/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * 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) 2001-2008, 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) 2001-2008, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
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- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
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+ * in the README & COPYING files - if they are missing, get the
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+ *
* 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.
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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "txtdump.h"
-#include "mdrun.h"
-#include "partdec.h"
-#include "mdatoms.h"
-#include "vsite.h"
-#include "network.h"
-#include "names.h"
-#include "constr.h"
-#include "domdec.h"
-#include "partdec.h"
-#include "physics.h"
-#include "copyrite.h"
-#include "shellfc.h"
-#include "mtop_util.h"
-#include "chargegroup.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/shellfc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/macros.h"
+
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
- int nnucl;
- atom_id shell; /* The shell id */
- atom_id nucl1,nucl2,nucl3; /* The nuclei connected to the shell */
- /* gmx_bool bInterCG; */ /* Coupled to nuclei outside cg? */
- real k; /* force constant */
- real k_1; /* 1 over force constant */
- rvec xold;
- rvec fold;
- rvec step;
+ int nnucl;
+ atom_id shell; /* The shell id */
+ atom_id nucl1, nucl2, nucl3; /* The nuclei connected to the shell */
+ /* gmx_bool bInterCG; */ /* Coupled to nuclei outside cg? */
+ real k; /* force constant */
+ real k_1; /* 1 over force constant */
+ rvec xold;
+ rvec fold;
+ rvec step;
} t_shell;
typedef struct gmx_shellfc {
- int nshell_gl; /* The number of shells in the system */
- t_shell *shell_gl; /* All the shells (for DD only) */
- int *shell_index_gl; /* Global shell index (for DD only) */
- gmx_bool bInterCG; /* Are there inter charge-group shells? */
- int nshell; /* The number of local shells */
- t_shell *shell; /* The local shells */
- int shell_nalloc; /* The allocation size of shell */
- gmx_bool bPredict; /* Predict shell positions */
- gmx_bool bRequireInit; /* Require initialization of shell positions */
- int nflexcon; /* The number of flexible constraints */
- rvec *x[2]; /* Array for iterative minimization */
- rvec *f[2]; /* Array for iterative minimization */
- int x_nalloc; /* The allocation size of x and f */
- rvec *acc_dir; /* Acceleration direction for flexcon */
- rvec *x_old; /* Old coordinates for flexcon */
- int flex_nalloc; /* The allocation size of acc_dir and x_old */
- rvec *adir_xnold; /* Work space for init_adir */
- rvec *adir_xnew; /* Work space for init_adir */
- int adir_nalloc; /* Work space for init_adir */
+ int nshell_gl; /* The number of shells in the system */
+ t_shell *shell_gl; /* All the shells (for DD only) */
+ int *shell_index_gl; /* Global shell index (for DD only) */
+ gmx_bool bInterCG; /* Are there inter charge-group shells? */
+ int nshell; /* The number of local shells */
+ t_shell *shell; /* The local shells */
+ int shell_nalloc; /* The allocation size of shell */
+ gmx_bool bPredict; /* Predict shell positions */
+ gmx_bool bRequireInit; /* Require initialization of shell positions */
+ int nflexcon; /* The number of flexible constraints */
+ rvec *x[2]; /* Array for iterative minimization */
+ rvec *f[2]; /* Array for iterative minimization */
+ int x_nalloc; /* The allocation size of x and f */
+ rvec *acc_dir; /* Acceleration direction for flexcon */
+ rvec *x_old; /* Old coordinates for flexcon */
+ int flex_nalloc; /* The allocation size of acc_dir and x_old */
+ rvec *adir_xnold; /* Work space for init_adir */
+ rvec *adir_xnew; /* Work space for init_adir */
+ int adir_nalloc; /* Work space for init_adir */
} t_gmx_shellfc;
-
-static void pr_shell(FILE *fplog,int ns,t_shell s[])
+
+static void pr_shell(FILE *fplog, int ns, t_shell s[])
{
- int i;
-
- fprintf(fplog,"SHELL DATA\n");
- fprintf(fplog,"%5s %8s %5s %5s %5s\n",
- "Shell","Force k","Nucl1","Nucl2","Nucl3");
- for(i=0; (i<ns); i++) {
- fprintf(fplog,"%5d %8.3f %5d",s[i].shell,1.0/s[i].k_1,s[i].nucl1);
- if (s[i].nnucl == 2)
- fprintf(fplog," %5d\n",s[i].nucl2);
- else if (s[i].nnucl == 3)
- fprintf(fplog," %5d %5d\n",s[i].nucl2,s[i].nucl3);
- else
- fprintf(fplog,"\n");
- }
+ int i;
+
+ fprintf(fplog, "SHELL DATA\n");
+ fprintf(fplog, "%5s %8s %5s %5s %5s\n",
+ "Shell", "Force k", "Nucl1", "Nucl2", "Nucl3");
+ for (i = 0; (i < ns); i++)
+ {
+ fprintf(fplog, "%5d %8.3f %5d", s[i].shell, 1.0/s[i].k_1, s[i].nucl1);
+ if (s[i].nnucl == 2)
+ {
+ fprintf(fplog, " %5d\n", s[i].nucl2);
+ }
+ else if (s[i].nnucl == 3)
+ {
+ fprintf(fplog, " %5d %5d\n", s[i].nucl2, s[i].nucl3);
+ }
+ else
+ {
+ fprintf(fplog, "\n");
+ }
+ }
}
-static void predict_shells(FILE *fplog,rvec x[],rvec v[],real dt,
- int ns,t_shell s[],
- real mass[],gmx_mtop_t *mtop,gmx_bool bInit)
+static void predict_shells(FILE *fplog, rvec x[], rvec v[], real dt,
+ int ns, t_shell s[],
+ real mass[], gmx_mtop_t *mtop, gmx_bool bInit)
{
- int i,m,s1,n1,n2,n3;
- real dt_1,dt_2,dt_3,fudge,tm,m1,m2,m3;
- rvec *ptr;
- gmx_mtop_atomlookup_t alook=NULL;
- t_atom *atom;
-
- if (mass == NULL) {
- alook = gmx_mtop_atomlookup_init(mtop);
- }
-
- /* We introduce a fudge factor for performance reasons: with this choice
- * the initial force on the shells is about a factor of two lower than
- * without
- */
- fudge = 1.0;
-
- if (bInit) {
- if (fplog)
- fprintf(fplog,"RELAX: Using prediction for initial shell placement\n");
- ptr = x;
- dt_1 = 1;
- }
- else {
- ptr = v;
- dt_1 = fudge*dt;
- }
-
- for(i=0; (i<ns); i++) {
- s1 = s[i].shell;
+ int i, m, s1, n1, n2, n3;
+ real dt_1, dt_2, dt_3, fudge, tm, m1, m2, m3;
+ rvec *ptr;
+ gmx_mtop_atomlookup_t alook = NULL;
+ t_atom *atom;
+
+ if (mass == NULL)
+ {
+ alook = gmx_mtop_atomlookup_init(mtop);
+ }
+
+ /* We introduce a fudge factor for performance reasons: with this choice
+ * the initial force on the shells is about a factor of two lower than
+ * without
+ */
+ fudge = 1.0;
+
if (bInit)
- clear_rvec(x[s1]);
- switch (s[i].nnucl) {
- case 1:
- n1 = s[i].nucl1;
- for(m=0; (m<DIM); m++)
- x[s1][m]+=ptr[n1][m]*dt_1;
- break;
- case 2:
- n1 = s[i].nucl1;
- n2 = s[i].nucl2;
- if (mass) {
- m1 = mass[n1];
- m2 = mass[n2];
- } else {
- /* Not the correct masses with FE, but it is just a prediction... */
- m1 = atom[n1].m;
- m2 = atom[n2].m;
- }
- tm = dt_1/(m1+m2);
- for(m=0; (m<DIM); m++)
- x[s1][m]+=(m1*ptr[n1][m]+m2*ptr[n2][m])*tm;
- break;
- case 3:
- n1 = s[i].nucl1;
- n2 = s[i].nucl2;
- n3 = s[i].nucl3;
- if (mass) {
- m1 = mass[n1];
- m2 = mass[n2];
- m3 = mass[n3];
- } else {
- /* Not the correct masses with FE, but it is just a prediction... */
- gmx_mtop_atomnr_to_atom(alook,n1,&atom);
- m1 = atom->m;
- gmx_mtop_atomnr_to_atom(alook,n2,&atom);
- m2 = atom->m;
- gmx_mtop_atomnr_to_atom(alook,n3,&atom);
- m3 = atom->m;
- }
- tm = dt_1/(m1+m2+m3);
- for(m=0; (m<DIM); m++)
- x[s1][m]+=(m1*ptr[n1][m]+m2*ptr[n2][m]+m3*ptr[n3][m])*tm;
- break;
- default:
- gmx_fatal(FARGS,"Shell %d has %d nuclei!",i,s[i].nnucl);
