static real *mk_nbfp(t_idef *idef,bool bBHAM)
{
real *nbfp;
int i,j,k,atnr;
atnr=idef->atnr;
if (bBHAM) {
snew(nbfp,3*atnr*atnr);
for(i=k=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++,k++) {
BHAMA(nbfp,atnr,i,j) = idef->iparams[k].bham.a;
BHAMB(nbfp,atnr,i,j) = idef->iparams[k].bham.b;
BHAMC(nbfp,atnr,i,j) = idef->iparams[k].bham.c;
}
}
}
else {
snew(nbfp,2*atnr*atnr);
for(i=k=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++,k++) {
C6(nbfp,atnr,i,j) = idef->iparams[k].lj.c6;
C12(nbfp,atnr,i,j) = idef->iparams[k].lj.c12;
}
}
}
return nbfp;
}
static void upd_nbfpbu(FILE *log,real *nbfp,int atnr,
real fa[],real fb[],real fc[])
{
int n,m,k;
/* Update the nonbonded force parameters */
for(k=n=0; (n<atnr); n++) {
for(m=0; (m<atnr); m++,k++) {
BHAMA(nbfp,atnr,n,m) *= fa[k];
BHAMB(nbfp,atnr,n,m) *= fb[k];
BHAMC(nbfp,atnr,n,m) *= fc[k];
}
}
}
static void pr_nbfp(FILE *fp,real *nbfp,bool bBHAM,int atnr)
{
int i,j;
if(fp)
{
for(i=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++) {
fprintf(fp,"%2d - %2d",i,j);
if (bBHAM)
fprintf(fp," a=%10g, b=%10g, c=%10g\n",BHAMA(nbfp,atnr,i,j),
BHAMB(nbfp,atnr,i,j),BHAMC(nbfp,atnr,i,j));
else
fprintf(fp," c6=%10g, c12=%10g\n",C6(nbfp,atnr,i,j),
C12(nbfp,atnr,i,j));
}
}
}
}
static void set_bham_b_max(FILE *log,t_forcerec *fr,t_mdatoms *mdatoms)
{
int i,j,tpi,tpj,ntypes,natoms,*type;
real b,bmin;
real *nbfp;
bool first;
if(log)
fprintf(log,"Determining largest Buckingham b parameter for table\n");
nbfp = fr->nbfp;
ntypes = fr->ntype;
type = mdatoms->typeA;
natoms = mdatoms->nr;
bmin = -1;
first = TRUE;
fr->bham_b_max = 0;
for(i=0; (i<natoms); i++) {
tpi = type[i];
if (tpi >= ntypes)
fatal_error(0,"Atomtype[%d] = %d, maximum = %d",i,tpi,ntypes);
for(j=0; (j<natoms); j++) {
tpj = type[j];
if (tpj >= ntypes)
fatal_error(0,"Atomtype[%d] = %d, maximum = %d",j,tpj,ntypes);
b = BHAMB(nbfp,ntypes,tpi,tpj);
if (b > fr->bham_b_max)
fr->bham_b_max = b;
if ((b < bmin) || first)
{
bmin = b;
first = FALSE;
}
}
}
if(log)
fprintf(log,"Buckingham b parameters, min: %g, max: %g\n",
bmin,fr->bham_b_max);
}
void do_coupling(FILE *log,int nfile,t_filenm fnm[],
t_coupl_rec *tcr,real t,int step,real ener[],
t_forcerec *fr,t_inputrec *ir,bool bMaster,
t_mdatoms *md,t_idef *idef,real mu_aver,int nmols,
t_commrec *cr,matrix box,tensor virial,
tensor pres,rvec mu_tot,
rvec x[],rvec f[],bool bDoIt)
{
#define enm2Debye 48.0321
