Merge release-4-5-patches into release-4-6

[alexxy/gromacs.git] / src / gmxlib / copyrite.c

diff --git a/src/gmxlib/copyrite.c b/src/gmxlib/copyrite.c
index d01a9c0a1b741bea7298f8785c44ca0b43a199f8..41bd02830c83ece5e28218edc9608214983e54c2 100644 (file)
--- a/src/gmxlib/copyrite.c
+++ b/src/gmxlib/copyrite.c
@@ -36,7 +36,7 @@
 #include <config.h>
 #endif
 
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
 #include <thread_mpi.h>
 #endif
 
@@ -48,7 +48,7 @@
 #include "smalloc.h"
 #include "string2.h"
 #include "macros.h"
-#include "time.h"
+#include <time.h>
 #include "random.h"
 #include "statutil.h"
 #include "copyrite.h"
@@ -404,10 +404,10 @@ void please_cite(FILE *fp,const char *key)
       "Phys. Chem. Chem. Phys.",
       13, 2011, "169-181" },
     { "Caleman2011b",
-      "C. Caleman and M. Hong and J. S. Hub and L. T. da Costa and P. J. van Maaren and D. van der Spoel",
-      "Force Field Benchmark 1: Density, Heat of Vaporization, Heat Capacity, Surface Tension and Dielectric Constant of 152 Organic Liquids",
-      "Submitted",
-      0, 2011, "" },
+      "C. Caleman and P. J. van Maaren and M. Hong and J. S. Hub and L. T. da Costa and D. van der Spoel",
+      "Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant",
+      "J. Chem. Theo. Comp.",
+      8, 2012, "61" },
     { "Lindahl2001a",
       "E. Lindahl and B. Hess and D. van der Spoel",
       "GROMACS 3.0: A package for molecular simulation and trajectory analysis",
@@ -522,18 +522,52 @@ void please_cite(FILE *fp,const char *key)
       "O. Engin, A. Villa, M. Sayar and B. Hess",
       "Driving Forces for Adsorption of Amphiphilic Peptides to Air-Water Interface",
       "J. Phys. Chem. B",
-      0, 2010, "???" },
+      114, 2010, "11093" },
+    { "Fritsch12",
+      "S. Fritsch, C. Junghans and K. Kremer",
+      "Adaptive molecular simulation study on structure formation of toluene around C60 using Gromacs",
+      "J. Chem. Theo. Comp.",
+      8, 2012, "398" },
+    { "Junghans10",
+      "C. Junghans and S. Poblete",
+      "A reference implementation of the adaptive resolution scheme in ESPResSo",
+      "Comp. Phys. Comm.",
+      181, 2010, "1449" },
     { "Wang2010",
       "H. Wang, F. Dommert, C.Holm",
       "Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency",
       "J. Chem. Phys. B",
-      133, 2010, "034117"
-    },
+      133, 2010, "034117" },
     { "Sugita1999a",
       "Y. Sugita, Y. Okamoto",
       "Replica-exchange molecular dynamics method for protein folding",
       "Chem. Phys. Lett.",
       314, 1999, "141-151" },
+    { "Kutzner2011",
+      "C. Kutzner and J. Czub and H. Grubmuller",
+      "Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS",
+      "J. Chem. Theory Comput.",
+      7, 2011, "1381-1393" },
+    { "Hoefling2011",
+      "M. Hoefling, N. Lima, D. Haenni, C.A.M. Seidel, B. Schuler, H. Grubmuller",
+      "Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach",
+      "PLoS ONE",
+      6, 2011, "e19791" },
+    { "Hockney1988",
+      "R. W. Hockney and J. W. Eastwood",
+      "Computer simulation using particles",
+      "IOP, Bristol",
+      1, 1988, "1" },
+    { "Ballenegger2012",
+      "V. Ballenegger, J.J. Cerda, and C. Holm",
+      "How to Convert SPME to P3M: Influence Functions and Error Estimates",
+      "J. Chem. Theory Comput.",
+      8, 2012, "936-947" },
+    { "Garmay2012",
+      "Garmay Yu, Shvetsov A, Karelov D, Lebedev D, Radulescu A, Petukhov M, Isaev-Ivanov V",
+      "Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament",
+      "Journal of Physics: Conference Series",
+      340, 2012, "012094" }
   };
 #define NSTR (int)asize(citedb)
   
@@ -607,7 +641,7 @@ void gmx_print_version_info(FILE *fp)
     fprintf(fp, "Precision:        single\n");
 #endif
 
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
     fprintf(fp, "Parallellization: thread_mpi\n");
 #elif defined(GMX_MPI)
     fprintf(fp, "Parallellization: MPI\n");
@@ -617,8 +651,6 @@ void gmx_print_version_info(FILE *fp)
 
 #ifdef GMX_FFT_FFTPACK
     fprintf(fp, "FFT Library:      fftpack\n");
-#elif defined(GMX_FFT_FFTW2)
-    fprintf(fp, "FFT Library:      fftw2\n");
 #elif defined(GMX_FFT_FFTW3)
     fprintf(fp, "FFT Library:      fftw3\n");
 #elif defined(GMX_FFT_MKL)