static double de_atof(std::string s) { string r = d2e(s); //double rval = Cantera::atofCheck(r.c_str()); double rval = atof(r.c_str()); return rval; }
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]; } }