#define d2e(x) (x)/enm2Debye
#define enm2kjmol(x) (x)*0.0143952 /* = 2.0*4.0*M_PI*EPSILON0 */
static real *f6,*f12,*fa,*fb,*fc,*fq;
static bool bFirst = TRUE;
int i,j,ati,atj,atnr2,type,ftype;
real deviation[eoObsNR],prdev[eoObsNR],epot0,dist,rmsf;
real ff6,ff12,ffa,ffb,ffc,ffq,factor,dt,mu_ind;
real Epol,Eintern,Virial,muabs,xiH=-1,xiS=-1,xi6,xi12;
rvec fmol[2];
bool bTest,bPrint;
t_coupl_LJ *tclj;
t_coupl_BU *tcbu;
t_coupl_Q *tcq;
t_coupl_iparams *tip;
atnr2 = idef->atnr * idef->atnr;
if (bFirst) {
if (PAR(cr))
fprintf(log,"GCT: this is parallel\n");
else
fprintf(log,"GCT: this is not parallel\n");
fflush(log);
snew(f6, atnr2);
snew(f12,atnr2);
snew(fa, atnr2);
snew(fb, atnr2);
snew(fc, atnr2);
snew(fq, idef->atnr);
if (tcr->bVirial) {
int nrdf = 0;
real TTT = 0;
real Vol = det(box);
for(i=0; (i<ir->opts.ngtc); i++) {
nrdf += ir->opts.nrdf[i];
TTT += ir->opts.nrdf[i]*ir->opts.ref_t[i];
}
TTT /= nrdf;
/* Calculate reference virial from reference temperature and pressure */
tcr->ref_value[eoVir] = 0.5*BOLTZ*nrdf*TTT - (3.0/2.0)*
Vol*tcr->ref_value[eoPres];
fprintf(log,"GCT: TTT = %g, nrdf = %d, vir0 = %g, Vol = %g\n",
TTT,nrdf,tcr->ref_value[eoVir],Vol);
fflush(log);
}
bFirst = FALSE;
}
bPrint = MASTER(cr) && do_per_step(step,ir->nstlog);
dt = ir->delta_t;
/* Initiate coupling to the reference pressure and temperature to start
* coupling slowly.
*/
if (step == 0) {
for(i=0; (i<eoObsNR); i++)
tcr->av_value[i] = tcr->ref_value[i];
if ((tcr->ref_value[eoDipole]) != 0.0) {
mu_ind = mu_aver - d2e(tcr->ref_value[eoDipole]); /* in e nm */
Epol = mu_ind*mu_ind/(enm2kjmol(tcr->ref_value[eoPolarizability]));
tcr->av_value[eoEpot] -= Epol;
fprintf(log,"GCT: mu_aver = %g(D), mu_ind = %g(D), Epol = %g (kJ/mol)\n",
mu_aver*enm2Debye,mu_ind*enm2Debye,Epol);
}
}
/* We want to optimize the LJ params, usually to the Vaporization energy
* therefore we only count intermolecular degrees of freedom.
* Note that this is now optional. switch UseEinter to yes in your gct file
* if you want this.
*/
dist = calc_dist(log,x);
muabs = norm(mu_tot);
Eintern = Ecouple(tcr,ener)/nmols;
Virial = virial[XX][XX]+virial[YY][YY]+virial[ZZ][ZZ];
/*calc_force(md->nr,f,fmol);*/
clear_rvec(fmol[0]);
/* Use a memory of tcr->nmemory steps, so we actually couple to the
* average observable over the last tcr->nmemory steps. This may help
* in avoiding local minima in parameter space.
