t_vcm *init_vcm(FILE *fp, gmx_groups_t *groups, t_inputrec *ir)
{
t_vcm *vcm;
int g;
snew(vcm, 1);
vcm->mode = (ir->nstcomm > 0) ? ir->comm_mode : ecmNO;
vcm->ndim = ndof_com(ir);
if (vcm->mode == ecmANGULAR && vcm->ndim < 3)
{
gmx_fatal(FARGS, "Can not have angular comm removal with pbc=%s",
epbc_names[ir->ePBC]);
}
if (vcm->mode != ecmNO)
{
vcm->nr = groups->grps[egcVCM].nr;
/* Allocate one extra for a possible rest group */
if (vcm->mode == ecmANGULAR)
{
snew(vcm->group_j, vcm->nr+1);
snew(vcm->group_x, vcm->nr+1);
snew(vcm->group_i, vcm->nr+1);
snew(vcm->group_w, vcm->nr+1);
}
snew(vcm->group_p, vcm->nr+1);
snew(vcm->group_v, vcm->nr+1);
snew(vcm->group_mass, vcm->nr+1);
snew(vcm->group_name, vcm->nr);
snew(vcm->group_ndf, vcm->nr);
for (g = 0; (g < vcm->nr); g++)
{
vcm->group_ndf[g] = ir->opts.nrdf[g];
}
/* Copy pointer to group names and print it. */
if (fp)
{
fprintf(fp, "Center of mass motion removal mode is %s\n",
ECOM(vcm->mode));
fprintf(fp, "We have the following groups for center of"
" mass motion removal:\n");
}
for (g = 0; (g < vcm->nr); g++)
{
vcm->group_name[g] = *groups->grpname[groups->grps[egcVCM].nm_ind[g]];
if (fp)
{
fprintf(fp, "%3d: %s\n", g, vcm->group_name[g]);
}
}
}
return vcm;
}
void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
gmx_bool bMDPformat)
{
const char *infbuf="inf";
int i;
if (available(fp,ir,indent,title)) {
if (!bMDPformat)
indent=pr_title(fp,indent,title);
PS("integrator",EI(ir->eI));
PSTEP("nsteps",ir->nsteps);
PSTEP("init-step",ir->init_step);
PS("ns-type",ENS(ir->ns_type));
PI("nstlist",ir->nstlist);
PI("ndelta",ir->ndelta);
PI("nstcomm",ir->nstcomm);
PS("comm-mode",ECOM(ir->comm_mode));
PI("nstlog",ir->nstlog);
PI("nstxout",ir->nstxout);
PI("nstvout",ir->nstvout);
PI("nstfout",ir->nstfout);
PI("nstcalcenergy",ir->nstcalcenergy);
PI("nstenergy",ir->nstenergy);
PI("nstxtcout",ir->nstxtcout);
PR("init-t",ir->init_t);
PR("delta-t",ir->delta_t);
PR("xtcprec",ir->xtcprec);
PI("nkx",ir->nkx);
PI("nky",ir->nky);
PI("nkz",ir->nkz);
PI("pme-order",ir->pme_order);
PR("ewald-rtol",ir->ewald_rtol);
PR("ewald-geometry",ir->ewald_geometry);
PR("epsilon-surface",ir->epsilon_surface);
PS("optimize-fft",BOOL(ir->bOptFFT));
PS("ePBC",EPBC(ir->ePBC));
PS("bPeriodicMols",BOOL(ir->bPeriodicMols));
PS("bContinuation",BOOL(ir->bContinuation));
PS("bShakeSOR",BOOL(ir->bShakeSOR));
PS("etc",ETCOUPLTYPE(ir->etc));
PI("nsttcouple",ir->nsttcouple);
PS("epc",EPCOUPLTYPE(ir->epc));
PS("epctype",EPCOUPLTYPETYPE(ir->epct));
PI("nstpcouple",ir->nstpcouple);
PR("tau-p",ir->tau_p);
pr_matrix(fp,indent,"ref-p",ir->ref_p,bMDPformat);
pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
PS("refcoord-scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
if (bMDPformat)
fprintf(fp,"posres-com = %g %g %g\n",ir->posres_com[XX],
ir->posres_com[YY],ir->posres_com[ZZ]);
else
pr_rvec(fp,indent,"posres-com",ir->posres_com,DIM,TRUE);
if (bMDPformat)
fprintf(fp,"posres-comB = %g %g %g\n",ir->posres_comB[XX],
