/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * 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,
* check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, 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.
- *
- * If you want to redistribute modifications, 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 www.gromacs.org.
- *
+ *
+ * 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 papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
#include <thread_mpi.h>
#endif
+#ifdef HAVE_LIBMKL
+#include <mkl.h>
+#endif
+#ifdef GMX_FFT_FFTW3
+#include <fftw3.h>
+#endif
+
/* This file is completely threadsafe - keep it that way! */
#include <string.h>
#include "smalloc.h"
#include "string2.h"
#include "macros.h"
-#include "time.h"
+#include <time.h>
#include "random.h"
#include "statutil.h"
#include "copyrite.h"
#include "strdb.h"
#include "futil.h"
+#include "vec.h"
+#include "buildinfo.h"
+#include "gmx_cpuid.h"
-static void pr_two(FILE *out,int c,int i)
+static void pr_two(FILE *out, int c, int i)
{
- if (i < 10)
- fprintf(out,"%c0%1d",c,i);
- else
- fprintf(out,"%c%2d",c,i);
+ if (i < 10)
+ {
+ fprintf(out, "%c0%1d", c, i);
+ }
+ else
+ {
+ fprintf(out, "%c%2d", c, i);
+ }
}
-void pr_difftime(FILE *out,double dt)
+void pr_difftime(FILE *out, double dt)
{
- int ndays,nhours,nmins,nsecs;
- gmx_bool bPrint,bPrinted;
-
- ndays = dt/(24*3600);
- dt = dt-24*3600*ndays;
- nhours= dt/3600;
- dt = dt-3600*nhours;
- nmins = dt/60;
- dt = dt-nmins*60;
- nsecs = dt;
- bPrint= (ndays > 0);
- bPrinted=bPrint;
- if (bPrint)
- fprintf(out,"%d",ndays);
- bPrint=bPrint || (nhours > 0);
- if (bPrint) {
- if (bPrinted)
- pr_two(out,'d',nhours);
- else
- fprintf(out,"%d",nhours);
- }
- bPrinted=bPrinted || bPrint;
- bPrint=bPrint || (nmins > 0);
- if (bPrint) {
+ int ndays, nhours, nmins, nsecs;
+ gmx_bool bPrint, bPrinted;
+
+ ndays = dt/(24*3600);
+ dt = dt-24*3600*ndays;
+ nhours = dt/3600;
+ dt = dt-3600*nhours;
+ nmins = dt/60;
+ dt = dt-nmins*60;
+ nsecs = dt;
+ bPrint = (ndays > 0);
+ bPrinted = bPrint;
+ if (bPrint)
+ {
+ fprintf(out, "%d", ndays);
+ }
+ bPrint = bPrint || (nhours > 0);
+ if (bPrint)
+ {
+ if (bPrinted)
+ {
+ pr_two(out, 'd', nhours);
+ }
+ else
+ {
+ fprintf(out, "%d", nhours);
+ }
+ }
+ bPrinted = bPrinted || bPrint;
+ bPrint = bPrint || (nmins > 0);
+ if (bPrint)
+ {
+ if (bPrinted)
+ {
+ pr_two(out, 'h', nmins);
+ }
+ else
+ {
+ fprintf(out, "%d", nmins);
+ }
+ }
+ bPrinted = bPrinted || bPrint;
if (bPrinted)
- pr_two(out,'h',nmins);
- else
- fprintf(out,"%d",nmins);
- }
- bPrinted=bPrinted || bPrint;
- if (bPrinted)
- pr_two(out,':',nsecs);
- else
- fprintf(out,"%ds",nsecs);
- fprintf(out,"\n");
+ {
+ pr_two(out, ':', nsecs);
+ }
+ else
+ {
+ fprintf(out, "%ds", nsecs);
+ }
+ fprintf(out, "\n");
}
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...
- */
-#ifdef GMX_FAHCORE
- /*be uncool*/
- return FALSE;
+ /* 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...