*/
set_act_value(tcr,eoPres, ener[F_PRES],step);
set_act_value(tcr,eoEpot, Eintern, step);
set_act_value(tcr,eoVir, Virial, step);
set_act_value(tcr,eoDist, dist, step);
set_act_value(tcr,eoMu, muabs, step);
set_act_value(tcr,eoFx, fmol[0][XX], step);
set_act_value(tcr,eoFy, fmol[0][YY], step);
set_act_value(tcr,eoFz, fmol[0][ZZ], step);
set_act_value(tcr,eoPx, pres[XX][XX],step);
set_act_value(tcr,eoPy, pres[YY][YY],step);
set_act_value(tcr,eoPz, pres[ZZ][ZZ],step);
epot0 = tcr->ref_value[eoEpot];
/* If dipole != 0.0 assume we want to use polarization corrected coupling */
if ((tcr->ref_value[eoDipole]) != 0.0) {
mu_ind = mu_aver - d2e(tcr->ref_value[eoDipole]); /* in e nm */
Epol = mu_ind*mu_ind/(enm2kjmol(tcr->ref_value[eoPolarizability]));
epot0 -= Epol;
if (debug) {
fprintf(debug,"mu_ind: %g (%g D) mu_aver: %g (%g D)\n",
mu_ind,mu_ind*enm2Debye,mu_aver,mu_aver*enm2Debye);
fprintf(debug,"Eref %g Epol %g Erunav %g Eact %g\n",
tcr->ref_value[eoEpot],Epol,tcr->av_value[eoEpot],
tcr->act_value[eoEpot]);
}
}
if (bPrint) {
pr_ff(tcr,t,idef,cr,nfile,fnm);
}
/* Calculate the deviation of average value from the target value */
for(i=0; (i<eoObsNR); i++) {
deviation[i] = calc_deviation(tcr->av_value[i],tcr->act_value[i],
tcr->ref_value[i]);
prdev[i] = tcr->ref_value[i] - tcr->act_value[i];
}
deviation[eoEpot] = calc_deviation(tcr->av_value[eoEpot],tcr->act_value[eoEpot],
epot0);
prdev[eoEpot] = epot0 - tcr->act_value[eoEpot];
if (bPrint)
pr_dev(tcr,t,prdev,cr,nfile,fnm);
/* First set all factors to 1 */
for(i=0; (i<atnr2); i++) {
f6[i] = f12[i] = fa[i] = fb[i] = fc[i] = 1.0;
}
for(i=0; (i<idef->atnr); i++)
fq[i] = 1.0;
/* Now compute the actual coupling compononents */
if (!fr->bBHAM) {
if (bDoIt) {
for(i=0; (i<tcr->nLJ); i++) {
tclj=&(tcr->tcLJ[i]);
ati=tclj->at_i;
atj=tclj->at_j;
ff6 = ff12 = 1.0;
if (tclj->eObs == eoForce) {
gmx_fatal(FARGS,"Hack code for this to work again ");
if (debug)
fprintf(debug,"Have computed derivatives: xiH = %g, xiS = %g\n",xiH,xiS);
if (ati == 1) {
/* Hydrogen */
ff12 += xiH;
}
else if (ati == 2) {
/* Shell */
ff12 += xiS;
}
else
gmx_fatal(FARGS,"No H, no Shell, edit code at %s, line %d\n",
__FILE__,__LINE__);
if (ff6 > 0)
set_factor_matrix(idef->atnr,f6, sqrt(ff6), ati,atj);
if (ff12 > 0)
set_factor_matrix(idef->atnr,f12,sqrt(ff12),ati,atj);
}
else {
if (debug)
fprintf(debug,"tcr->tcLJ[%d].xi_6 = %g, xi_12 = %g deviation = %g\n",i,
tclj->xi_6,tclj->xi_12,deviation[tclj->eObs]);
factor=deviation[tclj->eObs];
upd_f_value(log,idef->atnr,tclj->xi_6, dt,factor,f6, ati,atj);
upd_f_value(log,idef->atnr,tclj->xi_12,dt,factor,f12,ati,atj);
}
}
}
if (PAR(cr)) {
gprod(cr,atnr2,f6);
gprod(cr,atnr2,f12);
#ifdef DEBUGGCT
dump_fm(log,idef->atnr,f6,"f6");
dump_fm(log,idef->atnr,f12,"f12");
#endif
}
upd_nbfplj(log,fr->nbfp,idef->atnr,f6,f12,tcr->combrule);
/* Copy for printing */
for(i=0; (i<tcr->nLJ); i++) {
tclj=&(tcr->tcLJ[i]);
ati = tclj->at_i;
atj = tclj->at_j;
if (atj == -1)
atj = ati;
tclj->c6 = C6(fr->nbfp,fr->ntype,ati,atj);
tclj->c12 = C12(fr->nbfp,fr->ntype,ati,atj);
}
}
else {
if (bDoIt) {
for(i=0; (i<tcr->nBU); i++) {
tcbu = &(tcr->tcBU[i]);
factor = deviation[tcbu->eObs];
ati = tcbu->at_i;
atj = tcbu->at_j;
upd_f_value(log,idef->atnr,tcbu->xi_a,dt,factor,fa,ati,atj);
upd_f_value(log,idef->atnr,tcbu->xi_b,dt,factor,fb,ati,atj);
upd_f_value(log,idef->atnr,tcbu->xi_c,dt,factor,fc,ati,atj);
}
}
if (PAR(cr)) {
gprod(cr,atnr2,fa);
gprod(cr,atnr2,fb);
gprod(cr,atnr2,fc);
}
upd_nbfpbu(log,fr->nbfp,idef->atnr,fa,fb,fc);
/* Copy for printing */
for(i=0; (i<tcr->nBU); i++) {
tcbu=&(tcr->tcBU[i]);
ati = tcbu->at_i;
atj = tcbu->at_j;
if (atj == -1)
atj = ati;
tcbu->a = BHAMA(fr->nbfp,fr->ntype,ati,atj);
tcbu->b = BHAMB(fr->nbfp,fr->ntype,ati,atj);
tcbu->c = BHAMC(fr->nbfp,fr->ntype,ati,atj);
if (debug)
fprintf(debug,"buck (type=%d) = %e, %e, %e\n",
tcbu->at_i,tcbu->a,tcbu->b,tcbu->c);
}
}
if (bDoIt) {
for(i=0; (i<tcr->nQ); i++) {
tcq=&(tcr->tcQ[i]);
if (tcq->xi_Q)
ffq = 1.0 + (dt/tcq->xi_Q) * deviation[tcq->eObs];
else
ffq = 1.0;
fq[tcq->at_i] *= ffq;
}
}
if (PAR(cr))
gprod(cr,idef->atnr,fq);
for(j=0; (j<md->nr); j++) {
md->chargeA[j] *= fq[md->typeA[j]];
}
for(i=0; (i<tcr->nQ); i++) {
tcq=&(tcr->tcQ[i]);
for(j=0; (j<md->nr); j++) {
if (md->typeA[j] == tcq->at_i) {
tcq->Q = md->chargeA[j];
break;
}
}
if (j == md->nr)
gmx_fatal(FARGS,"Coupling type %d not found",tcq->at_i);
}
for(i=0; (i<tcr->nIP); i++) {
tip = &(tcr->tIP[i]);
type = tip->type;
ftype = idef->functype[type];
factor = dt*deviation[tip->eObs];
switch(ftype) {
case F_BONDS:
if (tip->xi.harmonic.krA) idef->iparams[type].harmonic.krA *= (1+factor/tip->xi.harmonic.krA);
if (tip->xi.harmonic.rA) idef->iparams[type].harmonic.rA *= (1+factor/tip->xi.harmonic.rA);
break;
default:
break;
}
tip->iprint=idef->iparams[type];
}
}
static void update_ff(t_forcerec *fr,int nparm,t_range range[],int param_val[])
{
static double *sigma=NULL,*eps=NULL,*c6=NULL,*cn=NULL,*bhama=NULL,*bhamb=NULL,*bhamc=NULL;
real val,*nbfp;
int i,j,atnr;
atnr = fr->ntype;
nbfp = fr->nbfp;
if (fr->bBHAM) {
if (bhama == NULL) {
snew(bhama,atnr);
snew(bhamb,atnr);
snew(bhamc,atnr);
}
}
else {
if (sigma == NULL) {
snew(sigma,atnr);
snew(eps,atnr);
snew(c6,atnr);
snew(cn,atnr);
}
}
/* Get current values for everything */
for(i=0; (i<nparm); i++) {
if (ga)
val = range[i].rval;
else
val = value_range(&range[i],param_val[i]);
if(debug)
fprintf(debug,"val = %g\n",val);
switch (range[i].ptype) {
case eseSIGMA:
sigma[range[i].atype] = val;
break;
case eseEPSILON:
eps[range[i].atype] = val;
break;
case eseBHAMA:
bhama[range[i].atype] = val;
break;
case eseBHAMB:
bhamb[range[i].atype] = val;
break;
case eseBHAMC:
bhamc[range[i].atype] = val;
break;
case eseCELLX:
scale[XX] = val;
break;
case eseCELLY:
scale[YY] = val;
break;
case eseCELLZ:
scale[ZZ] = val;
break;
default:
gmx_fatal(FARGS,"Unknown ptype");
}
}
if (fr->bBHAM) {
for(i=0; (i<atnr); i++) {
for(j=0; (j<=i); j++) {
BHAMA(nbfp,atnr,i,j) = BHAMA(nbfp,atnr,j,i) = sqrt(bhama[i]*bhama[j]);
BHAMB(nbfp,atnr,i,j) = BHAMB(nbfp,atnr,j,i) = sqrt(bhamb[i]*bhamb[j]);
BHAMC(nbfp,atnr,i,j) = BHAMC(nbfp,atnr,j,i) = sqrt(bhamc[i]*bhamc[j]);
}
}
}
else {
/* Now build a new matrix */
for(i=0; (i<atnr); i++) {
c6[i] = 4*eps[i]*pow(sigma[i],6.0);
cn[i] = 4*eps[i]*pow(sigma[i],ff.npow);
}
for(i=0; (i<atnr); i++) {
for(j=0; (j<=i); j++) {
C6(nbfp,atnr,i,j) = C6(nbfp,atnr,j,i) = sqrt(c6[i]*c6[j]);
C12(nbfp,atnr,i,j) = C12(nbfp,atnr,j,i) = sqrt(cn[i]*cn[j]);
}
}
}
if (debug) {
if (!fr->bBHAM)
for(i=0; (i<atnr); i++)
fprintf(debug,"atnr = %2d sigma = %8.4f eps = %8.4f\n",i,sigma[i],eps[i]);
for(i=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++) {
if (fr->bBHAM)
fprintf(debug,"i: %2d j: %2d A: %10.5e B: %10.5e C: %10.5e\n",i,j,
BHAMA(nbfp,atnr,i,j),BHAMB(nbfp,atnr,i,j),BHAMC(nbfp,atnr,i,j));
else
fprintf(debug,"i: %2d j: %2d c6: %10.5e cn: %10.5e\n",i,j,
C6(nbfp,atnr,i,j),C12(nbfp,atnr,i,j));
}
}
}
}
static void check_solvent(FILE *fp,t_topology *top,t_forcerec *fr,
t_mdatoms *md,t_nsborder *nsb)
{
/* This routine finds out whether a charge group can be used as
* solvent in the innerloops. The routine should be called once
* at the beginning of the MD program.
*/
t_block *cgs,*excl,*mols;
atom_id *cgid;
int i,j,m,j0,j1,nj,k,aj,ak,tjA,tjB,nl_m,nl_n,nl_o;
int warncount;
bool bOneCG;
bool *bAllExcl,bAE,bOrder;
bool *bHaveLJ,*bHaveCoul;
cgs = &(top->blocks[ebCGS]);
excl = &(top->atoms.excl);
mols = &(top->blocks[ebMOLS]);
if (fp)
fprintf(fp,"Going to determine what solvent types we have.\n");
snew(fr->solvent_type,cgs->nr+1);
snew(fr->mno_index,(cgs->nr+1)*3);
/* Generate charge group number for all atoms */
cgid = make_invblock(cgs,cgs->nra);
warncount=0;
/* Loop over molecules */
if (fp)
fprintf(fp,"There are %d molecules, %d charge groups and %d atoms\n",
mols->nr,cgs->nr,cgs->nra);
for(i=0; (i<mols->nr); i++) {
/* Set boolean that determines whether the molecules consists of one CG */
bOneCG = TRUE;
/* Set some counters */
j0 = mols->index[i];
j1 = mols->index[i+1];
nj = j1-j0;
for(j=j0+1; (j<j1); j++) {
bOneCG = bOneCG && (cgid[mols->a[j]] == cgid[mols->a[j-1]]);
}
if (fr->bSolvOpt && bOneCG && nj>1) {
/* Check whether everything is excluded */
snew(bAllExcl,nj);
bAE = TRUE;
/* Loop over all atoms in molecule */
for(j=j0; (j<j1) && bAE; j++) {
/* Set a flag for each atom in the molecule that determines whether
* it is excluded or not
*/
for(k=0; (k<nj); k++)
bAllExcl[k] = FALSE;
/* Now check all the exclusions of this atom */
for(k=excl->index[j]; (k<excl->index[j+1]); k++) {
ak = excl->a[k];
/* Consistency and range check */
if ((ak < j0) || (ak >= j1))
fatal_error(0,"Exclusion outside molecule? ak = %d, j0 = %d, j1 = 5d, mol is %d",ak,j0,j1,i);
bAllExcl[ak-j0] = TRUE;
}
/* Now sum up the booleans */
for(k=0; (k<nj); k++)
bAE = bAE && bAllExcl[k];
}
if (bAE) {
snew(bHaveCoul,nj);
snew(bHaveLJ,nj);
for(j=j0; (j<j1); j++) {
/* Check for coulomb */
aj = mols->a[j];
bHaveCoul[j-j0] = ( (fabs(top->atoms.atom[aj].q ) > GMX_REAL_MIN) ||
(fabs(top->atoms.atom[aj].qB) > GMX_REAL_MIN));
/* Check for LJ. */
tjA = top->atoms.atom[aj].type;
tjB = top->atoms.atom[aj].typeB;
bHaveLJ[j-j0] = FALSE;
for(k=0; (k<fr->ntype); k++) {
if (fr->bBHAM)
bHaveLJ[j-j0] = (bHaveLJ[j-j0] ||
(fabs(BHAMA(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(BHAMB(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(BHAMC(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(BHAMA(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN) ||
(fabs(BHAMB(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN) ||
(fabs(BHAMC(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN));
else
bHaveLJ[j-j0] = (bHaveLJ[j-j0] ||
(fabs(C6(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(C12(fr->nbfp,fr->ntype,tjA,k)) > GMX_REAL_MIN) ||
(fabs(C6(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN) ||
(fabs(C12(fr->nbfp,fr->ntype,tjB,k)) > GMX_REAL_MIN));
}
}
/* Now we have determined what particles have which interactions
* In the case of water-like molecules we only check for the number
* of particles and the LJ, not for the Coulomb. Let's just assume
* that the water loops are faster than the MNO loops anyway. DvdS
*/
/* No - there's another problem: To optimize the water
* innerloop assumes the charge of the first i atom is constant
* qO, and charge on atoms 2/3 is constant qH. /EL
*/
/* I won't write any altivec versions of the general solvent inner
* loops. Thus, when USE_PPC_ALTIVEC is defined it is faster
* to use the normal loops instead of the MNO solvent version. /EL
*/
aj=mols->a[j0];
if((nj==3) && bHaveCoul[0] && bHaveLJ[0] &&
!bHaveLJ[1] && !bHaveLJ[2] &&
fabs(top->atoms.atom[aj+1].q - top->atoms.atom[aj+2].q) < GMX_REAL_MIN)
fr->solvent_type[cgid[aj]] = esolWATER;
else {
#ifdef USE_PPC_ALTIVEC
fr->solvent_type[cgid[aj]] = esolNO;
#else
/* Time to compute M & N & O */
for(k=0; (k<nj) && (bHaveLJ[k] && bHaveCoul[k]); k++)
;
nl_n = k;
for(; (k<nj) && (!bHaveLJ[k] && bHaveCoul[k]); k++)
;
nl_o = k;
for(; (k<nj) && (bHaveLJ[k] && !bHaveCoul[k]); k++)
;
nl_m = k;
/* Now check whether we're at the end of the pack */
bOrder = FALSE;
for(; (k<nj); k++)
bOrder = bOrder || (bHaveLJ[k] || bHaveCoul[k]);
if (bOrder) {
/* If we have a solvent molecule with LJC everywhere, then
* we shouldn't issue a warning. Only if we suspect something
* could be better.
*/
if (nl_n != nj) {
warncount++;
if(warncount<11 && fp)
fprintf(fp,"The order in molecule %d could be optimized"
" for better performance\n",i);
if(warncount==10 && fp)
fprintf(fp,"(More than 10 molecules where the order can be optimized)\n");
}
nl_m = nl_n = nl_o = nj;
}
fr->mno_index[cgid[aj]*3] = nl_m;
fr->mno_index[cgid[aj]*3+1] = nl_n;
fr->mno_index[cgid[aj]*3+2] = nl_o;
fr->solvent_type[cgid[aj]] = esolMNO;
#endif /* MNO solvent if not using altivec */
}
/* Last check for perturbed atoms */
for(j=j0; (j<j1); j++)
if (md->bPerturbed[mols->a[j]])
fr->solvent_type[cgid[mols->a[j0]]] = esolNO;
sfree(bHaveLJ);
sfree(bHaveCoul);
}
else {
/* Turn off solvent optimization for all cg's in the molecule,
* here there is only one.
*/
fr->solvent_type[cgid[mols->a[j0]]] = esolNO;
}
sfree(bAllExcl);
}
else {
/* Turn off solvent optimization for all cg's in the molecule */
for(j=mols->index[i]; (j<mols->index[i+1]); j++) {
fr->solvent_type[cgid[mols->a[j]]] = esolNO;
}
}
}
if (debug) {
for(i=0; (i<cgs->nr); i++)
fprintf(debug,"MNO: cg = %5d, m = %2d, n = %2d, o = %2d\n",
i,fr->mno_index[3*i],fr->mno_index[3*i+1],fr->mno_index[3*i+2]);
}
/* Now compute the number of solvent molecules, could be merged with code above */
fr->nMNOMol = 0;
fr->nWatMol = 0;
for(m=0; m<3; m++)
fr->nMNOav[m] = 0;
for(i=0; i<mols->nr; i++) {
j = mols->a[mols->index[i]];
if (j>=START(nsb) && j<START(nsb)+HOMENR(nsb)) {
if (fr->solvent_type[cgid[j]] == esolMNO) {
fr->nMNOMol++;
for(m=0; m<3; m++)
fr->nMNOav[m] += fr->mno_index[3*cgid[j]+m];
}
else if (fr->solvent_type[cgid[j]] == esolWATER)
fr->nWatMol++;
}
}
if (fr->nMNOMol > 0)
for(m=0; (m<3); m++)
fr->nMNOav[m] /= fr->nMNOMol;
sfree(cgid);
if (fp) {
fprintf(fp,"There are %d optimized solvent molecules on node %d\n",
fr->nMNOMol,nsb->nodeid);
if (fr->nMNOMol > 0)
fprintf(fp," aver. nr. of atoms per molecule: vdwc %.1f coul %.1f vdw %.1f\n",
fr->nMNOav[1],fr->nMNOav[2]-fr->nMNOav[1],fr->nMNOav[0]-fr->nMNOav[2]);
fprintf(fp,"There are %d optimized water molecules on node %d\n",
fr->nWatMol,nsb->nodeid);
}
}