ir->posres_comB[YY],ir->posres_comB[ZZ]);
else
pr_rvec(fp,indent,"posres-comB",ir->posres_comB,DIM,TRUE);
PI("andersen-seed",ir->andersen_seed);
PR("rlist",ir->rlist);
PR("rlistlong",ir->rlistlong);
PR("rtpi",ir->rtpi);
PS("coulombtype",EELTYPE(ir->coulombtype));
PR("rcoulomb-switch",ir->rcoulomb_switch);
PR("rcoulomb",ir->rcoulomb);
PS("vdwtype",EVDWTYPE(ir->vdwtype));
PR("rvdw-switch",ir->rvdw_switch);
PR("rvdw",ir->rvdw);
if (ir->epsilon_r != 0)
PR("epsilon-r",ir->epsilon_r);
else
PS("epsilon-r",infbuf);
if (ir->epsilon_rf != 0)
PR("epsilon-rf",ir->epsilon_rf);
else
PS("epsilon-rf",infbuf);
PR("tabext",ir->tabext);
PS("implicit-solvent",EIMPLICITSOL(ir->implicit_solvent));
PS("gb-algorithm",EGBALGORITHM(ir->gb_algorithm));
PR("gb-epsilon-solvent",ir->gb_epsilon_solvent);
PI("nstgbradii",ir->nstgbradii);
PR("rgbradii",ir->rgbradii);
PR("gb-saltconc",ir->gb_saltconc);
PR("gb-obc-alpha",ir->gb_obc_alpha);
PR("gb-obc-beta",ir->gb_obc_beta);
PR("gb-obc-gamma",ir->gb_obc_gamma);
PR("gb-dielectric-offset",ir->gb_dielectric_offset);
PS("sa-algorithm",ESAALGORITHM(ir->gb_algorithm));
PR("sa-surface-tension",ir->sa_surface_tension);
PS("DispCorr",EDISPCORR(ir->eDispCorr));
PS("free-energy",EFEPTYPE(ir->efep));
PR("init-lambda",ir->init_lambda);
PR("delta-lambda",ir->delta_lambda);
if (!bMDPformat)
{
PI("n-foreign-lambda",ir->n_flambda);
}
if (ir->n_flambda > 0)
{
pr_indent(fp,indent);
fprintf(fp,"foreign-lambda%s",bMDPformat ? " = " : ":");
for(i=0; i<ir->n_flambda; i++)
{
fprintf(fp," %10g",ir->flambda[i]);
}
fprintf(fp,"\n");
}
PR("sc-alpha",ir->sc_alpha);
PI("sc-power",ir->sc_power);
PR("sc-sigma",ir->sc_sigma);
PR("sc-sigma-min",ir->sc_sigma_min);
PI("nstdhdl", ir->nstdhdl);
PS("separate-dhdl-file", SEPDHDLFILETYPE(ir->separate_dhdl_file));
PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(ir->dhdl_derivatives));
PI("dh-hist-size", ir->dh_hist_size);
PD("dh-hist-spacing", ir->dh_hist_spacing);
PI("nwall",ir->nwall);
PS("wall-type",EWALLTYPE(ir->wall_type));
PI("wall-atomtype[0]",ir->wall_atomtype[0]);
PI("wall-atomtype[1]",ir->wall_atomtype[1]);
PR("wall-density[0]",ir->wall_density[0]);
PR("wall-density[1]",ir->wall_density[1]);
PR("wall-ewald-zfac",ir->wall_ewald_zfac);
PS("pull",EPULLTYPE(ir->ePull));
if (ir->ePull != epullNO)
pr_pull(fp,indent,ir->pull);
PS("rotation",BOOL(ir->bRot));
if (ir->bRot)
pr_rot(fp,indent,ir->rot);
PS("disre",EDISRETYPE(ir->eDisre));
PS("disre-weighting",EDISREWEIGHTING(ir->eDisreWeighting));
PS("disre-mixed",BOOL(ir->bDisreMixed));
PR("dr-fc",ir->dr_fc);
PR("dr-tau",ir->dr_tau);
PR("nstdisreout",ir->nstdisreout);
PR("orires-fc",ir->orires_fc);
PR("orires-tau",ir->orires_tau);
PR("nstorireout",ir->nstorireout);
PR("dihre-fc",ir->dihre_fc);
PR("em-stepsize",ir->em_stepsize);
PR("em-tol",ir->em_tol);
PI("niter",ir->niter);
PR("fc-stepsize",ir->fc_stepsize);
PI("nstcgsteep",ir->nstcgsteep);
PI("nbfgscorr",ir->nbfgscorr);
PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