+ */
+#ifdef GMX_COOL_QUOTES
+ return (getenv("GMX_NO_QUOTES") == NULL);
#else
- return (getenv("GMX_NO_QUOTES") == NULL);
+ /*be uncool*/
+ return FALSE;
#endif
}
void space(FILE *out, int n)
{
- fprintf(out,"%*s",n,"");
+ fprintf(out, "%*s", n, "");
}
-static void sp_print(FILE *out,const char *s)
+static void sp_print(FILE *out, const char *s)
{
- int slen;
-
- slen=strlen(s);
- space(out,(80-slen)/2);
- fprintf(out,"%s\n",s);
+ int slen;
+
+ slen = strlen(s);
+ space(out, (80-slen)/2);
+ fprintf(out, "%s\n", s);
}
-static void ster_print(FILE *out,const char *s)
+static void ster_print(FILE *out, const char *s)
{
- int slen;
- char buf[128];
-
- snprintf(buf,128,":-) %s (-:",s);
- slen=strlen(buf);
- space(out,(80-slen)/2);
- fprintf(out,"%s\n",buf);
+ int slen;
+ char buf[128];
+
+ snprintf(buf, 128, ":-) %s (-:", s);
+ slen = strlen(buf);
+ space(out, (80-slen)/2);
+ fprintf(out, "%s\n", buf);
}
-static void pukeit(const char *db,const char *defstring, char *retstring,
- int retsize, int *cqnum)
+static void pukeit(const char *db, const char *defstring, char *retstring,
+ int retsize, int *cqnum)
{
- FILE *fp;
- char **help;
- int i,nhlp;
- int seed;
-
- if (be_cool() && ((fp = low_libopen(db,FALSE)) != NULL)) {
- nhlp=fget_lines(fp,&help);
- /* for libraries we can use the low-level close routines */
- ffclose(fp);
- seed=time(NULL);
- *cqnum=nhlp*rando(&seed);
- if (strlen(help[*cqnum]) >= STRLEN)
- help[*cqnum][STRLEN-1] = '\0';
- strncpy(retstring,help[*cqnum],retsize);
- for(i=0; (i<nhlp); i++)
- sfree(help[i]);
- sfree(help);
- }
- else
- strncpy(retstring,defstring,retsize);
+ FILE *fp;
+ char **help;
+ int i, nhlp;
+ int seed;
+
+ if (be_cool() && ((fp = low_libopen(db, FALSE)) != NULL))
+ {
+ nhlp = fget_lines(fp, &help);
+ /* for libraries we can use the low-level close routines */
+ ffclose(fp);
+ seed = time(NULL);
+ *cqnum = nhlp*rando(&seed);
+ if (strlen(help[*cqnum]) >= STRLEN)
+ {
+ help[*cqnum][STRLEN-1] = '\0';
+ }
+ strncpy(retstring, help[*cqnum], retsize);
+ for (i = 0; (i < nhlp); i++)
+ {
+ sfree(help[i]);
+ }
+ sfree(help);
+ }
+ else
+ {
+ strncpy(retstring, defstring, retsize);
+ }
}
void bromacs(char *retstring, int retsize)
{
- int dum;
+ int dum;
- pukeit("bromacs.dat",
- "Groningen Machine for Chemical Simulation",
- retstring,retsize,&dum);
+ pukeit("bromacs.dat",
+ "Groningen Machine for Chemical Simulation",
+ retstring, retsize, &dum);
}
void cool_quote(char *retstring, int retsize, int *cqnum)
{
- char *tmpstr;
- char *s,*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 = strchr(tmpstr,'_')) != NULL) {
- *ptr='\0';
- ptr++;
- sprintf(retstring,"\"%s\" %s",tmpstr,ptr);
- }
- else {
- strcpy(retstring,tmpstr);
- }
- sfree(tmpstr);
+ char *tmpstr;
+ char *s, *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 = strchr(tmpstr, '_')) != NULL)
+ {
+ *ptr = '\0';
+ ptr++;
+ sprintf(retstring, "\"%s\" %s", tmpstr, ptr);
+ }
+ else
+ {
+ strcpy(retstring, tmpstr);
+ }
+ sfree(tmpstr);
}
-void CopyRight(FILE *out,const char *szProgram)
+void CopyRight(FILE *out, const char *szProgram)
{
- /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
- * name of a file. Otherwise, we won't be able to find the library dir.
- */
+ /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
+ * name of a file. Otherwise, we won't be able to find the library dir.
+ */
#define NCR (int)asize(CopyrightText)
+/* TODO: Is this exception still needed? */
#ifdef GMX_FAHCORE
-#define NGPL 0 /*FAH has an exception permission from GPL to allow digital signatures in Gromacs*/
+#define NLICENSE 0 /*FAH has an exception permission from GPL to allow digital signatures in Gromacs*/
#else
-#define NGPL (int)asize(GPLText)
+#define NLICENSE (int)asize(LicenseText)
#endif
- char buf[256],tmpstr[1024];
- int i;
+ char buf[256], tmpstr[1024];
+ int i;
#ifdef GMX_FAHCORE
- set_program_name("Gromacs");
+ set_program_name("Gromacs");
#else
- set_program_name(szProgram);
+ set_program_name(szProgram);
#endif
- ster_print(out,"G R O M A C S");
- fprintf(out,"\n");
-
- bromacs(tmpstr,1023);
- sp_print(out,tmpstr);
- fprintf(out,"\n");
+ ster_print(out, "G R O M A C S");
+ fprintf(out, "\n");
- ster_print(out,GromacsVersion());
- fprintf(out,"\n");
+ bromacs(tmpstr, 1023);
+ sp_print(out, tmpstr);
+ fprintf(out, "\n");
- /* fprintf(out,"\n");*/
+ ster_print(out, GromacsVersion());
+ fprintf(out, "\n");
- /* sp_print(out,"PLEASE NOTE: THIS IS A BETA VERSION\n");
-
- fprintf(out,"\n"); */
+ /* fprintf(out,"\n");*/
- for(i=0; (i<NCR); i++)
- sp_print(out,CopyrightText[i]);
- for(i=0; (i<NGPL); i++)
- sp_print(out,GPLText[i]);
+ /* sp_print(out,"PLEASE NOTE: THIS IS A BETA VERSION\n");
- fprintf(out,"\n");
+ fprintf(out,"\n"); */
- snprintf(buf,256,"%s",Program());
+ for (i = 0; (i < NCR); i++)
+ {
+ sp_print(out, CopyrightText[i]);
+ }
+ for (i = 0; (i < NLICENSE); i++)
+ {
+ sp_print(out, LicenseText[i]);
+ }
+
+ fprintf(out, "\n");
+
+ snprintf(buf, 256, "%s", Program());
#ifdef GMX_DOUBLE
- strcat(buf," (double precision)");
+ strcat(buf, " (double precision)");
#endif
- ster_print(out,buf);
- fprintf(out,"\n");
+ ster_print(out, buf);
+ fprintf(out, "\n");
}
void thanx(FILE *fp)
{
- char cq[1024];
- int cqnum;
-
- /* protect the audience from suggestive discussions */
- cool_quote(cq,1023,&cqnum);
-
- if (be_cool())
- fprintf(fp,"\ngcq#%d: %s\n\n",cqnum,cq);
- else
- fprintf(fp,"\n%s\n\n",cq);
+ char cq[1024];
+ int cqnum;
+
+ /* protect the audience from suggestive discussions */
+ cool_quote(cq, 1023, &cqnum);
+
+ if (be_cool())
+ {
+ fprintf(fp, "\ngcq#%d: %s\n\n", cqnum, cq);
+ }
+ else
+ {
+ fprintf(fp, "\n%s\n\n", cq);
+ }
}
typedef struct {
- const char *key;
- const char *author;
- const char *title;
- const char *journal;
- int volume,year;
- const char *pages;
+ 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)
+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" },
- { "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" },
- { "Caleman2011b",
- "C. Caleman and M. Hong and J. S. Hub and L. T. da Costa and P. J. van Maaren and D. van der Spoel",
- "Force Field Benchmark 1: Density, Heat of Vaporization, Heat Capacity, Surface Tension and Dielectric Constant of 152 Organic Liquids",
- "Submitted",
- 0, 2011, "" },
- { "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" },
- { "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",
- 0, 2010, "???" },
- { "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" },
- };
+ 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" },
+ { "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" },
+ { "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" },
+ { "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" }
+ };
#define NSTR (int)asize(citedb)
-
- int j,index;
- char *author;
- char *title;
+
+ int j, 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);
+
+ 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);
}
#ifdef USE_VERSION_H
#include "version.h"
#else
/* Fall back to statically defined version. */
-static const char _gmx_ver_string[]="VERSION " VERSION;
+static const char _gmx_ver_string[] = "VERSION " VERSION;
#endif
-/* This routine only returns a static (constant) string, so we use a
- * mutex to initialize it. Since the string is only written to the
- * first time, there is no risk with multiple calls overwriting the
- * output for each other.
