static void pr_cosine(FILE *fp,int indent,const char *title,t_cosines *cos,
gmx_bool bMDPformat)
{
int j;
if (bMDPformat) {
fprintf(fp,"%s = %d\n",title,cos->n);
}
else {
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
fprintf(fp,"n = %d\n",cos->n);
if (cos->n > 0) {
(void) pr_indent(fp,indent+2);
fprintf(fp,"a =");
for(j=0; (j<cos->n); j++)
fprintf(fp," %e",cos->a[j]);
fprintf(fp,"\n");
(void) pr_indent(fp,indent+2);
fprintf(fp,"phi =");
for(j=0; (j<cos->n); j++)
fprintf(fp," %e",cos->phi[j]);
fprintf(fp,"\n");
}
}
}
void pr_header(FILE *fp,int indent,const char *title,t_tpxheader *sh)
{
char buf[22];
if (available(fp,sh,indent,title))
{
indent=pr_title(fp,indent,title);
pr_indent(fp,indent);
fprintf(fp,"bIr = %spresent\n",sh->bIr?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bBox = %spresent\n",sh->bBox?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bTop = %spresent\n",sh->bTop?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bX = %spresent\n",sh->bX?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bV = %spresent\n",sh->bV?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"bF = %spresent\n",sh->bF?"":"not ");
pr_indent(fp,indent);
fprintf(fp,"natoms = %d\n",sh->natoms);
pr_indent(fp,indent);
fprintf(fp,"lambda = %e\n",sh->lambda);
}
}
void list_xtc(const char *fn)
{
t_fileio *xd;
int indent;
char buf[256];
rvec *x;
matrix box;
int nframe, natoms, step;
real prec, time;
gmx_bool bOK;
xd = open_xtc(fn, "r");
read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
nframe = 0;
do
{
sprintf(buf, "%s frame %d", fn, nframe);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
fprintf(stdout, "natoms=%10d step=%10d time=%12.7e prec=%10g\n",
natoms, step, time, prec);
pr_rvecs(stdout, indent, "box", box, DIM);
pr_rvecs(stdout, indent, "x", x, natoms);
nframe++;
}
while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK));
if (!bOK)
{
fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
}
sfree(x);
close_xtc(xd);
}
/*! \brief Callback used by list_tng_for_gmx_dump. */
static void list_tng_inner(const char *fn,
gmx_bool bFirstFrame,
real *values,
gmx_int64_t step,
double frame_time,
gmx_int64_t n_values_per_frame,
gmx_int64_t n_atoms,
real prec,
gmx_int64_t nframe,
char *block_name)
{
char buf[256];
int indent = 0;
if (bFirstFrame)
{
sprintf(buf, "%s frame %" GMX_PRId64, fn, nframe);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
fprintf(stdout, "natoms=%10" GMX_PRId64 " step=%10" GMX_PRId64 " time=%12.7e",
n_atoms, step, frame_time);
if (prec > 0)
{
fprintf(stdout, " prec=%10g", prec);
}
fprintf(stdout, "\n");
}
pr_reals_of_dim(stdout, indent, block_name, values, n_atoms, n_values_per_frame);
}
void pr_top(FILE *fp,int indent,char *title,t_topology *top)
{
if (available(fp,top,title)) {
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"name=\"%s\"\n",*(top->name));
pr_atoms(fp,indent,"atoms",&(top->atoms));
pr_blocks(fp,indent,"blocks",top->blocks,ebNR,eblock_names);
pr_idef(fp,indent,"idef",&top->idef);
}
}
void pr_atoms(FILE *fp,int indent,const char *title,t_atoms *atoms,
gmx_bool bShownumbers)
{
if (available(fp,atoms,indent,title))
{
indent=pr_title(fp,indent,title);
pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr,bShownumbers);
pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr,bShownumbers);
pr_resinfo(fp,indent,"residue",atoms->resinfo,atoms->nres,bShownumbers);
}
}
static int pr_block_title(FILE *fp,int indent,const char *title,t_block *block)
{
int i;
if (available(fp,block,indent,title))
{
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"nr=%d\n",block->nr);
}
return indent;
}
static void list_trn(char *fn)
{
int fpread,fpwrite,nframe,indent;
char buf[256];
rvec *x,*v,*f;
matrix box;
t_trnheader trn;
bool bOK;
fpread = open_trn(fn,"r");
fpwrite = open_tpx(NULL,"w");
gmx_fio_setdebug(fpwrite,TRUE);
nframe = 0;
while (fread_trnheader(fpread,&trn,&bOK)) {
snew(x,trn.natoms);
snew(v,trn.natoms);
snew(f,trn.natoms);
if (fread_htrn(fpread,&trn,
trn.box_size ? box : NULL,
trn.x_size ? x : NULL,
trn.v_size ? v : NULL,
trn.f_size ? f : NULL)) {
sprintf(buf,"%s frame %d",fn,nframe);
indent=0;
indent=pr_title(stdout,indent,buf);
pr_indent(stdout,indent);
fprintf(stdout,"natoms=%10d step=%10d time=%12.7e lambda=%10g\n",
trn.natoms,trn.step,trn.t,trn.lambda);
if (trn.box_size)
pr_rvecs(stdout,indent,"box",box,DIM);
if (trn.x_size)
pr_rvecs(stdout,indent,"x",x,trn.natoms);
if (trn.v_size)
pr_rvecs(stdout,indent,"v",v,trn.natoms);
if (trn.f_size)
pr_rvecs(stdout,indent,"f",f,trn.natoms);
}
else
fprintf(stderr,"\nWARNING: Incomplete frame: nr %d, t=%g\n",
nframe,trn.t);
sfree(x);
sfree(v);
sfree(f);
nframe++;
}
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
nframe,trn.t);
close_tpx(fpwrite);
close_trn(fpread);
}
static void pr_atoms(FILE *fp,int indent,char *title,t_atoms *atoms)
{
if (available(fp,atoms,title))
{
indent=pr_title(fp,indent,title);
pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
pr_grps(fp,indent,"grp",atoms->grps,egcNR,atoms->grpname);
pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr);
pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr);
pr_strings(fp,indent,"residue",atoms->resname,atoms->nres);
pr_strings(fp,indent,"grpname",atoms->grpname,atoms->ngrpname);
pr_block(fp,indent,"excl",&atoms->excl);
}
}
void pr_top(FILE *fp,int indent,const char *title,t_topology *top, gmx_bool bShowNumbers)
{
if (available(fp,top,indent,title)) {
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"name=\"%s\"\n",*(top->name));
pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
}
}
void pr_atomtypes(FILE *fp,int indent,const char *title,t_atomtypes *atomtypes,
bool bShowNumbers)
{
int i;
if (available(fp,atomtypes,indent,title))
{
indent=pr_title(fp,indent,title);
for(i=0;i<atomtypes->nr;i++) {
pr_indent(fp,indent);
fprintf(fp,
"atomtype[%3d]={radius=%12.5e, volume=%12.5e, surftens=%12.5e, atomnumber=%4d)}\n",
bShowNumbers?i:-1,atomtypes->radius[i],atomtypes->vol[i],
atomtypes->surftens[i],atomtypes->atomnumber[i]);
}
}
}
void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers)
{
if (available(fp, top, indent, title))
{
indent = pr_title(fp, indent, title);
pr_indent(fp, indent);
fprintf(fp, "name=\"%s\"\n", *(top->name));
pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
pr_block(fp, indent, "cgs", &top->cgs, bShowNumbers);
pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
pr_str(fp, indent, "bIntermolecularInteractions",
gmx::boolToString(top->bIntermolecularInteractions));
pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
pr_idef(fp, indent, "idef", &top->idef, bShowNumbers);
}
}
static int pr_block_title(FILE *fp,int indent,char *title,t_block *block)
{
int i;
if (available(fp,block,title))
{
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
fprintf(fp,"multinr[division over processors]:");
for (i=0; (i<MAXNODES); i++)
(void) fprintf(fp," %d",block->multinr[i]);
fprintf(fp,"\n");
(void) pr_indent(fp,indent);
(void) fprintf(fp,"nr=%d\n",block->nr);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"nra=%d\n",block->nra);
}
return indent;
}