+ {
+ if (fplog)
+ {
+ fprintf(fplog, "RELAX: Using prediction for initial shell placement\n");
+ }
+ ptr = x;
+ dt_1 = 1;
+ }
+ else
+ {
+ ptr = v;
+ dt_1 = fudge*dt;
}
- }
- if (mass == NULL) {
- gmx_mtop_atomlookup_destroy(alook);
- }
+ for (i = 0; (i < ns); i++)
+ {
+ s1 = s[i].shell;
+ if (bInit)
+ {
+ clear_rvec(x[s1]);
+ }
+ switch (s[i].nnucl)
+ {
+ case 1:
+ n1 = s[i].nucl1;
+ for (m = 0; (m < DIM); m++)
+ {
+ x[s1][m] += ptr[n1][m]*dt_1;
+ }
+ break;
+ case 2:
+ n1 = s[i].nucl1;
+ n2 = s[i].nucl2;
+ if (mass)
+ {
+ m1 = mass[n1];
+ m2 = mass[n2];
+ }
+ else
+ {
+ /* Not the correct masses with FE, but it is just a prediction... */
+ m1 = atom[n1].m;
+ m2 = atom[n2].m;
+ }
+ tm = dt_1/(m1+m2);
+ for (m = 0; (m < DIM); m++)
+ {
+ x[s1][m] += (m1*ptr[n1][m]+m2*ptr[n2][m])*tm;
+ }
+ break;
+ case 3:
+ n1 = s[i].nucl1;
+ n2 = s[i].nucl2;
+ n3 = s[i].nucl3;
+ if (mass)
+ {
+ m1 = mass[n1];
+ m2 = mass[n2];
+ m3 = mass[n3];
+ }
+ else
+ {
+ /* Not the correct masses with FE, but it is just a prediction... */
+ gmx_mtop_atomnr_to_atom(alook, n1, &atom);
+ m1 = atom->m;
+ gmx_mtop_atomnr_to_atom(alook, n2, &atom);
+ m2 = atom->m;
+ gmx_mtop_atomnr_to_atom(alook, n3, &atom);
+ m3 = atom->m;
+ }
+ tm = dt_1/(m1+m2+m3);
+ for (m = 0; (m < DIM); m++)
+ {
+ x[s1][m] += (m1*ptr[n1][m]+m2*ptr[n2][m]+m3*ptr[n3][m])*tm;
+ }
+ break;
+ default:
+ gmx_fatal(FARGS, "Shell %d has %d nuclei!", i, s[i].nnucl);
+ }
+ }
+
+ if (mass == NULL)
+ {
+ gmx_mtop_atomlookup_destroy(alook);
+ }
}
gmx_shellfc_t init_shell_flexcon(FILE *fplog,
- gmx_mtop_t *mtop,int nflexcon,
- rvec *x)
+ gmx_mtop_t *mtop, int nflexcon,
+ rvec *x)
{
- struct gmx_shellfc *shfc;
- t_shell *shell;
- int *shell_index=NULL,*at2cg;
- t_atom *atom;
- int n[eptNR],ns,nshell,nsi;
- int i,j,nmol,type,mb,mt,a_offset,cg,mol,ftype,nra;
- real qS,alpha;
- int aS,aN=0; /* Shell and nucleus */
- int bondtypes[] = { F_BONDS, F_HARMONIC, F_CUBICBONDS, F_POLARIZATION, F_ANHARM_POL, F_WATER_POL };
+ struct gmx_shellfc *shfc;
+ t_shell *shell;
+ int *shell_index = NULL, *at2cg;
+ t_atom *atom;
+ int n[eptNR], ns, nshell, nsi;
+ int i, j, nmol, type, mb, mt, a_offset, cg, mol, ftype, nra;
+ real qS, alpha;
+ int aS, aN = 0; /* Shell and nucleus */
+ int bondtypes[] = { F_BONDS, F_HARMONIC, F_CUBICBONDS, F_POLARIZATION, F_ANHARM_POL, F_WATER_POL };
#define NBT asize(bondtypes)
- t_iatom *ia;
- gmx_mtop_atomloop_block_t aloopb;
- gmx_mtop_atomloop_all_t aloop;
- gmx_ffparams_t *ffparams;
- gmx_molblock_t *molb;
- gmx_moltype_t *molt;
- t_block *cgs;
-
- /* Count number of shells, and find their indices */
- for(i=0; (i<eptNR); i++) {
- n[i] = 0;
- }
-
- aloopb = gmx_mtop_atomloop_block_init(mtop);
- while (gmx_mtop_atomloop_block_next(aloopb,&atom,&nmol)) {
- n[atom->ptype] += nmol;
- }
-
- if (fplog) {
- /* Print the number of each particle type */
- for(i=0; (i<eptNR); i++) {
- if (n[i] != 0) {
- fprintf(fplog,"There are: %d %ss\n",n[i],ptype_str[i]);
- }
+ t_iatom *ia;
+ gmx_mtop_atomloop_block_t aloopb;
+ gmx_mtop_atomloop_all_t aloop;
+ gmx_ffparams_t *ffparams;
+ gmx_molblock_t *molb;
+ gmx_moltype_t *molt;
+ t_block *cgs;
+
+ /* Count number of shells, and find their indices */
+ for (i = 0; (i < eptNR); i++)
+ {
+ n[i] = 0;
}
- }
- nshell = n[eptShell];
-
- if (nshell == 0 && nflexcon == 0) {
- return NULL;
- }
+ aloopb = gmx_mtop_atomloop_block_init(mtop);
+ while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
+ {
+ n[atom->ptype] += nmol;
+ }
- snew(shfc,1);
- shfc->nflexcon = nflexcon;
+ if (fplog)
+ {
+ /* Print the number of each particle type */
+ for (i = 0; (i < eptNR); i++)
+ {
+ if (n[i] != 0)
+ {
+ fprintf(fplog, "There are: %d %ss\n", n[i], ptype_str[i]);
+ }
+ }
+ }
- if (nshell == 0) {
- return shfc;
- }
+ nshell = n[eptShell];
- /* We have shells: fill the shell data structure */
+ if (nshell == 0 && nflexcon == 0)
+ {
+ /* We're not doing shells or flexible constraints */
+ return NULL;
+ }
+
+ snew(shfc, 1);
+ shfc->nflexcon = nflexcon;
+
+ if (nshell == 0)
+ {
+ return shfc;
+ }
+
+ /* We have shells: fill the shell data structure */
- /* Global system sized array, this should be avoided */
- snew(shell_index,mtop->natoms);
+ /* Global system sized array, this should be avoided */
+ snew(shell_index, mtop->natoms);
- aloop = gmx_mtop_atomloop_all_init(mtop);
- nshell = 0;
- while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
- if (atom->ptype == eptShell) {
- shell_index[i] = nshell++;
+ aloop = gmx_mtop_atomloop_all_init(mtop);
+ nshell = 0;
+ while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
+ {
+ if (atom->ptype == eptShell)
+ {
+ shell_index[i] = nshell++;
+ }
}
- }
-
- snew(shell,nshell);
-
- /* Initiate the shell structures */
- for(i=0; (i<nshell); i++) {
- shell[i].shell = NO_ATID;
- shell[i].nnucl = 0;
- shell[i].nucl1 = NO_ATID;
- shell[i].nucl2 = NO_ATID;
- shell[i].nucl3 = NO_ATID;
- /* shell[i].bInterCG=FALSE; */
- shell[i].k_1 = 0;
- shell[i].k = 0;
- }
-
- ffparams = &mtop->ffparams;
-
- /* Now fill the structures */
- shfc->bInterCG = FALSE;
- ns = 0;
- a_offset = 0;
- for(mb=0; mb<mtop->nmolblock; mb++) {
- molb = &mtop->molblock[mb];
- molt = &mtop->moltype[molb->type];
-
- cgs = &molt->cgs;
- snew(at2cg,molt->atoms.nr);
- for(cg=0; cg<cgs->nr; cg++) {
- for(i=cgs->index[cg]; i<cgs->index[cg+1]; i++) {
- at2cg[i] = cg;
- }
+
+ snew(shell, nshell);
+
+ /* Initiate the shell structures */
+ for (i = 0; (i < nshell); i++)
+ {
+ shell[i].shell = NO_ATID;
+ shell[i].nnucl = 0;
+ shell[i].nucl1 = NO_ATID;
+ shell[i].nucl2 = NO_ATID;
+ shell[i].nucl3 = NO_ATID;
+ /* shell[i].bInterCG=FALSE; */
+ shell[i].k_1 = 0;
+ shell[i].k = 0;
}
- atom = molt->atoms.atom;
- for(mol=0; mol<molb->nmol; mol++) {
- for(j=0; (j<NBT); j++) {
- ia = molt->ilist[bondtypes[j]].iatoms;
- for(i=0; (i<molt->ilist[bondtypes[j]].nr); ) {
- type = ia[0];
- ftype = ffparams->functype[type];
- nra = interaction_function[ftype].nratoms;
-
- /* Check whether we have a bond with a shell */
- aS = NO_ATID;
-
- switch (bondtypes[j]) {
- case F_BONDS:
- case F_HARMONIC:
- case F_CUBICBONDS:
- case F_POLARIZATION:
- case F_ANHARM_POL:
- if (atom[ia[1]].ptype == eptShell) {
- aS = ia[1];
- aN = ia[2];
- }
- else if (atom[ia[2]].ptype == eptShell) {
- aS = ia[2];
- aN = ia[1];
- }
- break;
- case F_WATER_POL:
- aN = ia[4]; /* Dummy */
- aS = ia[5]; /* Shell */
- break;
- default:
- gmx_fatal(FARGS,"Death Horror: %s, %d",__FILE__,__LINE__);
- }
-
- if (aS != NO_ATID) {
- qS = atom[aS].q;
-
- /* Check whether one of the particles is a shell... */
- nsi = shell_index[a_offset+aS];
- if ((nsi < 0) || (nsi >= nshell))
- gmx_fatal(FARGS,"nsi is %d should be within 0 - %d. aS = %d",
- nsi,nshell,aS);
- if (shell[nsi].shell == NO_ATID) {
- shell[nsi].shell = a_offset + aS;
- ns ++;
- }
- else if (shell[nsi].shell != a_offset+aS)
- gmx_fatal(FARGS,"Weird stuff in %s, %d",__FILE__,__LINE__);
-
- if (shell[nsi].nucl1 == NO_ATID) {
- shell[nsi].nucl1 = a_offset + aN;
- } else if (shell[nsi].nucl2 == NO_ATID) {
- shell[nsi].nucl2 = a_offset + aN;
- } else if (shell[nsi].nucl3 == NO_ATID) {
- shell[nsi].nucl3 = a_offset + aN;
- } else {
- if (fplog)
- pr_shell(fplog,ns,shell);
