src/gmxlib/copyrite.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GROningen Mixture of Alchemy and Childrens' Stories
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #ifdef GMX_THREADS
  40 #include <thread_mpi.h>
  41 #endif
  42
  43 /* This file is completely threadsafe - keep it that way! */
  44
  45 #include <string.h>
  46 #include <ctype.h>
  47 #include "sysstuff.h"
  48 #include "smalloc.h"
  49 #include "string2.h"
  50 #include "macros.h"
  51 #include "time.h"
  52 #include "random.h"
  53 #include "statutil.h"
  54 #include "copyrite.h"
  55 #include "strdb.h"
  56 #include "futil.h"
  57
  58 static void pr_two(FILE *out,int c,int i)
  59 {
  60   if (i < 10)
  61     fprintf(out,"%c0%1d",c,i);
  62   else
  63     fprintf(out,"%c%2d",c,i);
  64 }
  65
  66 void pr_difftime(FILE *out,double dt)
  67 {
  68   int    ndays,nhours,nmins,nsecs;
  69   bool   bPrint,bPrinted;
  70
  71   ndays = dt/(24*3600);
  72   dt    = dt-24*3600*ndays;
  73   nhours= dt/3600;
  74   dt    = dt-3600*nhours;
  75   nmins = dt/60;
  76   dt    = dt-nmins*60;
  77   nsecs = dt;
  78   bPrint= (ndays > 0);
  79   bPrinted=bPrint;
  80   if (bPrint)
  81     fprintf(out,"%d",ndays);
  82   bPrint=bPrint || (nhours > 0);
  83   if (bPrint) {
  84     if (bPrinted)
  85       pr_two(out,'d',nhours);
  86     else
  87       fprintf(out,"%d",nhours);
  88   }
  89   bPrinted=bPrinted || bPrint;
  90   bPrint=bPrint || (nmins > 0);
  91   if (bPrint) {
  92     if (bPrinted)
  93       pr_two(out,'h',nmins);
  94     else
  95       fprintf(out,"%d",nmins);
  96   }
  97   bPrinted=bPrinted || bPrint;
  98   if (bPrinted)
  99     pr_two(out,':',nsecs);
 100   else
 101     fprintf(out,"%ds",nsecs);
 102   fprintf(out,"\n");
 103 }
 104
 105
 106 bool be_cool(void)
 107 {
 108   /* Yes, it is bad to check the environment variable every call,
 109    * but we dont call this routine often, and it avoids using
 110    * a mutex for locking the variable...
 111    */
 112   return (getenv("GMX_NO_QUOTES") == NULL);
 113 }
 114
 115 void space(FILE *out, int n)
 116 {
 117   fprintf(out,"%*s",n,"");
 118 }
 119
 120 void f(char *a)
 121 {
 122     int i;
 123     int len=strlen(a);
 124
 125     for(i=0;i<len;i++)
 126         a[i]=~a[i];
 127 }
 128
 129 static void sp_print(FILE *out,const char *s)
 130 {
 131   int slen;
 132
 133   slen=strlen(s);
 134   space(out,(80-slen)/2);
 135   fprintf(out,"%s\n",s);
 136 }
 137
 138 static void ster_print(FILE *out,const char *s)
 139 {
 140   int  slen;
 141   char buf[128];
 142
 143   sprintf(buf,":-)  %s  (-:",s);
 144   slen=strlen(buf);
 145   space(out,(80-slen)/2);
 146   fprintf(out,"%s\n",buf);
 147 }
 148
 149
 150 static void pukeit(const char *db,const char *defstring, char *retstring,
 151                    int retsize, int *cqnum)
 152 {
 153   FILE *fp;
 154   char **help;
 155   int  i,nhlp;
 156   int  seed;
 157
 158   if (be_cool() && ((fp = low_libopen(db,FALSE)) != NULL)) {
 159     nhlp=fget_lines(fp,&help);
 160     /* for libraries we can use the low-level close routines */
 161     ffclose(fp);
 162     seed=time(NULL);
 163     *cqnum=nhlp*rando(&seed);
 164     if (strlen(help[*cqnum]) >= STRLEN)
 165       help[*cqnum][STRLEN-1] = '\0';
 166     strncpy(retstring,help[*cqnum],retsize);
 167     f(retstring);
 168     for(i=0; (i<nhlp); i++)
 169       sfree(help[i]);
 170     sfree(help);
 171   }
 172   else
 173     strncpy(retstring,defstring,retsize);
 174 }
 175
 176 void bromacs(char *retstring, int retsize)
 177 {
 178   int dum;
 179
 180   pukeit("bromacs.dat",
 181          "Groningen Machine for Chemical Simulation",
 182          retstring,retsize,&dum);
 183 }
 184
 185 void cool_quote(char *retstring, int retsize, int *cqnum)
 186 {
 187   char *tmpstr;
 188   char *s,*ptr;
 189   int tmpcq,*p;
 190
 191   if (cqnum!=NULL)
 192     p = cqnum;
 193   else
 194     p = &tmpcq;
 195
 196   /* protect audience from explicit lyrics */
 197   snew(tmpstr,retsize+1);
 198   pukeit("gurgle.dat","Thanx for Using GROMACS - Have a Nice Day",
 199          tmpstr,retsize-2,p);
 200
 201   if ((ptr = strchr(tmpstr,'_')) != NULL) {
 202     *ptr='\0';
 203     ptr++;
 204     sprintf(retstring,"\"%s\" %s",tmpstr,ptr);
 205   }
 206   else {
 207     strcpy(retstring,tmpstr);
 208   }
 209   sfree(tmpstr);
 210 }
 211
 212 void CopyRight(FILE *out,const char *szProgram)
 213 {
 214   /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
 215    * name of a file. Otherwise, we won't be able to find the library dir.
