added Verlet scheme and NxN non-bonded functionality

[gromacs.git] / src / gmxlib / disre.c

/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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 *                This source code is part of
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 * 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.

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/* This file is completely threadsafe - keep it that way! */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <math.h>
#include "typedefs.h"
#include "sysstuff.h"
#include "smalloc.h"
#include "macros.h"
#include "vec.h"
#include "futil.h"
#include "xvgr.h"
#include "gmx_fatal.h"
#include "bondf.h"
#include "copyrite.h"
#include "disre.h"
#include "main.h"
#include "mtop_util.h"

void init_disres(FILE *fplog,const gmx_mtop_t *mtop,
                 t_inputrec *ir,const t_commrec *cr,gmx_bool bPartDecomp,
                 t_fcdata *fcd,t_state *state)
{
    int          fa,nmol,i,npair,np;
    t_iparams    *ip;
    t_disresdata *dd;
    history_t    *hist;
    gmx_mtop_ilistloop_t iloop;
    t_ilist      *il;
    char         *ptr;
    
    dd = &(fcd->disres);

    if (gmx_mtop_ftype_count(mtop,F_DISRES) == 0)
    {
        dd->nres = 0;

        return;
    }
    
    if (fplog)
    {
        fprintf(fplog,"Initializing the distance restraints\n");
    }
    

    if (ir->eDisre == edrEnsemble)
    {
        gmx_fatal(FARGS,"Sorry, distance restraints with ensemble averaging over multiple molecules in one system are not functional in this version of GROMACS");
    }

    dd->dr_weighting = ir->eDisreWeighting;
    dd->dr_fc        = ir->dr_fc;
    if (EI_DYNAMICS(ir->eI))
    {
        dd->dr_tau   = ir->dr_tau;
    }
    else
    {
        dd->dr_tau   = 0.0;
    }
    if (dd->dr_tau == 0.0)
    {
        dd->dr_bMixed = FALSE;
        dd->ETerm = 0.0;
    }
    else
    {
        dd->dr_bMixed = ir->bDisreMixed;
        dd->ETerm = exp(-(ir->delta_t/ir->dr_tau));
    }
    dd->ETerm1        = 1.0 - dd->ETerm;
    
    ip = mtop->ffparams.iparams;

    dd->nres  = 0;
    dd->npair = 0;
    iloop = gmx_mtop_ilistloop_init(mtop);
    while (gmx_mtop_ilistloop_next(iloop,&il,&nmol)) {
        np = 0;
        for(fa=0; fa<il[F_DISRES].nr; fa+=3)
        {
            np++;
            npair = mtop->ffparams.iparams[il[F_DISRES].iatoms[fa]].disres.npair;
            if (np == npair)
            {
                dd->nres  += (ir->eDisre==edrEnsemble ? 1 : nmol)*npair;
                dd->npair += nmol*npair;
                np = 0;
            }
        }
    }

    if (cr && PAR(cr) && !bPartDecomp)
    {
        /* Temporary check, will be removed when disre is implemented with DD */
        const char *notestr="NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd)";
        
        if (MASTER(cr))
            fprintf(stderr,"\n%s\n\n",notestr);
        if (fplog)
            fprintf(fplog,"%s\n",notestr);

        if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL ||
            dd->nres != dd->npair)
        {
            gmx_fatal(FARGS,"Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)");
        }
        if (ir->nstdisreout != 0)
        {
            if (fplog)
            {
                fprintf(fplog,"\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n\n");
            }
            if (MASTER(cr))
            {
                fprintf(stderr,"\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n");
            }
            ir->nstdisreout = 0;
        }
    }

    snew(dd->rt,dd->npair);
    
    if (dd->dr_tau != 0.0)
    {
        hist = &state->hist;
        /* Set the "history lack" factor to 1 */
        state->flags |= (1<<estDISRE_INITF);
        hist->disre_initf = 1.0;
        /* Allocate space for the r^-3 time averages */
        state->flags |= (1<<estDISRE_RM3TAV);
        hist->ndisrepairs = dd->npair;
        snew(hist->disre_rm3tav,hist->ndisrepairs);
    }
    /* Allocate space for a copy of rm3tav,
     * so we can call do_force without modifying the state.
     */
    snew(dd->rm3tav,dd->npair);

    /* Allocate Rt_6 and Rtav_6 consecutively in memory so they can be
     * averaged over the processors in one call (in calc_disre_R_6)
     */
    snew(dd->Rt_6,2*dd->nres);
    dd->Rtav_6 = &(dd->Rt_6[dd->nres]);

    ptr = getenv("GMX_DISRE_ENSEMBLE_SIZE");
    if (cr && cr->ms != NULL && ptr != NULL)
    {
#ifdef GMX_MPI
        dd->nsystems = 0;
        sscanf(ptr,"%d",&dd->nsystems);
        if (fplog)
        {
            fprintf(fplog,"Found GMX_DISRE_ENSEMBLE_SIZE set to %d systems per ensemble\n",dd->nsystems);
        }
        check_multi_int(fplog,cr->ms,dd->nsystems,
                        "the number of systems per ensemble");
        /* We use to allow any value of nsystems which was a divisor
         * of ms->nsim. But this required an extra communicator which
         * was stored in t_fcdata. This pulled in mpi.h in nearly all C files.
         */
        if (!(cr->ms->nsim == 1 || cr->ms->nsim == dd->nsystems))
        {
            gmx_fatal(FARGS,"GMX_DISRE_ENSEMBLE_SIZE (%d) is not equal to 1 or the number of systems (option -multi) %d",dd->nsystems,cr->ms->nsim);
        }

        if (fplog)
        {
            fprintf(fplog,"Our ensemble consists of systems:");
            for(i=0; i<dd->nsystems; i++)
            {
                fprintf(fplog," %d",
                        (cr->ms->sim/dd->nsystems)*dd->nsystems+i);
            }
            fprintf(fplog,"\n");
            }
        snew(dd->Rtl_6,dd->nres);
#endif
    }
    else
    {
        dd->nsystems = 1;
        dd->Rtl_6 = dd->Rt_6;
    }
    
    if (dd->npair > 0)
    {
        if (fplog) {
            fprintf(fplog,"There are %d distance restraints involving %d atom pairs\n",dd->nres,dd->npair);
        }
        if (cr && cr->ms)
        {
            check_multi_int(fplog,cr->ms,fcd->disres.nres,
                            "the number of distance restraints");
        }
        please_cite(fplog,"Tropp80a");
        please_cite(fplog,"Torda89a");
    }
}

void calc_disres_R_6(const gmx_multisim_t *ms,
                     int nfa,const t_iatom forceatoms[],const t_iparams ip[],
                     const rvec x[],const t_pbc *pbc,
                     t_fcdata *fcd,history_t *hist)
{
    atom_id     ai,aj;
    int         fa,res,i,pair,ki,kj,m;
    int         type,npair,np;
    rvec        dx;
    real        *rt,*rm3tav,*Rtl_6,*Rt_6,*Rtav_6;
    real        rt_1,rt_3,rt2;
    ivec        it,jt,dt;
    t_disresdata *dd;
    real        ETerm,ETerm1,cf1=0,cf2=0,invn=0;
    gmx_bool        bTav;

    dd = &(fcd->disres);
    bTav         = (dd->dr_tau != 0);
    ETerm        = dd->ETerm;
    ETerm1       = dd->ETerm1;
    rt           = dd->rt;
    rm3tav       = dd->rm3tav;
    Rtl_6        = dd->Rtl_6;
    Rt_6         = dd->Rt_6;
    Rtav_6       = dd->Rtav_6;
    
    if (bTav)
    {
        /* scaling factor to smoothly turn on the restraint forces *
         * when using time averaging                               */
        dd->exp_min_t_tau = hist->disre_initf*ETerm;
        
        cf1 = dd->exp_min_t_tau;
        cf2 = 1.0/(1.0 - dd->exp_min_t_tau);
    }
    
    if (dd->nsystems > 1)
    {
        invn = 1.0/dd->nsystems;
    }
    
    /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
     * the total number of atoms pairs is nfa/3                          */
    res = 0;
    fa  = 0;
    while (fa < nfa)
    {
        type  = forceatoms[fa];
        npair = ip[type].disres.npair;
        
        Rtav_6[res] = 0.0;
        Rt_6[res]   = 0.0;
        
        /* Loop over the atom pairs of 'this' restraint */
        np = 0;
        while (fa < nfa && np < npair)
        {
            pair = fa/3;
            ai   = forceatoms[fa+1];
            aj   = forceatoms[fa+2];
            
            if (pbc)
            {
                pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
            }
            else
            {
                rvec_sub(x[ai],x[aj],dx);
            }
            rt2  = iprod(dx,dx);
            rt_1 = gmx_invsqrt(rt2);
            rt_3 = rt_1*rt_1*rt_1;
            
            rt[pair]         = sqrt(rt2);
            if (bTav)
            {
                /* Here we update rm3tav in t_fcdata using the data
                 * in history_t.
                 * Thus the results stay correct when this routine
                 * is called multiple times.
                 */
                rm3tav[pair] = cf2*((ETerm - cf1)*hist->disre_rm3tav[pair] +
                                    ETerm1*rt_3);
            }
            else
            {
                rm3tav[pair] = rt_3;
            }

            Rt_6[res]       += rt_3*rt_3;
            Rtav_6[res]     += rm3tav[pair]*rm3tav[pair];

            fa += 3;
            np++;
        }
        if (dd->nsystems > 1)
        {
            Rtl_6[res]   = Rt_6[res];
            Rt_6[res]   *= invn;
            Rtav_6[res] *= invn;
        }

        res++;
    }
    
#ifdef GMX_MPI
    if (dd->nsystems > 1)
    {
        gmx_sum_sim(2*dd->nres,Rt_6,ms);
    }
#endif
}

real ta_disres(int nfa,const t_iatom forceatoms[],const t_iparams ip[],
               const rvec x[],rvec f[],rvec fshift[],
               const t_pbc *pbc,const t_graph *g,
               real lambda,real *dvdlambda,
               const t_mdatoms *md,t_fcdata *fcd,
               int *global_atom_index)
{
    const real sixth=1.0/6.0;
    const real seven_three=7.0/3.0;
    
    atom_id     ai,aj;
    int         fa,res,npair,p,pair,ki=CENTRAL,m;
    int         type;
    rvec        dx;
    real        weight_rt_1;
    real        smooth_fc,Rt,Rtav,rt2,*Rtl_6,*Rt_6,*Rtav_6;
    real        k0,f_scal=0,fmax_scal,fk_scal,fij;
    real        tav_viol,instant_viol,mixed_viol,violtot,vtot;
    real        tav_viol_Rtav7,instant_viol_Rtav7;
    real        up1,up2,low;
    gmx_bool        bConservative,bMixed,bViolation;
    ivec        it,jt,dt;
    t_disresdata *dd;
    int         dr_weighting;
    gmx_bool        dr_bMixed;
    
    dd = &(fcd->disres);
    dr_weighting = dd->dr_weighting;
    dr_bMixed    = dd->dr_bMixed;
    Rtl_6        = dd->Rtl_6;
    Rt_6         = dd->Rt_6;
    Rtav_6       = dd->Rtav_6;

    tav_viol=instant_viol=mixed_viol=tav_viol_Rtav7=instant_viol_Rtav7=0;

    smooth_fc = dd->dr_fc;
    if (dd->dr_tau != 0)
    {
        /* scaling factor to smoothly turn on the restraint forces *
         * when using time averaging                               */
        smooth_fc *= (1.0 - dd->exp_min_t_tau); 
    }
    
    violtot = 0;
    vtot    = 0;
    
    /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
     * the total number of atoms pairs is nfa/3                          */
    res  = 0;
    fa   = 0;
    while (fa < nfa)
    {
        type  = forceatoms[fa];
        /* Take action depending on restraint, calculate scalar force */
        npair = ip[type].disres.npair;
        up1   = ip[type].disres.up1;
        up2   = ip[type].disres.up2;
        low   = ip[type].disres.low;
        k0    = smooth_fc*ip[type].disres.kfac;
        
        /* save some flops when there is only one pair */
        if (ip[type].disres.type != 2)
        {
            bConservative = (dr_weighting == edrwConservative) && (npair > 1);
            bMixed        = dr_bMixed;
            Rt   = pow(Rt_6[res],-sixth);
            Rtav = pow(Rtav_6[res],-sixth);
        }
        else
        {
            /* When rtype=2 use instantaneous not ensemble avereged distance */
            bConservative = (npair > 1);
            bMixed        = FALSE;
            Rt   = pow(Rtl_6[res],-sixth);
            Rtav = Rt;
        }
        
        if (Rtav > up1)
        {
            bViolation = TRUE;
            tav_viol = Rtav - up1;
        }
        else if (Rtav < low)
        {
            bViolation = TRUE;
            tav_viol = Rtav - low;
        }
        else
        {
            bViolation = FALSE;
        }
        
        if (bViolation)
        {
            /* NOTE:
             * there is no real potential when time averaging is applied
             */
            vtot += 0.5*k0*sqr(tav_viol);
            if (1/vtot == 0)
            {
                printf("vtot is inf: %f\n",vtot);
            }
            if (!bMixed)
            {
                f_scal   = -k0*tav_viol;
                violtot += fabs(tav_viol);
            }
            else
            {
                if (Rt > up1)
                {
                    if (tav_viol > 0)
                    {
                        instant_viol = Rt - up1;
                    }
                    else
                    {
                        bViolation = FALSE;
                    }
                }
                else if (Rt < low)
                {
                    if (tav_viol < 0)
                    {
                        instant_viol = Rt - low;
                    }
                    else
                    {
                        bViolation = FALSE;
                    }
                }
                else
                {
                    bViolation = FALSE;
                }
                if (bViolation)
                {
                    mixed_viol = sqrt(tav_viol*instant_viol);
                    f_scal     = -k0*mixed_viol;
                    violtot   += mixed_viol;
                }
            }
        }

        if (bViolation)
        {
            fmax_scal = -k0*(up2-up1);
            /* Correct the force for the number of restraints */
            if (bConservative)
            {
                f_scal  = max(f_scal,fmax_scal);
                if (!bMixed)
                {
                    f_scal *= Rtav/Rtav_6[res];
                }
                else
                {
                    f_scal /= 2*mixed_viol;
                    tav_viol_Rtav7     = tav_viol*Rtav/Rtav_6[res];
                    instant_viol_Rtav7 = instant_viol*Rt/Rt_6[res];
                }
            }
            else
            {
                f_scal /= (real)npair;
                f_scal  = max(f_scal,fmax_scal);
            }    
            
            /* Exert the force ... */
            
            /* Loop over the atom pairs of 'this' restraint */
            for(p=0; p<npair; p++)
            {
                pair = fa/3;
                ai   = forceatoms[fa+1];
                aj   = forceatoms[fa+2];
                
                if (pbc)
                {
                    ki = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
                }
                else
                {
                    rvec_sub(x[ai],x[aj],dx);
                }
                rt2 = iprod(dx,dx);
                
                weight_rt_1 = gmx_invsqrt(rt2);
                
                if (bConservative)
                {
                    if (!dr_bMixed)
                    {
                        weight_rt_1 *= pow(dd->rm3tav[pair],seven_three);
                    }
                    else
                    {
                        weight_rt_1 *= tav_viol_Rtav7*pow(dd->rm3tav[pair],seven_three)+
                            instant_viol_Rtav7*pow(dd->rt[pair],-7);
                    }
                }
                
                fk_scal  = f_scal*weight_rt_1;
                
                if (g)
                {
                    ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
                    ki=IVEC2IS(dt);
                }
                
                for(m=0; m<DIM; m++)
                {
                    fij            = fk_scal*dx[m];
                    
                    f[ai][m]      += fij;
                    f[aj][m]      -= fij;
                    fshift[ki][m] += fij;
                    fshift[CENTRAL][m] -= fij;
                }
                fa += 3;
            }
        }
        else
        {
            /* No violation so force and potential contributions */
            fa += 3*npair;
        }
        res++;
    }
    
    dd->sumviol = violtot;
    
    /* Return energy */
    return vtot;
}

void update_disres_history(t_fcdata *fcd,history_t *hist)
{
    t_disresdata *dd;
    int pair;
    
    dd = &(fcd->disres);
    if (dd->dr_tau != 0)
    {
        /* Copy the new time averages that have been calculated
         * in calc_disres_R_6.
         */
        hist->disre_initf = dd->exp_min_t_tau;
        for(pair=0; pair<dd->npair; pair++)
        {
            hist->disre_rm3tav[pair] = dd->rm3tav[pair];
        }
    }
}