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, "");
155 static void sp_print(FILE *out, const char *s)
160 space(out, (80-slen)/2);
161 fprintf(out, "%s\n", s);
164 static void ster_print(FILE *out, const char *s)
169 snprintf(buf, 128, ":-) %s (-:", s);
171 space(out, (80-slen)/2);
172 fprintf(out, "%s\n", buf);
176 static void pukeit(const char *db, const char *defstring, char *retstring,
177 int retsize, int *cqnum)
184 if (be_cool() && ((fp = low_libopen(db, FALSE)) != NULL))
186 nhlp = fget_lines(fp, &help);
187 /* for libraries we can use the low-level close routines */
190 *cqnum = nhlp*rando(&seed);
191 if (strlen(help[*cqnum]) >= STRLEN)
193 help[*cqnum][STRLEN-1] = '\0';
195 strncpy(retstring, help[*cqnum], retsize);
196 for (i = 0; (i < nhlp); i++)
204 strncpy(retstring, defstring, retsize);
208 void bromacs(char *retstring, int retsize)
212 pukeit("bromacs.dat",
213 "Groningen Machine for Chemical Simulation",
214 retstring, retsize, &dum);
217 void cool_quote(char *retstring, int retsize, int *cqnum)
232 /* protect audience from explicit lyrics */
233 snew(tmpstr, retsize+1);
234 pukeit("gurgle.dat", "Thanx for Using GROMACS - Have a Nice Day",
235 tmpstr, retsize-2, p);
237 if ((ptr = strchr(tmpstr, '_')) != NULL)
241 sprintf(retstring, "\"%s\" %s", tmpstr, ptr);
245 strcpy(retstring, tmpstr);
250 void CopyRight(FILE *out, const char *szProgram)
252 static const char * CopyrightText[] = {
253 "Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,",
254 "Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, ",
255 "Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, ",
256 "Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, ",
257 "Michael Shirts, Alfons Sijbers, Peter Tieleman,\n",
258 "Berk Hess, David van der Spoel, and Erik Lindahl.\n",
259 "Copyright (c) 1991-2000, University of Groningen, The Netherlands.",
260 "Copyright (c) 2001-2010, The GROMACS development team at",
261 "Uppsala University & The Royal Institute of Technology, Sweden.",
262 "check out http://www.gromacs.org for more information.\n"
265 static const char * LicenseText[] = {
266 "This program is free software; you can redistribute it and/or",
267 "modify it under the terms of the GNU Lesser General Public License",
268 "as published by the Free Software Foundation; either version 2.1",
269 "of the License, or (at your option) any later version."
272 /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
273 * name of a file. Otherwise, we won't be able to find the library dir.
275 #define NCR (int)asize(CopyrightText)
276 /* TODO: Is this exception still needed? */
278 #define NLICENSE 0 /*FAH has an exception permission from GPL to allow digital signatures in Gromacs*/
280 #define NLICENSE (int)asize(LicenseText)
283 char buf[256], tmpstr[1024];
287 set_program_name("Gromacs");
289 set_program_name(szProgram);
292 ster_print(out, "G R O M A C S");
295 bromacs(tmpstr, 1023);
296 sp_print(out, tmpstr);
299 ster_print(out, GromacsVersion());
302 /* fprintf(out,"\n");*/
304 /* sp_print(out,"PLEASE NOTE: THIS IS A BETA VERSION\n");
306 fprintf(out,"\n"); */
308 for (i = 0; (i < NCR); i++)
310 sp_print(out, CopyrightText[i]);
312 for (i = 0; (i < NLICENSE); i++)
314 sp_print(out, LicenseText[i]);
319 snprintf(buf, 256, "%s", Program());
321 strcat(buf, " (double precision)");
323 ster_print(out, buf);
333 /* protect the audience from suggestive discussions */
334 cool_quote(cq, 1023, &cqnum);
338 fprintf(fp, "\ngcq#%d: %s\n\n", cqnum, cq);
342 fprintf(fp, "\n%s\n\n", cq);
355 void please_cite(FILE *fp, const char *key)
357 static const t_citerec citedb[] = {
359 "M. P. Allen and D. J. Tildesley",
360 "Computer simulation of liquids",
361 "Oxford Science Publications",
364 "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
365 "GROMACS: A message-passing parallel molecular dynamics implementation",
369 "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
370 "Molecular dynamics with coupling to an external bath",
372 81, 1984, "3684-3690" },
374 "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
375 "Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes",
377 23, 1977, "327-341" },
379 "S. Miyamoto and P. A. Kollman",
380 "SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models",
382 13, 1992, "952-962" },
384 "D. T. Cromer & J. B. Mann",
385 "X-ray scattering factors computed from numerical Hartree-Fock wave functions",
389 "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
390 "Algorithms for Constrained Molecular Dynamics",
392 16, 1995, "1192-1209" },
394 "U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen ",
395 "A smooth particle mesh Ewald method",
397 103, 1995, "8577-8592" },
399 "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
400 "Time-dependent distance restraints in molecular dynamics simulations",
402 157, 1989, "289-294" },
404 "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
405 "Generalized reaction field method for molecular dynamics simulations",
407 102, 1995, "5451-5459" },
409 "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
410 "LINCS: A Linear Constraint Solver for molecular simulations",
412 18, 1997, "1463-1472" },
415 "P-LINCS: A Parallel Linear Constraint Solver for molecular simulation",
416 "J. Chem. Theory Comput.",
417 4, 2008, "116-122" },
419 "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
420 "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation",
421 "J. Chem. Theory Comput.",
422 4, 2008, "435-447" },
424 "J. S. Hub, B. L. de Groot and D. van der Spoel",
425 "g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates",
426 "J. Chem. Theory Comput.",
427 6, 2010, "3713-3720"},
429 "Y. In-Chul and M. L. Berkowitz",
430 "Ewald summation for systems with slab geometry",
432 111, 1999, "3155-3162" },
434 "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",
435 "Prediction of Protein Conformational Freedom From Distance Constrains",
437 29, 1997, "240-251" },
439 "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
440 "A systematic study of water models for molecular simulation. Derivation of models optimized for use with a reaction-field.",
442 108, 1998, "10220-10230" },
444 "D. S. Wishart and A. M. Nip",
445 "Protein Chemical Shift Analysis: A Practical Guide",
446 "Biochem. Cell Biol.",
447 76, 1998, "153-163" },
449 "V. N. Maiorov and G. M. Crippen",
450 "Size-Independent Comparison of Protein Three-Dimensional Structures",
451 "PROTEINS: Struct. Funct. Gen.",
452 22, 1995, "273-283" },
454 "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
455 "Improving Efficiency of Large Time-scale Molecular Dynamics Simulations of Hydrogen-rich Systems",
457 20, 1999, "786-798" },
459 "N. Timneanu and C. Caleman and J. Hajdu and D. van der Spoel",
460 "Auger Electron Cascades in Water and Ice",
462 299, 2004, "277-283" },
464 "T. A. Pascal and S. T. Lin and W. A. Goddard III",
465 "Thermodynamics of liquids: standard molar entropies and heat capacities of common solvents from 2PT molecular dynamics",
466 "Phys. Chem. Chem. Phys.",
467 13, 2011, "169-181" },
469 "C. Caleman and P. J. van Maaren and M. Hong and J. S. Hub and L. T. da Costa and D. van der Spoel",
470 "Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant",
471 "J. Chem. Theo. Comp.",
474 "E. Lindahl and B. Hess and D. van der Spoel",
475 "GROMACS 3.0: A package for molecular simulation and trajectory analysis",
477 7, 2001, "306-317" },
479 "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
480 "Solvation model based on weighted solvent accessible surface area",
482 105, 2001, "5055-5067" },
484 "D. Eisenberg and A. D. McLachlan",
485 "Solvation energy in protein folding and binding",
487 319, 1986, "199-203" },
490 "van der Waals Volumes and Radii",
492 68, 1964,"441-451" },
494 "Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf",
495 "The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",
497 16, 1995, "273-284" },
499 "B. Hess, H. Saint-Martin and H.J.C. Berendsen",
500 "Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water",
502 116, 2002, "9602-9610" },
504 "Csaba Hetenyi and David van der Spoel",
505 "Efficient docking of peptides to proteins without prior knowledge of the binding site.",
507 11, 2002, "1729-1737" },
509 "B. Hess and R.M. Scheek",
510 "Orientation restraints in molecular dynamics simulations using time and ensemble averaging",
512 164, 2003, "19-27" },
514 "A. K. Rappe and W. A. Goddard III",
515 "Charge Equillibration for Molecular Dynamics Simulations",
517 95, 1991, "3358-3363" },
519 "Y. Mu, P. H. Nguyen and G. Stock",
520 "Energy landscape of a small peptide revelaed by dihedral angle principal component analysis",
521 "Prot. Struct. Funct. Bioinf.",
524 "T. Okabe and M. Kawata and Y. Okamoto and M. Mikami",
525 "Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble",
527 335, 2001, "435-439" },
529 "K. Hukushima and K. Nemoto",
530 "Exchange Monte Carlo Method and Application to Spin Glass Simulations",
531 "J. Phys. Soc. Jpn.",
532 65, 1996, "1604-1608" },
535 "Dipolar Relaxation and Nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances",
537 72, 1980, "6035-6043" },
539 "P. Bultinck and W. Langenaeker and P. Lahorte and F. De Proft and P. Geerlings and M. Waroquier and J. P. Tollenaere",
540 "The electronegativity equalization method I: Parametrization and validation for atomic charge calculations",
542 106, 2002, "7887-7894" },
544 "Q. Y. Yang and K. A. Sharp",
545 "Atomic charge parameters for the finite difference Poisson-Boltzmann method using electronegativity neutralization",
546 "J. Chem. Theory Comput.",
547 2, 2006, "1152-1167" },
549 "D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen",
550 "GROMACS: Fast, Flexible and Free",
552 26, 2005, "1701-1719" },
554 "D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu",
555 "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media",
557 110, 2006, "4393-4398" },
559 "D. van der Spoel and M. M. Seibert",
560 "Protein folding kinetics and thermodynamics from atomistic simulations",
561 "Phys. Rev. Letters",
562 96, 2006, "238102" },
565 "Transverse-current autocorrelation-function calculations of the shear viscosity for molecular liquids",
567 49, 1994, "359-366" },
569 "G. Bussi, D. Donadio and M. Parrinello",
570 "Canonical sampling through velocity rescaling",
572 126, 2007, "014101" },
574 "J. S. Hub and B. L. de Groot",
575 "Does CO2 permeate through Aquaporin-1?",
577 91, 2006, "842-848" },
579 "J. S. Hub and B. L. de Groot",
580 "Mechanism of selectivity in aquaporins and aquaglyceroporins",
582 105, 2008, "1198-1203" },
584 "M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, and V. S. Pande",
585 "Accelerating Molecular Dynamic Simulation on Graphics Processing Units",
587 30, 2009, "864-872" },
589 "O. Engin, A. Villa, M. Sayar and B. Hess",
590 "Driving Forces for Adsorption of Amphiphilic Peptides to Air-Water Interface",
592 114, 2010, "11093" },
594 "S. Fritsch, C. Junghans and K. Kremer",
595 "Adaptive molecular simulation study on structure formation of toluene around C60 using Gromacs",
596 "J. Chem. Theo. Comp.",
599 "C. Junghans and S. Poblete",
600 "A reference implementation of the adaptive resolution scheme in ESPResSo",
604 "H. Wang, F. Dommert, C.Holm",
605 "Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency",
607 133, 2010, "034117" },
609 "Y. Sugita, Y. Okamoto",
610 "Replica-exchange molecular dynamics method for protein folding",
612 314, 1999, "141-151" },
614 "C. Kutzner and J. Czub and H. Grubmuller",
615 "Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS",
616 "J. Chem. Theory Comput.",
617 7, 2011, "1381-1393" },
619 "M. Hoefling, N. Lima, D. Haenni, C.A.M. Seidel, B. Schuler, H. Grubmuller",
620 "Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach",
624 "R. W. Hockney and J. W. Eastwood",
625 "Computer simulation using particles",
629 "V. Ballenegger, J.J. Cerda, and C. Holm",
630 "How to Convert SPME to P3M: Influence Functions and Error Estimates",
631 "J. Chem. Theory Comput.",
632 8, 2012, "936-947" },
634 "Garmay Yu, Shvetsov A, Karelov D, Lebedev D, Radulescu A, Petukhov M, Isaev-Ivanov V",
635 "Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament",
636 "Journal of Physics: Conference Series",
637 340, 2012, "012094" }
639 #define NSTR (int)asize(citedb)
644 #define LINE_WIDTH 79
651 for (index = 0; (index < NSTR) && (strcmp(citedb[index].key, key) != 0); index++)
656 fprintf(fp, "\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n");
659 /* Insert newlines */
660 author = wrap_lines(citedb[index].author, LINE_WIDTH, 0, FALSE);
661 title = wrap_lines(citedb[index].title, LINE_WIDTH, 0, FALSE);
662 fprintf(fp, "%s\n%s\n%s %d (%d) pp. %s\n",
663 author, title, citedb[index].journal,
664 citedb[index].volume, citedb[index].year,
665 citedb[index].pages);
671 fprintf(fp, "Entry %s not found in citation database\n", key);
673 fprintf(fp, "-------- -------- --- Thank You --- -------- --------\n\n");
677 #ifdef GMX_GIT_VERSION_INFO
678 /* Version information generated at compile time. */
679 #include "gromacs/utility/gitversion.h"
681 /* Fall back to statically defined version. */
682 static const char _gmx_ver_string[] = "VERSION " VERSION;
685 const char *GromacsVersion()
687 return _gmx_ver_string;
690 void gmx_print_version_info_gpu(FILE *fp);
692 void gmx_print_version_info(FILE *fp)
694 fprintf(fp, "Gromacs version: %s\n", _gmx_ver_string);
695 #ifdef GMX_GIT_VERSION_INFO
696 fprintf(fp, "GIT SHA1 hash: %s\n", _gmx_full_git_hash);
697 /* Only print out the branch information if present.