 216    */
 217 #define NCR (int)asize(CopyrightText)
 218 #ifdef GMX_FAHCORE
 219 #define NGPL 0 /*FAH has an exception permission from GPL to allow digital signatures in Gromacs*/
 220 #else
 221 #define NGPL (int)asize(GPLText)
 222 #endif
 223
 224   char buf[256],tmpstr[1024];
 225   int i;
 226
 227   set_program_name(szProgram);
 228
 229   ster_print(out,"G  R  O  M  A  C  S");
 230   fprintf(out,"\n");
 231
 232   bromacs(tmpstr,1023);
 233   sp_print(out,tmpstr);
 234   fprintf(out,"\n");
 235
 236   ster_print(out,GromacsVersion());
 237   fprintf(out,"\n\n");
 238
 239   /* fprintf(out,"\n");*/
 240
 241   /* sp_print(out,"PLEASE NOTE: THIS IS A BETA VERSION\n");
 242
 243   fprintf(out,"\n"); */
 244
 245   for(i=0; (i<NCR); i++)
 246     sp_print(out,CopyrightText[i]);
 247   for(i=0; (i<NGPL); i++)
 248     sp_print(out,GPLText[i]);
 249
 250   fprintf(out,"\n");
 251
 252   sprintf(buf,"%s",Program());
 253 #ifdef GMX_DOUBLE
 254   strcat(buf," (double precision)");
 255 #endif
 256   ster_print(out,buf);
 257   fprintf(out,"\n");
 258 }
 259
 260
 261 void thanx(FILE *fp)
 262 {
 263   char cq[1024];
 264   int  cqnum;
 265
 266   /* protect the audience from suggestive discussions */
 267   cool_quote(cq,1023,&cqnum);
 268
 269   if (be_cool())
 270     fprintf(fp,"\ngcq#%d: %s\n\n",cqnum,cq);
 271   else
 272     fprintf(fp,"\n%s\n\n",cq);
 273 }
 274
 275 typedef struct {
 276   const char *key;
 277   const char *author;
 278   const char *title;
 279   const char *journal;
 280   int volume,year;
 281   const char *pages;
 282 } t_citerec;
 283
 284 void please_cite(FILE *fp,const char *key)
 285 {
 286   static const t_citerec citedb[] = {
 287     { "Allen1987a",
 288       "M. P. Allen and D. J. Tildesley",
 289       "Computer simulation of liquids",
 290       "Oxford Science Publications",
 291       1, 1987, "1" },
 292     { "Berendsen95a",
 293       "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
 294       "GROMACS: A message-passing parallel molecular dynamics implementation",
 295       "Comp. Phys. Comm.",
 296       91, 1995, "43-56" },
 297     { "Berendsen84a",
 298       "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
 299       "Molecular dynamics with coupling to an external bath",
 300       "J. Chem. Phys.",
 301       81, 1984, "3684-3690" },
 302     { "Ryckaert77a",
 303       "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
 304       "Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes",
 305       "J. Comp. Phys.",
 306       23, 1977, "327-341" },
 307     { "Miyamoto92a",
 308       "S. Miyamoto and P. A. Kollman",
 309       "SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models",
 310       "J. Comp. Chem.",
 311       13, 1992, "952-962" },
 312     { "Barth95a",
 313       "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
 314       "Algorithms for Constrained Molecular Dynamics",
 315       "J. Comp. Chem.",
 316       16, 1995, "1192-1209" },
 317     { "Essman95a",
 318       "U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen ",
 319       "A smooth particle mesh Ewald method",
 320       "J. Chem. Phys.",
 321       103, 1995, "8577-8592" },
 322     { "Torda89a",
 323       "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
 324       "Time-dependent distance restraints in molecular dynamics simulations",
 325       "Chem. Phys. Lett.",
 326       157, 1989, "289-294" },
 327     { "Tironi95a",
 328       "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
 329       "Generalized reaction field method for molecular dynamics simulations",
 330       "J. Chem. Phys",
 331       102, 1995, "5451-5459" },
 332     { "Hess97a",
 333       "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
 334       "LINCS: A Linear Constraint Solver for molecular simulations",
 335       "J. Comp. Chem.",
 336       18, 1997, "1463-1472" },
 337     { "Hess2008a",
 338       "B. Hess",
 339       "P-LINCS: A Parallel Linear Constraint Solver for molecular simulation",
 340       "J. Chem. Theory Comput.",
 341       4, 2008, "116-122" },
 342     { "Hess2008b",