PR("shake-tol",ir->shake_tol);
PI("lincs-order",ir->nProjOrder);
PR("lincs-warnangle",ir->LincsWarnAngle);
PI("lincs-iter",ir->nLincsIter);
PR("bd-fric",ir->bd_fric);
PI("ld-seed",ir->ld_seed);
PR("cos-accel",ir->cos_accel);
pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
PS("adress",BOOL(ir->bAdress));
if (ir->bAdress){
PS("adress_type",EADRESSTYPE(ir->adress->type));
PR("adress_const_wf",ir->adress->const_wf);
PR("adress_ex_width",ir->adress->ex_width);
PR("adress_hy_width",ir->adress->hy_width);
PS("adress_interface_correction",EADRESSICTYPE(ir->adress->icor));
PS("adress_site",EADRESSSITETYPE(ir->adress->site));
PR("adress_ex_force_cap",ir->adress->ex_forcecap);
PS("adress_do_hybridpairs", BOOL(ir->adress->do_hybridpairs));
pr_rvec(fp,indent,"adress_reference_coords",ir->adress->refs,DIM,TRUE);
}
PI("userint1",ir->userint1);
PI("userint2",ir->userint2);
PI("userint3",ir->userint3);
PI("userint4",ir->userint4);
PR("userreal1",ir->userreal1);
PR("userreal2",ir->userreal2);
PR("userreal3",ir->userreal3);
PR("userreal4",ir->userreal4);
pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
PS("bQMMM",BOOL(ir->bQMMM));
PI("QMconstraints",ir->QMconstraints);
PI("QMMMscheme",ir->QMMMscheme);
PR("scalefactor",ir->scalefactor);
pr_qm_opts(fp,indent,"qm-opts",&(ir->opts));
}
}
void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
bool bMDPformat)
{
char *infbuf="inf";
if (available(fp,ir,indent,title)) {
if (!bMDPformat)
indent=pr_title(fp,indent,title);
PS("integrator",EI(ir->eI));
PI("nsteps",ir->nsteps);
PI("init_step",ir->init_step);
PS("ns_type",ENS(ir->ns_type));
PI("nstlist",ir->nstlist);
PI("ndelta",ir->ndelta);
PI("nstcomm",ir->nstcomm);
PS("comm_mode",ECOM(ir->comm_mode));
PI("nstlog",ir->nstlog);
PI("nstxout",ir->nstxout);
PI("nstvout",ir->nstvout);
PI("nstfout",ir->nstfout);
PI("nstenergy",ir->nstenergy);
PI("nstxtcout",ir->nstxtcout);
PR("init_t",ir->init_t);
PR("delta_t",ir->delta_t);
PR("xtcprec",ir->xtcprec);
PI("nkx",ir->nkx);
PI("nky",ir->nky);
PI("nkz",ir->nkz);
PI("pme_order",ir->pme_order);
PR("ewald_rtol",ir->ewald_rtol);
PR("ewald_geometry",ir->ewald_geometry);
PR("epsilon_surface",ir->epsilon_surface);
PS("optimize_fft",BOOL(ir->bOptFFT));
PS("ePBC",EPBC(ir->ePBC));
PS("bPeriodicMols",BOOL(ir->bPeriodicMols));
PS("bContinuation",BOOL(ir->bContinuation));
PS("bShakeSOR",BOOL(ir->bShakeSOR));
PS("etc",ETCOUPLTYPE(ir->etc));
PS("epc",EPCOUPLTYPE(ir->epc));
PS("epctype",EPCOUPLTYPETYPE(ir->epct));
PR("tau_p",ir->tau_p);
pr_matrix(fp,indent,"ref_p",ir->ref_p,bMDPformat);
pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
PS("refcoord_scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
if (bMDPformat)
fprintf(fp,"posres_com = %g %g %g\n",ir->posres_com[XX],
ir->posres_com[YY],ir->posres_com[ZZ]);
else
pr_rvec(fp,indent,"posres_com",ir->posres_com,DIM,TRUE);
if (bMDPformat)
fprintf(fp,"posres_comB = %g %g %g\n",ir->posres_comB[XX],
ir->posres_comB[YY],ir->posres_comB[ZZ]);
else
pr_rvec(fp,indent,"posres_comB",ir->posres_comB,DIM,TRUE);
PI("andersen_seed",ir->andersen_seed);
PR("rlist",ir->rlist);
PR("rtpi",ir->rtpi);
PS("coulombtype",EELTYPE(ir->coulombtype));
PR("rcoulomb_switch",ir->rcoulomb_switch);
PR("rcoulomb",ir->rcoulomb);
PS("vdwtype",EVDWTYPE(ir->vdwtype));
PR("rvdw_switch",ir->rvdw_switch);
PR("rvdw",ir->rvdw);
if (ir->epsilon_r != 0)
PR("epsilon_r",ir->epsilon_r);
else
PS("epsilon_r",infbuf);
if (ir->epsilon_rf != 0)
PR("epsilon_rf",ir->epsilon_rf);
else
PS("epsilon_rf",infbuf);
PR("tabext",ir->tabext);
PS("implicit_solvent",EIMPLICITSOL(ir->implicit_solvent));
PS("gb_algorithm",EGBALGORITHM(ir->gb_algorithm));
PR("gb_epsilon_solvent",ir->gb_epsilon_solvent);
PI("nstgbradii",ir->nstgbradii);
PR("rgbradii",ir->rgbradii);
PR("gb_saltconc",ir->gb_saltconc);
PR("gb_obc_alpha",ir->gb_obc_alpha);
PR("gb_obc_beta",ir->gb_obc_beta);
PR("gb_obc_gamma",ir->gb_obc_gamma);
PR("sa_surface_tension",ir->sa_surface_tension);
PS("DispCorr",EDISPCORR(ir->eDispCorr));
PS("free_energy",EFEPTYPE(ir->efep));
PR("init_lambda",ir->init_lambda);
PR("sc_alpha",ir->sc_alpha);
PI("sc_power",ir->sc_power);
PR("sc_sigma",ir->sc_sigma);
PR("delta_lambda",ir->delta_lambda);
PI("nwall",ir->nwall);
PS("wall_type",EWALLTYPE(ir->wall_type));
PI("wall_atomtype[0]",ir->wall_atomtype[0]);
PI("wall_atomtype[1]",ir->wall_atomtype[1]);
PR("wall_density[0]",ir->wall_density[0]);
PR("wall_density[1]",ir->wall_density[1]);
PR("wall_ewald_zfac",ir->wall_ewald_zfac);
PS("pull",EPULLTYPE(ir->ePull));
if (ir->ePull != epullNO)
pr_pull(fp,indent,ir->pull);
PS("disre",EDISRETYPE(ir->eDisre));
PS("disre_weighting",EDISREWEIGHTING(ir->eDisreWeighting));
PS("disre_mixed",BOOL(ir->bDisreMixed));
PR("dr_fc",ir->dr_fc);
PR("dr_tau",ir->dr_tau);
PR("nstdisreout",ir->nstdisreout);
PR("orires_fc",ir->orires_fc);
PR("orires_tau",ir->orires_tau);
PR("nstorireout",ir->nstorireout);
PR("dihre-fc",ir->dihre_fc);
PR("em_stepsize",ir->em_stepsize);
PR("em_tol",ir->em_tol);
PI("niter",ir->niter);
PR("fc_stepsize",ir->fc_stepsize);
PI("nstcgsteep",ir->nstcgsteep);
PI("nbfgscorr",ir->nbfgscorr);
PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
PR("shake_tol",ir->shake_tol);
PI("lincs_order",ir->nProjOrder);
PR("lincs_warnangle",ir->LincsWarnAngle);
PI("lincs_iter",ir->nLincsIter);
PR("bd_fric",ir->bd_fric);
PI("ld_seed",ir->ld_seed);
PR("cos_accel",ir->cos_accel);
pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
PI("userint1",ir->userint1);
PI("userint2",ir->userint2);
PI("userint3",ir->userint3);
PI("userint4",ir->userint4);
PR("userreal1",ir->userreal1);
PR("userreal2",ir->userreal2);
PR("userreal3",ir->userreal3);
PR("userreal4",ir->userreal4);
pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
PS("bQMMM",BOOL(ir->bQMMM));
PI("QMconstraints",ir->QMconstraints);
PI("QMMMscheme",ir->QMMMscheme);
PR("scalefactor",ir->scalefactor);
pr_qm_opts(fp,indent,"qm_opts",&(ir->opts));
}
}