698 * The generating script checks whether the branch point actually
699 * coincides with the hash reported above, and produces an empty string
701 if (_gmx_central_base_hash[0] != 0)
703 fprintf(fp, "Branched from: %s\n", _gmx_central_base_hash);
708 fprintf(fp, "Precision: double\n");
710 fprintf(fp, "Precision: single\n");
712 fprintf(fp, "Memory model: %lu bit\n", 8*sizeof(void *));
714 #ifdef GMX_THREAD_MPI
715 fprintf(fp, "MPI library: thread_mpi\n");
716 #elif defined(GMX_MPI)
717 fprintf(fp, "MPI library: MPI\n");
719 fprintf(fp, "MPI library: none\n");
722 fprintf(fp, "OpenMP support: enabled\n");
724 fprintf(fp, "OpenMP support: disabled\n");
727 fprintf(fp, "GPU support: enabled\n");
729 fprintf(fp, "GPU support: disabled\n");
731 /* A preprocessor trick to avoid duplicating logic from vec.h */
732 #define gmx_stringify2(x) #x
733 #define gmx_stringify(x) gmx_stringify2(x)
734 fprintf(fp, "invsqrt routine: %s\n", gmx_stringify(gmx_invsqrt(x)));
735 fprintf(fp, "CPU acceleration: %s\n", GMX_CPU_ACCELERATION_STRING);
737 /* TODO: Would be nicer to wrap this in a gmx_fft_version() call, but
738 * since that is currently in mdlib, can wait for master. */
739 #ifdef GMX_FFT_FFTPACK
740 fprintf(fp, "FFT library: fftpack (built-in)\n");
741 #elif defined(GMX_FFT_FFTW3) && defined(GMX_NATIVE_WINDOWS)
742 fprintf(fp, "FFT library: %s\n", "fftw3");
743 #elif defined(GMX_FFT_FFTW3) && defined(GMX_DOUBLE)
744 fprintf(fp, "FFT library: %s\n", fftw_version);
745 #elif defined(GMX_FFT_FFTW3)
746 fprintf(fp, "FFT library: %s\n", fftwf_version);
747 #elif defined(GMX_FFT_MKL)
748 fprintf(fp, "FFT library: MKL\n");
750 fprintf(fp, "FFT library: unknown\n");
752 #ifdef GMX_LARGEFILES
753 fprintf(fp, "Large file support: enabled\n");
755 fprintf(fp, "Large file support: disabled\n");
758 fprintf(fp, "RDTSCP usage: enabled\n");
760 fprintf(fp, "RDTSCP usage: disabled\n");
763 fprintf(fp, "Built on: %s\n", BUILD_TIME);
764 fprintf(fp, "Built by: %s\n", BUILD_USER);
765 fprintf(fp, "Build OS/arch: %s\n", BUILD_HOST);
766 fprintf(fp, "Build CPU vendor: %s\n", BUILD_CPU_VENDOR);
767 fprintf(fp, "Build CPU brand: %s\n", BUILD_CPU_BRAND);
768 fprintf(fp, "Build CPU family: %d Model: %d Stepping: %d\n",
769 BUILD_CPU_FAMILY, BUILD_CPU_MODEL, BUILD_CPU_STEPPING);
770 /* TODO: The below strings can be quite long, so it would be nice to wrap
771 * them. Can wait for later, as the master branch has ready code to do all
773 fprintf(fp, "Build CPU features: %s\n", BUILD_CPU_FEATURES);
774 fprintf(fp, "C compiler: %s\n", BUILD_C_COMPILER);
775 fprintf(fp, "C compiler flags: %s\n", BUILD_CFLAGS);
776 if (BUILD_CXX_COMPILER[0] != '\0')
778 fprintf(fp, "C++ compiler: %s\n", BUILD_CXX_COMPILER);
779 fprintf(fp, "C++ compiler flags: %s\n", BUILD_CXXFLAGS);
782 /* MKL might be used for LAPACK/BLAS even if FFTs use FFTW, so keep it separate */
783 fprintf(fp, "Linked with Intel MKL version %s.%s.%s.\n",
784 __INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__);
787 gmx_print_version_info_gpu(fp);