Merge branch 'master' into malloc

configure.ac

@@ -701,8 +701,7 @@ cat <<EOF
 ****************************************************************
 EOF
 AC_MSG_CHECKING([whether to build with h5md support])
-AC_ARG_WITH(h5md, AS_HELP_STRING([--with-h5md],[wether to build with h5mdsupport]),
-    , [with_h5md=yes])
+AC_ARG_WITH(h5md, AS_HELP_STRING([--with-h5md],[wether to build with h5mdsupport]), , [with_h5md=no])
 AC_MSG_RESULT($with_h5md)
 if test .$with_h5md = .yes; then
   ES_ADDPATH_CHECK_LIB(hdf5,H5open,,AC_MSG_FAILURE([could not link against the hdf5 library]),)
@@ -713,6 +712,7 @@ if test .$with_h5md = .yes; then
 		]
 		,$extrapaths)
 fi
+AM_CONDITIONAL(H5MD, [test x$with_h5md == xyes])
 cat <<EOF
 ****************************************************************
 *                   Other settings                             *
@@ -842,6 +842,7 @@ Libraries
 ---------
 FFTW                    = $fftw_found
 efence                  = $with_efence
+h5md			= $with_h5md
 
 EOF
 

maintainer/jenkins/configs/maxset.hpp

@@ -75,4 +75,4 @@
 #define BOND_ENDANGLEDIST_HARMONIC
 
 #define VIRTUAL_SITES_RELATIVE
-#define H5MD
+

maintainer/jenkins/configs/nocheck-maxset.hpp

@@ -106,6 +106,10 @@
 #define LB_DEBUG
 #define VIRTUAL_SITES_DEBUG
 #define LE_DEBUG
+#ifdef
+#define CUDA_DEBUG
+#endif
+#define ESIF_DEBUG
 
 #define MPI_CORE
 #define FORCE_CORE

src/core/Makefile.am

@@ -215,7 +215,8 @@ CUDA_HEADER_FILES = \
 	integrate_sd_cuda.hpp \
 	integrate_sd_cuda_device.hpp \
 	integrate_sd_matrix.hpp \
-	fd-electrostatics.hpp
+	fd-electrostatics.hpp \
+	actor/DipolarDirectSum_cuda.hpp
 
 CUDA_SOURCE_FILES = \
 	cuda_init_cuda.cu \

src/core/constraint.cpp

@@ -1088,6 +1088,9 @@ void calculate_pore_dist(Particle *p1, double ppos[3], Particle *c_p, Constraint
   /* upper left smoothing circle */
   if (p2_z <= c1_z && r >= c1_or ) {
     /* distance from the smoothing center */
+    // Since: c2_or_or seems to be set to numeric_limits<double>max(), 
+    // this case being true means, that r is out of numerical limits.
+    // I suggest deleting it!
     norm = sqrt( (z - c1_z)*(z - c1_z) + (r - c1_or)*(r - c1_or) );
     *dist = norm - c->smoothing_radius;
     dist_vector_r=(c->smoothing_radius/norm -1)*(r - c1_or);
@@ -1099,13 +1102,16 @@ void calculate_pore_dist(Particle *p1, double ppos[3], Particle *c_p, Constraint
   if (p1_z >= c2_z && r <= c2_r ) {
     norm = sqrt( (z - c2_z)*(z - c2_z) + (r - c2_r)*(r - c2_r) );
     *dist = norm - c->smoothing_radius;
-    dist_vector_r=(c->smoothing_radius/norm -1)*(r - c2_or);
+    dist_vector_r=(c->smoothing_radius/norm -1)*(r - c2_r);
     dist_vector_z=(c->smoothing_radius/norm - 1)*(z - c2_z);
     for (i=0; i<3; i++) vec[i]=-dist_vector_r*e_r[i] - dist_vector_z*e_z[i];
     return;
   }
   /* Check if we are in the range of the upper right smoothing circle */
   if (p2_z >= c2_z && r >= c2_or ) {
+    // Since: c2_or_or seems to be set to numeric_limits<double>max(), 
+    // this case being true means, that r is out of numerical limits.
+    // I suggest deleting it!
     norm = sqrt( (z - c2_z)*(z - c2_z) + (r - c2_or)*(r - c2_or) );
     *dist = norm - c->smoothing_radius;
     dist_vector_r=(c->smoothing_radius/norm -1)*(r - c2_or);

src/core/forces_inline.hpp

@@ -153,18 +153,9 @@ inline void init_local_particle_force(Particle *part) {
     // the particle's orientation axis
     if ( part->swim.swimming )
     {
-      if ( thermo_switch & THERMO_LANGEVIN )
-      {
-        part->f.f[0] += part->swim.f_swim * part->p.mass * part->r.quatu[0];
-        part->f.f[1] += part->swim.f_swim * part->p.mass * part->r.quatu[1];
-        part->f.f[2] += part->swim.f_swim * part->p.mass * part->r.quatu[2];
-      }
-      else
-      {
-        part->f.f[0] += part->swim.f_swim * part->r.quatu[0];
-        part->f.f[1] += part->swim.f_swim * part->r.quatu[1];
-        part->f.f[2] += part->swim.f_swim * part->r.quatu[2];
-      }
+      part->f.f[0] += part->swim.f_swim * part->r.quatu[0];
+      part->f.f[1] += part->swim.f_swim * part->r.quatu[1];
+      part->f.f[2] += part->swim.f_swim * part->r.quatu[2];
     }
 #endif
 

src/features.def

@@ -227,6 +227,5 @@ ONEPART_DEBUG
 CUDA external
 FFTW external
 TK   external
+H5MD external
 
-/*Else*/
-H5MD

src/tcl/Makefile.am

@@ -65,7 +65,7 @@ libEspressoTcl_la_SOURCES = \
 	pressure_tcl.cpp pressure_tcl.hpp \
 	random_tcl.cpp random_tcl.hpp \
 	reaction_tcl.cpp reaction_tcl.hpp \
-	rattle_tcl.cpp rattle_ tcl.hpp \
+	rattle_tcl.cpp rattle_tcl.hpp \
 	statistics_chain_tcl.cpp statistics_chain_tcl.hpp \
 	statistics_cluster_tcl.cpp statistics_cluster_tcl.hpp \
 	statistics_correlation_tcl.cpp statistics_correlation_tcl.hpp \

src/tcl/h5mdfile_tcl.cpp

@@ -9,7 +9,6 @@
 #include <iostream>
 
 #ifdef H5MD
-
 #include "hdf5.h"
 
 typedef char h5string[1000];

src/tcl/h5mdfile_tcl.hpp

@@ -1,7 +1,33 @@
+/*
+  Copyright (C) 2010,2012,2013,2014 The ESPResSo project
+  Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010 
+    Max-Planck-Institute for Polymer Research, Theory Group
+  
+  This file is part of ESPResSo.
+  
+  ESPResSo is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+  
+  ESPResSo is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+  
+  You should have received a copy of the GNU General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>. 
+*/
+
+#ifndef __H5MD_HPP
+#define __H5MD_HPP
+
 #ifdef H5MD
 #include "parser.hpp"
 #include "config.hpp"
 #include <hdf5.h>
 
 int tclcommand_h5mdfile(ClientData data, Tcl_Interp *interp, int argc, char **argv);
 #endif
+
+#endif