/*
- *
- * 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, "");
}
- void f(char *a)
- {
- int i;
- int len = strlen(a);
-
- for (i = 0; i < len; i++)
- {
- a[i] = ~a[i];
- }
- }
-
-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);
- f(retstring);
+ 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
}
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * 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.
* 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:
- * GROwing Monsters And Cloning Shrimps
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#include "domdec.h"
#include "partdec.h"
#include "mtop_util.h"
+#include "gmx_omp_nthreads.h"
+#include "gmx_omp.h"
/* Routines to send/recieve coordinates and force
- * of constructing atoms.
- */
+ * of constructing atoms.
+ */
static void move_construct_x(t_comm_vsites *vsitecomm, rvec x[], t_commrec *cr)
{
- rvec *sendbuf;
- rvec *recvbuf;
- int i,ia;
-
- sendbuf = vsitecomm->send_buf;
- recvbuf = vsitecomm->recv_buf;
-
-
- /* Prepare pulse left by copying to send buffer */
- for(i=0;i<vsitecomm->left_export_nconstruct;i++)
- {
- ia = vsitecomm->left_export_construct[i];
- copy_rvec(x[ia],sendbuf[i]);
- }
-
- /* Pulse coordinates left */
- gmx_tx_rx_real(cr,GMX_LEFT,(real *)sendbuf,3*vsitecomm->left_export_nconstruct,GMX_RIGHT,(real *)recvbuf,3*vsitecomm->right_import_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for(i=0;i<vsitecomm->right_import_nconstruct;i++)
- {
- ia = vsitecomm->right_import_construct[i];
- copy_rvec(recvbuf[i],x[ia]);
- }
-
- /* Prepare pulse right by copying to send buffer */
- for(i=0;i<vsitecomm->right_export_nconstruct;i++)
- {
- ia = vsitecomm->right_export_construct[i];
- copy_rvec(x[ia],sendbuf[i]);
- }
-
- /* Pulse coordinates right */
- gmx_tx_rx_real(cr,GMX_RIGHT,(real *)sendbuf,3*vsitecomm->right_export_nconstruct,GMX_LEFT,(real *)recvbuf,3*vsitecomm->left_import_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for(i=0;i<vsitecomm->left_import_nconstruct;i++)
- {
- ia = vsitecomm->left_import_construct[i];
- copy_rvec(recvbuf[i],x[ia]);
- }
+ rvec *sendbuf;
+ rvec *recvbuf;
+ int i, ia;
+
+ sendbuf = vsitecomm->send_buf;
+ recvbuf = vsitecomm->recv_buf;
+
+
+ /* Prepare pulse left by copying to send buffer */
+ for (i = 0; i < vsitecomm->left_export_nconstruct; i++)
+ {
+ ia = vsitecomm->left_export_construct[i];
+ copy_rvec(x[ia], sendbuf[i]);
+ }
+
+ /* Pulse coordinates left */
+ gmx_tx_rx_real(cr, GMX_LEFT, (real *)sendbuf, 3*vsitecomm->left_export_nconstruct, GMX_RIGHT, (real *)recvbuf, 3*vsitecomm->right_import_nconstruct);
+
+ /* Copy from receive buffer to coordinate array */
+ for (i = 0; i < vsitecomm->right_import_nconstruct; i++)
+ {
+ ia = vsitecomm->right_import_construct[i];
+ copy_rvec(recvbuf[i], x[ia]);
+ }
+
+ /* Prepare pulse right by copying to send buffer */
+ for (i = 0; i < vsitecomm->right_export_nconstruct; i++)
+ {
+ ia = vsitecomm->right_export_construct[i];
+ copy_rvec(x[ia], sendbuf[i]);
+ }
+
+ /* Pulse coordinates right */
+ gmx_tx_rx_real(cr, GMX_RIGHT, (real *)sendbuf, 3*vsitecomm->right_export_nconstruct, GMX_LEFT, (real *)recvbuf, 3*vsitecomm->left_import_nconstruct);
+
+ /* Copy from receive buffer to coordinate array */
+ for (i = 0; i < vsitecomm->left_import_nconstruct; i++)
+ {
+ ia = vsitecomm->left_import_construct[i];
+ copy_rvec(recvbuf[i], x[ia]);
+ }
}
static void move_construct_f(t_comm_vsites *vsitecomm, rvec f[], t_commrec *cr)
{
- rvec *sendbuf;
- rvec *recvbuf;
- int i,ia;
-
- sendbuf = vsitecomm->send_buf;
- recvbuf = vsitecomm->recv_buf;
-
- /* Prepare pulse right by copying to send buffer */
- for(i=0;i<vsitecomm->right_import_nconstruct;i++)
- {
- ia = vsitecomm->right_import_construct[i];
- copy_rvec(f[ia],sendbuf[i]);
- clear_rvec(f[ia]); /* Zero it here after moving, just to simplify debug book-keeping... */
- }
-
- /* Pulse forces right */
- gmx_tx_rx_real(cr,GMX_RIGHT,(real *)sendbuf,3*vsitecomm->right_import_nconstruct,GMX_LEFT,(real *)recvbuf,3*vsitecomm->left_export_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for(i=0;i<vsitecomm->left_export_nconstruct;i++)
- {
- ia = vsitecomm->left_export_construct[i];
- rvec_inc(f[ia],recvbuf[i]);
- }
-
- /* Prepare pulse left by copying to send buffer */
- for(i=0;i<vsitecomm->left_import_nconstruct;i++)
- {
- ia = vsitecomm->left_import_construct[i];
- copy_rvec(f[ia],sendbuf[i]);
- clear_rvec(f[ia]); /* Zero it here after moving, just to simplify debug book-keeping... */
- }
-
- /* Pulse coordinates left */
- gmx_tx_rx_real(cr,GMX_LEFT,(real *)sendbuf,3*vsitecomm->left_import_nconstruct,GMX_RIGHT,(real *)recvbuf,3*vsitecomm->right_export_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for(i=0;i<vsitecomm->right_export_nconstruct;i++)
- {
- ia = vsitecomm->right_export_construct[i];
- rvec_inc(f[ia],recvbuf[i]);
- }
-
- /* All forces are now on the home processors */
+ rvec *sendbuf;
+ rvec *recvbuf;
+ int i, ia;
+
+ sendbuf = vsitecomm->send_buf;
+ recvbuf = vsitecomm->recv_buf;
+
+ /* Prepare pulse right by copying to send buffer */
+ for (i = 0; i < vsitecomm->right_import_nconstruct; i++)
+ {
+ ia = vsitecomm->right_import_construct[i];
+ copy_rvec(f[ia], sendbuf[i]);
+ clear_rvec(f[ia]); /* Zero it here after moving, just to simplify debug book-keeping... */
+ }
+
+ /* Pulse forces right */
+ gmx_tx_rx_real(cr, GMX_RIGHT, (real *)sendbuf, 3*vsitecomm->right_import_nconstruct, GMX_LEFT, (real *)recvbuf, 3*vsitecomm->left_export_nconstruct);
+
+ /* Copy from receive buffer to coordinate array */
+ for (i = 0; i < vsitecomm->left_export_nconstruct; i++)
+ {
+ ia = vsitecomm->left_export_construct[i];
+ rvec_inc(f[ia], recvbuf[i]);
+ }
+
+ /* Prepare pulse left by copying to send buffer */
+ for (i = 0; i < vsitecomm->left_import_nconstruct; i++)
+ {
+ ia = vsitecomm->left_import_construct[i];
+ copy_rvec(f[ia], sendbuf[i]);
+ clear_rvec(f[ia]); /* Zero it here after moving, just to simplify debug book-keeping... */
+ }
+
+ /* Pulse coordinates left */
+ gmx_tx_rx_real(cr, GMX_LEFT, (real *)sendbuf, 3*vsitecomm->left_import_nconstruct, GMX_RIGHT, (real *)recvbuf, 3*vsitecomm->right_export_nconstruct);
+
+ /* Copy from receive buffer to coordinate array */
+ for (i = 0; i < vsitecomm->right_export_nconstruct; i++)
+ {
+ ia = vsitecomm->right_export_construct[i];
+ rvec_inc(f[ia], recvbuf[i]);
+ }
+
+ /* All forces are now on the home processors */
}
-
+
static void
pd_clear_nonlocal_constructs(t_comm_vsites *vsitecomm, rvec f[])
{
- int i,ia;
-
- for(i=0;i<vsitecomm->left_import_nconstruct;i++)
- {
- ia = vsitecomm->left_import_construct[i];
- clear_rvec(f[ia]);
- }
- for(i=0;i<vsitecomm->right_import_nconstruct;i++)
- {
- ia = vsitecomm->right_import_construct[i];
- clear_rvec(f[ia]);
- }
+ int i, ia;
+
+ for (i = 0; i < vsitecomm->left_import_nconstruct; i++)
+ {
+ ia = vsitecomm->left_import_construct[i];
+ clear_rvec(f[ia]);
+ }
+ for (i = 0; i < vsitecomm->right_import_nconstruct; i++)
+ {
+ ia = vsitecomm->right_import_construct[i];
+ clear_rvec(f[ia]);
+ }
}
-static int pbc_rvec_sub(const t_pbc *pbc,const rvec xi,const rvec xj,rvec dx)
+static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
{
- if (pbc) {
- return pbc_dx_aiuc(pbc,xi,xj,dx);
- }
- else {
- rvec_sub(xi,xj,dx);
- return CENTRAL;
- }
+ if (pbc)
+ {
+ return pbc_dx_aiuc(pbc, xi, xj, dx);
+ }
+ else
+ {
+ rvec_sub(xi, xj, dx);
+ return CENTRAL;
+ }
}
/* Vsite construction routines */
-static void constr_vsite2(rvec xi,rvec xj,rvec x,real a,t_pbc *pbc)
+static void constr_vsite2(rvec xi, rvec xj, rvec x, real a, t_pbc *pbc)
{
- real b;
- rvec dx;
-
- b=1.0-a;
- /* 1 flop */
-
- if (pbc) {
- pbc_dx_aiuc(pbc,xj,xi,dx);
- x[XX] = xi[XX] + a*dx[XX];
- x[YY] = xi[YY] + a*dx[YY];
- x[ZZ] = xi[ZZ] + a*dx[ZZ];
- } else {
- x[XX] = b*xi[XX] + a*xj[XX];
- x[YY] = b*xi[YY] + a*xj[YY];
- x[ZZ] = b*xi[ZZ] + a*xj[ZZ];
- /* 9 Flops */
- }
-
- /* TOTAL: 10 flops */
+ real b;
+ rvec dx;
+
+ b = 1.0-a;
+ /* 1 flop */
+
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, xj, xi, dx);
+ x[XX] = xi[XX] + a*dx[XX];
+ x[YY] = xi[YY] + a*dx[YY];
+ x[ZZ] = xi[ZZ] + a*dx[ZZ];
+ }
+ else
+ {
+ x[XX] = b*xi[XX] + a*xj[XX];
+ x[YY] = b*xi[YY] + a*xj[YY];
+ x[ZZ] = b*xi[ZZ] + a*xj[ZZ];
+ /* 9 Flops */
+ }
+
+ /* TOTAL: 10 flops */
}
-static void constr_vsite3(rvec xi,rvec xj,rvec xk,rvec x,real a,real b,
- t_pbc *pbc)
+static void constr_vsite3(rvec xi, rvec xj, rvec xk, rvec x, real a, real b,
+ t_pbc *pbc)
{
- real c;
- rvec dxj,dxk;
-
- c=1.0-a-b;
- /* 2 flops */
-
- if (pbc) {
- pbc_dx_aiuc(pbc,xj,xi,dxj);
- pbc_dx_aiuc(pbc,xk,xi,dxk);
- x[XX] = xi[XX] + a*dxj[XX] + b*dxk[XX];
- x[YY] = xi[YY] + a*dxj[YY] + b*dxk[YY];
- x[ZZ] = xi[ZZ] + a*dxj[ZZ] + b*dxk[ZZ];
- } else {
- x[XX] = c*xi[XX] + a*xj[XX] + b*xk[XX];
- x[YY] = c*xi[YY] + a*xj[YY] + b*xk[YY];
- x[ZZ] = c*xi[ZZ] + a*xj[ZZ] + b*xk[ZZ];
- /* 15 Flops */
- }
-
- /* TOTAL: 17 flops */
+ real c;
+ rvec dxj, dxk;
+
+ c = 1.0-a-b;
+ /* 2 flops */
+
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, xj, xi, dxj);
+ pbc_dx_aiuc(pbc, xk, xi, dxk);
+ x[XX] = xi[XX] + a*dxj[XX] + b*dxk[XX];
+ x[YY] = xi[YY] + a*dxj[YY] + b*dxk[YY];
+ x[ZZ] = xi[ZZ] + a*dxj[ZZ] + b*dxk[ZZ];
+ }
+ else
+ {
+ x[XX] = c*xi[XX] + a*xj[XX] + b*xk[XX];
+ x[YY] = c*xi[YY] + a*xj[YY] + b*xk[YY];
+ x[ZZ] = c*xi[ZZ] + a*xj[ZZ] + b*xk[ZZ];
+ /* 15 Flops */
+ }
+
+ /* TOTAL: 17 flops */
}
-static void constr_vsite3FD(rvec xi,rvec xj,rvec xk,rvec x,real a,real b,
- t_pbc *pbc)
+static void constr_vsite3FD(rvec xi, rvec xj, rvec xk, rvec x, real a, real b,
+ t_pbc *pbc)
{
- rvec xij,xjk,temp;
- real c;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xj,xjk);
- /* 6 flops */
-
- /* temp goes from i to a point on the line jk */
- temp[XX] = xij[XX] + a*xjk[XX];
- temp[YY] = xij[YY] + a*xjk[YY];
- temp[ZZ] = xij[ZZ] + a*xjk[ZZ];
- /* 6 flops */
-
- c=b*gmx_invsqrt(iprod(temp,temp));
- /* 6 + 10 flops */
-
- x[XX] = xi[XX] + c*temp[XX];
- x[YY] = xi[YY] + c*temp[YY];
- x[ZZ] = xi[ZZ] + c*temp[ZZ];
- /* 6 Flops */
-
- /* TOTAL: 34 flops */
+ rvec xij, xjk, temp;
+ real c;
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xj, xjk);
+ /* 6 flops */
+
+ /* temp goes from i to a point on the line jk */
+ temp[XX] = xij[XX] + a*xjk[XX];
+ temp[YY] = xij[YY] + a*xjk[YY];
+ temp[ZZ] = xij[ZZ] + a*xjk[ZZ];
+ /* 6 flops */
+
+ c = b*gmx_invsqrt(iprod(temp, temp));
+ /* 6 + 10 flops */
+
+ x[XX] = xi[XX] + c*temp[XX];
+ x[YY] = xi[YY] + c*temp[YY];
+ x[ZZ] = xi[ZZ] + c*temp[ZZ];
+ /* 6 Flops */
+
+ /* TOTAL: 34 flops */
}
-static void constr_vsite3FAD(rvec xi,rvec xj,rvec xk,rvec x,real a,real b, t_pbc *pbc)
+static void constr_vsite3FAD(rvec xi, rvec xj, rvec xk, rvec x, real a, real b, t_pbc *pbc)
{
- rvec xij,xjk,xp;
- real a1,b1,c1,invdij;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xj,xjk);
- /* 6 flops */
-
- invdij = gmx_invsqrt(iprod(xij,xij));
- c1 = invdij * invdij * iprod(xij,xjk);
- xp[XX] = xjk[XX] - c1*xij[XX];
- xp[YY] = xjk[YY] - c1*xij[YY];
- xp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
- a1 = a*invdij;
- b1 = b*gmx_invsqrt(iprod(xp,xp));
- /* 45 */
-
- x[XX] = xi[XX] + a1*xij[XX] + b1*xp[XX];
- x[YY] = xi[YY] + a1*xij[YY] + b1*xp[YY];
- x[ZZ] = xi[ZZ] + a1*xij[ZZ] + b1*xp[ZZ];
- /* 12 Flops */
-
- /* TOTAL: 63 flops */
+ rvec xij, xjk, xp;
+ real a1, b1, c1, invdij;
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xj, xjk);
+ /* 6 flops */
+
+ invdij = gmx_invsqrt(iprod(xij, xij));
+ c1 = invdij * invdij * iprod(xij, xjk);
+ xp[XX] = xjk[XX] - c1*xij[XX];
+ xp[YY] = xjk[YY] - c1*xij[YY];
+ xp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
+ a1 = a*invdij;
+ b1 = b*gmx_invsqrt(iprod(xp, xp));
+ /* 45 */
+
+ x[XX] = xi[XX] + a1*xij[XX] + b1*xp[XX];
+ x[YY] = xi[YY] + a1*xij[YY] + b1*xp[YY];
+ x[ZZ] = xi[ZZ] + a1*xij[ZZ] + b1*xp[ZZ];
+ /* 12 Flops */
+
+ /* TOTAL: 63 flops */
}
-static void constr_vsite3OUT(rvec xi,rvec xj,rvec xk,rvec x,
- real a,real b,real c,t_pbc *pbc)
+static void constr_vsite3OUT(rvec xi, rvec xj, rvec xk, rvec x,
+ real a, real b, real c, t_pbc *pbc)
{
- rvec xij,xik,temp;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xi,xik);
- cprod(xij,xik,temp);
- /* 15 Flops */
-
- x[XX] = xi[XX] + a*xij[XX] + b*xik[XX] + c*temp[XX];
- x[YY] = xi[YY] + a*xij[YY] + b*xik[YY] + c*temp[YY];
- x[ZZ] = xi[ZZ] + a*xij[ZZ] + b*xik[ZZ] + c*temp[ZZ];
- /* 18 Flops */
-
- /* TOTAL: 33 flops */
+ rvec xij, xik, temp;
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xi, xik);
+ cprod(xij, xik, temp);
+ /* 15 Flops */
+
+ x[XX] = xi[XX] + a*xij[XX] + b*xik[XX] + c*temp[XX];
+ x[YY] = xi[YY] + a*xij[YY] + b*xik[YY] + c*temp[YY];
+ x[ZZ] = xi[ZZ] + a*xij[ZZ] + b*xik[ZZ] + c*temp[ZZ];
+ /* 18 Flops */
+
+ /* TOTAL: 33 flops */
}
-static void constr_vsite4FD(rvec xi,rvec xj,rvec xk,rvec xl,rvec x,
- real a,real b,real c,t_pbc *pbc)
+static void constr_vsite4FD(rvec xi, rvec xj, rvec xk, rvec xl, rvec x,
+ real a, real b, real c, t_pbc *pbc)
{
- rvec xij,xjk,xjl,temp;
- real d;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xj,xjk);
- pbc_rvec_sub(pbc,xl,xj,xjl);
- /* 9 flops */
-
- /* temp goes from i to a point on the plane jkl */
- temp[XX] = xij[XX] + a*xjk[XX] + b*xjl[XX];
- temp[YY] = xij[YY] + a*xjk[YY] + b*xjl[YY];
- temp[ZZ] = xij[ZZ] + a*xjk[ZZ] + b*xjl[ZZ];
- /* 12 flops */
-
- d=c*gmx_invsqrt(iprod(temp,temp));
- /* 6 + 10 flops */
-
- x[XX] = xi[XX] + d*temp[XX];
- x[YY] = xi[YY] + d*temp[YY];
- x[ZZ] = xi[ZZ] + d*temp[ZZ];
- /* 6 Flops */
-
- /* TOTAL: 43 flops */
+ rvec xij, xjk, xjl, temp;
+ real d;
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xj, xjk);
+ pbc_rvec_sub(pbc, xl, xj, xjl);
+ /* 9 flops */
+
+ /* temp goes from i to a point on the plane jkl */
+ temp[XX] = xij[XX] + a*xjk[XX] + b*xjl[XX];
+ temp[YY] = xij[YY] + a*xjk[YY] + b*xjl[YY];
+ temp[ZZ] = xij[ZZ] + a*xjk[ZZ] + b*xjl[ZZ];
+ /* 12 flops */
+
+ d = c*gmx_invsqrt(iprod(temp, temp));
+ /* 6 + 10 flops */
+
+ x[XX] = xi[XX] + d*temp[XX];
+ x[YY] = xi[YY] + d*temp[YY];
+ x[ZZ] = xi[ZZ] + d*temp[ZZ];
+ /* 6 Flops */
+
+ /* TOTAL: 43 flops */
}
-static void constr_vsite4FDN(rvec xi,rvec xj,rvec xk,rvec xl,rvec x,
- real a,real b,real c,t_pbc *pbc)
+static void constr_vsite4FDN(rvec xi, rvec xj, rvec xk, rvec xl, rvec x,
+ real a, real b, real c, t_pbc *pbc)
{
- rvec xij,xik,xil,ra,rb,rja,rjb,rm;
+ rvec xij, xik, xil, ra, rb, rja, rjb, rm;
real d;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xi,xik);
- pbc_rvec_sub(pbc,xl,xi,xil);
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xi, xik);
+ pbc_rvec_sub(pbc, xl, xi, xil);
/* 9 flops */
ra[XX] = a*xik[XX];
ra[YY] = a*xik[YY];
ra[ZZ] = a*xik[ZZ];
-
+
rb[XX] = b*xil[XX];
rb[YY] = b*xil[YY];
rb[ZZ] = b*xil[ZZ];
/* 6 flops */
- rvec_sub(ra,xij,rja);
- rvec_sub(rb,xij,rjb);
+ rvec_sub(ra, xij, rja);
+ rvec_sub(rb, xij, rjb);
/* 6 flops */
-
- cprod(rja,rjb,rm);
+
+ cprod(rja, rjb, rm);
/* 9 flops */
-
- d=c*gmx_invsqrt(norm2(rm));
+
+ d = c*gmx_invsqrt(norm2(rm));
/* 5+5+1 flops */
-
+
x[XX] = xi[XX] + d*rm[XX];
x[YY] = xi[YY] + d*rm[YY];
x[ZZ] = xi[ZZ] + d*rm[ZZ];
/* 6 Flops */
-
+
/* TOTAL: 47 flops */
}
static int constr_vsiten(t_iatom *ia, t_iparams ip[],
- rvec *x, t_pbc *pbc)
+ rvec *x, t_pbc *pbc)
{
- rvec xs,x1,dx;
- dvec dsum;
- int n3,av,ai,i;
- real a;
-
- n3 = 3*ip[ia[0]].vsiten.n;
- av = ia[1];
- ai = ia[2];
- copy_rvec(x[ai],x1);
- clear_dvec(dsum);
- for(i=3; i<n3; i+=3) {
- ai = ia[i+2];
- a = ip[ia[i]].vsiten.a;
- if (pbc) {
- pbc_dx_aiuc(pbc,x[ai],x1,dx);
- } else {
- rvec_sub(x[ai],x1,dx);
- }
- dsum[XX] += a*dx[XX];
- dsum[YY] += a*dx[YY];
- dsum[ZZ] += a*dx[ZZ];
- /* 9 Flops */
- }
+ rvec xs, x1, dx;
+ dvec dsum;
+ int n3, av, ai, i;
+ real a;
+
+ n3 = 3*ip[ia[0]].vsiten.n;
+ av = ia[1];
+ ai = ia[2];
+ copy_rvec(x[ai], x1);
+ clear_dvec(dsum);
+ for (i = 3; i < n3; i += 3)
+ {
+ ai = ia[i+2];
+ a = ip[ia[i]].vsiten.a;
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, x[ai], x1, dx);
+ }
+ else
+ {
+ rvec_sub(x[ai], x1, dx);
+ }
+ dsum[XX] += a*dx[XX];
+ dsum[YY] += a*dx[YY];
+ dsum[ZZ] += a*dx[ZZ];
+ /* 9 Flops */
+ }
- x[av][XX] = x1[XX] + dsum[XX];
- x[av][YY] = x1[YY] + dsum[YY];
- x[av][ZZ] = x1[ZZ] + dsum[ZZ];
+ x[av][XX] = x1[XX] + dsum[XX];
+ x[av][YY] = x1[YY] + dsum[YY];
+ x[av][ZZ] = x1[ZZ] + dsum[ZZ];
- return n3;
+ return n3;
}
-void construct_vsites(FILE *log,gmx_vsite_t *vsite,
- rvec x[],t_nrnb *nrnb,
- real dt,rvec *v,
- t_iparams ip[],t_ilist ilist[],
- int ePBC,gmx_bool bMolPBC,t_graph *graph,
- t_commrec *cr,matrix box)
+void construct_vsites_thread(gmx_vsite_t *vsite,
+ rvec x[], t_nrnb *nrnb,
+ real dt, rvec *v,
+ t_iparams ip[], t_ilist ilist[],
+ t_pbc *pbc_null)
{
- rvec xpbc,xv,vv,dx;
- real a1,b1,c1,inv_dt;
- int i,inc,ii,nra,nr,tp,ftype;
- t_iatom avsite,ai,aj,ak,al,pbc_atom;
- t_iatom *ia;
- t_pbc pbc,*pbc_null,*pbc_null2;
- gmx_bool bDomDec;
- int *vsite_pbc,ishift;
- rvec reftmp,vtmp,rtmp;
-
- bDomDec = cr && DOMAINDECOMP(cr);
-
- /* We only need to do pbc when we have inter-cg vsites */
- if (ePBC != epbcNONE && (bDomDec || bMolPBC) && vsite->n_intercg_vsite) {
- /* This is wasting some CPU time as we now do this multiple times
- * per MD step. But how often do we have vsites with full pbc?
- */
- pbc_null = set_pbc_dd(&pbc,ePBC,cr!=NULL ? cr->dd : NULL,FALSE,box);
- } else {
- pbc_null = NULL;
- }
-
- if (cr) {
- if (bDomDec) {
- dd_move_x_vsites(cr->dd,box,x);
- } else if (vsite->bPDvsitecomm) {
- /* I'm not sure whether the periodicity and shift are guaranteed
- * to be consistent between different nodes when running e.g. polymers
- * in parallel. In this special case we thus unshift/shift,
- * but only when necessary. This is to make sure the coordinates
- * we move don't end up a box away...
- */
- if (graph)
- unshift_self(graph,box,x);
-
- move_construct_x(vsite->vsitecomm,x,cr);
-
- if (graph)
- shift_self(graph,box,x);
- }
- }
-
- if (v) {
- inv_dt = 1.0/dt;
- } else {
- inv_dt = 1.0;
- }
-
- pbc_null2 = NULL;
- for(ftype=0; (ftype<F_NRE); ftype++) {
- if (interaction_function[ftype].flags & IF_VSITE) {
- nra = interaction_function[ftype].nratoms;
- nr = ilist[ftype].nr;
- ia = ilist[ftype].iatoms;
-
- if (pbc_null) {
- vsite_pbc = vsite->vsite_pbc_loc[ftype-F_VSITE2];
- } else {
- vsite_pbc = NULL;
- }
-
- for(i=0; (i<nr); ) {
- tp = ia[0];
- /*
- if (ftype != idef->functype[tp])
- gmx_incons("Function types for vsites wrong");
- */
-
- /* The vsite and constructing atoms */
- avsite = ia[1];
- ai = ia[2];
-
- /* Constants for constructing vsites */
- a1 = ip[tp].vsite.a;
- /* Check what kind of pbc we need to use */
- if (vsite_pbc) {
- pbc_atom = vsite_pbc[i/(1+nra)];
- if (pbc_atom > -2) {
- if (pbc_atom >= 0) {
- /* We need to copy the coordinates here,
- * single for single atom cg's pbc_atom is the vsite itself.
