Moved copyrite.* to fileio from gmxlib and legacyheaders.

[gromacs.git] / src / gromacs / fileio / copyrite.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
#include "gmxpre.h"

#include "copyrite.h"

#include "config.h"

#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <ctime>

#include <algorithm>

#ifdef HAVE_LIBMKL
#include <mkl.h>
#endif
#if HAVE_EXTRAE
#include <extrae_user_events.h>
#endif

/* This file is completely threadsafe - keep it that way! */

#include "buildinfo.h"
#include "gromacs/fft/fft.h"
#include "gromacs/fileio/strdb.h"
#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"

static gmx_bool be_cool(void)
{
    /* Yes, it is bad to check the environment variable every call,
     * but we dont call this routine often, and it avoids using
     * a mutex for locking the variable...
     */
#if GMX_COOL_QUOTES
    return (getenv("GMX_NO_QUOTES") == NULL);
#else
    /*be uncool*/
    return FALSE;
#endif
}

static void pukeit(const char *db, const char *defstring, char *retstring,
                   int retsize, int *cqnum)
{
    FILE     *fp;
    char    **help;
    int       i, nhlp;
    gmx_rng_t rng;

    if (be_cool() && ((fp = low_libopen(db, FALSE)) != NULL))
    {
        nhlp = fget_lines(fp, &help);
        /* for libraries we can use the low-level close routines */
        gmx_ffclose(fp);
        rng    = gmx_rng_init(gmx_rng_make_seed());
        *cqnum = static_cast<int>(nhlp*gmx_rng_uniform_real(rng));
        gmx_rng_destroy(rng);
        if (std::strlen(help[*cqnum]) >= STRLEN)
        {
            help[*cqnum][STRLEN-1] = '\0';
        }
        std::strncpy(retstring, help[*cqnum], retsize);
        for (i = 0; (i < nhlp); i++)
        {
            sfree(help[i]);
        }
        sfree(help);
    }
    else
    {
        *cqnum = -1;
        std::strncpy(retstring, defstring, retsize);
    }
}

void bromacs(char *retstring, int retsize)
{
    int dum;

    pukeit("bromacs.dat",
           "Groningen Machine for Chemical Simulation",
           retstring, retsize, &dum);
}

void cool_quote(char *retstring, int retsize, int *cqnum)
{
    char *tmpstr;
    char *ptr;
    int   tmpcq, *p;

    if (cqnum != NULL)
    {
        p = cqnum;
    }
    else
    {
        p = &tmpcq;
    }

    /* protect audience from explicit lyrics */
    snew(tmpstr, retsize+1);
    pukeit("gurgle.dat", "Thanx for Using GROMACS - Have a Nice Day",
           tmpstr, retsize-2, p);

    if ((ptr = std::strchr(tmpstr, '_')) != NULL)
    {
        *ptr = '\0';
        ptr++;
        sprintf(retstring, "\"%s\" %s", tmpstr, ptr);
    }
    else
    {
        std::strcpy(retstring, tmpstr);
    }
    sfree(tmpstr);
}

static int centeringOffset(int width, int length)
{
    return std::max(width - length, 0) / 2;
}

static void printCentered(FILE *fp, int width, const char *text)
{
    const int offset = centeringOffset(width, std::strlen(text));
    fprintf(fp, "%*s%s", offset, "", text);
}