- gmx_fatal(FARGS,"Can not handle more than three bonds per shell\n");
- }
- if (at2cg[aS] != at2cg[aN]) {
- /* shell[nsi].bInterCG = TRUE; */
- shfc->bInterCG = TRUE;
- }
-
- switch (bondtypes[j]) {
- case F_BONDS:
- case F_HARMONIC:
- shell[nsi].k += ffparams->iparams[type].harmonic.krA;
- break;
- case F_CUBICBONDS:
- shell[nsi].k += ffparams->iparams[type].cubic.kb;
- break;
- case F_POLARIZATION:
- case F_ANHARM_POL:
- if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
- gmx_fatal(FARGS,"polarize can not be used with qA(%e) != qB(%e) for atom %d of molecule block %d", qS, atom[aS].qB, aS+1, mb+1);
- shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/
- ffparams->iparams[type].polarize.alpha;
- break;
- case F_WATER_POL:
- if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
- gmx_fatal(FARGS,"water_pol can not be used with qA(%e) != qB(%e) for atom %d of molecule block %d", qS, atom[aS].qB, aS+1, mb+1);
- alpha = (ffparams->iparams[type].wpol.al_x+
- ffparams->iparams[type].wpol.al_y+
- ffparams->iparams[type].wpol.al_z)/3.0;
- shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/alpha;
- break;
- default:
- gmx_fatal(FARGS,"Death Horror: %s, %d",__FILE__,__LINE__);
- }
- shell[nsi].nnucl++;
- }
- ia += nra+1;
- i += nra+1;
- }
- }
- a_offset += molt->atoms.nr;
+ ffparams = &mtop->ffparams;
+
+ /* Now fill the structures */
+ shfc->bInterCG = FALSE;
+ ns = 0;
+ a_offset = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ molt = &mtop->moltype[molb->type];
+
+ cgs = &molt->cgs;
+ snew(at2cg, molt->atoms.nr);
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ for (i = cgs->index[cg]; i < cgs->index[cg+1]; i++)
+ {
+ at2cg[i] = cg;
+ }
+ }
+
+ atom = molt->atoms.atom;
+ for (mol = 0; mol < molb->nmol; mol++)
+ {
+ for (j = 0; (j < NBT); j++)
+ {
+ ia = molt->ilist[bondtypes[j]].iatoms;
+ for (i = 0; (i < molt->ilist[bondtypes[j]].nr); )
+ {
+ type = ia[0];
+ ftype = ffparams->functype[type];
+ nra = interaction_function[ftype].nratoms;
+
+ /* Check whether we have a bond with a shell */
+ aS = NO_ATID;
+
+ switch (bondtypes[j])
+ {
+ case F_BONDS:
+ case F_HARMONIC:
+ case F_CUBICBONDS:
+ case F_POLARIZATION:
+ case F_ANHARM_POL:
+ if (atom[ia[1]].ptype == eptShell)
+ {
+ aS = ia[1];
+ aN = ia[2];
+ }
+ else if (atom[ia[2]].ptype == eptShell)
+ {
+ aS = ia[2];
+ aN = ia[1];
+ }
+ break;
+ case F_WATER_POL:
+ aN = ia[4]; /* Dummy */
+ aS = ia[5]; /* Shell */
+ break;
+ default:
+ gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
+ }
+
+ if (aS != NO_ATID)
+ {
+ qS = atom[aS].q;
+
+ /* Check whether one of the particles is a shell... */
+ nsi = shell_index[a_offset+aS];
+ if ((nsi < 0) || (nsi >= nshell))
+ {
+ gmx_fatal(FARGS, "nsi is %d should be within 0 - %d. aS = %d",
+ nsi, nshell, aS);
+ }
+ if (shell[nsi].shell == NO_ATID)
+ {
+ shell[nsi].shell = a_offset + aS;
+ ns++;
+ }
+ else if (shell[nsi].shell != a_offset+aS)
+ {
+ gmx_fatal(FARGS, "Weird stuff in %s, %d", __FILE__, __LINE__);
+ }
+
+ if (shell[nsi].nucl1 == NO_ATID)
+ {
+ shell[nsi].nucl1 = a_offset + aN;
+ }
+ else if (shell[nsi].nucl2 == NO_ATID)
+ {
+ shell[nsi].nucl2 = a_offset + aN;
+ }
+ else if (shell[nsi].nucl3 == NO_ATID)
+ {
+ shell[nsi].nucl3 = a_offset + aN;
+ }
+ else
+ {
+ if (fplog)
+ {
+ pr_shell(fplog, ns, shell);
+ }
+ gmx_fatal(FARGS, "Can not handle more than three bonds per shell\n");
+ }
+ if (at2cg[aS] != at2cg[aN])
+ {
+ /* shell[nsi].bInterCG = TRUE; */
+ shfc->bInterCG = TRUE;
+ }
+
+ switch (bondtypes[j])
+ {
+ case F_BONDS:
+ case F_HARMONIC:
+ shell[nsi].k += ffparams->iparams[type].harmonic.krA;
+ break;
+ case F_CUBICBONDS:
+ shell[nsi].k += ffparams->iparams[type].cubic.kb;
+ break;
+ case F_POLARIZATION:
+ case F_ANHARM_POL:
+ if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
+ {
+ gmx_fatal(FARGS, "polarize can not be used with qA(%e) != qB(%e) for atom %d of molecule block %d", qS, atom[aS].qB, aS+1, mb+1);
+ }
+ shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/
+ ffparams->iparams[type].polarize.alpha;
+ break;
+ case F_WATER_POL:
+ if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
+ {
+ gmx_fatal(FARGS, "water_pol can not be used with qA(%e) != qB(%e) for atom %d of molecule block %d", qS, atom[aS].qB, aS+1, mb+1);
+ }
+ alpha = (ffparams->iparams[type].wpol.al_x+
+ ffparams->iparams[type].wpol.al_y+
+ ffparams->iparams[type].wpol.al_z)/3.0;
+ shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/alpha;
+ break;
+ default:
+ gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
+ }
+ shell[nsi].nnucl++;
+ }
+ ia += nra+1;
+ i += nra+1;
+ }
+ }
+ a_offset += molt->atoms.nr;
+ }
+ /* Done with this molecule type */
+ sfree(at2cg);
}
- /* Done with this molecule type */
- sfree(at2cg);
- }
-
- /* Verify whether it's all correct */
- if (ns != nshell)
- gmx_fatal(FARGS,"Something weird with shells. They may not be bonded to something");
-
- for(i=0; (i<ns); i++)
- shell[i].k_1 = 1.0/shell[i].k;
-
- if (debug)
- pr_shell(debug,ns,shell);
-
-
- shfc->nshell_gl = ns;
- shfc->shell_gl = shell;
- shfc->shell_index_gl = shell_index;
-
- shfc->bPredict = (getenv("GMX_NOPREDICT") == NULL);
- shfc->bRequireInit = FALSE;
- if (!shfc->bPredict) {
- if (fplog)
- fprintf(fplog,"\nWill never predict shell positions\n");
- } else {
- shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != NULL);
- if (shfc->bRequireInit && fplog)
- fprintf(fplog,"\nWill always initiate shell positions\n");
- }
-
- if (shfc->bPredict) {
- if (x) {
- predict_shells(fplog,x,NULL,0,shfc->nshell_gl,shfc->shell_gl,
- NULL,mtop,TRUE);
+
+ /* Verify whether it's all correct */
+ if (ns != nshell)
+ {
+ gmx_fatal(FARGS, "Something weird with shells. They may not be bonded to something");
}
- if (shfc->bInterCG) {
- if (fplog)
- fprintf(fplog,"\nNOTE: there all shells that are connected to particles outside thier own charge group, will not predict shells positions during the run\n\n");
- shfc->bPredict = FALSE;
+ for (i = 0; (i < ns); i++)
+ {
+ shell[i].k_1 = 1.0/shell[i].k;
}
- }
- return shfc;
+ if (debug)
+ {
+ pr_shell(debug, ns, shell);
+ }
+
+
+ shfc->nshell_gl = ns;
+ shfc->shell_gl = shell;
+ shfc->shell_index_gl = shell_index;
+
+ shfc->bPredict = (getenv("GMX_NOPREDICT") == NULL);
+ shfc->bRequireInit = FALSE;
+ if (!shfc->bPredict)
+ {
+ if (fplog)
+ {
+ fprintf(fplog, "\nWill never predict shell positions\n");
+ }
+ }
+ else
+ {
+ shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != NULL);
+ if (shfc->bRequireInit && fplog)
+ {
+ fprintf(fplog, "\nWill always initiate shell positions\n");
+ }
+ }
+
+ if (shfc->bPredict)
+ {
+ if (x)
+ {
+ predict_shells(fplog, x, NULL, 0, shfc->nshell_gl, shfc->shell_gl,
+ NULL, mtop, TRUE);
+ }
+
+ if (shfc->bInterCG)
+ {
+ if (fplog)
+ {
+ fprintf(fplog, "\nNOTE: there all shells that are connected to particles outside thier own charge group, will not predict shells positions during the run\n\n");
+ }
+ /* Prediction improves performance, so we should implement either:
+ * 1. communication for the atoms needed for prediction
+ * 2. prediction using the velocities of shells; currently the
+ * shell velocities are zeroed, it's a bit tricky to keep
+ * track of the shell displacements and thus the velocity.
