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,char *title,t_inputrec *ir)
{
char *infbuf="inf";
if (available(fp,ir,title)) {
indent=pr_title(fp,indent,title);
#define PS(t,s) pr_str(fp,indent,t,s)
#define PI(t,s) pr_int(fp,indent,t,s)
#define PR(t,s) pr_real(fp,indent,t,s)
PS("integrator",EI(ir->eI));
PI("nsteps",ir->nsteps);
PS("ns_type",ENS(ir->ns_type));
PI("nstlist",ir->nstlist);
PI("ndelta",ir->ndelta);
PS("bDomDecomp",BOOL(ir->bDomDecomp));
PI("decomp_dir",ir->decomp_dir);
PI("nstcomm",ir->nstcomm);
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("bUncStart",BOOL(ir->bUncStart));
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_rvecs(fp,indent,"ref_p",ir->ref_p,DIM);
pr_rvecs(fp,indent,"compress",ir->compress,DIM);
PS("bSimAnn",BOOL(ir->bSimAnn));
PR("zero_temp_time",ir->zero_temp_time);
PR("rlist",ir->rlist);
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 (fabs(ir->epsilon_r) > GMX_REAL_MIN)
PR("epsilon_r",ir->epsilon_r);
else
PS("epsilon_r",infbuf);
PS("DispCorr",EDISPCORR(ir->eDispCorr));
PR("fudgeQQ",ir->fudgeQQ);
PS("free_energy",EFEPTYPE(ir->efep));
PR("init_lambda",ir->init_lambda);
PR("sc_alpha",ir->sc_alpha);
PR("sc_sigma",ir->sc_sigma);
PR("delta_lambda",ir->delta_lambda);
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("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);
PS("ConstAlg",ESHAKETYPE(ir->eConstrAlg));
PR("shake_tol",ir->shake_tol);
PI("lincs_order",ir->nProjOrder);
PR("lincs_warnangle",ir->LincsWarnAngle);
PR("bd_temp",ir->bd_temp);
PR("bd_fric",ir->bd_fric);
PI("ld_seed",ir->ld_seed);
PR("cos_accel",ir->cos_accel);
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);
#undef PS
#undef PR
#undef PI
pr_grp_opts(fp,indent,"grpopts",&(ir->opts));
pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]));
pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]));
pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]));
pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]));
pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]));
pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]));
}
}
void parrinellorahman_pcoupl(FILE *fplog,gmx_step_t step,
t_inputrec *ir,real dt,tensor pres,
tensor box,tensor box_rel,tensor boxv,
tensor M,matrix mu,bool bFirstStep)
{
/* This doesn't do any coordinate updating. It just
* integrates the box vector equations from the calculated
* acceleration due to pressure difference. We also compute
* the tensor M which is used in update to couple the particle
* coordinates to the box vectors.
*
* In Nose and Klein (Mol.Phys 50 (1983) no 5., p 1055) this is
* given as
* -1 . . -1
* M_nk = (h') * (h' * h + h' h) * h
*
* with the dots denoting time derivatives and h is the transformation from
* the scaled frame to the real frame, i.e. the TRANSPOSE of the box.
* This also goes for the pressure and M tensors - they are transposed relative
* to ours. Our equation thus becomes:
*
* -1 . . -1
* M_gmx = M_nk' = b * (b * b' + b * b') * b'
*
* where b is the gromacs box matrix.
* Our box accelerations are given by
* .. ..
* b = vol/W inv(box') * (P-ref_P) (=h')
*/
int d,n;
tensor winv;
real vol=box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
real atot,arel,change,maxchange,xy_pressure;
tensor invbox,pdiff,t1,t2;
real maxl;
m_inv_ur0(box,invbox);
if (!bFirstStep) {
/* Note that PRESFAC does not occur here.
* The pressure and compressibility always occur as a product,
* therefore the pressure unit drops out.
*/
maxl=max(box[XX][XX],box[YY][YY]);
maxl=max(maxl,box[ZZ][ZZ]);
for(d=0;d<DIM;d++)
for(n=0;n<DIM;n++)
winv[d][n]=
(4*M_PI*M_PI*ir->compress[d][n])/(3*ir->tau_p*ir->tau_p*maxl);
m_sub(pres,ir->ref_p,pdiff);
if(ir->epct==epctSURFACETENSION) {
/* Unlike Berendsen coupling it might not be trivial to include a z
* pressure correction here? On the other hand we don't scale the
* box momentarily, but change accelerations, so it might not be crucial.
*/
xy_pressure=0.5*(pres[XX][XX]+pres[YY][YY]);
for(d=0;d<ZZ;d++)
pdiff[d][d]=(xy_pressure-(pres[ZZ][ZZ]-ir->ref_p[d][d]/box[d][d]));
}
tmmul(invbox,pdiff,t1);
/* Move the off-diagonal elements of the 'force' to one side to ensure
* that we obey the box constraints.
*/
for(d=0;d<DIM;d++) {
for(n=0;n<d;n++) {
t1[d][n] += t1[n][d];
t1[n][d] = 0;
}
}
switch (ir->epct) {
case epctANISOTROPIC:
for(d=0;d<DIM;d++)
for(n=0;n<=d;n++)
t1[d][n] *= winv[d][n]*vol;
break;
case epctISOTROPIC:
/* calculate total volume acceleration */
atot=box[XX][XX]*box[YY][YY]*t1[ZZ][ZZ]+
box[XX][XX]*t1[YY][YY]*box[ZZ][ZZ]+
t1[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
arel=atot/(3*vol);
/* set all RELATIVE box accelerations equal, and maintain total V
* change speed */
for(d=0;d<DIM;d++)
for(n=0;n<=d;n++)
t1[d][n] = winv[0][0]*vol*arel*box[d][n];
break;
case epctSEMIISOTROPIC:
case epctSURFACETENSION:
/* Note the correction to pdiff above for surftens. coupling */
/* calculate total XY volume acceleration */
atot=box[XX][XX]*t1[YY][YY]+t1[XX][XX]*box[YY][YY];
arel=atot/(2*box[XX][XX]*box[YY][YY]);
/* set RELATIVE XY box accelerations equal, and maintain total V
* change speed. Dont change the third box vector accelerations */
for(d=0;d<ZZ;d++)
for(n=0;n<=d;n++)
t1[d][n] = winv[d][n]*vol*arel*box[d][n];
for(n=0;n<DIM;n++)
t1[ZZ][n] *= winv[d][n]*vol;
break;
default:
gmx_fatal(FARGS,"Parrinello-Rahman pressure coupling type %s "
"not supported yet\n",EPCOUPLTYPETYPE(ir->epct));
break;
}
maxchange=0;
for(d=0;d<DIM;d++)
for(n=0;n<=d;n++) {
boxv[d][n] += dt*t1[d][n];
/* We do NOT update the box vectors themselves here, since
* we need them for shifting later. It is instead done last
* in the update() routine.
*/
/* Calculate the change relative to diagonal elements -
* since it's perfectly ok for the off-diagonal ones to
* be zero it doesn't make sense to check the change relative
* to its current size.
*/
change=fabs(dt*boxv[d][n]/box[d][d]);
if(change>maxchange)
maxchange=change;
}
if (maxchange > 0.01 && fplog) {
char buf[22];
fprintf(fplog,"\nStep %s Warning: Pressure scaling more than 1%%.\n",
gmx_step_str(step,buf));
}
}
preserve_box_shape(ir,box_rel,boxv);
mtmul(boxv,box,t1); /* t1=boxv * b' */
mmul(invbox,t1,t2);
mtmul(t2,invbox,M);
/* Determine the scaling matrix mu for the coordinates */
for(d=0;d<DIM;d++)
for(n=0;n<=d;n++)
t1[d][n] = box[d][n] + dt*boxv[d][n];
preserve_box_shape(ir,box_rel,t1);
/* t1 is the box at t+dt, determine mu as the relative change */
mmul_ur0(invbox,t1,mu);
}
void berendsen_pcoupl(FILE *fplog,gmx_step_t step,
t_inputrec *ir,real dt,tensor pres,matrix box,
matrix mu)
{
int d,n;
real scalar_pressure, xy_pressure, p_corr_z;
char *ptr,buf[STRLEN];
/*
* Calculate the scaling matrix mu
*/
scalar_pressure=0;
xy_pressure=0;
for(d=0; d<DIM; d++) {
scalar_pressure += pres[d][d]/DIM;
if (d != ZZ)
xy_pressure += pres[d][d]/(DIM-1);
}
/* Pressure is now in bar, everywhere. */
#define factor(d,m) (ir->compress[d][m]*dt/ir->tau_p)
/* mu has been changed from pow(1+...,1/3) to 1+.../3, since this is
* necessary for triclinic scaling
*/
clear_mat(mu);
switch (ir->epct) {
case epctISOTROPIC:
for(d=0; d<DIM; d++)
mu[d][d] = 1.0 - factor(d,d)*(ir->ref_p[d][d] - scalar_pressure)/DIM;
break;
case epctSEMIISOTROPIC:
for(d=0; d<ZZ; d++)
mu[d][d] = 1.0 - factor(d,d)*(ir->ref_p[d][d]-xy_pressure)/DIM;
mu[ZZ][ZZ] =
1.0 - factor(ZZ,ZZ)*(ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ])/DIM;
break;
case epctANISOTROPIC:
for(d=0; d<DIM; d++)
for(n=0; n<DIM; n++)
mu[d][n] = (d==n ? 1.0 : 0.0)
-factor(d,n)*(ir->ref_p[d][n] - pres[d][n])/DIM;
break;
case epctSURFACETENSION:
/* ir->ref_p[0/1] is the reference surface-tension times *
* the number of surfaces */
if (ir->compress[ZZ][ZZ])
p_corr_z = dt/ir->tau_p*(ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]);
else
/* when the compressibity is zero, set the pressure correction *
* in the z-direction to zero to get the correct surface tension */
p_corr_z = 0;
mu[ZZ][ZZ] = 1.0 - ir->compress[ZZ][ZZ]*p_corr_z;
for(d=0; d<DIM-1; d++)
mu[d][d] = 1.0 + factor(d,d)*(ir->ref_p[d][d]/(mu[ZZ][ZZ]*box[ZZ][ZZ])
- (pres[ZZ][ZZ]+p_corr_z - xy_pressure))/(DIM-1);
break;
default:
gmx_fatal(FARGS,"Berendsen pressure coupling type %s not supported yet\n",
EPCOUPLTYPETYPE(ir->epct));
break;
}
/* To fullfill the orientation restrictions on triclinic boxes
* we will set mu_yx, mu_zx and mu_zy to 0 and correct
* the other elements of mu to first order.
*/
mu[YY][XX] += mu[XX][YY];
mu[ZZ][XX] += mu[XX][ZZ];
mu[ZZ][YY] += mu[YY][ZZ];
mu[XX][YY] = 0;
mu[XX][ZZ] = 0;
mu[YY][ZZ] = 0;
if (debug) {
pr_rvecs(debug,0,"PC: pres ",pres,3);
pr_rvecs(debug,0,"PC: mu ",mu,3);
}
if (mu[XX][XX]<0.99 || mu[XX][XX]>1.01 ||
mu[YY][YY]<0.99 || mu[YY][YY]>1.01 ||
mu[ZZ][ZZ]<0.99 || mu[ZZ][ZZ]>1.01) {
char buf2[22];
sprintf(buf,"\nStep %s Warning: pressure scaling more than 1%%, "
"mu: %g %g %g\n",
gmx_step_str(step,buf2),mu[XX][XX],mu[YY][YY],mu[ZZ][ZZ]);
if (fplog)
fprintf(fplog,"%s",buf);
fprintf(stderr,"%s",buf);
}
}
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));
}
}