static void printCopyright(FILE *fp)
{
    static const char * const Contributors[] = {
        "Emile Apol",
        "Rossen Apostolov",
        "Herman J.C. Berendsen",
        "Par Bjelkmar",
        "Aldert van Buuren",
        "Rudi van Drunen",
        "Anton Feenstra",
        "Sebastian Fritsch",
        "Gerrit Groenhof",
        "Christoph Junghans",
        "Anca Hamuraru",
        "Vincent Hindriksen",
        "Dimitrios Karkoulis",
        "Peter Kasson",
        "Jiri Kraus",
        "Carsten Kutzner",
        "Per Larsson",
        "Justin A. Lemkul",
        "Magnus Lundborg",
        "Pieter Meulenhoff",
        "Erik Marklund",
        "Teemu Murtola",
        "Szilard Pall",
        "Sander Pronk",
        "Roland Schulz",
        "Alexey Shvetsov",
        "Michael Shirts",
        "Alfons Sijbers",
        "Peter Tieleman",
        "Teemu Virolainen",
        "Christian Wennberg",
        "Maarten Wolf"
    };
    static const char * const CopyrightText[] = {
        "Copyright (c) 1991-2000, University of Groningen, The Netherlands.",
        "Copyright (c) 2001-2015, The GROMACS development team at",
        "Uppsala University, Stockholm University and",
        "the Royal Institute of Technology, Sweden.",
        "check out http://www.gromacs.org for more information."
    };
    static const char * const LicenseText[] = {
        "GROMACS is free software; you can redistribute it and/or modify it",
        "under the terms of the GNU Lesser General Public License",
        "as published by the Free Software Foundation; either version 2.1",
        "of the License, or (at your option) any later version."
    };

#define NCONTRIBUTORS (int)asize(Contributors)
#define NCR (int)asize(CopyrightText)

// FAH has an exception permission from LGPL to allow digital signatures in Gromacs.
#ifdef GMX_FAHCORE
#define NLICENSE 0
#else
#define NLICENSE (int)asize(LicenseText)
#endif

    printCentered(fp, 78, "GROMACS is written by:");
    fprintf(fp, "\n");
    for (int i = 0; i < NCONTRIBUTORS; )
    {
        for (int j = 0; j < 4 && i < NCONTRIBUTORS; ++j, ++i)
        {
            const int width = 18;
            char      buf[30];
            const int offset = centeringOffset(width, strlen(Contributors[i]));
            GMX_RELEASE_ASSERT(strlen(Contributors[i]) + offset < asize(buf),
                               "Formatting buffer is not long enough");
            std::fill(buf, buf+width, ' ');
            std::strcpy(buf+offset, Contributors[i]);
            fprintf(fp, " %-*s", width, buf);
        }
        fprintf(fp, "\n");
    }
    printCentered(fp, 78, "and the project leaders:");
    fprintf(fp, "\n");
    printCentered(fp, 78, "Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel");
    fprintf(fp, "\n\n");
    for (int i = 0; i < NCR; ++i)
    {
        fprintf(fp, "%s\n", CopyrightText[i]);
    }
    fprintf(fp, "\n");
    for (int i = 0; i < NLICENSE; ++i)
    {
        fprintf(fp, "%s\n", LicenseText[i]);
    }
}


typedef struct {
    const char *key;
    const char *author;
    const char *title;
    const char *journal;
    int         volume, year;
    const char *pages;
} t_citerec;

void please_cite(FILE *fp, const char *key)
{
    static const t_citerec citedb[] = {
        { "Allen1987a",
          "M. P. Allen and D. J. Tildesley",
          "Computer simulation of liquids",
          "Oxford Science Publications",
          1, 1987, "1" },
        { "Berendsen95a",
          "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
          "GROMACS: A message-passing parallel molecular dynamics implementation",
          "Comp. Phys. Comm.",
          91, 1995, "43-56" },
        { "Berendsen84a",
          "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
          "Molecular dynamics with coupling to an external bath",
          "J. Chem. Phys.",
          81, 1984, "3684-3690" },
        { "Ryckaert77a",
          "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
          "Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes",
          "J. Comp. Phys.",
          23, 1977, "327-341" },
        { "Miyamoto92a",
          "S. Miyamoto and P. A. Kollman",
          "SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models",
          "J. Comp. Chem.",
          13, 1992, "952-962" },
        { "Cromer1968a",
          "D. T. Cromer & J. B. Mann",
          "X-ray scattering factors computed from numerical Hartree-Fock wave functions",
          "Acta Cryst. A",
          24, 1968, "321" },
        { "Barth95a",
          "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
          "Algorithms for Constrained Molecular Dynamics",
          "J. Comp. Chem.",
          16, 1995, "1192-1209" },
        { "Essmann95a",
          "U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen ",
          "A smooth particle mesh Ewald method",
          "J. Chem. Phys.",
          103, 1995, "8577-8592" },
        { "Torda89a",
          "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
          "Time-dependent distance restraints in molecular dynamics simulations",
          "Chem. Phys. Lett.",
          157, 1989, "289-294" },
        { "Tironi95a",
          "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
          "Generalized reaction field method for molecular dynamics simulations",
          "J. Chem. Phys",
          102, 1995, "5451-5459" },
        { "Hess97a",
          "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
          "LINCS: A Linear Constraint Solver for molecular simulations",
          "J. Comp. Chem.",
          18, 1997, "1463-1472" },
        { "Hess2008a",
          "B. Hess",
          "P-LINCS: A Parallel Linear Constraint Solver for molecular simulation",
          "J. Chem. Theory Comput.",
          4, 2008, "116-122" },
        { "Hess2008b",
          "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
          "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation",
          "J. Chem. Theory Comput.",
          4, 2008, "435-447" },
        { "Hub2010",
          "J. S. Hub, B. L. de Groot and D. van der Spoel",
          "g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates",
          "J. Chem. Theory Comput.",
          6, 2010, "3713-3720"},
        { "In-Chul99a",
          "Y. In-Chul and M. L. Berkowitz",
          "Ewald summation for systems with slab geometry",
          "J. Chem. Phys.",
          111, 1999, "3155-3162" },
        { "DeGroot97a",
          "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",
          "Prediction of Protein Conformational Freedom From Distance Constrains",
          "Proteins",
          29, 1997, "240-251" },
        { "Spoel98a",
          "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
          "A systematic study of water models for molecular simulation. Derivation of models optimized for use with a reaction-field.",
          "J. Chem. Phys.",
          108, 1998, "10220-10230" },
        { "Wishart98a",
          "D. S. Wishart and A. M. Nip",
          "Protein Chemical Shift Analysis: A Practical Guide",
          "Biochem. Cell Biol.",
          76, 1998, "153-163" },
        { "Maiorov95",
          "V. N. Maiorov and G. M. Crippen",
          "Size-Independent Comparison of Protein Three-Dimensional Structures",
          "PROTEINS: Struct. Funct. Gen.",
          22, 1995, "273-283" },
        { "Feenstra99",
          "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
          "Improving Efficiency of Large Time-scale Molecular Dynamics Simulations of Hydrogen-rich Systems",
          "J. Comput. Chem.",
          20, 1999, "786-798" },
        { "Lourenco2013a",
          "Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David van der Spoel and Luciano T. Costa",
          "Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View",
          "Environ. Sci. Technol.",
          47, 2013, "7421-7429" },
        { "Timneanu2004a",
          "N. Timneanu and C. Caleman and J. Hajdu and D. van der Spoel",
          "Auger Electron Cascades in Water and Ice",
          "Chem. Phys.",
          299, 2004, "277-283" },
        { "Pascal2011a",
          "T. A. Pascal and S. T. Lin and W. A. Goddard III",
          "Thermodynamics of liquids: standard molar entropies and heat capacities of common solvents from 2PT molecular dynamics",
          "Phys. Chem. Chem. Phys.",
          13, 2011, "169-181" },
        { "Caleman2008a",
          "C. Caleman and D. van der Spoel",
          "Picosecond Melting of Ice by an Infrared Laser Pulse: A Simulation Study",
          "Angew. Chem. Int. Ed",
          47, 2008, "1417-1420" },
        { "Caleman2011b",
          "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",
          "J. Mol. Mod.",
          7, 2001, "306-317" },
        { "Wang2001a",
          "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
          "Solvation model based on weighted solvent accessible surface area",
          "J. Phys. Chem. B",
          105, 2001, "5055-5067" },
        { "Eisenberg86a",
          "D. Eisenberg and A. D. McLachlan",
          "Solvation energy in protein folding and binding",
          "Nature",
          319, 1986, "199-203" },
        { "Bondi1964a",
          "A. Bondi",
          "van der Waals Volumes and Radii",
          "J. Phys. Chem.",
          68, 1964, "441-451" },
        { "Eisenhaber95",
          "Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf",
          "The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",
          "J. Comp. Chem.",
          16, 1995, "273-284" },
        { "Hess2002",
          "B. Hess, H. Saint-Martin and H.J.C. Berendsen",
          "Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water",
          "J. Chem. Phys.",
          116, 2002, "9602-9610" },
        { "Hetenyi2002b",
          "Csaba Hetenyi and David van der Spoel",
          "Efficient docking of peptides to proteins without prior knowledge of the binding site.",
          "Prot. Sci.",
          11, 2002, "1729-1737" },
        { "Hess2003",
          "B. Hess and R.M. Scheek",
          "Orientation restraints in molecular dynamics simulations using time and ensemble averaging",
          "J. Magn. Res.",
          164, 2003, "19-27" },
        { "Rappe1991a",
          "A. K. Rappe and W. A. Goddard III",
          "Charge Equillibration for Molecular Dynamics Simulations",
          "J. Phys. Chem.",
          95, 1991, "3358-3363" },
        { "Mu2005a",
          "Y. Mu, P. H. Nguyen and G. Stock",
          "Energy landscape of a small peptide revelaed by dihedral angle principal component analysis",
          "Prot. Struct. Funct. Bioinf.",
          58, 2005, "45-52" },
        { "Okabe2001a",
          "T. Okabe and M. Kawata and Y. Okamoto and M. Mikami",
          "Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble",
          "Chem. Phys. Lett.",
          335, 2001, "435-439" },
        { "Hukushima96a",
          "K. Hukushima and K. Nemoto",
          "Exchange Monte Carlo Method and Application to Spin Glass Simulations",
          "J. Phys. Soc. Jpn.",
          65, 1996, "1604-1608" },
        { "Tropp80a",
          "J. Tropp",
          "Dipolar Relaxation and Nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances",
          "J. Chem. Phys.",
          72, 1980, "6035-6043" },
        { "Bultinck2002a",
          "P. Bultinck and W. Langenaeker and P. Lahorte and F. De Proft and P. Geerlings and M. Waroquier and J. P. Tollenaere",
          "The electronegativity equalization method I: Parametrization and validation for atomic charge calculations",
          "J. Phys. Chem. A",
          106, 2002, "7887-7894" },
        { "Yang2006b",
          "Q. Y. Yang and K. A. Sharp",
          "Atomic charge parameters for the finite difference Poisson-Boltzmann method using electronegativity neutralization",
          "J. Chem. Theory Comput.",
          2, 2006, "1152-1167" },
        { "Spoel2005a",
          "D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen",
          "GROMACS: Fast, Flexible and Free",
          "J. Comp. Chem.",
          26, 2005, "1701-1719" },
        { "Spoel2006b",
          "D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu",
          "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media",
          "J. Phys. Chem. B",
          110, 2006, "4393-4398" },
        { "Spoel2006d",
          "D. van der Spoel and M. M. Seibert",
          "Protein folding kinetics and thermodynamics from atomistic simulations",
          "Phys. Rev. Letters",
          96, 2006, "238102" },
        { "Palmer94a",
          "B. J. Palmer",
          "Transverse-current autocorrelation-function calculations of the shear viscosity for molecular liquids",
          "Phys. Rev. E",
          49, 1994, "359-366" },
        { "Bussi2007a",
          "G. Bussi, D. Donadio and M. Parrinello",
          "Canonical sampling through velocity rescaling",
          "J. Chem. Phys.",
          126, 2007, "014101" },
        { "Hub2006",
          "J. S. Hub and B. L. de Groot",
          "Does CO2 permeate through Aquaporin-1?",
          "Biophys. J.",
          91, 2006, "842-848" },
        { "Hub2008",
          "J. S. Hub and B. L. de Groot",
          "Mechanism of selectivity in aquaporins and aquaglyceroporins",
          "PNAS",
          105, 2008, "1198-1203" },
        { "Friedrich2009",
          "M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, and V. S. Pande",
          "Accelerating Molecular Dynamic Simulation on Graphics Processing Units",
          "J. Comp. Chem.",
          30, 2009, "864-872" },
        { "Engin2010",
          "O. Engin, A. Villa, M. Sayar and B. Hess",
          "Driving Forces for Adsorption of Amphiphilic Peptides to Air-Water Interface",
          "J. Phys. Chem. B",
          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" },
        { "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" },
        { "Kutzner2011b",
          "C. Kutzner, H. Grubmuller, B. L. de Groot, and U. Zachariae",
          "Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail",
          "Biophys. J.",
          101, 2011, "809-817"},
        { "Lundborg2014",
          "M. Lundborg, R. Apostolov, D. Spangberg, A. Gardenas, D. van der Spoel and E. Lindahl",
          "An efficient and extensible format, library, and API for binary trajectory data from molecular simulations",
          "J. Comput. Chem.",
          35, 2014, "260-269"},
        { "Goga2012",
          "N. Goga and A. J. Rzepiela and A. H. de Vries and S. J. Marrink and H. J. C. Berendsen",
          "Efficient Algorithms for Langevin and DPD Dynamics",
          "J. Chem. Theory Comput.",
          8, 2012, "3637--3649"},
        { "Pronk2013",
          "S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl",
          "GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit",
          "Bioinformatics",
          29, 2013, "845-54"},
        { "Pall2015",
          "S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl",
          "Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS",
          "In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale",
          8759, 2015, "3-27" },
        { "Abraham2015",
          "M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl",
          "GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers",
          "SoftwareX",
          1, 2015, "19-25" },
    };
#define NSTR (int)asize(citedb)

    int   index;
    char *author;
    char *title;
#define LINE_WIDTH 79

    if (fp == NULL)
    {
        return;
    }

    for (index = 0; (index < NSTR) && (strcmp(citedb[index].key, key) != 0); index++)
    {
        ;
    }

    fprintf(fp, "\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n");
    if (index < NSTR)
    {
        /* Insert newlines */
        author = wrap_lines(citedb[index].author, LINE_WIDTH, 0, FALSE);
        title  = wrap_lines(citedb[index].title, LINE_WIDTH, 0, FALSE);
        fprintf(fp, "%s\n%s\n%s %d (%d) pp. %s\n",
                author, title, citedb[index].journal,
                citedb[index].volume, citedb[index].year,
                citedb[index].pages);
        sfree(author);
        sfree(title);
    }
    else
    {
        fprintf(fp, "Entry %s not found in citation database\n", key);
    }
    fprintf(fp, "-------- -------- --- Thank You --- -------- --------\n\n");
    fflush(fp);
}

extern void gmx_print_version_info_cuda_gpu(FILE *fp);

static void gmx_print_version_info(FILE *fp)
{
    fprintf(fp, "GROMACS version:    %s\n", gmx_version());
    const char *const git_hash = gmx_version_git_full_hash();
    if (git_hash[0] != '\0')
    {
        fprintf(fp, "GIT SHA1 hash:      %s\n", git_hash);
    }
    const char *const base_hash = gmx_version_git_central_base_hash();
    if (base_hash[0] != '\0')
    {
        fprintf(fp, "Branched from:      %s\n", base_hash);
    }

#ifdef GMX_DOUBLE
    fprintf(fp, "Precision:          double\n");
#else
    fprintf(fp, "Precision:          single\n");
#endif
    fprintf(fp, "Memory model:       %u bit\n", (unsigned)(8*sizeof(void *)));

#ifdef GMX_THREAD_MPI
    fprintf(fp, "MPI library:        thread_mpi\n");
#elif defined(GMX_MPI)
    fprintf(fp, "MPI library:        MPI\n");
#else
    fprintf(fp, "MPI library:        none\n");
#endif
#ifdef GMX_OPENMP
    fprintf(fp, "OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = %d)\n", GMX_OPENMP_MAX_THREADS);
#else
    fprintf(fp, "OpenMP support:     disabled\n");
#endif
#ifdef GMX_GPU
    fprintf(fp, "GPU support:        enabled\n");
#else
    fprintf(fp, "GPU support:        disabled\n");
#endif
#if defined(GMX_GPU) && defined(GMX_USE_OPENCL)
    fprintf(fp, "OpenCL support:     enabled\n");
#else
    fprintf(fp, "OpenCL support:     disabled\n");
#endif
    /* A preprocessor trick to avoid duplicating logic from vec.h */
#define gmx_stringify2(x) #x
#define gmx_stringify(x) gmx_stringify2(x)
    fprintf(fp, "invsqrt routine:    %s\n", gmx_stringify(gmx_invsqrt_impl(x)));
    fprintf(fp, "SIMD instructions:  %s\n", GMX_SIMD_STRING);
    fprintf(fp, "FFT library:        %s\n", gmx_fft_get_version_info());
#ifdef HAVE_RDTSCP
    fprintf(fp, "RDTSCP usage:       enabled\n");
#else
    fprintf(fp, "RDTSCP usage:       disabled\n");
#endif
#ifdef GMX_USE_TNG
    fprintf(fp, "TNG support:        enabled\n");
#else
    fprintf(fp, "TNG support:        disabled\n");
#endif
#if HAVE_EXTRAE
    unsigned major, minor, revision;
    Extrae_get_version(&major, &minor, &revision);
    fprintf(fp, "Tracing support:    enabled. Using Extrae-%d.%d.%d\n", major, minor, revision);
#else
    fprintf(fp, "Tracing support:    disabled\n");
#endif


    fprintf(fp, "Built on:           %s\n", BUILD_TIME);
    fprintf(fp, "Built by:           %s\n", BUILD_USER);
    fprintf(fp, "Build OS/arch:      %s\n", BUILD_HOST);
    fprintf(fp, "Build CPU vendor:   %s\n", BUILD_CPU_VENDOR);
    fprintf(fp, "Build CPU brand:    %s\n", BUILD_CPU_BRAND);
    fprintf(fp, "Build CPU family:   %d   Model: %d   Stepping: %d\n",
            BUILD_CPU_FAMILY, BUILD_CPU_MODEL, BUILD_CPU_STEPPING);
    /* TODO: The below strings can be quite long, so it would be nice to wrap
     * them. Can wait for later, as the master branch has ready code to do all
     * that. */
    fprintf(fp, "Build CPU features: %s\n", BUILD_CPU_FEATURES);
    fprintf(fp, "C compiler:         %s\n", BUILD_C_COMPILER);
    fprintf(fp, "C compiler flags:   %s\n", BUILD_CFLAGS);
    fprintf(fp, "C++ compiler:       %s\n", BUILD_CXX_COMPILER);
    fprintf(fp, "C++ compiler flags: %s\n", BUILD_CXXFLAGS);
#ifdef HAVE_LIBMKL
    /* MKL might be used for LAPACK/BLAS even if FFTs use FFTW, so keep it separate */
    fprintf(fp, "Linked with Intel MKL version %d.%d.%d.\n",
            __INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__);
#endif
#if defined(GMX_GPU)
#ifdef GMX_USE_OPENCL
    fprintf(fp, "OpenCL include dir: %s\n", OPENCL_INCLUDE_DIR);
    fprintf(fp, "OpenCL library:     %s\n", OPENCL_LIBRARY);
    fprintf(fp, "OpenCL version:     %s\n", OPENCL_VERSION_STRING);
#else
    gmx_print_version_info_cuda_gpu(fp);
#endif
#endif
}

#ifdef GMX_DOUBLE
void gmx_is_double_precision()
{
    /* allow precision detection */
}
#else
void gmx_is_single_precision()
{
    /* allow precision detection */
}
#endif

namespace gmx
{

BinaryInformationSettings::BinaryInformationSettings()
    : bExtendedInfo_(false), bCopyright_(false),
      bGeneratedByHeader_(false), prefix_(""), suffix_("")
{
}

void printBinaryInformation(FILE                  *fp,
                            const IProgramContext &programContext)
{
    printBinaryInformation(fp, programContext, BinaryInformationSettings());
}

void printBinaryInformation(FILE                            *fp,
                            const IProgramContext           &programContext,
                            const BinaryInformationSettings &settings)
{
    const char *prefix          = settings.prefix_;
    const char *suffix          = settings.suffix_;
    const char *precisionString = "";
#ifdef GMX_DOUBLE
    precisionString = " (double precision)";
#endif
    const char *const name = programContext.displayName();
    if (settings.bGeneratedByHeader_)
    {
        fprintf(fp, "%sCreated by:%s\n", prefix, suffix);
    }
    // TODO: It would be nice to know here whether we are really running a
    // Gromacs binary or some other binary that is calling Gromacs; we
    // could then print "%s is part of GROMACS" or some alternative text.
    std::string title
        = formatString(":-) GROMACS - %s, %s%s (-:", name, gmx_version(), precisionString);
    const int   indent
        = centeringOffset(78 - std::strlen(prefix) - std::strlen(suffix), title.length()) + 1;
    fprintf(fp, "%s%*c%s%s\n", prefix, indent, ' ', title.c_str(), suffix);
    fprintf(fp, "%s%s\n", prefix, suffix);
    if (settings.bCopyright_)
    {
        GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
                           "Prefix/suffix not supported with copyright");
        printCopyright(fp);
        fprintf(fp, "\n");
        // This line is printed again after the copyright notice to make it
        // appear together with all the other information, so that it is not
        // necessary to read stuff above the copyright notice.
        // The line above the copyright notice puts the copyright notice is
        // context, though.
        fprintf(fp, "%sGROMACS:      %s, %s%s%s\n", prefix, name,
                gmx_version(), precisionString, suffix);
    }
    const char *const binaryPath = programContext.fullBinaryPath();
    if (!gmx::isNullOrEmpty(binaryPath))
    {
        fprintf(fp, "%sExecutable:   %s%s\n", prefix, binaryPath, suffix);
    }
    const gmx::InstallationPrefixInfo installPrefix = programContext.installationPrefix();
    if (!gmx::isNullOrEmpty(installPrefix.path))
    {
        fprintf(fp, "%sData prefix:  %s%s%s\n", prefix, installPrefix.path,
                installPrefix.bSourceLayout ? " (source tree)" : "", suffix);
    }
    const char *const commandLine = programContext.commandLine();
    if (!gmx::isNullOrEmpty(commandLine))
    {
        fprintf(fp, "%sCommand line:%s\n%s  %s%s\n",
                prefix, suffix, prefix, commandLine, suffix);
    }
    if (settings.bExtendedInfo_)
    {
        GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
                           "Prefix/suffix not supported with extended info");
        fprintf(fp, "\n");
        gmx_print_version_info(fp);
    }
}

} // namespace gmx