- */
const char *GromacsVersion()
{
- return _gmx_ver_string;
+ return _gmx_ver_string;
}
+void gmx_print_version_info_gpu(FILE *fp);
void gmx_print_version_info(FILE *fp)
{
- fprintf(fp, "Version: %s\n", _gmx_ver_string);
+ fprintf(fp, "Gromacs version: %s\n", _gmx_ver_string);
#ifdef USE_VERSION_H
- fprintf(fp, "GIT SHA1 hash: %s\n", _gmx_full_git_hash);
+ fprintf(fp, "GIT SHA1 hash: %s\n", _gmx_full_git_hash);
/* Only print out the branch information if present.
* The generating script checks whether the branch point actually
* coincides with the hash reported above, and produces an empty string
* in such cases. */
if (_gmx_central_base_hash[0] != 0)
{
- fprintf(fp, "Branched from: %s\n", _gmx_central_base_hash);
+ fprintf(fp, "Branched from: %s\n", _gmx_central_base_hash);
}
#endif
#ifdef GMX_DOUBLE
- fprintf(fp, "Precision: double\n");
+ fprintf(fp, "Precision: double\n");
#else
- fprintf(fp, "Precision: single\n");
+ fprintf(fp, "Precision: single\n");
#endif
+ fprintf(fp, "Memory model: %lu bit\n", 8*sizeof(void *));
-#ifdef GMX_THREADS
- fprintf(fp, "Parallellization: thread_mpi\n");
+#ifdef GMX_THREAD_MPI
+ fprintf(fp, "MPI library: thread_mpi\n");
#elif defined(GMX_MPI)
- fprintf(fp, "Parallellization: MPI\n");
+ fprintf(fp, "MPI library: MPI\n");
#else
- fprintf(fp, "Parallellization: none\n");
+ fprintf(fp, "MPI library: none\n");
#endif
-
+#ifdef GMX_OPENMP
+ fprintf(fp, "OpenMP support: enabled\n");
+#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
+ /* 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(x)));
+ fprintf(fp, "CPU acceleration: %s\n", GMX_CPU_ACCELERATION_STRING);
+
+ /* TODO: Would be nicer to wrap this in a gmx_fft_version() call, but
+ * since that is currently in mdlib, can wait for master. */
#ifdef GMX_FFT_FFTPACK
- fprintf(fp, "FFT Library: fftpack\n");
-#elif defined(GMX_FFT_FFTW2)
- fprintf(fp, "FFT Library: fftw2\n");
+ fprintf(fp, "FFT library: fftpack (built-in)\n");
+#elif defined(GMX_FFT_FFTW3) && defined(GMX_NATIVE_WINDOWS)
+ fprintf(fp, "FFT library: %s\n", "fftw3");
+#elif defined(GMX_FFT_FFTW3) && defined(GMX_DOUBLE)
+ fprintf(fp, "FFT library: %s\n", fftw_version);
#elif defined(GMX_FFT_FFTW3)
- fprintf(fp, "FFT Library: fftw3\n");
+ fprintf(fp, "FFT library: %s\n", fftwf_version);
#elif defined(GMX_FFT_MKL)
- fprintf(fp, "FFT Library: MKL\n");
+ fprintf(fp, "FFT library: MKL\n");
#else
- fprintf(fp, "FFT Library: unknown\n");
+ fprintf(fp, "FFT library: unknown\n");
+#endif
+#ifdef GMX_LARGEFILES
+ fprintf(fp, "Large file support: enabled\n");
+#else
+ fprintf(fp, "Large file support: disabled\n");
+#endif
+#ifdef HAVE_RDTSCP
+ fprintf(fp, "RDTSCP usage: enabled\n");
+#else
+ fprintf(fp, "RDTSCP usage: 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);
+ if (BUILD_CXX_COMPILER[0] != '\0')
+ {
+ 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 %s.%s.%s.\n",
+ __INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__);
+#endif
+#ifdef GMX_GPU
+ gmx_print_version_info_gpu(fp);
#endif
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff