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
40 #include <thread_mpi.h>
50 /* This file is completely threadsafe - keep it that way! */
65 #include "buildinfo.h"
66 #include "gmx_cpuid.h"
68 static void pr_two(FILE *out, int c, int i)
72 fprintf(out, "%c0%1d", c, i);
76 fprintf(out, "%c%2d", c, i);
80 void pr_difftime(FILE *out, double dt)
82 int ndays, nhours, nmins, nsecs;
83 gmx_bool bPrint, bPrinted;
86 dt = dt-24*3600*ndays;
96 fprintf(out, "%d", ndays);
98 bPrint = bPrint || (nhours > 0);
103 pr_two(out, 'd', nhours);
107 fprintf(out, "%d", nhours);
110 bPrinted = bPrinted || bPrint;
111 bPrint = bPrint || (nmins > 0);
116 pr_two(out, 'h', nmins);
120 fprintf(out, "%d", nmins);
123 bPrinted = bPrinted || bPrint;
126 pr_two(out, ':', nsecs);
130 fprintf(out, "%ds", nsecs);
136 gmx_bool be_cool(void)
138 /* Yes, it is bad to check the environment variable every call,
139 * but we dont call this routine often, and it avoids using
140 * a mutex for locking the variable...
142 #ifdef GMX_COOL_QUOTES
143 return (getenv("GMX_NO_QUOTES") == NULL);
150 void space(FILE *out, int n)
152 fprintf(out, "%*s", n, "");
160 for (i = 0; i < len; i++)
166 static void sp_print(FILE *out, const char *s)
171 space(out, (80-slen)/2);
172 fprintf(out, "%s\n", s);
175 static void ster_print(FILE *out, const char *s)
180 snprintf(buf, 128, ":-) %s (-:", s);
182 space(out, (80-slen)/2);
183 fprintf(out, "%s\n", buf);
187 static void pukeit(const char *db, const char *defstring, char *retstring,
188 int retsize, int *cqnum)
195 if (be_cool() && ((fp = low_libopen(db, FALSE)) != NULL))
197 nhlp = fget_lines(fp, &help);
198 /* for libraries we can use the low-level close routines */
201 *cqnum = nhlp*rando(&seed);
202 if (strlen(help[*cqnum]) >= STRLEN)
204 help[*cqnum][STRLEN-1] = '\0';
206 strncpy(retstring, help[*cqnum], retsize);
208 for (i = 0; (i < nhlp); i++)
216 strncpy(retstring, defstring, retsize);
220 void bromacs(char *retstring, int retsize)
224 pukeit("bromacs.dat",
225 "Groningen Machine for Chemical Simulation",
226 retstring, retsize, &dum);
229 void cool_quote(char *retstring, int retsize, int *cqnum)
244 /* protect audience from explicit lyrics */
245 snew(tmpstr, retsize+1);
246 pukeit("gurgle.dat", "Thanx for Using GROMACS - Have a Nice Day",
247 tmpstr, retsize-2, p);
249 if ((ptr = strchr(tmpstr, '_')) != NULL)
253 sprintf(retstring, "\"%s\" %s", tmpstr, ptr);
257 strcpy(retstring, tmpstr);
262 void CopyRight(FILE *out, const char *szProgram)
264 static const char * CopyrightText[] = {
265 "Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,",
266 "Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, ",
267 "Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, ",
268 "Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, ",
269 "Michael Shirts, Alfons Sijbers, Peter Tieleman,\n",
270 "Berk Hess, David van der Spoel, and Erik Lindahl.\n",
271 "Copyright (c) 1991-2000, University of Groningen, The Netherlands.",
272 "Copyright (c) 2001-2010, The GROMACS development team at",
273 "Uppsala University & The Royal Institute of Technology, Sweden.",
274 "check out http://www.gromacs.org for more information.\n"
277 static const char * LicenseText[] = {
278 "This program is free software; you can redistribute it and/or",
279 "modify it under the terms of the GNU Lesser General Public License",
280 "as published by the Free Software Foundation; either version 2.1",
281 "of the License, or (at your option) any later version."