 343       "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
 344       "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation",
 345       "J. Chem. Theory Comput.",
 346       4, 2008, "435-447" },
 347     { "In-Chul99a",
 348       "Y. In-Chul and M. L. Berkowitz",
 349       "Ewald summation for systems with slab geometry",
 350       "J. Chem. Phys.",
 351       111, 1999, "3155-3162" },
 352     { "DeGroot97a",
 353       "B. L. de Groot and D. M. F. van Aalten and R. M. Scheek and A. Amadei and G. Vriend and H. J. C. Berendsen",
 354       "Prediction of Protein Conformational Freedom From Distance Constrains",
 355       "Proteins",
 356       29, 1997, "240-251" },
 357     { "Spoel98a",
 358       "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
 359       "A systematic study of water models for molecular simulation. Derivation of models optimized for use with a reaction-field.",
 360       "J. Chem. Phys.",
 361       108, 1998, "10220-10230" },
 362     { "Wishart98a",
 363       "D. S. Wishart and A. M. Nip",
 364       "Protein Chemical Shift Analysis: A Practical Guide",
 365       "Biochem. Cell Biol.",
 366       76, 1998, "153-163" },
 367     { "Maiorov95",
 368       "V. N. Maiorov and G. M. Crippen",
 369       "Size-Independent Comparison of Protein Three-Dimensional Structures",
 370       "PROTEINS: Struct. Funct. Gen.",
 371       22, 1995, "273-283" },
 372     { "Feenstra99",
 373       "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
 374       "Improving Efficiency of Large Time-scale Molecular Dynamics Simulations of Hydrogen-rich Systems",
 375       "J. Comput. Chem.",
 376       20, 1999, "786-798" },
 377     { "Timneanu2004a",
 378       "N. Timneanu and C. Caleman and J. Hajdu and D. van der Spoel",
 379       "Auger Electron Cascades in Water and Ice",
 380       "Chem. Phys.",
 381       299, 2004, "277-283" },
 382     { "Lindahl2001a",
 383       "E. Lindahl and B. Hess and D. van der Spoel",
 384       "GROMACS 3.0: A package for molecular simulation and trajectory analysis",
 385       "J. Mol. Mod.",
 386       7, 2001, "306-317" },
 387     { "Wang2001a",
 388       "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
 389       "Solvation model based on weighted solvent accessible surface area",
 390       "J. Phys. Chem. B",
 391       105, 2001, "5055-5067" },
 392     { "Eisenberg86a",
 393       "D. Eisenberg and A. D. McLachlan",
 394       "Solvation energy in protein folding and binding",
 395       "Nature",
 396       319, 1986, "199-203" },
 397     { "Eisenhaber95",
 398       "Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf",
 399       "The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",
 400       "J. Comp. Chem.",
 401       16, 1995, "273-284" },
 402     { "Hess2002",
 403       "B. Hess, H. Saint-Martin and H.J.C. Berendsen",
 404       "Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water",
 405       "J. Chem. Phys.",
 406       116, 2002, "9602-9610" },
 407     { "Hetenyi2002b",
 408       "Csaba Hetenyi and David van der Spoel",
 409       "Efficient docking of peptides to proteins without prior knowledge of the binding site.",
 410       "Prot. Sci.",
 411       11, 2002, "1729-1737" },
 412     { "Hess2003",
 413       "B. Hess and R.M. Scheek",
 414       "Orientation restraints in molecular dynamics simulations using time and ensemble averaging",
 415       "J. Magn. Res.",
 416       164, 2003, "19-27" },
 417     { "Rappe1991a",
 418       "A. K. Rappe and W. A. Goddard III",
 419       "Charge Equillibration for Molecular Dynamics Simulations",
 420       "J. Phys. Chem.",
 421       95, 1991, "3358-3363" },
 422     { "Mu2005a",
 423       "Y. Mu, P. H. Nguyen and G. Stock",
 424       "Energy landscape of a small peptide revelaed by dihedral angle principal component analysis",
 425       "Prot. Struct. Funct. Bioinf.",
 426       58, 2005, "45-52" },
 427     { "Okabe2001a",
 428       "T. Okabe and M. Kawata and Y. Okamoto and M. Mikami",
 429       "Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble",
 430       "Chem. Phys. Lett.",
 431       335, 2001, "435-439" },
 432     { "Hukushima96a",
 433       "K. Hukushima and K. Nemoto",
 434       "Exchange Monte Carlo Method and Application to Spin Glass Simulations",
 435       "J. Phys. Soc. Jpn.",
 436       65, 1996, "1604-1608" },
 437     { "Tropp80a",
 438       "J. Tropp",
 439       "Dipolar Relaxation and Nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances",
 440       "J. Chem. Phys.",
 441       72, 1980, "6035-6043" },
 442     { "Bultinck2002a",
 443        "P. Bultinck and W. Langenaeker and P. Lahorte and F. De Proft and P. Geerlings and M. Waroquier and J. P. Tollenaere",
 444       "The electronegativity equalization method I: Parametrization and validation for atomic charge calculations",
 445       "J. Phys. Chem. A",
 446       106, 2002, "7887-7894" },
 447     { "Yang2006b",
 448       "Q. Y. Yang and K. A. Sharp",
 449       "Atomic charge parameters for the finite difference Poisson-Boltzmann method using electronegativity neutralization",
 450       "J. Chem. Theory Comput.",
 451       2, 2006, "1152-1167" },
 452     { "Spoel2005a",
 453       "D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen",
 454       "GROMACS: Fast, Flexible and Free",
 455       "J. Comp. Chem.",
 456       26, 2005, "1701-1719" },
 457     { "Spoel2006b",
 458       "D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu",
 459       "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media",
 460       "J. Phys. Chem. B",
 461       110, 2006, "4393-4398" },
 462     { "Spoel2006d",
 463       "D. van der Spoel and M. M. Seibert",
 464       "Protein folding kinetics and thermodynamics from atomistic simulations",
 465       "Phys. Rev. Letters",
 466       96, 2006, "238102" },
 467     { "Palmer94a",
 468       "B. J. Palmer",
 469       "Transverse-current autocorrelation-function calculations of the shear viscosity for molecular liquids",
 470       "Phys. Rev. E",
 471       49, 1994, "359-366" },
 472     { "Bussi2007a",
 473       "G. Bussi, D. Donadio and M. Parrinello",
 474       "Canonical sampling through velocity rescaling",
 475       "J. Chem. Phys.",
 476       126, 2007, "014101" },
 477     { "Hub2006",
 478       "J. S. Hub and B. L. de Groot",
 479       "Does CO2 permeate through Aquaporin-1?",
 480       "Biophys. J.",
 481       91, 2006, "842-848" },
 482     { "Hub2008",
 483       "J. S. Hub and B. L. de Groot",
 484       "Mechanism of selectivity in aquaporins and aquaglyceroporins",
 485       "PNAS",
 486       105, 2008, "1198-1203" }
 487   };
 488 #define NSTR (int)asize(citedb)
 489
 490   int  j,index;
 491   char *author;
 492   char *title;
 493 #define LINE_WIDTH 79
 494
 495   if (fp == NULL)
 496     return;
 497
 498   for(index=0; (index<NSTR) && (strcmp(citedb[index].key,key) != 0); index++)
 499     ;
 500
 501   fprintf(fp,"\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n");
 502   if (index < NSTR) {
 503     /* Insert newlines */
 504     author = wrap_lines(citedb[index].author,LINE_WIDTH,0,FALSE);
 505     title  = wrap_lines(citedb[index].title,LINE_WIDTH,0,FALSE);
 506     fprintf(fp,"%s\n%s\n%s %d (%d) pp. %s\n",
 507             author,title,citedb[index].journal,
 508             citedb[index].volume,citedb[index].year,
 509             citedb[index].pages);
 510     sfree(author);
 511     sfree(title);
 512   }
 513   else {
 514     fprintf(fp,"Entry %s not found in citation database\n",key);
 515   }
 516   fprintf(fp,"-------- -------- --- Thank You --- -------- --------\n\n");
 517   fflush(fp);
 518 }
 519
 520 /* This routine only returns a static (constant) string, so we use a
 521  * mutex to initialize it. Since the string is only written to the
 522  * first time, there is no risk with multiple calls overwriting the
 523  * output for each other.
 524  */
 525 const char *GromacsVersion()
 526 {
 527 #ifdef USE_VERSION_H
 528   /* Version generated at compile time. */
 529   #include "version.h"
 530 #else
 531   /* Fall back to statically defined version. */
 532   static const char ver_string[]="VERSION " VERSION;
 533 #endif
 534
 535   return ver_string;
 536 }