+ */
+ shfc->bPredict = FALSE;
+ }
+ }
+
+ return shfc;
}
-void make_local_shells(t_commrec *cr,t_mdatoms *md,
- struct gmx_shellfc *shfc)
+void make_local_shells(t_commrec *cr, t_mdatoms *md,
+ struct gmx_shellfc *shfc)
{
- t_shell *shell;
- int a0,a1,*ind,nshell,i;
- gmx_domdec_t *dd=NULL;
-
- if (PAR(cr)) {
- if (DOMAINDECOMP(cr)) {
- dd = cr->dd;
- a0 = 0;
- a1 = dd->nat_home;
- } else {
- pd_at_range(cr,&a0,&a1);
+ t_shell *shell;
+ int a0, a1, *ind, nshell, i;
+ gmx_domdec_t *dd = NULL;
+
+ if (DOMAINDECOMP(cr))
+ {
+ dd = cr->dd;
+ a0 = 0;
+ a1 = dd->nat_home;
}
- } else {
- /* Single node: we need all shells, just copy the pointer */
- shfc->nshell = shfc->nshell_gl;
- shfc->shell = shfc->shell_gl;
-
- return;
- }
-
- ind = shfc->shell_index_gl;
-
- nshell = 0;
- shell = shfc->shell;
- for(i=a0; i<a1; i++) {
- if (md->ptype[i] == eptShell) {
- if (nshell+1 > shfc->shell_nalloc) {
- shfc->shell_nalloc = over_alloc_dd(nshell+1);
- srenew(shell,shfc->shell_nalloc);
- }
- if (dd) {
- shell[nshell] = shfc->shell_gl[ind[dd->gatindex[i]]];
- } else {
- shell[nshell] = shfc->shell_gl[ind[i]];
- }
- /* With inter-cg shells we can no do shell prediction,
- * so we do not need the nuclei numbers.
- */
- if (!shfc->bInterCG) {
- shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
- if (shell[nshell].nnucl > 1)
- shell[nshell].nucl2 = i + shell[nshell].nucl2 - shell[nshell].shell;
- if (shell[nshell].nnucl > 2)
- shell[nshell].nucl3 = i + shell[nshell].nucl3 - shell[nshell].shell;
- }
- shell[nshell].shell = i;
- nshell++;
+ else
+ {
+ /* Single node: we need all shells, just copy the pointer */
+ shfc->nshell = shfc->nshell_gl;
+ shfc->shell = shfc->shell_gl;
+
+ return;
+ }
+
+ ind = shfc->shell_index_gl;
+
+ nshell = 0;
+ shell = shfc->shell;
+ for (i = a0; i < a1; i++)
+ {
+ if (md->ptype[i] == eptShell)
+ {
+ if (nshell+1 > shfc->shell_nalloc)
+ {
+ shfc->shell_nalloc = over_alloc_dd(nshell+1);
+ srenew(shell, shfc->shell_nalloc);
+ }
+ if (dd)
+ {
+ shell[nshell] = shfc->shell_gl[ind[dd->gatindex[i]]];
+ }
+ else
+ {
+ shell[nshell] = shfc->shell_gl[ind[i]];
+ }
+
+ /* With inter-cg shells we can no do shell prediction,
+ * so we do not need the nuclei numbers.
+ */
+ if (!shfc->bInterCG)
+ {
+ shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
+ if (shell[nshell].nnucl > 1)
+ {
+ shell[nshell].nucl2 = i + shell[nshell].nucl2 - shell[nshell].shell;
+ }
+ if (shell[nshell].nnucl > 2)
+ {
+ shell[nshell].nucl3 = i + shell[nshell].nucl3 - shell[nshell].shell;
+ }
+ }
+ shell[nshell].shell = i;
+ nshell++;
+ }
}
- }
- shfc->nshell = nshell;
- shfc->shell = shell;
+ shfc->nshell = nshell;
+ shfc->shell = shell;
}
-static void do_1pos(rvec xnew,rvec xold,rvec f,real step)
+static void do_1pos(rvec xnew, rvec xold, rvec f, real step)
{
- real xo,yo,zo;
- real dx,dy,dz;
-
- xo=xold[XX];
- yo=xold[YY];
- zo=xold[ZZ];
-
- dx=f[XX]*step;
- dy=f[YY]*step;
- dz=f[ZZ]*step;
-
- xnew[XX]=xo+dx;
- xnew[YY]=yo+dy;
- xnew[ZZ]=zo+dz;
+ real xo, yo, zo;
+ real dx, dy, dz;
+
+ xo = xold[XX];
+ yo = xold[YY];
+ zo = xold[ZZ];
+
+ dx = f[XX]*step;
+ dy = f[YY]*step;
+ dz = f[ZZ]*step;
+
+ xnew[XX] = xo+dx;
+ xnew[YY] = yo+dy;
+ xnew[ZZ] = zo+dz;
}
-static void do_1pos3(rvec xnew,rvec xold,rvec f,rvec step)
+static void do_1pos3(rvec xnew, rvec xold, rvec f, rvec step)
{
- real xo,yo,zo;
- real dx,dy,dz;
-
- xo=xold[XX];
- yo=xold[YY];
- zo=xold[ZZ];
-
- dx=f[XX]*step[XX];
- dy=f[YY]*step[YY];
- dz=f[ZZ]*step[ZZ];
-
- xnew[XX]=xo+dx;
- xnew[YY]=yo+dy;
- xnew[ZZ]=zo+dz;
+ real xo, yo, zo;
+ real dx, dy, dz;
+
+ xo = xold[XX];
+ yo = xold[YY];
+ zo = xold[ZZ];
+
+ dx = f[XX]*step[XX];
+ dy = f[YY]*step[YY];
+ dz = f[ZZ]*step[ZZ];
+
+ xnew[XX] = xo+dx;
+ xnew[YY] = yo+dy;
+ xnew[ZZ] = zo+dz;
}
-static void directional_sd(FILE *log,rvec xold[],rvec xnew[],rvec acc_dir[],
- int start,int homenr,real step)
+static void directional_sd(rvec xold[], rvec xnew[], rvec acc_dir[],
+ int start, int homenr, real step)
{
- int i;
+ int i;
- for(i=start; i<homenr; i++)
- do_1pos(xnew[i],xold[i],acc_dir[i],step);
+ for (i = start; i < homenr; i++)
+ {
+ do_1pos(xnew[i], xold[i], acc_dir[i], step);
+ }
}
-static void shell_pos_sd(FILE *log,rvec xcur[],rvec xnew[],rvec f[],
- int ns,t_shell s[],int count)
+static void shell_pos_sd(rvec xcur[], rvec xnew[], rvec f[],
+ int ns, t_shell s[], int count)
{
- const real step_scale_min = 0.8,
- step_scale_increment = 0.2,
- step_scale_max = 1.2,
- step_scale_multiple = (step_scale_max - step_scale_min) / step_scale_increment;
- int i,shell,d;
- real dx,df,k_est;
-#ifdef PRINT_STEP
- real step_min,step_max;
-
- step_min = 1e30;
- step_max = 0;
-#endif
- for(i=0; (i<ns); i++) {
- shell = s[i].shell;
- if (count == 1) {
- for(d=0; d<DIM; d++) {
- s[i].step[d] = s[i].k_1;
+ const real step_scale_min = 0.8,
+ step_scale_increment = 0.2,
+ step_scale_max = 1.2,
+ step_scale_multiple = (step_scale_max - step_scale_min) / step_scale_increment;
+ int i, shell, d;
+ real dx, df, k_est;
#ifdef PRINT_STEP
- step_min = min(step_min,s[i].step[d]);
- step_max = max(step_max,s[i].step[d]);
+ real step_min, step_max;
+
+ step_min = 1e30;
+ step_max = 0;
#endif
- }
- } else {
- for(d=0; d<DIM; d++) {
- dx = xcur[shell][d] - s[i].xold[d];
- df = f[shell][d] - s[i].fold[d];
- /* -dx/df gets used to generate an interpolated value, but would
- * cause a NaN if df were binary-equal to zero. Values close to
- * zero won't cause problems (because of the min() and max()), so
- * just testing for binary inequality is OK. */
- if (0.0 != df)
- {
- k_est = -dx/df;
- /* Scale the step size by a factor interpolated from
- * step_scale_min to step_scale_max, as k_est goes from 0 to
- * step_scale_multiple * s[i].step[d] */
- s[i].step[d] =
- step_scale_min * s[i].step[d] +
- step_scale_increment * min(step_scale_multiple * s[i].step[d], max(k_est, 0));
- }
- else
+ for (i = 0; (i < ns); i++)
{
- /* Here 0 == df */
- if (gmx_numzero(dx)) /* 0 == dx */
+ shell = s[i].shell;
+ if (count == 1)
{
- /* Likely this will never happen, but if it does just
- * don't scale the step. */
+ for (d = 0; d < DIM; d++)
+ {
+ s[i].step[d] = s[i].k_1;
+#ifdef PRINT_STEP
+ step_min = min(step_min, s[i].step[d]);
+ step_max = max(step_max, s[i].step[d]);
+#endif
+ }
}
- else /* 0 != dx */
+ else
{
- s[i].step[d] *= step_scale_max;
- }
- }
+ for (d = 0; d < DIM; d++)
+ {
+ dx = xcur[shell][d] - s[i].xold[d];
+ df = f[shell][d] - s[i].fold[d];
+ /* -dx/df gets used to generate an interpolated value, but would
+ * cause a NaN if df were binary-equal to zero. Values close to
+ * zero won't cause problems (because of the min() and max()), so
+ * just testing for binary inequality is OK. */
+ if (0.0 != df)
+ {
+ k_est = -dx/df;
+ /* Scale the step size by a factor interpolated from
+ * step_scale_min to step_scale_max, as k_est goes from 0 to
+ * step_scale_multiple * s[i].step[d] */
+ s[i].step[d] =
+ step_scale_min * s[i].step[d] +
+ step_scale_increment * min(step_scale_multiple * s[i].step[d], max(k_est, 0));
+ }
+ else
+ {
+ /* Here 0 == df */
+ if (gmx_numzero(dx)) /* 0 == dx */
+ {
+ /* Likely this will never happen, but if it does just
+ * don't scale the step. */
+ }
+ else /* 0 != dx */
+ {
+ s[i].step[d] *= step_scale_max;
+ }
+ }
#ifdef PRINT_STEP
- step_min = min(step_min,s[i].step[d]);
- step_max = max(step_max,s[i].step[d]);
+ step_min = min(step_min, s[i].step[d]);
+ step_max = max(step_max, s[i].step[d]);
#endif
- }
- }
- copy_rvec(xcur[shell],s[i].xold);
- copy_rvec(f[shell], s[i].fold);
+ }
+ }
+ copy_rvec(xcur[shell], s[i].xold);
+ copy_rvec(f[shell], s[i].fold);
- do_1pos3(xnew[shell],xcur[shell],f[shell],s[i].step);
+ do_1pos3(xnew[shell], xcur[shell], f[shell], s[i].step);
- if (gmx_debug_at) {
- fprintf(debug,"shell[%d] = %d\n",i,shell);
- pr_rvec(debug,0,"fshell",f[shell],DIM,TRUE);
- pr_rvec(debug,0,"xold",xcur[shell],DIM,TRUE);
- pr_rvec(debug,0,"step",s[i].step,DIM,TRUE);
- pr_rvec(debug,0,"xnew",xnew[shell],DIM,TRUE);
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "shell[%d] = %d\n", i, shell);
+ pr_rvec(debug, 0, "fshell", f[shell], DIM, TRUE);
+ pr_rvec(debug, 0, "xold", xcur[shell], DIM, TRUE);
+ pr_rvec(debug, 0, "step", s[i].step, DIM, TRUE);
+ pr_rvec(debug, 0, "xnew", xnew[shell], DIM, TRUE);
+ }
}
- }
#ifdef PRINT_STEP
- printf("step %.3e %.3e\n",step_min,step_max);
+ printf("step %.3e %.3e\n", step_min, step_max);
#endif
}
-static void decrease_step_size(int nshell,t_shell s[])
+static void decrease_step_size(int nshell, t_shell s[])
{
- int i;
-
- for(i=0; i<nshell; i++)
- svmul(0.8,s[i].step,s[i].step);
+ int i;
+
+ for (i = 0; i < nshell; i++)
+ {
+ svmul(0.8, s[i].step, s[i].step);
+ }
}
-static void print_epot(FILE *fp,gmx_large_int_t mdstep,int count,real epot,real df,
- int ndir,real sf_dir)
+static void print_epot(FILE *fp, gmx_int64_t mdstep, int count, real epot, real df,
+ int ndir, real sf_dir)
{
- char buf[22];
-
- fprintf(fp,"MDStep=%5s/%2d EPot: %12.8e, rmsF: %6.2e",
- gmx_step_str(mdstep,buf),count,epot,df);
- if (ndir)
- fprintf(fp,", dir. rmsF: %6.2e\n",sqrt(sf_dir/ndir));
- else
- fprintf(fp,"\n");
+ char buf[22];
+
+ fprintf(fp, "MDStep=%5s/%2d EPot: %12.8e, rmsF: %6.2e",
+ gmx_step_str(mdstep, buf), count, epot, df);
+ if (ndir)
+ {
+ fprintf(fp, ", dir. rmsF: %6.2e\n", sqrt(sf_dir/ndir));
+ }
+ else
+ {
+ fprintf(fp, "\n");
+ }
}
-static real rms_force(t_commrec *cr,rvec f[],int ns,t_shell s[],
- int ndir,real *sf_dir,real *Epot)
+static real rms_force(t_commrec *cr, rvec f[], int ns, t_shell s[],
+ int ndir, real *sf_dir, real *Epot)
{
- int i,shell,ntot;
- double buf[4];
-
- buf[0] = *sf_dir;
- for(i=0; i<ns; i++) {
- shell = s[i].shell;
- buf[0] += norm2(f[shell]);
- }
- ntot = ns;
-
- if (PAR(cr)) {
- buf[1] = ntot;
- buf[2] = *sf_dir;
- buf[3] = *Epot;
- gmx_sumd(4,buf,cr);
- ntot = (int)(buf[1] + 0.5);
- *sf_dir = buf[2];
- *Epot = buf[3];
- }
- ntot += ndir;
-
- return (ntot ? sqrt(buf[0]/ntot) : 0);
+ int i, shell, ntot;
+ double buf[4];
+
+ buf[0] = *sf_dir;
+ for (i = 0; i < ns; i++)
+ {
+ shell = s[i].shell;
+ buf[0] += norm2(f[shell]);
+ }
+ ntot = ns;
+
+ if (PAR(cr))
+ {
+ buf[1] = ntot;
+ buf[2] = *sf_dir;
+ buf[3] = *Epot;
+ gmx_sumd(4, buf, cr);
+ ntot = (int)(buf[1] + 0.5);
+ *sf_dir = buf[2];
+ *Epot = buf[3];
+ }
+ ntot += ndir;
+
+ return (ntot ? sqrt(buf[0]/ntot) : 0);
}
-static void check_pbc(FILE *fp,rvec x[],int shell)
+static void check_pbc(FILE *fp, rvec x[], int shell)
{
- int m,now;
-
- now = shell-4;
- for(m=0; (m<DIM); m++)
- if (fabs(x[shell][m]-x[now][m]) > 0.3) {
- pr_rvecs(fp,0,"SHELL-X",x+now,5);
- break;
+ int m, now;
+
+ now = shell-4;
+ for (m = 0; (m < DIM); m++)
+ {
+ if (fabs(x[shell][m]-x[now][m]) > 0.3)
+ {
+ pr_rvecs(fp, 0, "SHELL-X", x+now, 5);
+ break;
+ }
}
}
-static void dump_shells(FILE *fp,rvec x[],rvec f[],real ftol,int ns,t_shell s[])
+static void dump_shells(FILE *fp, rvec x[], rvec f[], real ftol, int ns, t_shell s[])
{
- int i,shell;
- real ft2,ff2;
-
- ft2 = sqr(ftol);
-
- for(i=0; (i<ns); i++) {
- shell = s[i].shell;
- ff2 = iprod(f[shell],f[shell]);
- if (ff2 > ft2)
- fprintf(fp,"SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n",
- shell,f[shell][XX],f[shell][YY],f[shell][ZZ],sqrt(ff2));
- check_pbc(fp,x,shell);
- }
+ int i, shell;
+ real ft2, ff2;
+
+ ft2 = sqr(ftol);
+
+ for (i = 0; (i < ns); i++)
+ {
+ shell = s[i].shell;
+ ff2 = iprod(f[shell], f[shell]);
+ if (ff2 > ft2)
+ {
+ fprintf(fp, "SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n",
+ shell, f[shell][XX], f[shell][YY], f[shell][ZZ], sqrt(ff2));
+ }
+ check_pbc(fp, x, shell);
+ }
}
-static void init_adir(FILE *log,gmx_shellfc_t shfc,
- gmx_constr_t constr,t_idef *idef,t_inputrec *ir,
- t_commrec *cr,int dd_ac1,
- gmx_large_int_t step,t_mdatoms *md,int start,int end,
- rvec *x_old,rvec *x_init,rvec *x,
- rvec *f,rvec *acc_dir,
- gmx_bool bMolPBC,matrix box,
- real *lambda,real *dvdlambda,t_nrnb *nrnb)
+static void init_adir(FILE *log, gmx_shellfc_t shfc,
+ gmx_constr_t constr, t_idef *idef, t_inputrec *ir,
+ t_commrec *cr, int dd_ac1,
+ gmx_int64_t step, t_mdatoms *md, int start, int end,
+ rvec *x_old, rvec *x_init, rvec *x,
+ rvec *f, rvec *acc_dir,
+ gmx_bool bMolPBC, matrix box,
+ real *lambda, real *dvdlambda, t_nrnb *nrnb)
{
- rvec *xnold,*xnew;
- double w_dt;
- int gf,ga,gt;
- real dt,scale;
- int n,d;
- unsigned short *ptype;
- rvec p,dx;
-
- if (DOMAINDECOMP(cr))
- n = dd_ac1;
- else
- n = end - start;
- if (n > shfc->adir_nalloc) {
- shfc->adir_nalloc = over_alloc_dd(n);
- srenew(shfc->adir_xnold,shfc->adir_nalloc);
- srenew(shfc->adir_xnew ,shfc->adir_nalloc);
- }
- xnold = shfc->adir_xnold;
- xnew = shfc->adir_xnew;
-
- ptype = md->ptype;
-
- dt = ir->delta_t;
-
- /* Does NOT work with freeze or acceleration groups (yet) */
- for (n=start; n<end; n++) {
- w_dt = md->invmass[n]*dt;
-
- for (d=0; d<DIM; d++) {
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell)) {
- xnold[n-start][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
- xnew[n-start][d] = 2*x[n][d] - x_old[n][d] + f[n][d]*w_dt*dt;
- } else {
- xnold[n-start][d] = x[n][d];
- xnew[n-start][d] = x[n][d];
- }
+ rvec *xnold, *xnew;
+ double w_dt;
+ int gf, ga, gt;
+ real dt, scale;
+ int n, d;
+ unsigned short *ptype;
+ rvec p, dx;
+
+ if (DOMAINDECOMP(cr))
+ {
+ n = dd_ac1;
+ }
+ else
+ {
+ n = end - start;
+ }
+ if (n > shfc->adir_nalloc)
+ {
+ shfc->adir_nalloc = over_alloc_dd(n);
+ srenew(shfc->adir_xnold, shfc->adir_nalloc);
+ srenew(shfc->adir_xnew, shfc->adir_nalloc);
}
- }
- constrain(log,FALSE,FALSE,constr,idef,ir,NULL,cr,step,0,md,
- x,xnold-start,NULL,bMolPBC,box,
- lambda[efptBONDED],&(dvdlambda[efptBONDED]),
- NULL,NULL,nrnb,econqCoord,FALSE,0,0);
- constrain(log,FALSE,FALSE,constr,idef,ir,NULL,cr,step,0,md,
- x,xnew-start,NULL,bMolPBC,box,
- lambda[efptBONDED],&(dvdlambda[efptBONDED]),
- NULL,NULL,nrnb,econqCoord,FALSE,0,0);
-
- for (n=start; n<end; n++) {
- for(d=0; d<DIM; d++)
- xnew[n-start][d] =
- -(2*x[n][d]-xnold[n-start][d]-xnew[n-start][d])/sqr(dt)
- - f[n][d]*md->invmass[n];
- clear_rvec(acc_dir[n]);
- }
-
- /* Project the acceleration on the old bond directions */
- constrain(log,FALSE,FALSE,constr,idef,ir,NULL,cr,step,0,md,
- x_old,xnew-start,acc_dir,bMolPBC,box,
- lambda[efptBONDED],&(dvdlambda[efptBONDED]),
- NULL,NULL,nrnb,econqDeriv_FlexCon,FALSE,0,0);
+ xnold = shfc->adir_xnold;
+ xnew = shfc->adir_xnew;
+
+ ptype = md->ptype;
+
+ dt = ir->delta_t;
+
+ /* Does NOT work with freeze or acceleration groups (yet) */
+ for (n = start; n < end; n++)
+ {
+ w_dt = md->invmass[n]*dt;
+
+ for (d = 0; d < DIM; d++)
+ {
+ if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
+ {
+ xnold[n-start][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
+ xnew[n-start][d] = 2*x[n][d] - x_old[n][d] + f[n][d]*w_dt*dt;
+ }
+ else
+ {
+ xnold[n-start][d] = x[n][d];
+ xnew[n-start][d] = x[n][d];
+ }
+ }
+ }
+ constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
+ x, xnold-start, NULL, bMolPBC, box,
+ lambda[efptBONDED], &(dvdlambda[efptBONDED]),
+ NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
+ constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
+ x, xnew-start, NULL, bMolPBC, box,
+ lambda[efptBONDED], &(dvdlambda[efptBONDED]),
+ NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
+
+ for (n = start; n < end; n++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ xnew[n-start][d] =
+ -(2*x[n][d]-xnold[n-start][d]-xnew[n-start][d])/sqr(dt)
+ - f[n][d]*md->invmass[n];
+ }
+ clear_rvec(acc_dir[n]);
+ }
+
+ /* Project the acceleration on the old bond directions */
+ constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
+ x_old, xnew-start, acc_dir, bMolPBC, box,
+ lambda[efptBONDED], &(dvdlambda[efptBONDED]),
+ NULL, NULL, nrnb, econqDeriv_FlexCon, FALSE, 0, 0);
}
-int relax_shell_flexcon(FILE *fplog,t_commrec *cr,gmx_bool bVerbose,
- gmx_large_int_t mdstep,t_inputrec *inputrec,
- gmx_bool bDoNS,int force_flags,
- gmx_bool bStopCM,
- gmx_localtop_t *top,
- gmx_mtop_t* mtop,
- gmx_constr_t constr,
- gmx_enerdata_t *enerd,t_fcdata *fcd,
- t_state *state,rvec f[],
- tensor force_vir,
- t_mdatoms *md,
- t_nrnb *nrnb,gmx_wallcycle_t wcycle,
- t_graph *graph,
- gmx_groups_t *groups,
- struct gmx_shellfc *shfc,
- t_forcerec *fr,
- gmx_bool bBornRadii,
- double t,rvec mu_tot,
- int natoms,gmx_bool *bConverged,
- gmx_vsite_t *vsite,
- FILE *fp_field)
+int relax_shell_flexcon(FILE *fplog, t_commrec *cr, gmx_bool bVerbose,
+ gmx_int64_t mdstep, t_inputrec *inputrec,
+ gmx_bool bDoNS, int force_flags,
+ gmx_localtop_t *top,
+ gmx_constr_t constr,
+ gmx_enerdata_t *enerd, t_fcdata *fcd,
+ t_state *state, rvec f[],
+ tensor force_vir,
+ t_mdatoms *md,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ t_graph *graph,
+ gmx_groups_t *groups,
+ struct gmx_shellfc *shfc,
+ t_forcerec *fr,
+ gmx_bool bBornRadii,
+ double t, rvec mu_tot,
+ gmx_bool *bConverged,
+ gmx_vsite_t *vsite,
+ FILE *fp_field)
{
- int nshell;
- t_shell *shell;
- t_idef *idef;
- rvec *pos[2],*force[2],*acc_dir=NULL,*x_old=NULL;
- real Epot[2],df[2];
- rvec dx;
- real sf_dir,invdt;
- real ftol,xiH,xiS,dum=0;
- char sbuf[22];
- gmx_bool bCont,bInit;
- int nat,dd_ac0,dd_ac1=0,i;
- int start=md->start,homenr=md->homenr,end=start+homenr,cg0,cg1;
- int nflexcon,g,number_steps,d,Min=0,count=0;
+ int nshell;
+ t_shell *shell;
+ t_idef *idef;
+ rvec *pos[2], *force[2], *acc_dir = NULL, *x_old = NULL;
+ real Epot[2], df[2];
+ rvec dx;
+ real sf_dir, invdt;
+ real ftol, xiH, xiS, dum = 0;
+ char sbuf[22];
+ gmx_bool bCont, bInit;
+ int nat, dd_ac0, dd_ac1 = 0, i;
+ int start = 0, homenr = md->homenr, end = start+homenr, cg0, cg1;
+ int nflexcon, g, number_steps, d, Min = 0, count = 0;
#define Try (1-Min) /* At start Try = 1 */
- bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
- bInit = (mdstep == inputrec->init_step) || shfc->bRequireInit;
- ftol = inputrec->em_tol;
- number_steps = inputrec->niter;
- nshell = shfc->nshell;
- shell = shfc->shell;
- nflexcon = shfc->nflexcon;
-
- idef = &top->idef;
-
- if (DOMAINDECOMP(cr)) {
- nat = dd_natoms_vsite(cr->dd);
- if (nflexcon > 0) {
- dd_get_constraint_range(cr->dd,&dd_ac0,&dd_ac1);
- nat = max(nat,dd_ac1);
+ bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
+ bInit = (mdstep == inputrec->init_step) || shfc->bRequireInit;
+ ftol = inputrec->em_tol;
+ number_steps = inputrec->niter;
+ nshell = shfc->nshell;
+ shell = shfc->shell;
+ nflexcon = shfc->nflexcon;
+
+ idef = &top->idef;
+
+ if (DOMAINDECOMP(cr))
+ {
+ nat = dd_natoms_vsite(cr->dd);
+ if (nflexcon > 0)
+ {
+ dd_get_constraint_range(cr->dd, &dd_ac0, &dd_ac1);
+ nat = max(nat, dd_ac1);
+ }
}
- } else {
- nat = state->natoms;
- }
-
- if (nat > shfc->x_nalloc) {
- /* Allocate local arrays */
- shfc->x_nalloc = over_alloc_dd(nat);
- for(i=0; (i<2); i++) {
- srenew(shfc->x[i],shfc->x_nalloc);
- srenew(shfc->f[i],shfc->x_nalloc);
+ else
+ {
+ nat = state->natoms;
}
- }
- for(i=0; (i<2); i++) {
- pos[i] = shfc->x[i];
- force[i] = shfc->f[i];
- }
-
- /* With particle decomposition this code only works
- * when all particles involved with each shell are in the same cg.
- */
-
- if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr)) {
- /* This is the only time where the coordinates are used
- * before do_force is called, which normally puts all
- * charge groups in the box.
- */
- if (PARTDECOMP(cr)) {
- pd_cg_range(cr,&cg0,&cg1);
- } else {
- cg0 = 0;
- cg1 = top->cgs.nr;
+
+ if (nat > shfc->x_nalloc)
+ {
+ /* Allocate local arrays */
+ shfc->x_nalloc = over_alloc_dd(nat);
+ for (i = 0; (i < 2); i++)
+ {
+ srenew(shfc->x[i], shfc->x_nalloc);
+ srenew(shfc->f[i], shfc->x_nalloc);
+ }
+ }
+ for (i = 0; (i < 2); i++)
+ {
+ pos[i] = shfc->x[i];
+ force[i] = shfc->f[i];
+ }
+
+ if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr))
+ {
+ /* This is the only time where the coordinates are used
+ * before do_force is called, which normally puts all
+ * charge groups in the box.
+ */
+ if (inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ put_atoms_in_box_omp(fr->ePBC, state->box, md->homenr, state->x);
+ }
+ else
+ {
+ cg0 = 0;
+ cg1 = top->cgs.nr;
+ put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, state->box,
+ &(top->cgs), state->x, fr->cg_cm);
+ }
+
+ if (graph)
+ {
+ mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
+ }
}
- put_charge_groups_in_box(fplog,cg0,cg1,fr->ePBC,state->box,
- &(top->cgs),state->x,fr->cg_cm);
+
+ /* After this all coordinate arrays will contain whole charge groups */
if (graph)
- mk_mshift(fplog,graph,fr->ePBC,state->box,state->x);
- }
-
- /* After this all coordinate arrays will contain whole molecules */
- if (graph)
- shift_self(graph,state->box,state->x);
-
- if (nflexcon) {
- if (nat > shfc->flex_nalloc) {
- shfc->flex_nalloc = over_alloc_dd(nat);
- srenew(shfc->acc_dir,shfc->flex_nalloc);
- srenew(shfc->x_old,shfc->flex_nalloc);
+ {
+ shift_self(graph, state->box, state->x);
}
- acc_dir = shfc->acc_dir;
- x_old = shfc->x_old;
- for(i=0; i<homenr; i++) {
- for(d=0; d<DIM; d++)
- shfc->x_old[i][d] =
- state->x[start+i][d] - state->v[start+i][d]*inputrec->delta_t;
+
+ if (nflexcon)
+ {
+ if (nat > shfc->flex_nalloc)
+ {
+ shfc->flex_nalloc = over_alloc_dd(nat);
+ srenew(shfc->acc_dir, shfc->flex_nalloc);
+ srenew(shfc->x_old, shfc->flex_nalloc);
+ }
+ acc_dir = shfc->acc_dir;
+ x_old = shfc->x_old;
+ for (i = 0; i < homenr; i++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ shfc->x_old[i][d] =
+ state->x[start+i][d] - state->v[start+i][d]*inputrec->delta_t;
+ }
+ }
}
- }
-
- /* Do a prediction of the shell positions */
- if (shfc->bPredict && !bCont) {
- predict_shells(fplog,state->x,state->v,inputrec->delta_t,nshell,shell,
- md->massT,NULL,bInit);
- }
-
- /* do_force expected the charge groups to be in the box */
- if (graph)
- unshift_self(graph,state->box,state->x);
-
- /* Calculate the forces first time around */
- if (gmx_debug_at) {
- pr_rvecs(debug,0,"x b4 do_force",state->x + start,homenr);
- }
- do_force(fplog,cr,inputrec,mdstep,nrnb,wcycle,top,mtop,groups,
- state->box,state->x,&state->hist,
- force[Min],force_vir,md,enerd,fcd,
- state->lambda,graph,
- fr,vsite,mu_tot,t,fp_field,NULL,bBornRadii,
- (bDoNS ? GMX_FORCE_NS : 0) | force_flags);
-
- sf_dir = 0;
- if (nflexcon) {
- init_adir(fplog,shfc,
- constr,idef,inputrec,cr,dd_ac1,mdstep,md,start,end,
- shfc->x_old-start,state->x,state->x,force[Min],
- shfc->acc_dir-start,
- fr->bMolPBC,state->box,state->lambda,&dum,nrnb);
-
- for(i=start; i<end; i++)
- sf_dir += md->massT[i]*norm2(shfc->acc_dir[i-start]);
- }
-
- Epot[Min] = enerd->term[F_EPOT];
-
- df[Min]=rms_force(cr,shfc->f[Min],nshell,shell,nflexcon,&sf_dir,&Epot[Min]);
- df[Try]=0;
- if (debug) {
- fprintf(debug,"df = %g %g\n",df[Min],df[Try]);
- }
-
- if (gmx_debug_at) {
- pr_rvecs(debug,0,"force0",force[Min],md->nr);
- }
-
- if (nshell+nflexcon > 0) {
- /* Copy x to pos[Min] & pos[Try]: during minimization only the
- * shell positions are updated, therefore the other particles must
- * be set here.
- */
- memcpy(pos[Min],state->x,nat*sizeof(state->x[0]));
- memcpy(pos[Try],state->x,nat*sizeof(state->x[0]));
- }
-
- if (bVerbose && MASTER(cr))
- print_epot(stdout,mdstep,0,Epot[Min],df[Min],nflexcon,sf_dir);
-
- if (debug) {
- fprintf(debug,"%17s: %14.10e\n",
- interaction_function[F_EKIN].longname,enerd->term[F_EKIN]);
- fprintf(debug,"%17s: %14.10e\n",
- interaction_function[F_EPOT].longname,enerd->term[F_EPOT]);
- fprintf(debug,"%17s: %14.10e\n",
- interaction_function[F_ETOT].longname,enerd->term[F_ETOT]);
- fprintf(debug,"SHELLSTEP %s\n",gmx_step_str(mdstep,sbuf));
- }
-
- /* First check whether we should do shells, or whether the force is
- * low enough even without minimization.
- */
- *bConverged = (df[Min] < ftol);
-
- for(count=1; (!(*bConverged) && (count < number_steps)); count++) {
- if (vsite)
- construct_vsites(fplog,vsite,pos[Min],nrnb,inputrec->delta_t,state->v,
- idef->iparams,idef->il,
- fr->ePBC,fr->bMolPBC,graph,cr,state->box);
-
- if (nflexcon) {
- init_adir(fplog,shfc,
- constr,idef,inputrec,cr,dd_ac1,mdstep,md,start,end,
- x_old-start,state->x,pos[Min],force[Min],acc_dir-start,
- fr->bMolPBC,state->box,state->lambda,&dum,nrnb);
-
- directional_sd(fplog,pos[Min],pos[Try],acc_dir-start,start,end,
- fr->fc_stepsize);
+
+ /* Do a prediction of the shell positions */
+ if (shfc->bPredict && !bCont)
+ {
+ predict_shells(fplog, state->x, state->v, inputrec->delta_t, nshell, shell,
+ md->massT, NULL, bInit);
}
-
- /* New positions, Steepest descent */
- shell_pos_sd(fplog,pos[Min],pos[Try],force[Min],nshell,shell,count);
/* do_force expected the charge groups to be in the box */
if (graph)
- unshift_self(graph,state->box,pos[Try]);
-
- if (gmx_debug_at) {
- pr_rvecs(debug,0,"RELAX: pos[Min] ",pos[Min] + start,homenr);
- pr_rvecs(debug,0,"RELAX: pos[Try] ",pos[Try] + start,homenr);
+ {
+ unshift_self(graph, state->box, state->x);
}
- /* Try the new positions */
- do_force(fplog,cr,inputrec,1,nrnb,wcycle,
- top,mtop,groups,state->box,pos[Try],&state->hist,
- force[Try],force_vir,
- md,enerd,fcd,state->lambda,graph,
- fr,vsite,mu_tot,t,fp_field,NULL,bBornRadii,
- force_flags);
-
- if (gmx_debug_at) {
- pr_rvecs(debug,0,"RELAX: force[Min]",force[Min] + start,homenr);
- pr_rvecs(debug,0,"RELAX: force[Try]",force[Try] + start,homenr);
+
+ /* Calculate the forces first time around */
+ if (gmx_debug_at)
+ {
+ pr_rvecs(debug, 0, "x b4 do_force", state->x + start, homenr);
}
+ do_force(fplog, cr, inputrec, mdstep, nrnb, wcycle, top, groups,
+ state->box, state->x, &state->hist,
+ force[Min], force_vir, md, enerd, fcd,
+ state->lambda, graph,
+ fr, vsite, mu_tot, t, fp_field, NULL, bBornRadii,
+ (bDoNS ? GMX_FORCE_NS : 0) | force_flags);
+
sf_dir = 0;
- if (nflexcon) {
- init_adir(fplog,shfc,
- constr,idef,inputrec,cr,dd_ac1,mdstep,md,start,end,
- x_old-start,state->x,pos[Try],force[Try],acc_dir-start,
- fr->bMolPBC,state->box,state->lambda,&dum,nrnb);
-
- for(i=start; i<end; i++)
- sf_dir += md->massT[i]*norm2(acc_dir[i-start]);
+ if (nflexcon)
+ {
+ init_adir(fplog, shfc,
+ constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end,
+ shfc->x_old-start, state->x, state->x, force[Min],
+ shfc->acc_dir-start,
+ fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
+
+ for (i = start; i < end; i++)
+ {
+ sf_dir += md->massT[i]*norm2(shfc->acc_dir[i-start]);
+ }
}
- Epot[Try] = enerd->term[F_EPOT];
-
- df[Try]=rms_force(cr,force[Try],nshell,shell,nflexcon,&sf_dir,&Epot[Try]);
+ Epot[Min] = enerd->term[F_EPOT];
+ df[Min] = rms_force(cr, shfc->f[Min], nshell, shell, nflexcon, &sf_dir, &Epot[Min]);
+ df[Try] = 0;
if (debug)
- fprintf(debug,"df = %g %g\n",df[Min],df[Try]);
-
- if (debug) {
- if (gmx_debug_at)
- pr_rvecs(debug,0,"F na do_force",force[Try] + start,homenr);
- if (gmx_debug_at) {
- fprintf(debug,"SHELL ITER %d\n",count);
- dump_shells(debug,pos[Try],force[Try],ftol,nshell,shell);
- }
+ {
+ fprintf(debug, "df = %g %g\n", df[Min], df[Try]);
+ }
+
+ if (gmx_debug_at)
+ {
+ pr_rvecs(debug, 0, "force0", force[Min], md->nr);
+ }
+
+ if (nshell+nflexcon > 0)
+ {
+ /* Copy x to pos[Min] & pos[Try]: during minimization only the
+ * shell positions are updated, therefore the other particles must
+ * be set here.
+ */
+ memcpy(pos[Min], state->x, nat*sizeof(state->x[0]));
+ memcpy(pos[Try], state->x, nat*sizeof(state->x[0]));
}
if (bVerbose && MASTER(cr))
- print_epot(stdout,mdstep,count,Epot[Try],df[Try],nflexcon,sf_dir);
-
- *bConverged = (df[Try] < ftol);
-
- if ((df[Try] < df[Min])) {
- if (debug)
- fprintf(debug,"Swapping Min and Try\n");
- if (nflexcon) {
- /* Correct the velocities for the flexible constraints */
- invdt = 1/inputrec->delta_t;
- for(i=start; i<end; i++) {
- for(d=0; d<DIM; d++)
- state->v[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt;
- }
- }
- Min = Try;
- } else {
- decrease_step_size(nshell,shell);
+ {
+ print_epot(stdout, mdstep, 0, Epot[Min], df[Min], nflexcon, sf_dir);
}
- }
- if (MASTER(cr) && !(*bConverged)) {
- /* Note that the energies and virial are incorrect when not converged */
- if (fplog)
- fprintf(fplog,
- "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
- gmx_step_str(mdstep,sbuf),number_steps,df[Min]);
- fprintf(stderr,
- "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
- gmx_step_str(mdstep,sbuf),number_steps,df[Min]);
- }
-
- /* Copy back the coordinates and the forces */
- memcpy(state->x,pos[Min],nat*sizeof(state->x[0]));
- memcpy(f,force[Min],nat*sizeof(f[0]));
-
- return count;
-}
+ if (debug)
+ {
+ fprintf(debug, "%17s: %14.10e\n",
+ interaction_function[F_EKIN].longname, enerd->term[F_EKIN]);
+ fprintf(debug, "%17s: %14.10e\n",
+ interaction_function[F_EPOT].longname, enerd->term[F_EPOT]);
+ fprintf(debug, "%17s: %14.10e\n",
+ interaction_function[F_ETOT].longname, enerd->term[F_ETOT]);
+ fprintf(debug, "SHELLSTEP %s\n", gmx_step_str(mdstep, sbuf));
+ }
+
+ /* First check whether we should do shells, or whether the force is
+ * low enough even without minimization.
+ */
+ *bConverged = (df[Min] < ftol);
+
+ for (count = 1; (!(*bConverged) && (count < number_steps)); count++)
+ {
+ if (vsite)
+ {
+ construct_vsites(vsite, pos[Min], inputrec->delta_t, state->v,
+ idef->iparams, idef->il,
+ fr->ePBC, fr->bMolPBC, cr, state->box);
+ }
+
+ if (nflexcon)
+ {
+ init_adir(fplog, shfc,
+ constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end,
+ x_old-start, state->x, pos[Min], force[Min], acc_dir-start,
+ fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
+
+ directional_sd(pos[Min], pos[Try], acc_dir-start, start, end,
+ fr->fc_stepsize);
+ }
+
+ /* New positions, Steepest descent */
+ shell_pos_sd(pos[Min], pos[Try], force[Min], nshell, shell, count);
+
+ /* do_force expected the charge groups to be in the box */
+ if (graph)
+ {
+ unshift_self(graph, state->box, pos[Try]);
+ }
+
+ if (gmx_debug_at)
+ {
+ pr_rvecs(debug, 0, "RELAX: pos[Min] ", pos[Min] + start, homenr);
+ pr_rvecs(debug, 0, "RELAX: pos[Try] ", pos[Try] + start, homenr);
+ }
+ /* Try the new positions */
+ do_force(fplog, cr, inputrec, 1, nrnb, wcycle,
+ top, groups, state->box, pos[Try], &state->hist,
+ force[Try], force_vir,
+ md, enerd, fcd, state->lambda, graph,
+ fr, vsite, mu_tot, t, fp_field, NULL, bBornRadii,
+ force_flags);
+
+ if (gmx_debug_at)
+ {
+ pr_rvecs(debug, 0, "RELAX: force[Min]", force[Min] + start, homenr);
+ pr_rvecs(debug, 0, "RELAX: force[Try]", force[Try] + start, homenr);
+ }
+ sf_dir = 0;
+ if (nflexcon)
+ {
+ init_adir(fplog, shfc,
+ constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end,
+ x_old-start, state->x, pos[Try], force[Try], acc_dir-start,
+ fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
+
+ for (i = start; i < end; i++)
+ {
+ sf_dir += md->massT[i]*norm2(acc_dir[i-start]);
+ }
+ }
+
+ Epot[Try] = enerd->term[F_EPOT];
+
+ df[Try] = rms_force(cr, force[Try], nshell, shell, nflexcon, &sf_dir, &Epot[Try]);
+
+ if (debug)
+ {
+ fprintf(debug, "df = %g %g\n", df[Min], df[Try]);
+ }
+
+ if (debug)
+ {
+ if (gmx_debug_at)
+ {
+ pr_rvecs(debug, 0, "F na do_force", force[Try] + start, homenr);
+ }
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "SHELL ITER %d\n", count);
+ dump_shells(debug, pos[Try], force[Try], ftol, nshell, shell);
+ }
+ }
+
+ if (bVerbose && MASTER(cr))
+ {
+ print_epot(stdout, mdstep, count, Epot[Try], df[Try], nflexcon, sf_dir);
+ }
+
+ *bConverged = (df[Try] < ftol);
+
+ if ((df[Try] < df[Min]))
+ {
+ if (debug)
+ {
+ fprintf(debug, "Swapping Min and Try\n");
+ }
+ if (nflexcon)
+ {
+ /* Correct the velocities for the flexible constraints */
+ invdt = 1/inputrec->delta_t;
+ for (i = start; i < end; i++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ state->v[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt;
+ }
+ }
+ }
+ Min = Try;
+ }
+ else
+ {
+ decrease_step_size(nshell, shell);
+ }
+ }
+ if (MASTER(cr) && !(*bConverged))
+ {
+ /* Note that the energies and virial are incorrect when not converged */
+ if (fplog)
+ {
+ fprintf(fplog,
+ "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
+ gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
+ }
+ fprintf(stderr,
+ "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
+ gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
+ }
+
+ /* Copy back the coordinates and the forces */
+ memcpy(state->x, pos[Min], nat*sizeof(state->x[0]));
+ memcpy(f, force[Min], nat*sizeof(f[0]));
+
+ return count;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff