTROSTATICS
-      coulomb.method != COULOMB_NONE
-#else
-      0
+#if defined(ELECTROSTATICS) && defined(DIPOLES) 
+     coulomb.method != COULOMB_NONE || coulomb.Dmethod != DIPOLAR_NONE
+#elif defined(ELECTROSTATICS)
+     coulomb.method != COULOMB_NONE
+#elif defined(DIPOLES)     
+     coulomb.Dmethod != DIPOLAR_NONE
 #endif
-      ||
-#ifdef DIPOLES
-      coulomb.Dmethod != DIPOLAR_NONE
-#else
-      0
-#endif 
-      ) {
+     ) {
     /* total Coulomb energy */
     value = 0;
     for (i = 0; i < total_energy.n_coulomb; i++)
@@ -281,34 +277,31 @@ static void tclcommand_analyze_print_all(Tcl_Interp *interp)
     Tcl_PrintDouble(interp, value, buffer);
 
 #if defined(ELECTROSTATICS) && defined(DIPOLES) 
-
     Tcl_AppendResult(interp, "{ coulomb+magdipoles ", buffer, (char *)NULL);  
-
-#else
-
-#ifndef DIPOLES
+#elif defined(ELECTROSTATICS)
     Tcl_AppendResult(interp, "{ coulomb ", buffer, (char *)NULL);
-#endif
-
-#ifndef ELECTROSTATICS
+#elif defined(DIPOLES)
     Tcl_AppendResult(interp, "{ magdipoles ", buffer, (char *)NULL);  
-#endif
-
 #endif
 
     /* if it is split up, then print the split up parts */
+#ifdef ELECTROSTATICS
     if (total_energy.n_coulomb > 1) {
       for (i = 0; i < total_energy.n_coulomb; i++) {
 	Tcl_PrintDouble(interp, total_energy.coulomb[i], buffer);
 	Tcl_AppendResult(interp, " ", buffer, (char *)NULL);
       }
-     } 
+    }
+#endif
+
+#ifdef DIPOLES
     if (total_energy.n_dipolar > 1) {
       for (i = 0; i < total_energy.n_dipolar; i++) {
  	Tcl_PrintDouble(interp, total_energy.dipolar[i], buffer);
 	Tcl_AppendResult(interp, " ", buffer, (char *)NULL);
       }
     }
+#endif
     Tcl_AppendResult(interp, " }", (char *)NULL);
   }
 #endif
@@ -385,7 +378,7 @@ int tclcommand_analyze_parse_and_print_energy(Tcl_Interp *interp, int argc, char
       for (i = 0; i < total_energy.n_coulomb; i++)
 	value += total_energy.coulomb[i];
 #else
-      Tcl_AppendResult(interp, "ELECTROSTATICS not compiled (see config.h)\n", (char *)NULL);
+      Tcl_AppendResult(interp, "ELECTROSTATICS not compiled (see myconfig.h)\n", (char *)NULL);
 #endif
     }    
     else if( ARG0_IS_S("magnetic")) {
@@ -394,7 +387,7 @@ int tclcommand_analyze_parse_and_print_energy(Tcl_Interp *interp, int argc, char
       for (i = 0; i < total_energy.n_dipolar; i++)
 	value += total_energy.dipolar[i];
 #else
-      Tcl_AppendResult(interp, "DIPOLES not compiled (see config.h)\n", (char *)NULL);
+      Tcl_AppendResult(interp, "DIPOLES not compiled (see myconfig.h)\n", (char *)NULL);
 #endif
     }
 

src/p3m.c

@@ -1435,9 +1435,11 @@ double p3m_perform_aliasing_sums_energy(int n[3])
 
 #define P3M_TUNE_MAX_CUTS 50
 
-/** get the minimal error for this combination of parameters. In fact, the real space error is tuned such that it
-    contributes half of the total error, and then the Fourier space error is calculated. Returns the error and the
-    optimal alpha, or 0 if this combination does not work at all */
+/** get the minimal error for this combination of parameters. In fact,
+    the real space error is tuned such that it contributes half of the
+    total error, and then the Fourier space error is
+    calculated. Returns the error and the optimal alpha, or 0 if this
+    combination does not work at all */
 static double p3m_get_accuracy(int mesh[3], int cao, double r_cut_iL, double *_alpha_L, double *_rs_err, double *_ks_err)
 {
    double rs_err, ks_err;

src/statistics.h

@@ -34,9 +34,10 @@
 /*@{*/
 
 typedef struct {
-  /** Status flag for observable calculation. 
-      For 'analyze energy': 0 re-initialize observable struct, else every thing is fine, calculation can start. 
-      For 'analyze pressure' and 'analyze p_inst': 0 or !(1+v_comp) re-initialize, else all OK. */
+  /** Status flag for observable calculation.  For 'analyze energy': 0
+      re-initialize observable struct, else everything is fine,
+      calculation can start.  For 'analyze pressure' and 'analyze
+      p_inst': 0 or !(1+v_comp) re-initialize, else all OK. */
   int init_status;
 
   /** Array for observables on each node. */