- */
- copy_rvec(x[pbc_atom],xpbc);
- }
- pbc_null2 = pbc_null;
- } else {
- pbc_null2 = NULL;
- }
- } else {
- pbc_atom = -2;
- }
- /* Copy the old position */
- copy_rvec(x[avsite],xv);
-
- /* Construct the vsite depending on type */
- inc = nra+1;
- switch (ftype) {
- case F_VSITE2:
- aj = ia[3];
- constr_vsite2(x[ai],x[aj],x[avsite],a1,pbc_null2);
- break;
- case F_VSITE3:
- aj = ia[3];
- ak = ia[4];
- b1 = ip[tp].vsite.b;
- constr_vsite3(x[ai],x[aj],x[ak],x[avsite],a1,b1,pbc_null2);
- break;
- case F_VSITE3FD:
- aj = ia[3];
- ak = ia[4];
- b1 = ip[tp].vsite.b;
- constr_vsite3FD(x[ai],x[aj],x[ak],x[avsite],a1,b1,pbc_null2);
- break;
- case F_VSITE3FAD:
- aj = ia[3];
- ak = ia[4];
- b1 = ip[tp].vsite.b;
- constr_vsite3FAD(x[ai],x[aj],x[ak],x[avsite],a1,b1,pbc_null2);
- break;
- case F_VSITE3OUT:
- aj = ia[3];
- ak = ia[4];
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- constr_vsite3OUT(x[ai],x[aj],x[ak],x[avsite],a1,b1,c1,pbc_null2);
- break;
- case F_VSITE4FD:
- aj = ia[3];
- ak = ia[4];
- al = ia[5];
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- constr_vsite4FD(x[ai],x[aj],x[ak],x[al],x[avsite],a1,b1,c1,
- pbc_null2);
- break;
- case F_VSITE4FDN:
- aj = ia[3];
- ak = ia[4];
- al = ia[5];
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- constr_vsite4FDN(x[ai],x[aj],x[ak],x[al],x[avsite],a1,b1,c1,
- pbc_null2);
- break;
- case F_VSITEN:
- inc = constr_vsiten(ia,ip,x,pbc_null2);
- break;
- default:
- gmx_fatal(FARGS,"No such vsite type %d in %s, line %d",
- ftype,__FILE__,__LINE__);
- }
-
- if (pbc_atom >= 0) {
- /* Match the pbc of this vsite to the rest of its charge group */
- ishift = pbc_dx_aiuc(pbc_null,x[avsite],xpbc,dx);
- if (ishift != CENTRAL)
- rvec_add(xpbc,dx,x[avsite]);
- }
- if (v) {
- /* Calculate velocity of vsite... */
- rvec_sub(x[avsite],xv,vv);
- svmul(inv_dt,vv,v[avsite]);
- }
-
- /* Increment loop variables */
- i += inc;
- ia += inc;
- }
- }
- }
-}
+ gmx_bool bPBCAll;
+ rvec xpbc, xv, vv, dx;
+ real a1, b1, c1, inv_dt;
+ int i, inc, ii, nra, nr, tp, ftype;
+ t_iatom avsite, ai, aj, ak, al, pbc_atom;
+ t_iatom *ia;
+ t_pbc *pbc_null2;
+ int *vsite_pbc, ishift;
+ rvec reftmp, vtmp, rtmp;
+
+ if (v != NULL)
+ {
+ inv_dt = 1.0/dt;
+ }
+ else
+ {
+ inv_dt = 1.0;
+ }
-static void spread_vsite2(t_iatom ia[],real a,
- rvec x[],rvec f[],rvec fshift[],
- t_pbc *pbc,t_graph *g)
-{
- rvec fi,fj,dx;
- t_iatom av,ai,aj;
- ivec di;
- real b;
- int siv,sij;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
-
- svmul(1-a,f[av],fi);
- svmul( a,f[av],fj);
- /* 7 flop */
-
- rvec_inc(f[ai],fi);
- rvec_inc(f[aj],fj);
- /* 6 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,av),di);
- siv = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),di);
- sij = IVEC2IS(di);
- } else if (pbc) {
- siv = pbc_dx_aiuc(pbc,x[ai],x[av],dx);
- sij = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
- } else {
- siv = CENTRAL;
- sij = CENTRAL;
- }
-
- if (fshift && (siv != CENTRAL || sij != CENTRAL)) {
- rvec_inc(fshift[siv],f[av]);
- rvec_dec(fshift[CENTRAL],fi);
- rvec_dec(fshift[sij],fj);
- }
-
- /* TOTAL: 13 flops */
-}
+ bPBCAll = (pbc_null != NULL && !vsite->bHaveChargeGroups);
-void construct_vsites_mtop(FILE *log,gmx_vsite_t *vsite,
- gmx_mtop_t *mtop,rvec x[])
-{
- int as,mb,mol;
- gmx_molblock_t *molb;
- gmx_moltype_t *molt;
-
- as = 0;
- for(mb=0; mb<mtop->nmolblock; mb++) {
- molb = &mtop->molblock[mb];
- molt = &mtop->moltype[molb->type];
- for(mol=0; mol<molb->nmol; mol++) {
- construct_vsites(log,vsite,x+as,NULL,0.0,NULL,
- mtop->ffparams.iparams,molt->ilist,
- epbcNONE,TRUE,NULL,NULL,NULL);
- as += molt->atoms.nr;
- }
- }
-}
+ pbc_null2 = NULL;
+ vsite_pbc = NULL;
+ for (ftype = 0; (ftype < F_NRE); ftype++)
+ {
+ if ((interaction_function[ftype].flags & IF_VSITE) &&
+ ilist[ftype].nr > 0)
+ {
+ nra = interaction_function[ftype].nratoms;
+ inc = 1 + nra;
+ nr = ilist[ftype].nr;
+ ia = ilist[ftype].iatoms;
-static void spread_vsite3(t_iatom ia[],real a,real b,
- rvec x[],rvec f[],rvec fshift[],
- t_pbc *pbc,t_graph *g)
-{
- rvec fi,fj,fk,dx;
- atom_id av,ai,aj,ak;
- ivec di;
- int siv,sij,sik;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
-
- svmul(1-a-b,f[av],fi);
- svmul( a,f[av],fj);
- svmul( b,f[av],fk);
- /* 11 flops */
-
- rvec_inc(f[ai],fi);
- rvec_inc(f[aj],fj);
- rvec_inc(f[ak],fk);
- /* 9 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,ia[1]),di);
- siv = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),di);
- sij = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,ak),di);
- sik = IVEC2IS(di);
- } else if (pbc) {
- siv = pbc_dx_aiuc(pbc,x[ai],x[av],dx);
- sij = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
- sik = pbc_dx_aiuc(pbc,x[ai],x[ak],dx);
- } else {
- siv = CENTRAL;
- sij = CENTRAL;
- sik = CENTRAL;
- }
-
- if (fshift && (siv!=CENTRAL || sij!=CENTRAL || sik!=CENTRAL)) {
- rvec_inc(fshift[siv],f[av]);
- rvec_dec(fshift[CENTRAL],fi);
- rvec_dec(fshift[sij],fj);
- rvec_dec(fshift[sik],fk);
- }
-
- /* TOTAL: 20 flops */
+ if (bPBCAll)
+ {
+ pbc_null2 = pbc_null;
+ }
+ else if (pbc_null != NULL)
+ {
+ vsite_pbc = vsite->vsite_pbc_loc[ftype-F_VSITE2];
+ }
+
+ for (i = 0; i < nr; )
+ {
+ tp = ia[0];
+
+ /* The vsite and constructing atoms */
+ avsite = ia[1];
+ ai = ia[2];
- aj = ia[3];
+
+ /* Constants for constructing vsites */
+ a1 = ip[tp].vsite.a;
+ /* Check what kind of pbc we need to use */
+ if (bPBCAll)
+ {
+ /* No charge groups, vsite follows its own pbc */
+ pbc_atom = avsite;
+ copy_rvec(x[avsite], xpbc);
+ }
+ else if (vsite_pbc != NULL)
+ {
+ pbc_atom = vsite_pbc[i/(1+nra)];
+ if (pbc_atom > -2)
+ {
+ if (pbc_atom >= 0)
+ {
+ /* We need to copy the coordinates here,
+ * single for single atom cg's pbc_atom
+ * is the vsite itself.
+ */
+ copy_rvec(x[pbc_atom], xpbc);
+ }
+ pbc_null2 = pbc_null;
+ }
+ else
+ {
+ pbc_null2 = NULL;
+ }
+ }
+ else
+ {
+ pbc_atom = -2;
+ }
+ /* Copy the old position */
+ copy_rvec(x[avsite], xv);
+
+ /* Construct the vsite depending on type */
+ switch (ftype)
+ {
+ case F_VSITE2:
++ aj = ia[3];
+ constr_vsite2(x[ai], x[aj], x[avsite], a1, pbc_null2);
+ break;
+ case F_VSITE3:
++ aj = ia[3];
+ ak = ia[4];
+ b1 = ip[tp].vsite.b;
+ constr_vsite3(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ break;
+ case F_VSITE3FD:
++ aj = ia[3];
+ ak = ia[4];
+ b1 = ip[tp].vsite.b;
+ constr_vsite3FD(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ break;
+ case F_VSITE3FAD:
++ aj = ia[3];
+ ak = ia[4];
+ b1 = ip[tp].vsite.b;
+ constr_vsite3FAD(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ break;
+ case F_VSITE3OUT:
++ aj = ia[3];
+ ak = ia[4];
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ constr_vsite3OUT(x[ai], x[aj], x[ak], x[avsite], a1, b1, c1, pbc_null2);
+ break;
+ case F_VSITE4FD:
++ aj = ia[3];
+ ak = ia[4];
+ al = ia[5];
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ constr_vsite4FD(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1,
+ pbc_null2);
+ break;
+ case F_VSITE4FDN:
++ aj = ia[3];
+ ak = ia[4];
+ al = ia[5];
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ constr_vsite4FDN(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1,
+ pbc_null2);
+ break;
+ case F_VSITEN:
+ inc = constr_vsiten(ia, ip, x, pbc_null2);
+ break;
+ default:
+ gmx_fatal(FARGS, "No such vsite type %d in %s, line %d",
+ ftype, __FILE__, __LINE__);
+ }
+
+ if (pbc_atom >= 0)
+ {
+ /* Match the pbc of this vsite to the rest of its charge group */
+ ishift = pbc_dx_aiuc(pbc_null, x[avsite], xpbc, dx);
+ if (ishift != CENTRAL)
+ {
+ rvec_add(xpbc, dx, x[avsite]);
+ }
+ }
+ if (v != NULL)
+ {
+ /* Calculate velocity of vsite... */
+ rvec_sub(x[avsite], xv, vv);
+ svmul(inv_dt, vv, v[avsite]);
+ }
+
+ /* Increment loop variables */
+ i += inc;
+ ia += inc;
+ }
+ }
+ }
}
-static void spread_vsite3FD(t_iatom ia[],real a,real b,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+void construct_vsites(FILE *log, gmx_vsite_t *vsite,
+ rvec x[], t_nrnb *nrnb,
+ real dt, rvec *v,
+ t_iparams ip[], t_ilist ilist[],
+ int ePBC, gmx_bool bMolPBC, t_graph *graph,
+ t_commrec *cr, matrix box)
{
- real fx,fy,fz,c,invl,fproj,a1;
- rvec xvi,xij,xjk,xix,fv,temp;
- t_iatom av,ai,aj,ak;
- int svi,sji,skj,d;
- ivec di;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
- copy_rvec(f[av],fv);
-
- sji = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- skj = pbc_rvec_sub(pbc,x[ak],x[aj],xjk);
- /* 6 flops */
-
- /* xix goes from i to point x on the line jk */
- xix[XX]=xij[XX]+a*xjk[XX];
- xix[YY]=xij[YY]+a*xjk[YY];
- xix[ZZ]=xij[ZZ]+a*xjk[ZZ];
- /* 6 flops */
-
- invl=gmx_invsqrt(iprod(xix,xix));
- c=b*invl;
- /* 4 + ?10? flops */
-
- fproj=iprod(xix,fv)*invl*invl; /* = (xix . f)/(xix . xix) */
-
- temp[XX]=c*(fv[XX]-fproj*xix[XX]);
- temp[YY]=c*(fv[YY]-fproj*xix[YY]);
- temp[ZZ]=c*(fv[ZZ]-fproj*xix[ZZ]);
- /* 16 */
-
- /* c is already calculated in constr_vsite3FD
- storing c somewhere will save 26 flops! */
-
- a1=1-a;
- f[ai][XX] += fv[XX] - temp[XX];
- f[ai][YY] += fv[YY] - temp[YY];
- f[ai][ZZ] += fv[ZZ] - temp[ZZ];
- f[aj][XX] += a1*temp[XX];
- f[aj][YY] += a1*temp[YY];
- f[aj][ZZ] += a1*temp[ZZ];
- f[ak][XX] += a*temp[XX];
- f[ak][YY] += a*temp[YY];
- f[ak][ZZ] += a*temp[ZZ];
- /* 19 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ia[1]),SHIFT_IVEC(g,ai),di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,aj),di);
- skj = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
- svi = CENTRAL;
- }
-
- if (fshift && (svi!=CENTRAL || sji!=CENTRAL || skj!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
- fshift[CENTRAL][XX] += fv[XX] - (1 + a)*temp[XX];
- fshift[CENTRAL][YY] += fv[YY] - (1 + a)*temp[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - (1 + a)*temp[ZZ];
- fshift[ sji][XX] += temp[XX];
- fshift[ sji][YY] += temp[YY];
- fshift[ sji][ZZ] += temp[ZZ];
- fshift[ skj][XX] += a*temp[XX];
- fshift[ skj][YY] += a*temp[YY];
- fshift[ skj][ZZ] += a*temp[ZZ];
- }
+ t_pbc pbc, *pbc_null;
+ gmx_bool bDomDec;
+ int nthreads;
- if (VirCorr)
+ bDomDec = cr && DOMAINDECOMP(cr);
+
+ /* We only need to do pbc when we have inter-cg vsites */
+ if (ePBC != epbcNONE && (bDomDec || bMolPBC) && vsite->n_intercg_vsite)
{
- /* When VirCorr=TRUE, the virial for the current forces is not
- * calculated from the redistributed forces. This means that
- * the effect of non-linear virtual site constructions on the virial
- * needs to be added separately. This contribution can be calculated
- * in many ways, but the simplest and cheapest way is to use
- * the first constructing atom ai as a reference position in space:
- * subtract (xv-xi)*fv and add (xj-xi)*fj + (xk-xi)*fk.
+ /* This is wasting some CPU time as we now do this multiple times
+ * per MD step. But how often do we have vsites with full pbc?
*/
- rvec xiv;
- int i,j;
-
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ pbc_null = set_pbc_dd(&pbc, ePBC, cr != NULL ? cr->dd : NULL, FALSE, box);
+ }
+ else
+ {
+ pbc_null = NULL;
+ }
- for(i=0; i<DIM; i++)
+ if (cr)
+ {
+ if (bDomDec)
+ {
+ dd_move_x_vsites(cr->dd, box, x);
+ }
+ else if (vsite->bPDvsitecomm)
{
- for(j=0; j<DIM; j++)
+ /* I'm not sure whether the periodicity and shift are guaranteed
+ * to be consistent between different nodes when running e.g. polymers
+ * in parallel. In this special case we thus unshift/shift,
+ * but only when necessary. This is to make sure the coordinates
+ * we move don't end up a box away...
