3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
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.
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.
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.
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.
30 * For more info, check our website at http://www.gromacs.org
33 * GROningen Mixture of Alchemy and Childrens' Stories
50 /* This file is completely threadsafe - keep it that way! */
52 #include "gromacs/legacyheaders/futil.h"
53 #include "gromacs/legacyheaders/macros.h"
54 #include "gromacs/legacyheaders/random.h"
55 #include "gromacs/legacyheaders/smalloc.h"
56 #include "gromacs/legacyheaders/statutil.h"
57 #include "gromacs/legacyheaders/strdb.h"
58 #include "gromacs/legacyheaders/string2.h"
59 #include "gromacs/legacyheaders/vec.h"
61 #include "gromacs/fft/fft.h"
62 #include "gromacs/utility/gmxassert.h"
63 #include "gromacs/utility/programinfo.h"
65 #include "buildinfo.h"
67 static gmx_bool be_cool(void)
69 /* Yes, it is bad to check the environment variable every call,
70 * but we dont call this routine often, and it avoids using
71 * a mutex for locking the variable...
73 #ifdef GMX_COOL_QUOTES
74 return (getenv("GMX_NO_QUOTES") == NULL);
81 static void pukeit(const char *db, const char *defstring, char *retstring,
82 int retsize, int *cqnum)
89 if (be_cool() && ((fp = low_libopen(db, FALSE)) != NULL))
91 nhlp = fget_lines(fp, &help);
92 /* for libraries we can use the low-level close routines */
95 *cqnum = static_cast<int>(nhlp*rando(&seed));
96 if (strlen(help[*cqnum]) >= STRLEN)
98 help[*cqnum][STRLEN-1] = '\0';
100 strncpy(retstring, help[*cqnum], retsize);
101 for (i = 0; (i < nhlp); i++)
110 strncpy(retstring, defstring, retsize);
114 void bromacs(char *retstring, int retsize)
118 pukeit("bromacs.dat",
119 "Groningen Machine for Chemical Simulation",
120 retstring, retsize, &dum);
123 void cool_quote(char *retstring, int retsize, int *cqnum)
138 /* protect audience from explicit lyrics */
139 snew(tmpstr, retsize+1);
140 pukeit("gurgle.dat", "Thanx for Using GROMACS - Have a Nice Day",
141 tmpstr, retsize-2, p);
143 if ((ptr = strchr(tmpstr, '_')) != NULL)
147 sprintf(retstring, "\"%s\" %s", tmpstr, ptr);
151 strcpy(retstring, tmpstr);
156 static void printCopyright(FILE *fp)
158 static const char * const CopyrightText[] = {
159 "GROMACS is written by:",
160 "Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,",
161 "Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,",
162 "Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,",
163 "Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,",
164 "Michael Shirts, Alfons Sijbers, Peter Tieleman,\n",
165 "Berk Hess, David van der Spoel, and Erik Lindahl.\n",
166 "Copyright (c) 1991-2000, University of Groningen, The Netherlands.",
167 "Copyright (c) 2001-2013, The GROMACS development team at",
168 "Uppsala University & The Royal Institute of Technology, Sweden.",
169 "check out http://www.gromacs.org for more information."
172 static const char * const LicenseText[] = {
173 "GROMACS is free software; you can redistribute it and/or modify it",
174 "under the terms of the GNU Lesser General Public License",
175 "as published by the Free Software Foundation; either version 2.1",
176 "of the License, or (at your option) any later version."
179 #define NCR (int)asize(CopyrightText)
180 // FAH has an exception permission from LGPL to allow digital signatures in Gromacs.
184 #define NLICENSE (int)asize(LicenseText)
187 for (int i = 0; i < NCR; ++i)
189 fprintf(fp, "%s\n", CopyrightText[i]);
192 for (int i = 0; i < NLICENSE; ++i)
194 fprintf(fp, "%s\n", LicenseText[i]);
199 void gmx_thanx(FILE *fp)
204 /* protect the audience from suggestive discussions */
205 cool_quote(cq, 1023, &cqnum);
209 fprintf(fp, "\ngcq#%d: %s\n\n", cqnum, cq);
213 fprintf(fp, "\n%s\n\n", cq);
226 void please_cite(FILE *fp, const char *key)
228 static const t_citerec citedb[] = {
230 "M. P. Allen and D. J. Tildesley",
231 "Computer simulation of liquids",
232 "Oxford Science Publications",
235 "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
236 "GROMACS: A message-passing parallel molecular dynamics implementation",
240 "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
241 "Molecular dynamics with coupling to an external bath",
243 81, 1984, "3684-3690" },
245 "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
246 "Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes",
248 23, 1977, "327-341" },
250 "S. Miyamoto and P. A. Kollman",
251 "SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models",
253 13, 1992, "952-962" },
255 "D. T. Cromer & J. B. Mann",
256 "X-ray scattering factors computed from numerical Hartree-Fock wave functions",
260 "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
261 "Algorithms for Constrained Molecular Dynamics",
263 16, 1995, "1192-1209" },
265 "U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen ",
266 "A smooth particle mesh Ewald method",
268 103, 1995, "8577-8592" },
270 "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
271 "Time-dependent distance restraints in molecular dynamics simulations",
273 157, 1989, "289-294" },
275 "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
276 "Generalized reaction field method for molecular dynamics simulations",
278 102, 1995, "5451-5459" },
280 "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
281 "LINCS: A Linear Constraint Solver for molecular simulations",
283 18, 1997, "1463-1472" },
286 "P-LINCS: A Parallel Linear Constraint Solver for molecular simulation",
287 "J. Chem. Theory Comput.",
288 4, 2008, "116-122" },
290 "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
291 "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation",
292 "J. Chem. Theory Comput.",
293 4, 2008, "435-447" },
295 "J. S. Hub, B. L. de Groot and D. van der Spoel",
296 "g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates",
297 "J. Chem. Theory Comput.",
298 6, 2010, "3713-3720"},
300 "Y. In-Chul and M. L. Berkowitz",
301 "Ewald summation for systems with slab geometry",
303 111, 1999, "3155-3162" },
305 "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",
306 "Prediction of Protein Conformational Freedom From Distance Constrains",
308 29, 1997, "240-251" },
310 "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
311 "A systematic study of water models for molecular simulation. Derivation of models optimized for use with a reaction-field.",
313 108, 1998, "10220-10230" },
315 "D. S. Wishart and A. M. Nip",
316 "Protein Chemical Shift Analysis: A Practical Guide",
317 "Biochem. Cell Biol.",
318 76, 1998, "153-163" },
320 "V. N. Maiorov and G. M. Crippen",
321 "Size-Independent Comparison of Protein Three-Dimensional Structures",
322 "PROTEINS: Struct. Funct. Gen.",
323 22, 1995, "273-283" },
325 "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
326 "Improving Efficiency of Large Time-scale Molecular Dynamics Simulations of Hydrogen-rich Systems",
328 20, 1999, "786-798" },
330 "Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David van der Spoel and Luciano T. Costa",
331 "Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View",
332 "Environ. Sci. Technol.",
333 47, 2013, "7421-7429" },
335 "N. Timneanu and C. Caleman and J. Hajdu and D. van der Spoel",
336 "Auger Electron Cascades in Water and Ice",
338 299, 2004, "277-283" },
340 "T. A. Pascal and S. T. Lin and W. A. Goddard III",
341 "Thermodynamics of liquids: standard molar entropies and heat capacities of common solvents from 2PT molecular dynamics",
342 "Phys. Chem. Chem. Phys.",
343 13, 2011, "169-181" },
345 "C. Caleman and P. J. van Maaren and M. Hong and J. S. Hub and L. T. da Costa and D. van der Spoel",
346 "Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant",
347 "J. Chem. Theo. Comp.",
350 "E. Lindahl and B. Hess and D. van der Spoel",
351 "GROMACS 3.0: A package for molecular simulation and trajectory analysis",
353 7, 2001, "306-317" },
355 "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
356 "Solvation model based on weighted solvent accessible surface area",
358 105, 2001, "5055-5067" },
360 "D. Eisenberg and A. D. McLachlan",
361 "Solvation energy in protein folding and binding",
363 319, 1986, "199-203" },
366 "van der Waals Volumes and Radii",
368 68, 1964, "441-451" },
370 "Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf",
371 "The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",
373 16, 1995, "273-284" },
375 "B. Hess, H. Saint-Martin and H.J.C. Berendsen",
376 "Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water",
378 116, 2002, "9602-9610" },
380 "Csaba Hetenyi and David van der Spoel",
381 "Efficient docking of peptides to proteins without prior knowledge of the binding site.",
383 11, 2002, "1729-1737" },
385 "B. Hess and R.M. Scheek",
386 "Orientation restraints in molecular dynamics simulations using time and ensemble averaging",
388 164, 2003, "19-27" },
390 "A. K. Rappe and W. A. Goddard III",
391 "Charge Equillibration for Molecular Dynamics Simulations",
393 95, 1991, "3358-3363" },
395 "Y. Mu, P. H. Nguyen and G. Stock",
396 "Energy landscape of a small peptide revelaed by dihedral angle principal component analysis",
397 "Prot. Struct. Funct. Bioinf.",
400 "T. Okabe and M. Kawata and Y. Okamoto and M. Mikami",
401 "Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble",
403 335, 2001, "435-439" },
405 "K. Hukushima and K. Nemoto",
406 "Exchange Monte Carlo Method and Application to Spin Glass Simulations",
407 "J. Phys. Soc. Jpn.",
408 65, 1996, "1604-1608" },
411 "Dipolar Relaxation and Nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances",
413 72, 1980, "6035-6043" },
415 "P. Bultinck and W. Langenaeker and P. Lahorte and F. De Proft and P. Geerlings and M. Waroquier and J. P. Tollenaere",
416 "The electronegativity equalization method I: Parametrization and validation for atomic charge calculations",
418 106, 2002, "7887-7894" },
420 "Q. Y. Yang and K. A. Sharp",
421 "Atomic charge parameters for the finite difference Poisson-Boltzmann method using electronegativity neutralization",
422 "J. Chem. Theory Comput.",
423 2, 2006, "1152-1167" },
425 "D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen",
426 "GROMACS: Fast, Flexible and Free",
428 26, 2005, "1701-1719" },
430 "D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu",
431 "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media",
433 110, 2006, "4393-4398" },
435 "D. van der Spoel and M. M. Seibert",
436 "Protein folding kinetics and thermodynamics from atomistic simulations",
437 "Phys. Rev. Letters",
438 96, 2006, "238102" },
441 "Transverse-current autocorrelation-function calculations of the shear viscosity for molecular liquids",
443 49, 1994, "359-366" },
445 "G. Bussi, D. Donadio and M. Parrinello",
446 "Canonical sampling through velocity rescaling",
448 126, 2007, "014101" },
450 "J. S. Hub and B. L. de Groot",
451 "Does CO2 permeate through Aquaporin-1?",
453 91, 2006, "842-848" },
455 "J. S. Hub and B. L. de Groot",
456 "Mechanism of selectivity in aquaporins and aquaglyceroporins",
458 105, 2008, "1198-1203" },
460 "M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, and V. S. Pande",
461 "Accelerating Molecular Dynamic Simulation on Graphics Processing Units",
463 30, 2009, "864-872" },
465 "O. Engin, A. Villa, M. Sayar and B. Hess",
466 "Driving Forces for Adsorption of Amphiphilic Peptides to Air-Water Interface",
468 114, 2010, "11093" },
470 "S. Fritsch, C. Junghans and K. Kremer",
471 "Adaptive molecular simulation study on structure formation of toluene around C60 using Gromacs",
472 "J. Chem. Theo. Comp.",
475 "C. Junghans and S. Poblete",
476 "A reference implementation of the adaptive resolution scheme in ESPResSo",
480 "H. Wang, F. Dommert, C.Holm",
481 "Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency",
483 133, 2010, "034117" },
485 "Y. Sugita, Y. Okamoto",
486 "Replica-exchange molecular dynamics method for protein folding",
488 314, 1999, "141-151" },
490 "C. Kutzner and J. Czub and H. Grubmuller",
491 "Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS",
492 "J. Chem. Theory Comput.",
493 7, 2011, "1381-1393" },
495 "M. Hoefling, N. Lima, D. Haenni, C.A.M. Seidel, B. Schuler, H. Grubmuller",
496 "Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach",
500 "R. W. Hockney and J. W. Eastwood",
501 "Computer simulation using particles",
505 "V. Ballenegger, J.J. Cerda, and C. Holm",
506 "How to Convert SPME to P3M: Influence Functions and Error Estimates",
507 "J. Chem. Theory Comput.",
508 8, 2012, "936-947" },
510 "Garmay Yu, Shvetsov A, Karelov D, Lebedev D, Radulescu A, Petukhov M, Isaev-Ivanov V",
511 "Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament",
512 "Journal of Physics: Conference Series",
513 340, 2012, "012094" }
515 #define NSTR (int)asize(citedb)
520 #define LINE_WIDTH 79
527 for (index = 0; (index < NSTR) && (strcmp(citedb[index].key, key) != 0); index++)
532 fprintf(fp, "\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n");
535 /* Insert newlines */
536 author = wrap_lines(citedb[index].author, LINE_WIDTH, 0, FALSE);
537 title = wrap_lines(citedb[index].title, LINE_WIDTH, 0, FALSE);
538 fprintf(fp, "%s\n%s\n%s %d (%d) pp. %s\n",
539 author, title, citedb[index].journal,
540 citedb[index].volume, citedb[index].year,
541 citedb[index].pages);
547 fprintf(fp, "Entry %s not found in citation database\n", key);
549 fprintf(fp, "-------- -------- --- Thank You --- -------- --------\n\n");
553 #ifdef GMX_GIT_VERSION_INFO
554 /* Version information generated at compile time. */
555 #include "gromacs/utility/gitversion.h"
557 /* Fall back to statically defined version. */
558 static const char _gmx_ver_string[] = "VERSION " VERSION;
561 const char *GromacsVersion()
563 return _gmx_ver_string;
566 extern void gmx_print_version_info_gpu(FILE *fp);
568 static void gmx_print_version_info(FILE *fp)
570 fprintf(fp, "Gromacs version: %s\n", _gmx_ver_string);
571 #ifdef GMX_GIT_VERSION_INFO
572 fprintf(fp, "GIT SHA1 hash: %s\n", _gmx_full_git_hash);
573 /* Only print out the branch information if present.
574 * The generating script checks whether the branch point actually
575 * coincides with the hash reported above, and produces an empty string
577 if (_gmx_central_base_hash[0] != 0)
579 fprintf(fp, "Branched from: %s\n", _gmx_central_base_hash);
584 fprintf(fp, "Precision: double\n");
586 fprintf(fp, "Precision: single\n");
588 fprintf(fp, "Memory model: %lu bit\n", 8*sizeof(void *));
590 #ifdef GMX_THREAD_MPI
591 fprintf(fp, "MPI library: thread_mpi\n");
592 #elif defined(GMX_MPI)
593 fprintf(fp, "MPI library: MPI\n");
595 fprintf(fp, "MPI library: none\n");
598 fprintf(fp, "OpenMP support: enabled\n");
600 fprintf(fp, "OpenMP support: disabled\n");
603 fprintf(fp, "GPU support: enabled\n");
605 fprintf(fp, "GPU support: disabled\n");
607 /* A preprocessor trick to avoid duplicating logic from vec.h */
608 #define gmx_stringify2(x) #x
609 #define gmx_stringify(x) gmx_stringify2(x)
610 fprintf(fp, "invsqrt routine: %s\n", gmx_stringify(gmx_invsqrt(x)));
611 fprintf(fp, "CPU acceleration: %s\n", GMX_CPU_ACCELERATION_STRING);
613 fprintf(fp, "FFT library: %s\n", gmx_fft_get_version_info());
614 #ifdef GMX_LARGEFILES
615 fprintf(fp, "Large file support: enabled\n");
617 fprintf(fp, "Large file support: disabled\n");
620 fprintf(fp, "RDTSCP usage: enabled\n");
622 fprintf(fp, "RDTSCP usage: disabled\n");
625 fprintf(fp, "Built on: %s\n", BUILD_TIME);
626 fprintf(fp, "Built by: %s\n", BUILD_USER);
627 fprintf(fp, "Build OS/arch: %s\n", BUILD_HOST);
628 fprintf(fp, "Build CPU vendor: %s\n", BUILD_CPU_VENDOR);
629 fprintf(fp, "Build CPU brand: %s\n", BUILD_CPU_BRAND);
630 fprintf(fp, "Build CPU family: %d Model: %d Stepping: %d\n",
631 BUILD_CPU_FAMILY, BUILD_CPU_MODEL, BUILD_CPU_STEPPING);
632 /* TODO: The below strings can be quite long, so it would be nice to wrap
633 * them. Can wait for later, as the master branch has ready code to do all
635 fprintf(fp, "Build CPU features: %s\n", BUILD_CPU_FEATURES);
636 fprintf(fp, "C compiler: %s\n", BUILD_C_COMPILER);
637 fprintf(fp, "C compiler flags: %s\n", BUILD_CFLAGS);
638 fprintf(fp, "C++ compiler: %s\n", BUILD_CXX_COMPILER);
639 fprintf(fp, "C++ compiler flags: %s\n", BUILD_CXXFLAGS);
641 /* MKL might be used for LAPACK/BLAS even if FFTs use FFTW, so keep it separate */
642 fprintf(fp, "Linked with Intel MKL version %d.%d.%d.\n",
643 __INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__);
646 gmx_print_version_info_gpu(fp);
653 BinaryInformationSettings::BinaryInformationSettings()
654 : bExtendedInfo_(false), bCopyright_(false),
655 bGeneratedByHeader_(false), prefix_(""), suffix_("")
659 void printBinaryInformation(FILE *fp, const ProgramInfo &programInfo)
661 printBinaryInformation(fp, programInfo, BinaryInformationSettings());
664 void printBinaryInformation(FILE *fp, const ProgramInfo &programInfo,
665 const BinaryInformationSettings &settings)
667 const char *prefix = settings.prefix_;
668 const char *suffix = settings.suffix_;
669 const char *precisionString = "";
671 precisionString = " (double precision)";
673 const std::string &name = programInfo.displayName();
674 if (settings.bGeneratedByHeader_)
676 fprintf(fp, "%sCreated by:%s\n", prefix, suffix);
678 if (settings.bCopyright_)
680 GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
681 "Prefix/suffix not supported with copyright");
682 // This line is printed again after the copyright notice to make it
683 // appear together with all the other information, so that it is not
684 // necessary to read stuff above the copyright notice.
685 // The line above the copyright notice puts the copyright notice is
687 // TODO: It would be nice to know here whether we are really running a
688 // Gromacs binary or some other binary that is calling Gromacs; we
689 // could then print "%s is part of GROMACS" or some alternative text.
690 fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name.c_str(),
691 GromacsVersion(), precisionString, suffix);
696 fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name.c_str(),
697 GromacsVersion(), precisionString, suffix);
698 fprintf(fp, "%sExecutable: %s%s\n", prefix,
699 programInfo.programNameWithPath().c_str(), suffix);
700 fprintf(fp, "%sCommand line:%s\n%s %s%s\n",
701 prefix, suffix, prefix, programInfo.commandLine().c_str(), suffix);
702 if (settings.bExtendedInfo_)
704 GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
705 "Prefix/suffix not supported with extended info");
707 gmx_print_version_info(fp);