static void pr_cosine(FILE *fp,int indent,char *title,t_cosines *cos)
{
int j;
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
fprintf(fp,"n = %d\n",cos->n);
if (cos->n > 0) {
(void) pr_indent(fp,indent+2);
fprintf(fp,"a =");
for(j=0; (j<cos->n); j++)
fprintf(fp," %e",cos->a[j]);
fprintf(fp,"\n");
(void) pr_indent(fp,indent+2);
fprintf(fp,"phi =");
for(j=0; (j<cos->n); j++)
fprintf(fp," %e",cos->phi[j]);
fprintf(fp,"\n");
}
}
void pr_ffparams(FILE *fp,int indent,const char *title,
gmx_ffparams_t *ffparams,
bool bShowNumbers)
{
int i,j;
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
for (i=0; i<ffparams->ntypes; i++) {
(void) pr_indent(fp,indent+INDENT);
(void) fprintf(fp,"functype[%d]=%s, ",
bShowNumbers?i:-1,
interaction_function[ffparams->functype[i]].name);
pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
}
(void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
}
static void pr_ilist(FILE *fp,int indent,char *title,
t_idef *idef,t_ilist *ilist)
{
int i,j,k,type,ftype;
t_iatom *iatoms;
if (available(fp,ilist,title))
{
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
fprintf(fp,"nr: %d\n",ilist->nr);
if (ilist->nr > 0) {
(void) pr_indent(fp,indent);
fprintf(fp,"multinr[division over processors]:");
for (i=0; (i<MAXNODES) && (ilist->multinr[i] > 0); i++)
(void) fprintf(fp," %d",ilist->multinr[i]);
fprintf(fp,"\n");
(void) pr_indent(fp,indent);
fprintf(fp,"iatoms:\n");
iatoms=ilist->iatoms;
for (i=j=0; i<ilist->nr;) {
#ifndef DEBUG
(void) pr_indent(fp,indent+INDENT);
type=*(iatoms++);
ftype=idef->functype[type];
(void) fprintf(fp,"%d type=%d (%s)",
bShowNumbers?j:-1,bShowNumbers?type:-1,
interaction_function[ftype].name);
j++;
for (k=0; k<interaction_function[ftype].nratoms; k++)
(void) fprintf(fp," %u",*(iatoms++));
(void) fprintf(fp,"\n");
i+=1+interaction_function[ftype].nratoms;
#else
fprintf(fp,"%5d%5d\n",i,iatoms[i]);
i++;
#endif
}
}
}
}
void list_xtc(char *fn, bool bXVG)
{
int xd,indent;
char buf[256];
rvec *x;
matrix box;
int nframe,natoms,step;
real prec,time;
bool bOK;
xd = open_xtc(fn,"r");
read_first_xtc(xd,&natoms,&step,&time,box,&x,&prec,&bOK);
nframe=0;
do {
if (bXVG) {
int i,d;
fprintf(stdout,"%g",time);
for(i=0; i<natoms; i++)
for(d=0; d<DIM; d++)
fprintf(stdout," %g",x[i][d]);
fprintf(stdout,"\n");
} else {
sprintf(buf,"%s frame %d",fn,nframe);
indent=0;
indent=pr_title(stdout,indent,buf);
pr_indent(stdout,indent);
fprintf(stdout,"natoms=%10d step=%10d time=%12.7e prec=%10g\n",
natoms,step,time,prec);
pr_rvecs(stdout,indent,"box",box,DIM);
pr_rvecs(stdout,indent,"x",x,natoms);
}
nframe++;
} while (read_next_xtc(xd,natoms,&step,&time,box,x,&prec,&bOK));
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame at time %g\n",time);
close_xtc(xd);
}
void pr_trnheader(FILE *fp,int indent,char *title,t_trnheader *sh)
{
if (sh) {
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"box_size = %d\n",sh->box_size);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"x_size = %d\n",sh->x_size);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"v_size = %d\n",sh->v_size);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"f_size = %d\n",sh->f_size);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"natoms = %d\n",sh->natoms);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"step = %d\n",sh->step);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"t = %e\n",sh->t);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"lambda = %e\n",sh->lambda);
}
}
void pr_mtop(FILE *fp,int indent,const char *title,gmx_mtop_t *mtop,
gmx_bool bShowNumbers)
{
int mt,mb;
if (available(fp,mtop,indent,title)) {
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"name=\"%s\"\n",*(mtop->name));
pr_int(fp,indent,"#atoms",mtop->natoms);
for(mb=0; mb<mtop->nmolblock; mb++) {
pr_molblock(fp,indent,"molblock",&mtop->molblock[mb],mb,
mtop->moltype,bShowNumbers);
}
pr_ffparams(fp,indent,"ffparams",&(mtop->ffparams),bShowNumbers);
pr_atomtypes(fp,indent,"atomtypes",&(mtop->atomtypes),bShowNumbers);
for(mt=0; mt<mtop->nmoltype; mt++) {
pr_moltype(fp,indent,"moltype",&mtop->moltype[mt],mt,
&mtop->ffparams,bShowNumbers);
}
pr_groups(fp,indent,"groups",&mtop->groups,bShowNumbers);
}
}
void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
gmx_bool bShowNumbers)
{
int mt, mb, j;
if (available(fp, mtop, indent, title))
{
indent = pr_title(fp, indent, title);
pr_indent(fp, indent);
fprintf(fp, "name=\"%s\"\n", *(mtop->name));
pr_int(fp, indent, "#atoms", mtop->natoms);
pr_int(fp, indent, "#molblock", mtop->nmolblock);
for (mb = 0; mb < mtop->nmolblock; mb++)
{
pr_molblock(fp, indent, "molblock", &mtop->molblock[mb], mb, mtop->moltype);
}
pr_str(fp, indent, "bIntermolecularInteractions",
gmx::boolToString(mtop->bIntermolecularInteractions));
if (mtop->bIntermolecularInteractions)
{
for (j = 0; (j < F_NRE); j++)
{
pr_ilist(fp, indent, interaction_function[j].longname,
mtop->ffparams.functype,
&mtop->intermolecular_ilist[j], bShowNumbers);
}
}
pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
pr_atomtypes(fp, indent, "atomtypes", &(mtop->atomtypes), bShowNumbers);
for (mt = 0; mt < mtop->nmoltype; mt++)
{
pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt,
&mtop->ffparams, bShowNumbers);
}
pr_groups(fp, indent, &mtop->groups, bShowNumbers);
}
}
void pr_ilist(FILE *fp,int indent,const char *title,
t_functype *functype,t_ilist *ilist, gmx_bool bShowNumbers)
{
int i,j,k,type,ftype;
t_iatom *iatoms;
if (available(fp,ilist,indent,title) && ilist->nr > 0)
{
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
fprintf(fp,"nr: %d\n",ilist->nr);
if (ilist->nr > 0) {
(void) pr_indent(fp,indent);
fprintf(fp,"iatoms:\n");
iatoms=ilist->iatoms;
for (i=j=0; i<ilist->nr;) {
#ifndef DEBUG
(void) pr_indent(fp,indent+INDENT);
type=*(iatoms++);
ftype=functype[type];
(void) fprintf(fp,"%d type=%d (%s)",
bShowNumbers?j:-1,bShowNumbers?type:-1,
interaction_function[ftype].name);
j++;
for (k=0; k<interaction_function[ftype].nratoms; k++)
(void) fprintf(fp," %u",*(iatoms++));
(void) fprintf(fp,"\n");
i+=1+interaction_function[ftype].nratoms;
#else
fprintf(fp,"%5d%5d\n",i,iatoms[i]);
i++;
#endif
}
}
}
}
void pr_idef(FILE *fp,int indent,const char *title,t_idef *idef, gmx_bool bShowNumbers)
{
int i,j;
if (available(fp,idef,indent,title)) {
indent=pr_title(fp,indent,title);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"atnr=%d\n",idef->atnr);
(void) pr_indent(fp,indent);
(void) fprintf(fp,"ntypes=%d\n",idef->ntypes);
for (i=0; i<idef->ntypes; i++) {
(void) pr_indent(fp,indent+INDENT);
(void) fprintf(fp,"functype[%d]=%s, ",
bShowNumbers?i:-1,
interaction_function[idef->functype[i]].name);
pr_iparams(fp,idef->functype[i],&idef->iparams[i]);
}
(void) pr_real(fp,indent,"fudgeQQ",idef->fudgeQQ);
for(j=0; (j<F_NRE); j++)
pr_ilist(fp,indent,interaction_function[j].longname,
idef->functype,&idef->il[j],bShowNumbers);
}
}
static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
gmx_bool bSysTop)
{
FILE *gp;
int fp, indent, i, j, **gcount, atot;
t_state state;
rvec *f = NULL;
t_inputrec ir;
t_tpxheader tpx;
gmx_mtop_t mtop;
gmx_groups_t *groups;
t_topology top;
read_tpxheader(fn, &tpx, TRUE, NULL, NULL);
read_tpx_state(fn,
tpx.bIr ? &ir : NULL,
&state, tpx.bF ? f : NULL,
tpx.bTop ? &mtop : NULL);
if (mdpfn && tpx.bIr)
{
gp = gmx_fio_fopen(mdpfn, "w");
pr_inputrec(gp, 0, NULL, &(ir), TRUE);
gmx_fio_fclose(gp);
}
if (!mdpfn)
{
if (bSysTop)
{
top = gmx_mtop_t_to_t_topology(&mtop);
}
if (available(stdout, &tpx, 0, fn))
{
indent = 0;
indent = pr_title(stdout, indent, fn);
pr_inputrec(stdout, 0, "inputrec", tpx.bIr ? &(ir) : NULL, FALSE);
indent = 0;
pr_header(stdout, indent, "header", &(tpx));
if (!bSysTop)
{
pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers);
}
else
{
pr_top(stdout, indent, "topology", &(top), bShowNumbers);
}
pr_rvecs(stdout, indent, "box", tpx.bBox ? state.box : NULL, DIM);
pr_rvecs(stdout, indent, "box_rel", tpx.bBox ? state.box_rel : NULL, DIM);
pr_rvecs(stdout, indent, "boxv", tpx.bBox ? state.boxv : NULL, DIM);
pr_rvecs(stdout, indent, "pres_prev", tpx.bBox ? state.pres_prev : NULL, DIM);
pr_rvecs(stdout, indent, "svir_prev", tpx.bBox ? state.svir_prev : NULL, DIM);
pr_rvecs(stdout, indent, "fvir_prev", tpx.bBox ? state.fvir_prev : NULL, DIM);
/* leave nosehoover_xi in for now to match the tpr version */
pr_doubles(stdout, indent, "nosehoover_xi", state.nosehoover_xi, state.ngtc);
/*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
/*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
pr_rvecs(stdout, indent, "x", tpx.bX ? state.x : NULL, state.natoms);
pr_rvecs(stdout, indent, "v", tpx.bV ? state.v : NULL, state.natoms);
if (tpx.bF)
{
pr_rvecs(stdout, indent, "f", f, state.natoms);
}
}
groups = &mtop.groups;
snew(gcount, egcNR);
for (i = 0; (i < egcNR); i++)
{
snew(gcount[i], groups->grps[i].nr);
}
for (i = 0; (i < mtop.natoms); i++)
{
for (j = 0; (j < egcNR); j++)
{
gcount[j][ggrpnr(groups, j, i)]++;
}
}
printf("Group statistics\n");
for (i = 0; (i < egcNR); i++)
{
atot = 0;
printf("%-12s: ", gtypes[i]);
for (j = 0; (j < groups->grps[i].nr); j++)
{
printf(" %5d", gcount[i][j]);
atot += gcount[i][j];
}
printf(" (total %d atoms)\n", atot);
sfree(gcount[i]);
}
sfree(gcount);
}
done_state(&state);
sfree(f);
}
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));
}
}
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]));
}
}
static void list_trr(const char *fn)
{
t_fileio *fpread;
int nframe, indent;
char buf[256];
rvec *x, *v, *f;
matrix box;
gmx_trr_header_t trrheader;
gmx_bool bOK;
fpread = gmx_trr_open(fn, "r");
nframe = 0;
while (gmx_trr_read_frame_header(fpread, &trrheader, &bOK))
{
snew(x, trrheader.natoms);
snew(v, trrheader.natoms);
snew(f, trrheader.natoms);
if (gmx_trr_read_frame_data(fpread, &trrheader,
trrheader.box_size ? box : NULL,
trrheader.x_size ? x : NULL,
trrheader.v_size ? v : NULL,
trrheader.f_size ? f : NULL))
{
sprintf(buf, "%s frame %d", fn, nframe);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
fprintf(stdout, "natoms=%10d step=%10d time=%12.7e lambda=%10g\n",
trrheader.natoms, trrheader.step, trrheader.t, trrheader.lambda);
if (trrheader.box_size)
{
pr_rvecs(stdout, indent, "box", box, DIM);
}
if (trrheader.x_size)
{
pr_rvecs(stdout, indent, "x", x, trrheader.natoms);
}
if (trrheader.v_size)
{
pr_rvecs(stdout, indent, "v", v, trrheader.natoms);
}
if (trrheader.f_size)
{
pr_rvecs(stdout, indent, "f", f, trrheader.natoms);
}
}
else
{
fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n",
nframe, trrheader.t);
}
sfree(x);
sfree(v);
sfree(f);
nframe++;
}
if (!bOK)
{
fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n",
nframe, trrheader.t);
}
gmx_trr_close(fpread);
}