+ */
+ if (graph != NULL)
{
- /* As xix is a linear combination of j and k, use that here */
- dxdf[i][j] += -xiv[i]*fv[j] + xix[i]*temp[j];
+ unshift_self(graph, box, x);
+ }
+
+ move_construct_x(vsite->vsitecomm, x, cr);
+
+ if (graph != NULL)
+ {
+ shift_self(graph, box, x);
}
}
}
- /* TOTAL: 61 flops */
+ if (vsite->nthreads == 1)
+ {
+ construct_vsites_thread(vsite,
+ x, nrnb, dt, v,
+ ip, ilist,
+ pbc_null);
+ }
+ else
+ {
+#pragma omp parallel num_threads(vsite->nthreads)
+ {
+ construct_vsites_thread(vsite,
+ x, nrnb, dt, v,
+ ip, vsite->tdata[gmx_omp_get_thread_num()].ilist,
+ pbc_null);
+ }
+ /* Now we can construct the vsites that might depend on other vsites */
+ construct_vsites_thread(vsite,
+ x, nrnb, dt, v,
+ ip, vsite->tdata[vsite->nthreads].ilist,
+ pbc_null);
+ }
}
-static void spread_vsite3FAD(t_iatom ia[],real a,real b,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+static void spread_vsite2(t_iatom ia[], real a,
+ rvec x[], rvec f[], rvec fshift[],
+ t_pbc *pbc, t_graph *g)
{
- rvec xvi,xij,xjk,xperp,Fpij,Fppp,fv,f1,f2,f3;
- real a1,b1,c1,c2,invdij,invdij2,invdp,fproj;
- t_iatom av,ai,aj,ak;
- int svi,sji,skj,d;
- ivec di;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
- copy_rvec(f[ia[1]],fv);
-
- sji = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- skj = pbc_rvec_sub(pbc,x[ak],x[aj],xjk);
- /* 6 flops */
-
- invdij = gmx_invsqrt(iprod(xij,xij));
- invdij2 = invdij * invdij;
- c1 = iprod(xij,xjk) * invdij2;
- xperp[XX] = xjk[XX] - c1*xij[XX];
- xperp[YY] = xjk[YY] - c1*xij[YY];
- xperp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
- /* xperp in plane ijk, perp. to ij */
- invdp = gmx_invsqrt(iprod(xperp,xperp));
- a1 = a*invdij;
- b1 = b*invdp;
- /* 45 flops */
-
- /* a1, b1 and c1 are already calculated in constr_vsite3FAD
- storing them somewhere will save 45 flops! */
-
- fproj=iprod(xij ,fv)*invdij2;
- svmul(fproj, xij, Fpij); /* proj. f on xij */
- svmul(iprod(xperp,fv)*invdp*invdp,xperp,Fppp); /* proj. f on xperp */
- svmul(b1*fproj, xperp,f3);
- /* 23 flops */
-
- rvec_sub(fv,Fpij,f1); /* f1 = f - Fpij */
- rvec_sub(f1,Fppp,f2); /* f2 = f - Fpij - Fppp */
- for (d=0; (d<DIM); d++) {
- f1[d]*=a1;
- f2[d]*=b1;
- }
- /* 12 flops */
-
- c2=1+c1;
- f[ai][XX] += fv[XX] - f1[XX] + c1*f2[XX] + f3[XX];
- f[ai][YY] += fv[YY] - f1[YY] + c1*f2[YY] + f3[YY];
- f[ai][ZZ] += fv[ZZ] - f1[ZZ] + c1*f2[ZZ] + f3[ZZ];
- f[aj][XX] += f1[XX] - c2*f2[XX] - f3[XX];
- f[aj][YY] += f1[YY] - c2*f2[YY] - f3[YY];
- f[aj][ZZ] += f1[ZZ] - c2*f2[ZZ] - f3[ZZ];
- f[ak][XX] += f2[XX];
- f[ak][YY] += f2[YY];
- f[ak][ZZ] += f2[ZZ];
- /* 30 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ia[1]),SHIFT_IVEC(g,ai),di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,aj),di);
- skj = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
- svi = CENTRAL;
- }
-
- if (fshift && (svi!=CENTRAL || sji!=CENTRAL || skj!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
- fshift[CENTRAL][XX] += fv[XX] - f1[XX] - (1-c1)*f2[XX] + f3[XX];
- fshift[CENTRAL][YY] += fv[YY] - f1[YY] - (1-c1)*f2[YY] + f3[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - f1[ZZ] - (1-c1)*f2[ZZ] + f3[ZZ];
- fshift[ sji][XX] += f1[XX] - c1 *f2[XX] - f3[XX];
- fshift[ sji][YY] += f1[YY] - c1 *f2[YY] - f3[YY];
- fshift[ sji][ZZ] += f1[ZZ] - c1 *f2[ZZ] - f3[ZZ];
- fshift[ skj][XX] += f2[XX];
- fshift[ skj][YY] += f2[YY];
- fshift[ skj][ZZ] += f2[ZZ];
- }
+ rvec fi, fj, dx;
+ t_iatom av, ai, aj;
+ ivec di;
+ real b;
+ int siv, sij;
- if (VirCorr)
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+
+ svmul(1-a, f[av], fi);
+ svmul( a, f[av], fj);
+ /* 7 flop */
+
+ rvec_inc(f[ai], fi);
+ rvec_inc(f[aj], fj);
+ /* 6 Flops */
+
+ if (g)
{
- rvec xiv;
- int i,j;
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, av), di);
+ siv = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), di);
+ sij = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ siv = pbc_dx_aiuc(pbc, x[ai], x[av], dx);
+ sij = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
+ }
+ else
+ {
+ siv = CENTRAL;
+ sij = CENTRAL;
+ }
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ if (fshift && (siv != CENTRAL || sij != CENTRAL))
+ {
+ rvec_inc(fshift[siv], f[av]);
+ rvec_dec(fshift[CENTRAL], fi);
+ rvec_dec(fshift[sij], fj);
+ }
+
+ /* TOTAL: 13 flops */
+}
- for(i=0; i<DIM; i++)
+void construct_vsites_mtop(FILE *log, gmx_vsite_t *vsite,
+ gmx_mtop_t *mtop, rvec x[])
+{
+ int as, mb, mol;
+ gmx_molblock_t *molb;
+ gmx_moltype_t *molt;
+
+ as = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ molt = &mtop->moltype[molb->type];
+ for (mol = 0; mol < molb->nmol; mol++)
{
- for(j=0; j<DIM; j++)
- {
- /* Note that xik=xij+xjk, so we have to add xij*f2 */
- dxdf[i][j] +=
- - xiv[i]*fv[j]
- + xij[i]*(f1[j] + (1 - c2)*f2[j] - f3[j])
- + xjk[i]*f2[j];
- }
+ construct_vsites(log, vsite, x+as, NULL, 0.0, NULL,
+ mtop->ffparams.iparams, molt->ilist,
+ epbcNONE, TRUE, NULL, NULL, NULL);
+ as += molt->atoms.nr;
}
}
-
- /* TOTAL: 113 flops */
}
-static void spread_vsite3OUT(t_iatom ia[],real a,real b,real c,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+static void spread_vsite3(t_iatom ia[], real a, real b,
+ rvec x[], rvec f[], rvec fshift[],
+ t_pbc *pbc, t_graph *g)
{
- rvec xvi,xij,xik,fv,fj,fk;
- real cfx,cfy,cfz;
- atom_id av,ai,aj,ak;
- ivec di;
- int svi,sji,ski;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
-
- sji = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- ski = pbc_rvec_sub(pbc,x[ak],x[ai],xik);
- /* 6 Flops */
-
- copy_rvec(f[av],fv);
-
- cfx = c*fv[XX];
- cfy = c*fv[YY];
- cfz = c*fv[ZZ];
- /* 3 Flops */
-
- fj[XX] = a*fv[XX] - xik[ZZ]*cfy + xik[YY]*cfz;
- fj[YY] = xik[ZZ]*cfx + a*fv[YY] - xik[XX]*cfz;
- fj[ZZ] = -xik[YY]*cfx + xik[XX]*cfy + a*fv[ZZ];
-
- fk[XX] = b*fv[XX] + xij[ZZ]*cfy - xij[YY]*cfz;
- fk[YY] = -xij[ZZ]*cfx + b*fv[YY] + xij[XX]*cfz;
- fk[ZZ] = xij[YY]*cfx - xij[XX]*cfy + b*fv[ZZ];
- /* 30 Flops */
-
- f[ai][XX] += fv[XX] - fj[XX] - fk[XX];
- f[ai][YY] += fv[YY] - fj[YY] - fk[YY];
- f[ai][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
- rvec_inc(f[aj],fj);
- rvec_inc(f[ak],fk);
- /* 15 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ia[1]),SHIFT_IVEC(g,ai),di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,ai),di);
- ski = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
- svi = CENTRAL;
- }
-
- if (fshift && (svi!=CENTRAL || sji!=CENTRAL || ski!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
- fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX];
- fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
- rvec_inc(fshift[sji],fj);
- rvec_inc(fshift[ski],fk);
- }
+ rvec fi, fj, fk, dx;
+ atom_id av, ai, aj, ak;
+ ivec di;
+ int siv, sij, sik;
- if (VirCorr)
- {
- rvec xiv;
- int i,j;
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ svmul(1-a-b, f[av], fi);
+ svmul( a, f[av], fj);
+ svmul( b, f[av], fk);
+ /* 11 flops */
- for(i=0; i<DIM; i++)
- {
- for(j=0; j<DIM; j++)
- {
- dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j] + xik[i]*fk[j];
- }
- }
+ rvec_inc(f[ai], fi);
+ rvec_inc(f[aj], fj);
+ rvec_inc(f[ak], fk);
+ /* 9 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, ia[1]), di);
+ siv = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), di);
+ sij = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, ak), di);
+ sik = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ siv = pbc_dx_aiuc(pbc, x[ai], x[av], dx);
+ sij = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
+ sik = pbc_dx_aiuc(pbc, x[ai], x[ak], dx);
}
-
- /* TOTAL: 54 flops */
+ else
+ {
+ siv = CENTRAL;
+ sij = CENTRAL;
+ sik = CENTRAL;
+ }
+
+ if (fshift && (siv != CENTRAL || sij != CENTRAL || sik != CENTRAL))
+ {
+ rvec_inc(fshift[siv], f[av]);
+ rvec_dec(fshift[CENTRAL], fi);
+ rvec_dec(fshift[sij], fj);
+ rvec_dec(fshift[sik], fk);
+ }
+
+ /* TOTAL: 20 flops */
}
-static void spread_vsite4FD(t_iatom ia[],real a,real b,real c,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+static void spread_vsite3FD(t_iatom ia[], real a, real b,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
{
- real d,invl,fproj,a1;
- rvec xvi,xij,xjk,xjl,xix,fv,temp;
- atom_id av,ai,aj,ak,al;
- ivec di;
- int svi,sji,skj,slj,m;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
- al = ia[5];
-
- sji = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- skj = pbc_rvec_sub(pbc,x[ak],x[aj],xjk);
- slj = pbc_rvec_sub(pbc,x[al],x[aj],xjl);
- /* 9 flops */
-
- /* xix goes from i to point x on the plane jkl */
- for(m=0; m<DIM; m++)
- xix[m] = xij[m] + a*xjk[m] + b*xjl[m];
- /* 12 flops */
-
- invl=gmx_invsqrt(iprod(xix,xix));
- d=c*invl;
- /* 4 + ?10? flops */
-
- copy_rvec(f[av],fv);
-
- fproj=iprod(xix,fv)*invl*invl; /* = (xix . f)/(xix . xix) */
-
- for(m=0; m<DIM; m++)
- temp[m] = d*(fv[m] - fproj*xix[m]);
- /* 16 */
-
- /* c is already calculated in constr_vsite3FD
- storing c somewhere will save 35 flops! */
-
- a1 = 1 - a - b;
- for(m=0; m<DIM; m++) {
- f[ai][m] += fv[m] - temp[m];
- f[aj][m] += a1*temp[m];
- f[ak][m] += a*temp[m];
- f[al][m] += b*temp[m];
- }
- /* 26 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ia[1]),SHIFT_IVEC(g,ai),di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,aj),di);
- skj = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,al),SHIFT_IVEC(g,aj),di);
- slj = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
- svi = CENTRAL;
- }
-
- if (fshift &&
- (svi!=CENTRAL || sji!=CENTRAL || skj!=CENTRAL || slj!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
- for(m=0; m<DIM; m++) {
- fshift[CENTRAL][m] += fv[m] - (1 + a + b)*temp[m];
- fshift[ sji][m] += temp[m];
- fshift[ skj][m] += a*temp[m];
- fshift[ slj][m] += b*temp[m];
- }
- }
+ real fx, fy, fz, c, invl, fproj, a1;
+ rvec xvi, xij, xjk, xix, fv, temp;
+ t_iatom av, ai, aj, ak;
+ int svi, sji, skj, d;
+ ivec di;
+
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
+ copy_rvec(f[av], fv);
+
+ sji = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ skj = pbc_rvec_sub(pbc, x[ak], x[aj], xjk);
+ /* 6 flops */
+
+ /* xix goes from i to point x on the line jk */
+ xix[XX] = xij[XX]+a*xjk[XX];
+ xix[YY] = xij[YY]+a*xjk[YY];
+ xix[ZZ] = xij[ZZ]+a*xjk[ZZ];
+ /* 6 flops */
+
+ invl = gmx_invsqrt(iprod(xix, xix));
+ c = b*invl;
+ /* 4 + ?10? flops */
+
+ fproj = iprod(xix, fv)*invl*invl; /* = (xix . f)/(xix . xix) */
+
+ temp[XX] = c*(fv[XX]-fproj*xix[XX]);
+ temp[YY] = c*(fv[YY]-fproj*xix[YY]);
+ temp[ZZ] = c*(fv[ZZ]-fproj*xix[ZZ]);
+ /* 16 */
+
+ /* c is already calculated in constr_vsite3FD
+ storing c somewhere will save 26 flops! */
+
+ a1 = 1-a;
+ f[ai][XX] += fv[XX] - temp[XX];
+ f[ai][YY] += fv[YY] - temp[YY];
+ f[ai][ZZ] += fv[ZZ] - temp[ZZ];
+ f[aj][XX] += a1*temp[XX];
+ f[aj][YY] += a1*temp[YY];
+ f[aj][ZZ] += a1*temp[ZZ];
+ f[ak][XX] += a*temp[XX];
+ f[ak][YY] += a*temp[YY];
+ f[ak][ZZ] += a*temp[ZZ];
+ /* 19 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
+ svi = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
+ sji = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, aj), di);
+ skj = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = CENTRAL;
+ }
+
+ if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[CENTRAL][XX] += fv[XX] - (1 + a)*temp[XX];
+ fshift[CENTRAL][YY] += fv[YY] - (1 + a)*temp[YY];
+ fshift[CENTRAL][ZZ] += fv[ZZ] - (1 + a)*temp[ZZ];
+ fshift[ sji][XX] += temp[XX];
+ fshift[ sji][YY] += temp[YY];
+ fshift[ sji][ZZ] += temp[ZZ];
+ fshift[ skj][XX] += a*temp[XX];
+ fshift[ skj][YY] += a*temp[YY];
+ fshift[ skj][ZZ] += a*temp[ZZ];
+ }
if (VirCorr)
{
+ /* When VirCorr=TRUE, the virial for the current forces is not
+ * calculated from the redistributed forces. This means that
+ * the effect of non-linear virtual site constructions on the virial
+ * needs to be added separately. This contribution can be calculated
+ * in many ways, but the simplest and cheapest way is to use
+ * the first constructing atom ai as a reference position in space:
+ * subtract (xv-xi)*fv and add (xj-xi)*fj + (xk-xi)*fk.
+ */
rvec xiv;
- int i,j;
+ int i, j;
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
- for(i=0; i<DIM; i++)
+ for (i = 0; i < DIM; i++)
{
- for(j=0; j<DIM; j++)
+ for (j = 0; j < DIM; j++)
{
+ /* As xix is a linear combination of j and k, use that here */
dxdf[i][j] += -xiv[i]*fv[j] + xix[i]*temp[j];
}
}
}
- /* TOTAL: 77 flops */
+ /* TOTAL: 61 flops */
}
-
-static void spread_vsite4FDN(t_iatom ia[],real a,real b,real c,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+static void spread_vsite3FAD(t_iatom ia[], real a, real b,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
{
- rvec xvi,xij,xik,xil,ra,rb,rja,rjb,rab,rm,rt;
- rvec fv,fj,fk,fl;
- real invrm,denom;
- real cfx,cfy,cfz;
- ivec di;
- int av,ai,aj,ak,al;
- int svi,sij,sik,sil;
+ rvec xvi, xij, xjk, xperp, Fpij, Fppp, fv, f1, f2, f3;
+ real a1, b1, c1, c2, invdij, invdij2, invdp, fproj;
+ t_iatom av, ai, aj, ak;
+ int svi, sji, skj, d;
+ ivec di;
- /* DEBUG: check atom indices */
av = ia[1];
ai = ia[2];
aj = ia[3];
ak = ia[4];
- al = ia[5];
+ copy_rvec(f[ia[1]], fv);
- copy_rvec(f[av],fv);
-
- sij = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- sik = pbc_rvec_sub(pbc,x[ak],x[ai],xik);
- sil = pbc_rvec_sub(pbc,x[al],x[ai],xil);
- /* 9 flops */
-
- ra[XX] = a*xik[XX];
- ra[YY] = a*xik[YY];
- ra[ZZ] = a*xik[ZZ];
-
- rb[XX] = b*xil[XX];
- rb[YY] = b*xil[YY];
- rb[ZZ] = b*xil[ZZ];
-
+ sji = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ skj = pbc_rvec_sub(pbc, x[ak], x[aj], xjk);
/* 6 flops */
-
- rvec_sub(ra,xij,rja);
- rvec_sub(rb,xij,rjb);
- rvec_sub(rb,ra,rab);
- /* 9 flops */
-
- cprod(rja,rjb,rm);
- /* 9 flops */
-
- invrm=gmx_invsqrt(norm2(rm));
- denom=invrm*invrm;
- /* 5+5+2 flops */
-
- cfx = c*invrm*fv[XX];
- cfy = c*invrm*fv[YY];
- cfz = c*invrm*fv[ZZ];
- /* 6 Flops */
-
- cprod(rm,rab,rt);
- /* 9 flops */
+
+ invdij = gmx_invsqrt(iprod(xij, xij));
+ invdij2 = invdij * invdij;
+ c1 = iprod(xij, xjk) * invdij2;
+ xperp[XX] = xjk[XX] - c1*xij[XX];
+ xperp[YY] = xjk[YY] - c1*xij[YY];
+ xperp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
+ /* xperp in plane ijk, perp. to ij */
+ invdp = gmx_invsqrt(iprod(xperp, xperp));
+ a1 = a*invdij;
+ b1 = b*invdp;
+ /* 45 flops */
+
+ /* a1, b1 and c1 are already calculated in constr_vsite3FAD
+ storing them somewhere will save 45 flops! */
+
+ fproj = iprod(xij, fv)*invdij2;
+ svmul(fproj, xij, Fpij); /* proj. f on xij */
+ svmul(iprod(xperp, fv)*invdp*invdp, xperp, Fppp); /* proj. f on xperp */
+ svmul(b1*fproj, xperp, f3);
+ /* 23 flops */
+
+ rvec_sub(fv, Fpij, f1); /* f1 = f - Fpij */
+ rvec_sub(f1, Fppp, f2); /* f2 = f - Fpij - Fppp */
+ for (d = 0; (d < DIM); d++)
+ {
+ f1[d] *= a1;
+ f2[d] *= b1;
+ }
+ /* 12 flops */
+
+ c2 = 1+c1;
+ f[ai][XX] += fv[XX] - f1[XX] + c1*f2[XX] + f3[XX];
+ f[ai][YY] += fv[YY] - f1[YY] + c1*f2[YY] + f3[YY];
+ f[ai][ZZ] += fv[ZZ] - f1[ZZ] + c1*f2[ZZ] + f3[ZZ];
+ f[aj][XX] += f1[XX] - c2*f2[XX] - f3[XX];
+ f[aj][YY] += f1[YY] - c2*f2[YY] - f3[YY];
+ f[aj][ZZ] += f1[ZZ] - c2*f2[ZZ] - f3[ZZ];
+ f[ak][XX] += f2[XX];
+ f[ak][YY] += f2[YY];
+ f[ak][ZZ] += f2[ZZ];
+ /* 30 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
+ svi = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
+ sji = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, aj), di);
+ skj = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = CENTRAL;
+ }
+
+ if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[CENTRAL][XX] += fv[XX] - f1[XX] - (1-c1)*f2[XX] + f3[XX];
+ fshift[CENTRAL][YY] += fv[YY] - f1[YY] - (1-c1)*f2[YY] + f3[YY];
+ fshift[CENTRAL][ZZ] += fv[ZZ] - f1[ZZ] - (1-c1)*f2[ZZ] + f3[ZZ];
+ fshift[ sji][XX] += f1[XX] - c1 *f2[XX] - f3[XX];
+ fshift[ sji][YY] += f1[YY] - c1 *f2[YY] - f3[YY];
+ fshift[ sji][ZZ] += f1[ZZ] - c1 *f2[ZZ] - f3[ZZ];
+ fshift[ skj][XX] += f2[XX];
+ fshift[ skj][YY] += f2[YY];
+ fshift[ skj][ZZ] += f2[ZZ];
+ }
+
+ if (VirCorr)
+ {
+ rvec xiv;
+ int i, j;
+
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
+
+ for (i = 0; i < DIM; i++)
+ {
+ for (j = 0; j < DIM; j++)
+ {
+ /* Note that xik=xij+xjk, so we have to add xij*f2 */
+ dxdf[i][j] +=
+ -xiv[i]*fv[j]
+ + xij[i]*(f1[j] + (1 - c2)*f2[j] - f3[j])
+ + xjk[i]*f2[j];
+ }
+ }
+ }
+
+ /* TOTAL: 113 flops */
+}
+
+static void spread_vsite3OUT(t_iatom ia[], real a, real b, real c,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
+{
+ rvec xvi, xij, xik, fv, fj, fk;
+ real cfx, cfy, cfz;
+ atom_id av, ai, aj, ak;
+ ivec di;
+ int svi, sji, ski;
+
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
+
+ sji = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ ski = pbc_rvec_sub(pbc, x[ak], x[ai], xik);
+ /* 6 Flops */
+
+ copy_rvec(f[av], fv);
+
+ cfx = c*fv[XX];
+ cfy = c*fv[YY];
+ cfz = c*fv[ZZ];
+ /* 3 Flops */
+
+ fj[XX] = a*fv[XX] - xik[ZZ]*cfy + xik[YY]*cfz;
+ fj[YY] = xik[ZZ]*cfx + a*fv[YY] - xik[XX]*cfz;
+ fj[ZZ] = -xik[YY]*cfx + xik[XX]*cfy + a*fv[ZZ];
+
+ fk[XX] = b*fv[XX] + xij[ZZ]*cfy - xij[YY]*cfz;
+ fk[YY] = -xij[ZZ]*cfx + b*fv[YY] + xij[XX]*cfz;
+ fk[ZZ] = xij[YY]*cfx - xij[XX]*cfy + b*fv[ZZ];
+ /* 30 Flops */
+
+ f[ai][XX] += fv[XX] - fj[XX] - fk[XX];
+ f[ai][YY] += fv[YY] - fj[YY] - fk[YY];
+ f[ai][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
+ rvec_inc(f[aj], fj);
+ rvec_inc(f[ak], fk);
+ /* 15 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
+ svi = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
+ sji = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, ai), di);
+ ski = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = CENTRAL;
+ }
+
+ if (fshift && (svi != CENTRAL || sji != CENTRAL || ski != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX];
+ fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY];
+ fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
+ rvec_inc(fshift[sji], fj);
+ rvec_inc(fshift[ski], fk);
+ }
+
+ if (VirCorr)
+ {
+ rvec xiv;
+ int i, j;
+
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
+
+ for (i = 0; i < DIM; i++)
+ {
+ for (j = 0; j < DIM; j++)
+ {
+ dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j] + xik[i]*fk[j];
+ }
+ }
+ }
+
+ /* TOTAL: 54 flops */
+}
+
+static void spread_vsite4FD(t_iatom ia[], real a, real b, real c,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
+{
+ real d, invl, fproj, a1;
+ rvec xvi, xij, xjk, xjl, xix, fv, temp;
+ atom_id av, ai, aj, ak, al;
+ ivec di;
+ int svi, sji, skj, slj, m;
+
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
+ al = ia[5];
+
+ sji = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ skj = pbc_rvec_sub(pbc, x[ak], x[aj], xjk);
+ slj = pbc_rvec_sub(pbc, x[al], x[aj], xjl);
+ /* 9 flops */
+
+ /* xix goes from i to point x on the plane jkl */
+ for (m = 0; m < DIM; m++)
+ {
+ xix[m] = xij[m] + a*xjk[m] + b*xjl[m];
+ }
+ /* 12 flops */
+
+ invl = gmx_invsqrt(iprod(xix, xix));
+ d = c*invl;
+ /* 4 + ?10? flops */
+
+ copy_rvec(f[av], fv);
+
+ fproj = iprod(xix, fv)*invl*invl; /* = (xix . f)/(xix . xix) */
+
+ for (m = 0; m < DIM; m++)
+ {
+ temp[m] = d*(fv[m] - fproj*xix[m]);
+ }
+ /* 16 */
+
+ /* c is already calculated in constr_vsite3FD
+ storing c somewhere will save 35 flops! */
+
+ a1 = 1 - a - b;
+ for (m = 0; m < DIM; m++)
+ {
+ f[ai][m] += fv[m] - temp[m];
+ f[aj][m] += a1*temp[m];
+ f[ak][m] += a*temp[m];
+ f[al][m] += b*temp[m];
+ }
+ /* 26 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
+ svi = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
+ sji = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, aj), di);
+ skj = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, al), SHIFT_IVEC(g, aj), di);
+ slj = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = CENTRAL;
+ }
+
+ if (fshift &&
+ (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL || slj != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
+ for (m = 0; m < DIM; m++)
+ {
+ fshift[CENTRAL][m] += fv[m] - (1 + a + b)*temp[m];
+ fshift[ sji][m] += temp[m];
+ fshift[ skj][m] += a*temp[m];
+ fshift[ slj][m] += b*temp[m];
+ }
+ }
+
+ if (VirCorr)
+ {
+ rvec xiv;
+ int i, j;
+
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
+
+ for (i = 0; i < DIM; i++)
+ {
+ for (j = 0; j < DIM; j++)
+ {
+ dxdf[i][j] += -xiv[i]*fv[j] + xix[i]*temp[j];
+ }
+ }
+ }
+
+ /* TOTAL: 77 flops */
+}
+
+
+static void spread_vsite4FDN(t_iatom ia[], real a, real b, real c,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
+{
+ rvec xvi, xij, xik, xil, ra, rb, rja, rjb, rab, rm, rt;
+ rvec fv, fj, fk, fl;
+ real invrm, denom;
+ real cfx, cfy, cfz;
+ ivec di;
+ int av, ai, aj, ak, al;
+ int svi, sij, sik, sil;
+
+ /* DEBUG: check atom indices */
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
+ al = ia[5];
+
+ copy_rvec(f[av], fv);
+
+ sij = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ sik = pbc_rvec_sub(pbc, x[ak], x[ai], xik);
+ sil = pbc_rvec_sub(pbc, x[al], x[ai], xil);
+ /* 9 flops */
+
+ ra[XX] = a*xik[XX];
+ ra[YY] = a*xik[YY];
+ ra[ZZ] = a*xik[ZZ];
+
+ rb[XX] = b*xil[XX];
+ rb[YY] = b*xil[YY];
+ rb[ZZ] = b*xil[ZZ];
+
+ /* 6 flops */
+
+ rvec_sub(ra, xij, rja);
+ rvec_sub(rb, xij, rjb);
+ rvec_sub(rb, ra, rab);
+ /* 9 flops */
+
+ cprod(rja, rjb, rm);
+ /* 9 flops */
+
+ invrm = gmx_invsqrt(norm2(rm));
+ denom = invrm*invrm;
+ /* 5+5+2 flops */
+
+ cfx = c*invrm*fv[XX];
+ cfy = c*invrm*fv[YY];
+ cfz = c*invrm*fv[ZZ];
+ /* 6 Flops */
+
+ cprod(rm, rab, rt);
+ /* 9 flops */
rt[XX] *= denom;
rt[YY] *= denom;
rt[ZZ] *= denom;
/* 3flops */
-
+
fj[XX] = ( -rm[XX]*rt[XX]) * cfx + ( rab[ZZ]-rm[YY]*rt[XX]) * cfy + (-rab[YY]-rm[ZZ]*rt[XX]) * cfz;
fj[YY] = (-rab[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + ( rab[XX]-rm[ZZ]*rt[YY]) * cfz;
fj[ZZ] = ( rab[YY]-rm[XX]*rt[ZZ]) * cfx + (-rab[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
/* 30 flops */
-
- cprod(rjb,rm,rt);
+
+ cprod(rjb, rm, rt);
/* 9 flops */
rt[XX] *= denom*a;
rt[YY] *= denom*a;
rt[ZZ] *= denom*a;
/* 3flops */
-
+
fk[XX] = ( -rm[XX]*rt[XX]) * cfx + (-a*rjb[ZZ]-rm[YY]*rt[XX]) * cfy + ( a*rjb[YY]-rm[ZZ]*rt[XX]) * cfz;
fk[YY] = ( a*rjb[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + (-a*rjb[XX]-rm[ZZ]*rt[YY]) * cfz;
