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 init_pull(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
gmx_mtop_t *mtop, t_commrec *cr, const output_env_t oenv, real lambda,
gmx_bool bOutFile, unsigned long Flags)
{
t_pull *pull;
t_pull_group *pgrp;
int c, g, start = 0, end = 0, m;
pull = ir->pull;
pull->ePBC = ir->ePBC;
switch (pull->ePBC)
{
case epbcNONE: pull->npbcdim = 0; break;
case epbcXY: pull->npbcdim = 2; break;
default: pull->npbcdim = 3; break;
}
if (fplog)
{
gmx_bool bAbs, bCos;
bAbs = FALSE;
for (c = 0; c < pull->ncoord; c++)
{
if (pull->group[pull->coord[c].group[0]].nat == 0 ||
pull->group[pull->coord[c].group[1]].nat == 0)
{
bAbs = TRUE;
}
}
fprintf(fplog, "\nWill apply %s COM pulling in geometry '%s'\n",
EPULLTYPE(ir->ePull), EPULLGEOM(pull->eGeom));
fprintf(fplog, "with %d pull coordinate%s and %d group%s\n",
pull->ncoord, pull->ncoord == 1 ? "" : "s",
pull->ngroup, pull->ngroup == 1 ? "" : "s");
if (bAbs)
{
fprintf(fplog, "with an absolute reference\n");
}
bCos = FALSE;
for (g = 0; g < pull->ngroup; g++)
{
if (pull->group[g].nat > 1 &&
pull->group[g].pbcatom < 0)
{
/* We are using cosine weighting */
fprintf(fplog, "Cosine weighting is used for group %d\n", g);
bCos = TRUE;
}
}
if (bCos)
{
please_cite(fplog, "Engin2010");
}
}
/* We always add the virial contribution,
* except for geometry = direction_periodic where this is impossible.
*/
pull->bVirial = (pull->eGeom != epullgDIRPBC);
if (getenv("GMX_NO_PULLVIR") != NULL)
{
if (fplog)
{
fprintf(fplog, "Found env. var., will not add the virial contribution of the COM pull forces\n");
}
pull->bVirial = FALSE;
}
if (cr && PARTDECOMP(cr))
{
pd_at_range(cr, &start, &end);
}
pull->rbuf = NULL;
pull->dbuf = NULL;
pull->dbuf_cyl = NULL;
pull->bRefAt = FALSE;
pull->cosdim = -1;
for (g = 0; g < pull->ngroup; g++)
{
pgrp = &pull->group[g];
pgrp->epgrppbc = epgrppbcNONE;
if (pgrp->nat > 0)
{
/* Determine if we need to take PBC into account for calculating
* the COM's of the pull groups.
*/
for (m = 0; m < pull->npbcdim; m++)
{
if (pull->dim[m] && pgrp->nat > 1)
{
if (pgrp->pbcatom >= 0)
{
pgrp->epgrppbc = epgrppbcREFAT;
pull->bRefAt = TRUE;
}
else
{
if (pgrp->weight)
{
gmx_fatal(FARGS, "Pull groups can not have relative weights and cosine weighting at same time");
}
pgrp->epgrppbc = epgrppbcCOS;
if (pull->cosdim >= 0 && pull->cosdim != m)
{
gmx_fatal(FARGS, "Can only use cosine weighting with pulling in one dimension (use mdp option pull_dim)");
}
pull->cosdim = m;
}
}
}
/* Set the indices */
init_pull_group_index(fplog, cr, start, end, g, pgrp, pull->dim, mtop, ir, lambda);
if (PULL_CYL(pull) && pgrp->invtm == 0)
{
gmx_fatal(FARGS, "Can not have frozen atoms in a cylinder pull group");
}
}
else
{
/* Absolute reference, set the inverse mass to zero */
pgrp->invtm = 0;
pgrp->wscale = 1;
}
}
/* if we use dynamic reference groups, do some initialising for them */
if (PULL_CYL(pull))
{
if (ir->ePull == epullCONSTRAINT && pull->ncoord > 1)
{
/* We can't easily update the single reference group with multiple
* constraints. This would require recalculating COMs.
*/
gmx_fatal(FARGS, "Constraint COM pulling supports only one coordinate with geometry=cylinder, you can use umbrella pulling with multiple coordinates");
}
for (c = 0; c < pull->ncoord; c++)
{
if (pull->group[pull->coord[c].group[0]].nat == 0)
{
gmx_fatal(FARGS, "Dynamic reference groups are not supported when using absolute reference!\n");
}
}
snew(pull->dyna, pull->ncoord);
}
/* Only do I/O when we are doing dynamics and if we are the MASTER */
pull->out_x = NULL;
pull->out_f = NULL;
if (bOutFile)
{
if (pull->nstxout > 0)
{
pull->out_x = open_pull_out(opt2fn("-px", nfile, fnm), pull, oenv, TRUE, Flags);
}
if (pull->nstfout > 0)
{
pull->out_f = open_pull_out(opt2fn("-pf", nfile, fnm), pull, oenv,
FALSE, Flags);
}
}
}
/*! \brief
* Read parameters of an AWH bias dimension.
*
* \param[in,out] ninp_p Number of read input file entries.
* \param[in,out] inp_p Input file entries.
* \param[in] prefix Prefix for dimension parameters.
* \param[in,out] dimParams AWH dimensional parameters.
* \param[in] pull_params Pull parameters.
* \param[in,out] wi Struct for bookeeping warnings.
* \param[in] bComment True if comments should be printed.
*/
static void readDimParams(int *ninp_p, t_inpfile **inp_p, const char *prefix,
AwhDimParams *dimParams, const pull_params_t *pull_params,
warninp_t wi, bool bComment)
{
char warningmsg[STRLEN];
int ninp = *ninp_p;
t_inpfile *inp = *inp_p;
if (bComment)
{
CTYPE("The provider of the reaction coordinate, currently only pull is supported");
}
char opt[STRLEN];
sprintf(opt, "%s-coord-provider", prefix);
EETYPE(opt, dimParams->eCoordProvider, eawhcoordprovider_names);
if (bComment)
{
CTYPE("The coordinate index for this dimension");
}
sprintf(opt, "%s-coord-index", prefix);
int coordIndexInput;
ITYPE(opt, coordIndexInput, 1);
if (coordIndexInput < 1)
{
gmx_fatal(FARGS, "Failed to read a valid coordinate index for %s. "
"Note that the pull coordinate indexing starts at 1.", opt);
}
/* The pull coordinate indices start at 1 in the input file, at 0 internally */
dimParams->coordIndex = coordIndexInput - 1;
/* The pull settings need to be consistent with the AWH settings */
if (!(pull_params->coord[dimParams->coordIndex].eType == epullEXTERNAL) )
{
gmx_fatal(FARGS, "AWH biasing can only be applied to pull type %s",
EPULLTYPE(epullEXTERNAL));
}
if (dimParams->coordIndex >= pull_params->ncoord)
{
gmx_fatal(FARGS, "The given AWH coordinate index (%d) is larger than the number of pull coordinates (%d)",
coordIndexInput, pull_params->ncoord);
}
if (pull_params->coord[dimParams->coordIndex].rate != 0)
{
sprintf(warningmsg, "Setting pull-coord%d-rate (%g) is incompatible with AWH biasing this coordinate", coordIndexInput, pull_params->coord[dimParams->coordIndex].rate);
warning_error(wi, warningmsg);
}
/* Grid params for each axis */
int eGeom = pull_params->coord[dimParams->coordIndex].eGeom;
if (bComment)
{
CTYPE("Start and end values for each coordinate dimension");
}
sprintf(opt, "%s-start", prefix);
RTYPE(opt, dimParams->origin, 0.);
sprintf(opt, "%s-end", prefix);
RTYPE(opt, dimParams->end, 0.);
if (gmx_within_tol(dimParams->end - dimParams->origin, 0, GMX_REAL_EPS))
{
sprintf(warningmsg, "The given interval length given by %s-start (%g) and %s-end (%g) is zero. "
"This will result in only one point along this axis in the coordinate value grid.",
prefix, dimParams->origin, prefix, dimParams->end);
warning(wi, warningmsg);
}
/* Check that the requested interval is in allowed range */
if (eGeom == epullgDIST)
{
if (dimParams->origin < 0 || dimParams->end < 0)
{
gmx_fatal(FARGS, "%s-start (%g) or %s-end (%g) set to a negative value. With pull geometry distance coordinate values are non-negative. "
"Perhaps you want to use geometry %s instead?",
prefix, dimParams->origin, prefix, dimParams->end, EPULLGEOM(epullgDIR));
}
}
else if (eGeom == epullgANGLE || eGeom == epullgANGLEAXIS)
{
if (dimParams->origin < 0 || dimParams->end > 180)
{
gmx_fatal(FARGS, "%s-start (%g) and %s-end (%g) are outside of the allowed range 0 to 180 deg for pull geometries %s and %s ",
prefix, dimParams->origin, prefix, dimParams->end, EPULLGEOM(epullgANGLE), EPULLGEOM(epullgANGLEAXIS));
}
}
else if (eGeom == epullgDIHEDRAL)
{
if (dimParams->origin < -180 || dimParams->end > 180)
{
gmx_fatal(FARGS, "%s-start (%g) and %s-end (%g) are outside of the allowed range -180 to 180 deg for pull geometry %s. ",
prefix, dimParams->origin, prefix, dimParams->end, EPULLGEOM(epullgDIHEDRAL));
}
}
if (bComment)
{
CTYPE("The force constant for this coordinate (kJ/mol/nm^2 or kJ/mol/rad^2)");
}
sprintf(opt, "%s-force-constant", prefix);
RTYPE(opt, dimParams->forceConstant, 0);
if (dimParams->forceConstant <= 0)
{
warning_error(wi, "The force AWH bias force constant should be > 0");
}
if (bComment)
{
CTYPE("Estimated diffusion constant (nm^2/ps or rad^2/ps)");
}
sprintf(opt, "%s-diffusion", prefix);
RTYPE(opt, dimParams->diffusion, 0);
if (dimParams->diffusion <= 0)
{
const double diffusion_default = 1e-5;
sprintf(warningmsg, "%s not explicitly set by user."
" You can choose to use a default value (%g nm^2/ps or rad^2/ps) but this may very well be non-optimal for your system!",
opt, diffusion_default);
warning(wi, warningmsg);
dimParams->diffusion = diffusion_default;
}
if (bComment)
{
CTYPE("Diameter that needs to be sampled around a point before it is considered covered.");
}
sprintf(opt, "%s-cover-diameter", prefix);
RTYPE(opt, dimParams->coverDiameter, 0);
if (dimParams->coverDiameter < 0)
{
gmx_fatal(FARGS, "%s (%g) cannot be negative.",
opt, dimParams->coverDiameter);
}
*ninp_p = ninp;
*inp_p = inp;
}
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));
}
}