284 /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
285 * name of a file. Otherwise, we won't be able to find the library dir.
287 #define NCR (int)asize(CopyrightText)
288 /* TODO: Is this exception still needed? */
290 #define NLICENSE 0 /*FAH has an exception permission from GPL to allow digital signatures in Gromacs*/
292 #define NLICENSE (int)asize(LicenseText)
295 char buf[256], tmpstr[1024];
299 set_program_name("Gromacs");
301 set_program_name(szProgram);
304 ster_print(out, "G R O M A C S");
307 bromacs(tmpstr, 1023);
308 sp_print(out, tmpstr);
311 ster_print(out, GromacsVersion());
314 /* fprintf(out,"\n");*/
316 /* sp_print(out,"PLEASE NOTE: THIS IS A BETA VERSION\n");
318 fprintf(out,"\n"); */
320 for (i = 0; (i < NCR); i++)
322 sp_print(out, CopyrightText[i]);
324 for (i = 0; (i < NLICENSE); i++)
326 sp_print(out, LicenseText[i]);
331 snprintf(buf, 256, "%s", Program());
333 strcat(buf, " (double precision)");
335 ster_print(out, buf);
345 /* protect the audience from suggestive discussions */
346 cool_quote(cq, 1023, &cqnum);
350 fprintf(fp, "\ngcq#%d: %s\n\n", cqnum, cq);
354 fprintf(fp, "\n%s\n\n", cq);
367 void please_cite(FILE *fp, const char *key)
369 static const t_citerec citedb[] = {
371 "M. P. Allen and D. J. Tildesley",
372 "Computer simulation of liquids",
373 "Oxford Science Publications",
376 "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
377 "GROMACS: A message-passing parallel molecular dynamics implementation",
381 "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
382 "Molecular dynamics with coupling to an external bath",
384 81, 1984, "3684-3690" },
386 "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
387 "Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes",
389 23, 1977, "327-341" },
391 "S. Miyamoto and P. A. Kollman",
392 "SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models",
394 13, 1992, "952-962" },
396 "D. T. Cromer & J. B. Mann",
397 "X-ray scattering factors computed from numerical Hartree-Fock wave functions",
401 "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
402 "Algorithms for Constrained Molecular Dynamics",
404 16, 1995, "1192-1209" },
406 "U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen ",
407 "A smooth particle mesh Ewald method",
409 103, 1995, "8577-8592" },
411 "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
412 "Time-dependent distance restraints in molecular dynamics simulations",
414 157, 1989, "289-294" },
416 "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
417 "Generalized reaction field method for molecular dynamics simulations",
419 102, 1995, "5451-5459" },
421 "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
422 "LINCS: A Linear Constraint Solver for molecular simulations",
424 18, 1997, "1463-1472" },
427 "P-LINCS: A Parallel Linear Constraint Solver for molecular simulation",
428 "J. Chem. Theory Comput.",
429 4, 2008, "116-122" },
431 "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
432 "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation",
433 "J. Chem. Theory Comput.",
434 4, 2008, "435-447" },
436 "J. S. Hub, B. L. de Groot and D. van der Spoel",
437 "g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates",
438 "J. Chem. Theory Comput.",
439 6, 2010, "3713-3720"},
441 "Y. In-Chul and M. L. Berkowitz",
442 "Ewald summation for systems with slab geometry",
444 111, 1999, "3155-3162" },
446 "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",
447 "Prediction of Protein Conformational Freedom From Distance Constrains",
449 29, 1997, "240-251" },
451 "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
452 "A systematic study of water models for molecular simulation. Derivation of models optimized for use with a reaction-field.",
454 108, 1998, "10220-10230" },
456 "D. S. Wishart and A. M. Nip",
457 "Protein Chemical Shift Analysis: A Practical Guide",
458 "Biochem. Cell Biol.",
459 76, 1998, "153-163" },
461 "V. N. Maiorov and G. M. Crippen",
462 "Size-Independent Comparison of Protein Three-Dimensional Structures",
463 "PROTEINS: Struct. Funct. Gen.",
464 22, 1995, "273-283" },
466 "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
467 "Improving Efficiency of Large Time-scale Molecular Dynamics Simulations of Hydrogen-rich Systems",
469 20, 1999, "786-798" },
471 "N. Timneanu and C. Caleman and J. Hajdu and D. van der Spoel",
472 "Auger Electron Cascades in Water and Ice",
474 299, 2004, "277-283" },
476 "T. A. Pascal and S. T. Lin and W. A. Goddard III",
477 "Thermodynamics of liquids: standard molar entropies and heat capacities of common solvents from 2PT molecular dynamics",
478 "Phys. Chem. Chem. Phys.",
479 13, 2011, "169-181" },
481 "C. Caleman and P. J. van Maaren and M. Hong and J. S. Hub and L. T. da Costa and D. van der Spoel",
482 "Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant",
483 "J. Chem. Theo. Comp.",
486 "E. Lindahl and B. Hess and D. van der Spoel",
487 "GROMACS 3.0: A package for molecular simulation and trajectory analysis",
489 7, 2001, "306-317" },
491 "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
492 "Solvation model based on weighted solvent accessible surface area",
494 105, 2001, "5055-5067" },
496 "D. Eisenberg and A. D. McLachlan",
497 "Solvation energy in protein folding and binding",
499 319, 1986, "199-203" },
501 "Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf",
502 "The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",
504 16, 1995, "273-284" },
506 "B. Hess, H. Saint-Martin and H.J.C. Berendsen",
507 "Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water",
509 116, 2002, "9602-9610" },
511 "Csaba Hetenyi and David van der Spoel",
512 "Efficient docking of peptides to proteins without prior knowledge of the binding site.",
514 11, 2002, "1729-1737" },
516 "B. Hess and R.M. Scheek",
517 "Orientation restraints in molecular dynamics simulations using time and ensemble averaging",
519 164, 2003, "19-27" },
521 "A. K. Rappe and W. A. Goddard III",
522 "Charge Equillibration for Molecular Dynamics Simulations",
524 95, 1991, "3358-3363" },
526 "Y. Mu, P. H. Nguyen and G. Stock",
527 "Energy landscape of a small peptide revelaed by dihedral angle principal component analysis",
528 "Prot. Struct. Funct. Bioinf.",
531 "T. Okabe and M. Kawata and Y. Okamoto and M. Mikami",
532 "Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble",
534 335, 2001, "435-439" },
536 "K. Hukushima and K. Nemoto",
537 "Exchange Monte Carlo Method and Application to Spin Glass Simulations",
538 "J. Phys. Soc. Jpn.",
539 65, 1996, "1604-1608" },
542 "Dipolar Relaxation and Nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances",
544 72, 1980, "6035-6043" },
546 "P. Bultinck and W. Langenaeker and P. Lahorte and F. De Proft and P. Geerlings and M. Waroquier and J. P. Tollenaere",
547 "The electronegativity equalization method I: Parametrization and validation for atomic charge calculations",
549 106, 2002, "7887-7894" },
551 "Q. Y. Yang and K. A. Sharp",
552 "Atomic charge parameters for the finite difference Poisson-Boltzmann method using electronegativity neutralization",
553 "J. Chem. Theory Comput.",
554 2, 2006, "1152-1167" },
556 "D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen",
557 "GROMACS: Fast, Flexible and Free",
559 26, 2005, "1701-1719" },
561 "D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu",
562 "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media",
564 110, 2006, "4393-4398" },
566 "D. van der Spoel and M. M. Seibert",
567 "Protein folding kinetics and thermodynamics from atomistic simulations",
568 "Phys. Rev. Letters",
569 96, 2006, "238102" },
572 "Transverse-current autocorrelation-function calculations of the shear viscosity for molecular liquids",
574 49, 1994, "359-366" },
576 "G. Bussi, D. Donadio and M. Parrinello",
577 "Canonical sampling through velocity rescaling",
579 126, 2007, "014101" },
581 "J. S. Hub and B. L. de Groot",
582 "Does CO2 permeate through Aquaporin-1?",
584 91, 2006, "842-848" },
586 "J. S. Hub and B. L. de Groot",
587 "Mechanism of selectivity in aquaporins and aquaglyceroporins",
589 105, 2008, "1198-1203" },
591 "M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, and V. S. Pande",
592 "Accelerating Molecular Dynamic Simulation on Graphics Processing Units",
594 30, 2009, "864-872" },
596 "O. Engin, A. Villa, M. Sayar and B. Hess",
597 "Driving Forces for Adsorption of Amphiphilic Peptides to Air-Water Interface",
599 114, 2010, "11093" },
601 "S. Fritsch, C. Junghans and K. Kremer",
602 "Adaptive molecular simulation study on structure formation of toluene around C60 using Gromacs",
603 "J. Chem. Theo. Comp.",
606 "C. Junghans and S. Poblete",
607 "A reference implementation of the adaptive resolution scheme in ESPResSo",
611 "H. Wang, F. Dommert, C.Holm",
612 "Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency",
614 133, 2010, "034117" },
616 "Y. Sugita, Y. Okamoto",
617 "Replica-exchange molecular dynamics method for protein folding",
619 314, 1999, "141-151" },
621 "C. Kutzner and J. Czub and H. Grubmuller",
622 "Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS",
623 "J. Chem. Theory Comput.",
624 7, 2011, "1381-1393" },
626 "M. Hoefling, N. Lima, D. Haenni, C.A.M. Seidel, B. Schuler, H. Grubmuller",
627 "Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach",
631 "R. W. Hockney and J. W. Eastwood",
632 "Computer simulation using particles",
636 "V. Ballenegger, J.J. Cerda, and C. Holm",
637 "How to Convert SPME to P3M: Influence Functions and Error Estimates",
638 "J. Chem. Theory Comput.",
639 8, 2012, "936-947" },
641 "Garmay Yu, Shvetsov A, Karelov D, Lebedev D, Radulescu A, Petukhov M, Isaev-Ivanov V",
642 "Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament",
643 "Journal of Physics: Conference Series",
644 340, 2012, "012094" }
646 #define NSTR (int)asize(citedb)
651 #define LINE_WIDTH 79
658 for (index = 0; (index < NSTR) && (strcmp(citedb[index].key, key) != 0); index++)
663 fprintf(fp, "\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n");
666 /* Insert newlines */
667 author = wrap_lines(citedb[index].author, LINE_WIDTH, 0, FALSE);
668 title = wrap_lines(citedb[index].title, LINE_WIDTH, 0, FALSE);
669 fprintf(fp, "%s\n%s\n%s %d (%d) pp. %s\n",
670 author, title, citedb[index].journal,
671 citedb[index].volume, citedb[index].year,
672 citedb[index].pages);
678 fprintf(fp, "Entry %s not found in citation database\n", key);
680 fprintf(fp, "-------- -------- --- Thank You --- -------- --------\n\n");
684 #ifdef GMX_GIT_VERSION_INFO
685 /* Version information generated at compile time. */
686 #include "gromacs/utility/gitversion.h"
688 /* Fall back to statically defined version. */
689 static const char _gmx_ver_string[] = "VERSION " VERSION;
692 const char *GromacsVersion()
694 return _gmx_ver_string;
697 void gmx_print_version_info_gpu(FILE *fp);
699 void gmx_print_version_info(FILE *fp)
701 fprintf(fp, "Gromacs version: %s\n", _gmx_ver_string);
702 #ifdef GMX_GIT_VERSION_INFO
703 fprintf(fp, "GIT SHA1 hash: %s\n", _gmx_full_git_hash);
704 /* Only print out the branch information if present.
705 * The generating script checks whether the branch point actually
706 * coincides with the hash reported above, and produces an empty string
708 if (_gmx_central_base_hash[0] != 0)
710 fprintf(fp, "Branched from: %s\n", _gmx_central_base_hash);
715 fprintf(fp, "Precision: double\n");
717 fprintf(fp, "Precision: single\n");
719 fprintf(fp, "Memory model: %lu bit\n", 8*sizeof(void *));
721 #ifdef GMX_THREAD_MPI
722 fprintf(fp, "MPI library: thread_mpi\n");
723 #elif defined(GMX_MPI)
724 fprintf(fp, "MPI library: MPI\n");
726 fprintf(fp, "MPI library: none\n");
729 fprintf(fp, "OpenMP support: enabled\n");
731 fprintf(fp, "OpenMP support: disabled\n");
734 fprintf(fp, "GPU support: enabled\n");
736 fprintf(fp, "GPU support: disabled\n");
738 /* A preprocessor trick to avoid duplicating logic from vec.h */
739 #define gmx_stringify2(x) #x
740 #define gmx_stringify(x) gmx_stringify2(x)
741 fprintf(fp, "invsqrt routine: %s\n", gmx_stringify(gmx_invsqrt(x)));
742 fprintf(fp, "CPU acceleration: %s\n", GMX_CPU_ACCELERATION_STRING);
744 /* TODO: Would be nicer to wrap this in a gmx_fft_version() call, but
745 * since that is currently in mdlib, can wait for master. */
746 #ifdef GMX_FFT_FFTPACK
747 fprintf(fp, "FFT library: fftpack (built-in)\n");
748 #elif defined(GMX_FFT_FFTW3) && defined(GMX_NATIVE_WINDOWS)
749 fprintf(fp, "FFT library: %s\n", "fftw3");
750 #elif defined(GMX_FFT_FFTW3) && defined(GMX_DOUBLE)
751 fprintf(fp, "FFT library: %s\n", fftw_version);
752 #elif defined(GMX_FFT_FFTW3)
753 fprintf(fp, "FFT library: %s\n", fftwf_version);
754 #elif defined(GMX_FFT_MKL)
755 fprintf(fp, "FFT library: MKL\n");
757 fprintf(fp, "FFT library: unknown\n");
759 #ifdef GMX_LARGEFILES
760 fprintf(fp, "Large file support: enabled\n");
762 fprintf(fp, "Large file support: disabled\n");
765 fprintf(fp, "RDTSCP usage: enabled\n");
767 fprintf(fp, "RDTSCP usage: disabled\n");
770 fprintf(fp, "Built on: %s\n", BUILD_TIME);
771 fprintf(fp, "Built by: %s\n", BUILD_USER);
772 fprintf(fp, "Build OS/arch: %s\n", BUILD_HOST);
773 fprintf(fp, "Build CPU vendor: %s\n", BUILD_CPU_VENDOR);
774 fprintf(fp, "Build CPU brand: %s\n", BUILD_CPU_BRAND);
775 fprintf(fp, "Build CPU family: %d Model: %d Stepping: %d\n",
776 BUILD_CPU_FAMILY, BUILD_CPU_MODEL, BUILD_CPU_STEPPING);
777 /* TODO: The below strings can be quite long, so it would be nice to wrap
778 * them. Can wait for later, as the master branch has ready code to do all
780 fprintf(fp, "Build CPU features: %s\n", BUILD_CPU_FEATURES);
781 fprintf(fp, "C compiler: %s\n", BUILD_C_COMPILER);
782 fprintf(fp, "C compiler flags: %s\n", BUILD_CFLAGS);
783 if (BUILD_CXX_COMPILER[0] != '\0')
785 fprintf(fp, "C++ compiler: %s\n", BUILD_CXX_COMPILER);
786 fprintf(fp, "C++ compiler flags: %s\n", BUILD_CXXFLAGS);
789 /* MKL might be used for LAPACK/BLAS even if FFTs use FFTW, so keep it separate */
790 fprintf(fp, "Linked with Intel MKL version %s.%s.%s.\n",
791 __INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__);
794 gmx_print_version_info_gpu(fp);