fk[ZZ] = (-a*rjb[YY]-rm[XX]*rt[ZZ]) * cfx + ( a*rjb[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
/* 36 flops */
-
- cprod(rm,rja,rt);
+
+ cprod(rm, rja, rt);
/* 9 flops */
-
+
rt[XX] *= denom*b;
rt[YY] *= denom*b;
rt[ZZ] *= denom*b;
/* 3flops */
-
+
fl[XX] = ( -rm[XX]*rt[XX]) * cfx + ( b*rja[ZZ]-rm[YY]*rt[XX]) * cfy + (-b*rja[YY]-rm[ZZ]*rt[XX]) * cfz;
fl[YY] = (-b*rja[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + ( b*rja[XX]-rm[ZZ]*rt[YY]) * cfz;
fl[ZZ] = ( b*rja[YY]-rm[XX]*rt[ZZ]) * cfx + (-b*rja[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
f[ai][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
f[ai][YY] += fv[YY] - fj[YY] - fk[YY] - fl[YY];
f[ai][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ] - fl[ZZ];
- rvec_inc(f[aj],fj);
- rvec_inc(f[ak],fk);
- rvec_inc(f[al],fl);
+ rvec_inc(f[aj], fj);
+ rvec_inc(f[ak], fk);
+ rvec_inc(f[al], fl);
/* 21 flops */
- if (g) {
- ivec_sub(SHIFT_IVEC(g,av),SHIFT_IVEC(g,ai),di);
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, av), SHIFT_IVEC(g, ai), di);
svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
sij = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,ai),di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, ai), di);
sik = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,al),SHIFT_IVEC(g,ai),di);
+ ivec_sub(SHIFT_IVEC(g, al), SHIFT_IVEC(g, ai), di);
sil = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
svi = CENTRAL;
}
-
- if (fshift && (svi!=CENTRAL || sij!=CENTRAL || sik!=CENTRAL || sil!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
+
+ if (fshift && (svi != CENTRAL || sij != CENTRAL || sik != CENTRAL || sil != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY] - fl[YY];
fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ] - fl[ZZ];
- rvec_inc(fshift[sij],fj);
- rvec_inc(fshift[sik],fk);
- rvec_inc(fshift[sil],fl);
+ rvec_inc(fshift[sij], fj);
+ rvec_inc(fshift[sik], fk);
+ rvec_inc(fshift[sil], fl);
}
if (VirCorr)
{
rvec xiv;
- int i,j;
+ int i, j;
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
- for(i=0; i<DIM; i++)
+ for (i = 0; i < DIM; i++)
{
- for(j=0; j<DIM; j++)
+ for (j = 0; j < DIM; j++)
{
dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j] + xik[i]*fk[j] + xil[i]*fl[j];
}
}
}
-
+
/* Total: 207 flops (Yuck!) */
}
-static int spread_vsiten(t_iatom ia[],t_iparams ip[],
- rvec x[],rvec f[],rvec fshift[],
- t_pbc *pbc,t_graph *g)
+static int spread_vsiten(t_iatom ia[], t_iparams ip[],
+ rvec x[], rvec f[], rvec fshift[],
+ t_pbc *pbc, t_graph *g)
{
- rvec xv,dx,fi;
- int n3,av,i,ai;
- real a;
- ivec di;
- int siv;
-
- n3 = 3*ip[ia[0]].vsiten.n;
- av = ia[1];
- copy_rvec(x[av],xv);
-
- for(i=0; i<n3; i+=3) {
- ai = ia[i+2];
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,av),di);
- siv = IVEC2IS(di);
- } else if (pbc) {
- siv = pbc_dx_aiuc(pbc,x[ai],xv,dx);
- } else {
- siv = CENTRAL;
- }
- a = ip[ia[i]].vsiten.a;
- svmul(a,f[av],fi);
- rvec_inc(f[ai],fi);
- if (fshift && siv != CENTRAL) {
- rvec_inc(fshift[siv],fi);
- rvec_dec(fshift[CENTRAL],fi);
+ rvec xv, dx, fi;
+ int n3, av, i, ai;
+ real a;
+ ivec di;
+ int siv;
+
+ n3 = 3*ip[ia[0]].vsiten.n;
+ av = ia[1];
+ copy_rvec(x[av], xv);
+
+ for (i = 0; i < n3; i += 3)
+ {
+ ai = ia[i+2];
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, av), di);
+ siv = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ siv = pbc_dx_aiuc(pbc, x[ai], xv, dx);
+ }
+ else
+ {
+ siv = CENTRAL;
+ }
+ a = ip[ia[i]].vsiten.a;
+ svmul(a, f[av], fi);
+ rvec_inc(f[ai], fi);
+ if (fshift && siv != CENTRAL)
+ {
+ rvec_inc(fshift[siv], fi);
+ rvec_dec(fshift[CENTRAL], fi);
+ }
+ /* 6 Flops */
}
- /* 6 Flops */
- }
- return n3;
+ return n3;
}
-void spread_vsite_f(FILE *log,gmx_vsite_t *vsite,
- rvec x[],rvec f[],rvec *fshift,
- gmx_bool VirCorr,matrix vir,
- t_nrnb *nrnb,t_idef *idef,
- int ePBC,gmx_bool bMolPBC,t_graph *g,matrix box,
- t_commrec *cr)
+static int vsite_count(const t_ilist *ilist, int ftype)
{
- real a1,b1,c1;
- int i,inc,m,nra,nr,tp,ftype;
- int nd2,nd3,nd3FD,nd3FAD,nd3OUT,nd4FD,nd4FDN,ndN;
- t_iatom *ia;
- t_iparams *ip;
- t_pbc pbc,*pbc_null,*pbc_null2;
- int *vsite_pbc;
- matrix dxdf;
-
- /* We only need to do pbc when we have inter-cg vsites */
- if ((DOMAINDECOMP(cr) || bMolPBC) && vsite->n_intercg_vsite) {
- /* This is wasting some CPU time as we now do this multiple times
- * per MD step. But how often do we have vsites with full pbc?
- */
- pbc_null = set_pbc_dd(&pbc,ePBC,cr->dd,FALSE,box);
- } else {
- pbc_null = NULL;
- }
-
- if (DOMAINDECOMP(cr))
- {
- dd_clear_f_vsites(cr->dd,f);
- }
- else if (PARTDECOMP(cr) && vsite->vsitecomm != NULL)
- {
- pd_clear_nonlocal_constructs(vsite->vsitecomm,f);
- }
-
- if (vir != NULL)
+ if (ftype == F_VSITEN)
+ {
+ return ilist[ftype].nr/3;
+ }
+ else
+ {
+ return ilist[ftype].nr/(1 + interaction_function[ftype].nratoms);
+ }
+}
+
+static void spread_vsite_f_thread(gmx_vsite_t *vsite,
+ rvec x[], rvec f[], rvec *fshift,
+ gmx_bool VirCorr, matrix dxdf,
+ t_iparams ip[], t_ilist ilist[],
+ t_graph *g, t_pbc *pbc_null)
+{
+ gmx_bool bPBCAll;
+ real a1, b1, c1;
+ int i, inc, m, nra, nr, tp, ftype;
+ t_iatom *ia;
+ t_pbc *pbc_null2;
+ int *vsite_pbc;
+
+ if (VirCorr)
{
clear_mat(dxdf);
}
-
- ip = idef->iparams;
-
- nd2 = 0;
- nd3 = 0;
- nd3FD = 0;
- nd3FAD = 0;
- nd3OUT = 0;
- nd4FD = 0;
- nd4FDN = 0;
- ndN = 0;
-
- /* this loop goes backwards to be able to build *
- * higher type vsites from lower types */
- pbc_null2 = NULL;
- for(ftype=F_NRE-1; (ftype>=0); ftype--) {
- if (interaction_function[ftype].flags & IF_VSITE) {
- nra = interaction_function[ftype].nratoms;
- nr = idef->il[ftype].nr;
- ia = idef->il[ftype].iatoms;
-
- if (pbc_null) {
- vsite_pbc = vsite->vsite_pbc_loc[ftype-F_VSITE2];
- } else {
- vsite_pbc = NULL;
- }
-
- for(i=0; (i<nr); ) {
- /* Check if we need to apply pbc for this vsite */
- if (vsite_pbc) {
- if (vsite_pbc[i/(1+nra)] > -2)
- pbc_null2 = pbc_null;
- else
- pbc_null2 = NULL;
- }
-
- tp = ia[0];
- if (ftype != idef->functype[tp])
- gmx_incons("Functiontypes for vsites wrong");
-
- /* Constants for constructing */
- a1 = ip[tp].vsite.a;
- /* Construct the vsite depending on type */
- inc = nra+1;
- switch (ftype) {
- case F_VSITE2:
- spread_vsite2(ia,a1,x,f,fshift,pbc_null2,g);
- nd2++;
- break;
- case F_VSITE3:
- b1 = ip[tp].vsite.b;
- spread_vsite3(ia,a1,b1,x,f,fshift,pbc_null2,g);
- nd3++;
- break;
- case F_VSITE3FD:
- b1 = ip[tp].vsite.b;
- spread_vsite3FD(ia,a1,b1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- nd3FD++;
- break;
- case F_VSITE3FAD:
- b1 = ip[tp].vsite.b;
- spread_vsite3FAD(ia,a1,b1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- nd3FAD++;
- break;
- case F_VSITE3OUT:
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- spread_vsite3OUT(ia,a1,b1,c1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- nd3OUT++;
- break;
- case F_VSITE4FD:
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- spread_vsite4FD(ia,a1,b1,c1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- nd4FD++;
- break;
- case F_VSITE4FDN:
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- spread_vsite4FDN(ia,a1,b1,c1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- nd4FDN++;
- break;
- case F_VSITEN:
- inc = spread_vsiten(ia,ip,x,f,fshift,pbc_null2,g);
- ndN += inc;
- break;
- default:
- gmx_fatal(FARGS,"No such vsite type %d in %s, line %d",
- ftype,__FILE__,__LINE__);
- }
- clear_rvec(f[ia[1]]);
-
- /* Increment loop variables */
- i += inc;
- ia += inc;
- }
- }
- }
+
+ bPBCAll = (pbc_null != NULL && !vsite->bHaveChargeGroups);
+
+ /* this loop goes backwards to be able to build *
+ * higher type vsites from lower types */
+ pbc_null2 = NULL;
+ vsite_pbc = NULL;
+ for (ftype = F_NRE-1; (ftype >= 0); ftype--)
+ {
+ if ((interaction_function[ftype].flags & IF_VSITE) &&
+ ilist[ftype].nr > 0)
+ {
+ nra = interaction_function[ftype].nratoms;
+ inc = 1 + nra;
+ nr = ilist[ftype].nr;
+ ia = ilist[ftype].iatoms;
+
+ if (bPBCAll)
+ {
+ pbc_null2 = pbc_null;
+ }
+ else if (pbc_null != NULL)
+ {
+ vsite_pbc = vsite->vsite_pbc_loc[ftype-F_VSITE2];
+ }
+
+ for (i = 0; i < nr; )
+ {
+ if (vsite_pbc != NULL)
+ {
+ if (vsite_pbc[i/(1+nra)] > -2)
+ {
+ pbc_null2 = pbc_null;
+ }
+ else
+ {
+ pbc_null2 = NULL;
+ }
+ }
+
+ tp = ia[0];
+
+ /* Constants for constructing */
+ a1 = ip[tp].vsite.a;
+ /* Construct the vsite depending on type */
+ switch (ftype)
+ {
+ case F_VSITE2:
+ spread_vsite2(ia, a1, x, f, fshift, pbc_null2, g);
+ break;
+ case F_VSITE3:
+ b1 = ip[tp].vsite.b;
+ spread_vsite3(ia, a1, b1, x, f, fshift, pbc_null2, g);
+ break;
+ case F_VSITE3FD:
+ b1 = ip[tp].vsite.b;
+ spread_vsite3FD(ia, a1, b1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITE3FAD:
+ b1 = ip[tp].vsite.b;
+ spread_vsite3FAD(ia, a1, b1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITE3OUT:
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ spread_vsite3OUT(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITE4FD:
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ spread_vsite4FD(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITE4FDN:
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ spread_vsite4FDN(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITEN:
+ inc = spread_vsiten(ia, ip, x, f, fshift, pbc_null2, g);
+ break;
+ default:
+ gmx_fatal(FARGS, "No such vsite type %d in %s, line %d",
+ ftype, __FILE__, __LINE__);
+ }
+ clear_rvec(f[ia[1]]);
+
+ /* Increment loop variables */
+ i += inc;
+ ia += inc;
+ }
+ }
+ }
+}
+
+void spread_vsite_f(FILE *log, gmx_vsite_t *vsite,
+ rvec x[], rvec f[], rvec *fshift,
+ gmx_bool VirCorr, matrix vir,
+ t_nrnb *nrnb, t_idef *idef,
+ int ePBC, gmx_bool bMolPBC, t_graph *g, matrix box,
+ t_commrec *cr)
+{
+ t_pbc pbc, *pbc_null;
+ int th;
+
+ /* We only need to do pbc when we have inter-cg vsites */
+ if ((DOMAINDECOMP(cr) || bMolPBC) && vsite->n_intercg_vsite)
+ {
+ /* This is wasting some CPU time as we now do this multiple times
+ * per MD step. But how often do we have vsites with full pbc?
+ */
+ pbc_null = set_pbc_dd(&pbc, ePBC, cr->dd, FALSE, box);
+ }
+ else
+ {
+ pbc_null = NULL;
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ dd_clear_f_vsites(cr->dd, f);
+ }
+ else if (PARTDECOMP(cr) && vsite->vsitecomm != NULL)
+ {
+ pd_clear_nonlocal_constructs(vsite->vsitecomm, f);
+ }
+
+ if (vsite->nthreads == 1)
+ {
+ spread_vsite_f_thread(vsite,
+ x, f, fshift,
+ VirCorr, vsite->tdata[0].dxdf,
+ idef->iparams, idef->il,
+ g, pbc_null);
+ }
+ else
+ {
+ /* First spread the vsites that might depend on other vsites */
+ spread_vsite_f_thread(vsite,
+ x, f, fshift,
+ VirCorr, vsite->tdata[vsite->nthreads].dxdf,
+ idef->iparams,
+ vsite->tdata[vsite->nthreads].ilist,
+ g, pbc_null);
+
+#pragma omp parallel num_threads(vsite->nthreads)
+ {
+ int thread;
+ rvec *fshift_t;
+
+ thread = gmx_omp_get_thread_num();
+
+ if (thread == 0 || fshift == NULL)
+ {
+ fshift_t = fshift;
+ }
+ else
+ {
+ int i;
+
+ fshift_t = vsite->tdata[thread].fshift;
+
+ for (i = 0; i < SHIFTS; i++)
+ {
+ clear_rvec(fshift_t[i]);
+ }
+ }
+
+ spread_vsite_f_thread(vsite,
+ x, f, fshift_t,
+ VirCorr, vsite->tdata[thread].dxdf,
+ idef->iparams,
+ vsite->tdata[thread].ilist,
+ g, pbc_null);
+ }
+
+ if (fshift != NULL)
+ {
+ int i;
+
+ for (th = 1; th < vsite->nthreads; th++)
+ {
+ for (i = 0; i < SHIFTS; i++)
+ {
+ rvec_inc(fshift[i], vsite->tdata[th].fshift[i]);
+ }
+ }
+ }
+ }
if (VirCorr)
{
- int i,j;
+ int i, j;
- for(i=0; i<DIM; i++)
+ for (th = 0; th < (vsite->nthreads == 1 ? 1 : vsite->nthreads+1); th++)
{
- for(j=0; j<DIM; j++)
+ for (i = 0; i < DIM; i++)
{
- vir[i][j] += -0.5*dxdf[i][j];
+ for (j = 0; j < DIM; j++)
+ {
+ vir[i][j] += -0.5*vsite->tdata[th].dxdf[i][j];
+ }
}
}
}
- inc_nrnb(nrnb,eNR_VSITE2, nd2 );
- inc_nrnb(nrnb,eNR_VSITE3, nd3 );
- inc_nrnb(nrnb,eNR_VSITE3FD, nd3FD );
- inc_nrnb(nrnb,eNR_VSITE3FAD,nd3FAD );
- inc_nrnb(nrnb,eNR_VSITE3OUT,nd3OUT );
- inc_nrnb(nrnb,eNR_VSITE4FD, nd4FD );
- inc_nrnb(nrnb,eNR_VSITE4FDN,nd4FDN );
- inc_nrnb(nrnb,eNR_VSITEN, ndN );
-
- if (DOMAINDECOMP(cr)) {
- dd_move_f_vsites(cr->dd,f,fshift);
- } else if (vsite->bPDvsitecomm) {
- /* We only move forces here, and they are independent of shifts */
- move_construct_f(vsite->vsitecomm,f,cr);
- }
+ if (DOMAINDECOMP(cr))
+ {
+ dd_move_f_vsites(cr->dd, f, fshift);
+ }
+ else if (vsite->bPDvsitecomm)
+ {
+ /* We only move forces here, and they are independent of shifts */
+ move_construct_f(vsite->vsitecomm, f, cr);
+ }
+
+ inc_nrnb(nrnb, eNR_VSITE2, vsite_count(idef->il, F_VSITE2));
+ inc_nrnb(nrnb, eNR_VSITE3, vsite_count(idef->il, F_VSITE3));
+ inc_nrnb(nrnb, eNR_VSITE3FD, vsite_count(idef->il, F_VSITE3FD));
+ inc_nrnb(nrnb, eNR_VSITE3FAD, vsite_count(idef->il, F_VSITE3FAD));
+ inc_nrnb(nrnb, eNR_VSITE3OUT, vsite_count(idef->il, F_VSITE3OUT));
+ inc_nrnb(nrnb, eNR_VSITE4FD, vsite_count(idef->il, F_VSITE4FD));
+ inc_nrnb(nrnb, eNR_VSITE4FDN, vsite_count(idef->il, F_VSITE4FDN));
+ inc_nrnb(nrnb, eNR_VSITEN, vsite_count(idef->il, F_VSITEN));
}
static int *atom2cg(t_block *cgs)
{
- int *a2cg,cg,i;
-
- snew(a2cg,cgs->index[cgs->nr]);
- for(cg=0; cg<cgs->nr; cg++) {
- for(i=cgs->index[cg]; i<cgs->index[cg+1]; i++)
- a2cg[i] = cg;
- }
-
- return a2cg;
+ int *a2cg, cg, i;
+
+ snew(a2cg, cgs->index[cgs->nr]);
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ for (i = cgs->index[cg]; i < cgs->index[cg+1]; i++)
+ {
+ a2cg[i] = cg;
+ }
+ }
+
+ return a2cg;
}
-static int count_intercg_vsite(gmx_mtop_t *mtop)
+static int count_intercg_vsite(gmx_mtop_t *mtop,
+ gmx_bool *bHaveChargeGroups)
{
- int mb,mt,ftype,nral,i,cg,a;
- gmx_molblock_t *molb;
- gmx_moltype_t *molt;
- int *a2cg;
- t_ilist *il;
- t_iatom *ia;
- int n_intercg_vsite;
-
- n_intercg_vsite = 0;
- for(mb=0; mb<mtop->nmolblock; mb++) {
- molb = &mtop->molblock[mb];
- molt = &mtop->moltype[molb->type];
- a2cg = atom2cg(&molt->cgs);
- for(ftype=0; ftype<F_NRE; ftype++) {
- if (interaction_function[ftype].flags & IF_VSITE) {
- nral = NRAL(ftype);
- il = &molt->ilist[ftype];
- ia = il->iatoms;
- for(i=0; i<il->nr; i+=1+nral) {
- cg = a2cg[ia[1+i]];
- for(a=1; a<nral; a++) {
- if (a2cg[ia[1+a]] != cg) {
- n_intercg_vsite += molb->nmol;
- break;
- }
- }
- }
- }
- }
- sfree(a2cg);
- }
-
- return n_intercg_vsite;
+ int mb, mt, ftype, nral, i, cg, a;
+ gmx_molblock_t *molb;
+ gmx_moltype_t *molt;
+ int *a2cg;
+ t_ilist *il;
+ t_iatom *ia;
+ int n_intercg_vsite;
+
+ *bHaveChargeGroups = FALSE;
+
+ n_intercg_vsite = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ molt = &mtop->moltype[molb->type];
+
+ if (molt->cgs.nr < molt->atoms.nr)
+ {
+ *bHaveChargeGroups = TRUE;
+ }
+
+ a2cg = atom2cg(&molt->cgs);
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_VSITE)
+ {
+ nral = NRAL(ftype);
+ il = &molt->ilist[ftype];
+ ia = il->iatoms;
+ for (i = 0; i < il->nr; i += 1+nral)
+ {
+ cg = a2cg[ia[1+i]];
+ for (a = 1; a < nral; a++)
+ {
+ if (a2cg[ia[1+a]] != cg)
+ {
+ n_intercg_vsite += molb->nmol;
+ break;
+ }
+ }
+ }
+ }
+ }
+ sfree(a2cg);
+ }
+
+ return n_intercg_vsite;
}
-static int **get_vsite_pbc(t_iparams *iparams,t_ilist *ilist,
- t_atom *atom,t_mdatoms *md,
- t_block *cgs,int *a2cg)
+static int **get_vsite_pbc(t_iparams *iparams, t_ilist *ilist,
+ t_atom *atom, t_mdatoms *md,
+ t_block *cgs, int *a2cg)
{
- int ftype,nral,i,j,vsi,vsite,cg_v,cg_c,a,nc3=0;
- t_ilist *il;
- t_iatom *ia;
- int **vsite_pbc,*vsite_pbc_f;
- char *pbc_set;
- gmx_bool bViteOnlyCG_and_FirstAtom;
-
- /* Make an array that tells if the pbc of an atom is set */
- snew(pbc_set,cgs->index[cgs->nr]);
- /* PBC is set for all non vsites */
- for(a=0; a<cgs->index[cgs->nr]; a++) {
- if ((atom && atom[a].ptype != eptVSite) ||
- (md && md->ptype[a] != eptVSite)) {
- pbc_set[a] = 1;
- }
- }
-
- snew(vsite_pbc,F_VSITEN-F_VSITE2+1);
-
- for(ftype=0; ftype<F_NRE; ftype++) {
- if (interaction_function[ftype].flags & IF_VSITE) {
- nral = NRAL(ftype);
- il = &ilist[ftype];
- ia = il->iatoms;
-
- snew(vsite_pbc[ftype-F_VSITE2],il->nr/(1+nral));
- vsite_pbc_f = vsite_pbc[ftype-F_VSITE2];
-
- i = 0;
- while (i < il->nr) {
- vsi = i/(1+nral);
- vsite = ia[i+1];
- cg_v = a2cg[vsite];
- /* A value of -2 signals that this vsite and its contructing
- * atoms are all within the same cg, so no pbc is required.
- */
- vsite_pbc_f[vsi] = -2;
- /* Check if constructing atoms are outside the vsite's cg */
- nc3 = 0;
- if (ftype == F_VSITEN) {
- nc3 = 3*iparams[ia[i]].vsiten.n;
- for(j=0; j<nc3; j+=3) {
- if (a2cg[ia[i+j+2]] != cg_v)
- vsite_pbc_f[vsi] = -1;
- }
- } else {
- for(a=1; a<nral; a++) {
- if (a2cg[ia[i+1+a]] != cg_v)
- vsite_pbc_f[vsi] = -1;
- }
- }
- if (vsite_pbc_f[vsi] == -1) {
- /* Check if this is the first processed atom of a vsite only cg */
- bViteOnlyCG_and_FirstAtom = TRUE;
- for(a=cgs->index[cg_v]; a<cgs->index[cg_v+1]; a++) {
- /* Non-vsites already have pbc set, so simply check for pbc_set */
- if (pbc_set[a]) {
- bViteOnlyCG_and_FirstAtom = FALSE;
- break;
- }
- }
- if (bViteOnlyCG_and_FirstAtom) {
- /* First processed atom of a vsite only charge group.
- * The pbc of the input coordinates to construct_vsites
- * should be preserved.
- */
- vsite_pbc_f[vsi] = vsite;
- } else if (cg_v != a2cg[ia[1+i+1]]) {
- /* This vsite has a different charge group index
- * than it's first constructing atom
- * and the charge group has more than one atom,
- * search for the first normal particle
- * or vsite that already had its pbc defined.
- * If nothing is found, use full pbc for this vsite.
- */
- for(a=cgs->index[cg_v]; a<cgs->index[cg_v+1]; a++) {
- if (a != vsite && pbc_set[a]) {
- vsite_pbc_f[vsi] = a;
- if (gmx_debug_at)
- fprintf(debug,"vsite %d match pbc with atom %d\n",
- vsite+1,a+1);
- break;
- }
- }
- if (gmx_debug_at)
- fprintf(debug,"vsite atom %d cg %d - %d pbc atom %d\n",
- vsite+1,cgs->index[cg_v]+1,cgs->index[cg_v+1],
- vsite_pbc_f[vsi]+1);
- }
- }
- if (ftype == F_VSITEN) {
- /* The other entries in vsite_pbc_f are not used for center vsites */
- i += nc3;
- } else {
- i += 1+nral;
- }
-
- /* This vsite now has its pbc defined */
- pbc_set[vsite] = 1;
- }
- }
- }
-
- sfree(pbc_set);
-
- return vsite_pbc;
+ int ftype, nral, i, j, vsi, vsite, cg_v, cg_c, a, nc3 = 0;
+ t_ilist *il;
+ t_iatom *ia;
+ int **vsite_pbc, *vsite_pbc_f;
+ char *pbc_set;
+ gmx_bool bViteOnlyCG_and_FirstAtom;
+
+ /* Make an array that tells if the pbc of an atom is set */
+ snew(pbc_set, cgs->index[cgs->nr]);
+ /* PBC is set for all non vsites */
+ for (a = 0; a < cgs->index[cgs->nr]; a++)
+ {
+ if ((atom && atom[a].ptype != eptVSite) ||
+ (md && md->ptype[a] != eptVSite))
+ {
+ pbc_set[a] = 1;
+ }
+ }
+
+ snew(vsite_pbc, F_VSITEN-F_VSITE2+1);
+
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_VSITE)
+ {
+ nral = NRAL(ftype);
+ il = &ilist[ftype];
+ ia = il->iatoms;
+
+ snew(vsite_pbc[ftype-F_VSITE2], il->nr/(1+nral));
+ vsite_pbc_f = vsite_pbc[ftype-F_VSITE2];
+
+ i = 0;
+ while (i < il->nr)
+ {
+ vsi = i/(1+nral);
+ vsite = ia[i+1];
+ cg_v = a2cg[vsite];
+ /* A value of -2 signals that this vsite and its contructing
+ * atoms are all within the same cg, so no pbc is required.
+ */
+ vsite_pbc_f[vsi] = -2;
+ /* Check if constructing atoms are outside the vsite's cg */
+ nc3 = 0;
+ if (ftype == F_VSITEN)
+ {
+ nc3 = 3*iparams[ia[i]].vsiten.n;
+ for (j = 0; j < nc3; j += 3)
+ {
+ if (a2cg[ia[i+j+2]] != cg_v)
+ {
+ vsite_pbc_f[vsi] = -1;
+ }
+ }
+ }
+ else
+ {
+ for (a = 1; a < nral; a++)
+ {
+ if (a2cg[ia[i+1+a]] != cg_v)
+ {
+ vsite_pbc_f[vsi] = -1;
+ }
+ }
+ }
+ if (vsite_pbc_f[vsi] == -1)
+ {
+ /* Check if this is the first processed atom of a vsite only cg */
+ bViteOnlyCG_and_FirstAtom = TRUE;
+ for (a = cgs->index[cg_v]; a < cgs->index[cg_v+1]; a++)
+ {
+ /* Non-vsites already have pbc set, so simply check for pbc_set */
+ if (pbc_set[a])
+ {
+ bViteOnlyCG_and_FirstAtom = FALSE;
+ break;
+ }
+ }
+ if (bViteOnlyCG_and_FirstAtom)
+ {
+ /* First processed atom of a vsite only charge group.
+ * The pbc of the input coordinates to construct_vsites
+ * should be preserved.
+ */
+ vsite_pbc_f[vsi] = vsite;
+ }
+ else if (cg_v != a2cg[ia[1+i+1]])
+ {
+ /* This vsite has a different charge group index
+ * than it's first constructing atom
+ * and the charge group has more than one atom,
+ * search for the first normal particle
+ * or vsite that already had its pbc defined.
+ * If nothing is found, use full pbc for this vsite.
+ */
+ for (a = cgs->index[cg_v]; a < cgs->index[cg_v+1]; a++)
+ {
+ if (a != vsite && pbc_set[a])
+ {
+ vsite_pbc_f[vsi] = a;
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "vsite %d match pbc with atom %d\n",
+ vsite+1, a+1);
+ }
+ break;
+ }
+ }
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "vsite atom %d cg %d - %d pbc atom %d\n",
+ vsite+1, cgs->index[cg_v]+1, cgs->index[cg_v+1],
+ vsite_pbc_f[vsi]+1);
+ }
+ }
+ }
+ if (ftype == F_VSITEN)
+ {
+ /* The other entries in vsite_pbc_f are not used for center vsites */
+ i += nc3;
+ }
+ else
+ {
+ i += 1+nral;
+ }
+
+ /* This vsite now has its pbc defined */
+ pbc_set[vsite] = 1;
+ }
+ }
+ }
+
+ sfree(pbc_set);
+
+ return vsite_pbc;
}
-gmx_vsite_t *init_vsite(gmx_mtop_t *mtop,t_commrec *cr)
+
+gmx_vsite_t *init_vsite(gmx_mtop_t *mtop, t_commrec *cr,
+ gmx_bool bSerial_NoPBC)
{
- int nvsite,i;
- int *a2cg,cg;
- gmx_vsite_t *vsite;
- int mt;
- gmx_moltype_t *molt;
-
- /* check if there are vsites */
- nvsite = 0;
- for(i=0; i<F_NRE; i++) {
- if (interaction_function[i].flags & IF_VSITE) {
- nvsite += gmx_mtop_ftype_count(mtop,i);
- }
- }
-
- if (nvsite == 0) {
- return NULL;
- }
-
- snew(vsite,1);
-
- vsite->n_intercg_vsite = count_intercg_vsite(mtop);
-
- if (vsite->n_intercg_vsite > 0 && DOMAINDECOMP(cr)) {
- vsite->nvsite_pbc_molt = mtop->nmoltype;
- snew(vsite->vsite_pbc_molt,vsite->nvsite_pbc_molt);
- for(mt=0; mt<mtop->nmoltype; mt++) {
- molt = &mtop->moltype[mt];
- /* Make an atom to charge group index */
- a2cg = atom2cg(&molt->cgs);
- vsite->vsite_pbc_molt[mt] = get_vsite_pbc(mtop->ffparams.iparams,
- molt->ilist,
- molt->atoms.atom,NULL,
- &molt->cgs,a2cg);
- sfree(a2cg);
- }
-
- snew(vsite->vsite_pbc_loc_nalloc,F_VSITEN-F_VSITE2+1);
- snew(vsite->vsite_pbc_loc ,F_VSITEN-F_VSITE2+1);
- }
-
-
- return vsite;
+ int nvsite, i;
+ int *a2cg, cg;
+ gmx_vsite_t *vsite;
+ int mt;
+ gmx_moltype_t *molt;
+ int nthreads;
+
+ /* check if there are vsites */
+ nvsite = 0;
+ for (i = 0; i < F_NRE; i++)
+ {
+ if (interaction_function[i].flags & IF_VSITE)
+ {
+ nvsite += gmx_mtop_ftype_count(mtop, i);
+ }
+ }
+
+ if (nvsite == 0)
+ {
+ return NULL;
+ }
+
+ snew(vsite, 1);
+
+ vsite->n_intercg_vsite = count_intercg_vsite(mtop,
+ &vsite->bHaveChargeGroups);
+
+ /* If we don't have charge groups, the vsite follows its own pbc */
+ if (!bSerial_NoPBC &&
+ vsite->bHaveChargeGroups &&
+ vsite->n_intercg_vsite > 0 && DOMAINDECOMP(cr))
+ {
+ vsite->nvsite_pbc_molt = mtop->nmoltype;
+ snew(vsite->vsite_pbc_molt, vsite->nvsite_pbc_molt);
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ molt = &mtop->moltype[mt];
+ /* Make an atom to charge group index */
+ a2cg = atom2cg(&molt->cgs);
+ vsite->vsite_pbc_molt[mt] = get_vsite_pbc(mtop->ffparams.iparams,
+ molt->ilist,
+ molt->atoms.atom, NULL,
+ &molt->cgs, a2cg);
+ sfree(a2cg);
+ }
+
+ snew(vsite->vsite_pbc_loc_nalloc, F_VSITEN-F_VSITE2+1);
+ snew(vsite->vsite_pbc_loc, F_VSITEN-F_VSITE2+1);
+ }
+
+ if (bSerial_NoPBC)
+ {
+ vsite->nthreads = 1;
+ }
+ else
+ {
+ vsite->nthreads = gmx_omp_nthreads_get(emntVSITE);
+ }
+ if (!bSerial_NoPBC)
+ {
+ /* We need one extra thread data structure for the overlap vsites */
+ snew(vsite->tdata, vsite->nthreads+1);
+ }
+
+ vsite->th_ind = NULL;
+ vsite->th_ind_nalloc = 0;
+
+ return vsite;
}
-void set_vsite_top(gmx_vsite_t *vsite,gmx_localtop_t *top,t_mdatoms *md,
- t_commrec *cr)
+static void prepare_vsite_thread(const t_ilist *ilist,
+ gmx_vsite_thread_t *vsite_th)
{
- int *a2cg;
+ int ftype;
+
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_VSITE)
+ {
+ if (ilist[ftype].nr > vsite_th->ilist[ftype].nalloc)
+ {
+ vsite_th->ilist[ftype].nalloc = over_alloc_large(ilist[ftype].nr);
+ srenew(vsite_th->ilist[ftype].iatoms, vsite_th->ilist[ftype].nalloc);
+ }
+
+ vsite_th->ilist[ftype].nr = 0;
+ }
+ }
+}
+
+void split_vsites_over_threads(const t_ilist *ilist,
+ const t_mdatoms *mdatoms,
+ gmx_bool bLimitRange,
+ gmx_vsite_t *vsite)
+{
+ int th;
+ int vsite_atom_range, natperthread;
+ int *th_ind;
+ int ftype;
+ t_iatom *iat;
+ t_ilist *il_th;
+ int nral1, inc, i, j;
+
+ if (vsite->nthreads == 1)
+ {
+ /* Nothing to do */
+ return;
+ }
+
+#pragma omp parallel for num_threads(vsite->nthreads) schedule(static)
+ for (th = 0; th < vsite->nthreads; th++)
+ {
+ prepare_vsite_thread(ilist, &vsite->tdata[th]);
+ }
+ /* Master threads does the (potential) overlap vsites */
+ prepare_vsite_thread(ilist, &vsite->tdata[vsite->nthreads]);
+
+ /* The current way of distributing the vsites over threads in primitive.
+ * We divide the atom range 0 - natoms_in_vsite uniformly over threads,
+ * without taking into account how the vsites are distributed.
+ * Without domain decomposition we bLimitRange=TRUE and we at least
+ * tighten the upper bound of the range (useful for common systems
+ * such as a vsite-protein in 3-site water).
+ */
+ if (bLimitRange)
+ {
+ vsite_atom_range = -1;
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if ((interaction_function[ftype].flags & IF_VSITE) &&
+ ftype != F_VSITEN)
+ {
+ nral1 = 1 + NRAL(ftype);
+ iat = ilist[ftype].iatoms;
+ for (i = 0; i < ilist[ftype].nr; i += nral1)
+ {
+ for (j = i+1; j < i+nral1; j++)
+ {
+ vsite_atom_range = max(vsite_atom_range, iat[j]);
+ }
+ }
+ }
+ }
+ vsite_atom_range++;
+ }
+ else
+ {
+ vsite_atom_range = mdatoms->homenr;
+ }
+ natperthread = (vsite_atom_range + vsite->nthreads - 1)/vsite->nthreads;
- /* Make an atom to charge group index */
- a2cg = atom2cg(&top->cgs);
+ if (debug)
+ {
+ fprintf(debug, "virtual site thread dist: natoms %d, range %d, natperthread %d\n", mdatoms->nr, vsite_atom_range, natperthread);
+ }
- if (vsite->n_intercg_vsite > 0) {
- vsite->vsite_pbc_loc = get_vsite_pbc(top->idef.iparams,
- top->idef.il,NULL,md,
- &top->cgs,a2cg);
+ /* To simplify the vsite assignment, we make an index which tells us
+ * to which thread particles, both non-vsites and vsites, are assigned.
+ */
+ if (mdatoms->nr > vsite->th_ind_nalloc)
+ {
+ vsite->th_ind_nalloc = over_alloc_large(mdatoms->nr);
+ srenew(vsite->th_ind, vsite->th_ind_nalloc);
+ }
+ th_ind = vsite->th_ind;
+ th = 0;
+ for (i = 0; i < mdatoms->nr; i++)
+ {
+ if (mdatoms->ptype[i] == eptVSite)
+ {
+ /* vsites are not assigned to a thread yet */
+ th_ind[i] = -1;
+ }
+ else
+ {
+ /* assign non-vsite particles to thread th */
+ th_ind[i] = th;
+ }
+ if (i == (th + 1)*natperthread && th < vsite->nthreads)
+ {
+ th++;
+ }
+ }
- if (PARTDECOMP(cr)) {
- snew(vsite->vsitecomm,1);
- vsite->bPDvsitecomm =
- setup_parallel_vsites(&(top->idef),cr,vsite->vsitecomm);
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if ((interaction_function[ftype].flags & IF_VSITE) &&
+ ftype != F_VSITEN)
+ {
+ nral1 = 1 + NRAL(ftype);
+ inc = nral1;
+ iat = ilist[ftype].iatoms;
+ for (i = 0; i < ilist[ftype].nr; )
+ {
+ th = iat[1+i]/natperthread;
+ /* We would like to assign this vsite the thread th,
+ * but it might depend on atoms outside the atom range of th
+ * or on another vsite not assigned to thread th.
+ */
+ if (ftype != F_VSITEN)
+ {
+ for (j = i+2; j < i+nral1; j++)
+ {
+ if (th_ind[iat[j]] != th)
+ {
+ /* Some constructing atoms are not assigned to
+ * thread th, move this vsite to a separate batch.
+ */
+ th = vsite->nthreads;
+ }
+ }
+ }
+ else
+ {
+ inc = iat[i];
+ for (j = i+2; j < i+inc; j += 3)
+ {
+ if (th_ind[iat[j]] != th)
+ {
+ th = vsite->nthreads;
+ }
+ }
+ }
+ /* Copy this vsite to the thread data struct of thread th */
+ il_th = &vsite->tdata[th].ilist[ftype];
+ for (j = i; j < i+inc; j++)
+ {
+ il_th->iatoms[il_th->nr++] = iat[j];
+ }
+ /* Update this vsite's thread index entry */
+ th_ind[iat[1+i]] = th;
+
+ i += inc;
+ }
+ }
}
- }
- sfree(a2cg);
+ if (debug)
+ {
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if ((interaction_function[ftype].flags & IF_VSITE) &&
+ ilist[ftype].nr > 0)
+ {
+ fprintf(debug, "%-20s thread dist:",
+ interaction_function[ftype].longname);
+ for (th = 0; th < vsite->nthreads+1; th++)
+ {
+ fprintf(debug, " %4d", vsite->tdata[th].ilist[ftype].nr);
+ }
+ fprintf(debug, "\n");
+ }
+ }
+ }
+}
+
+void set_vsite_top(gmx_vsite_t *vsite, gmx_localtop_t *top, t_mdatoms *md,
+ t_commrec *cr)
+{
+ int *a2cg;
+
+ if (vsite->n_intercg_vsite > 0)
+ {
+ if (vsite->bHaveChargeGroups)
+ {
+ /* Make an atom to charge group index */
+ a2cg = atom2cg(&top->cgs);
+ vsite->vsite_pbc_loc = get_vsite_pbc(top->idef.iparams,
+ top->idef.il, NULL, md,
+ &top->cgs, a2cg);
+ sfree(a2cg);
+ }
+
+ if (PARTDECOMP(cr))
+ {
+ snew(vsite->vsitecomm, 1);
+ vsite->bPDvsitecomm =
+ setup_parallel_vsites(&(top->idef), cr, vsite->vsitecomm);
+ }
+ }
+
+ if (vsite->nthreads > 1)
+ {
+ if (vsite->bHaveChargeGroups || PARTDECOMP(cr))
+ {
+ gmx_incons("Can not use threads virtual sites combined with charge groups or particle decomposition");
+ }
+
+ split_vsites_over_threads(top->idef.il, md, !DOMAINDECOMP(cr), vsite);
+ }
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff