typedef struct
{
real deltaF0;
- gmx_bool bHarmonic; /* Use flooding for harmonic restraint on eigenvector */
+ gmx_bool bHarmonic; /* Use flooding for harmonic restraint on eigenvector */
real tau;
real deltaF;
real Efl;
typedef struct edpar
{
int nini; /* total Nr of atoms */
- gmx_bool fitmas; /* true if trans fit with cm */
- gmx_bool pcamas; /* true if mass-weighted PCA */
+ gmx_bool fitmas; /* true if trans fit with cm */
+ gmx_bool pcamas; /* true if mass-weighted PCA */
int presteps; /* number of steps to run without any
* perturbations ... just monitoring */
int outfrq; /* freq (in steps) of writing to edo */
/* all gmx_edx datasets are copied to all nodes in the parallel case */
struct gmx_edx sref; /* reference positions, to these fitting
* will be done */
- gmx_bool bRefEqAv; /* If true, reference & average indices
+ gmx_bool bRefEqAv; /* If true, reference & average indices
* are the same. Used for optimization */
struct gmx_edx sav; /* average positions */
struct gmx_edx star; /* target positions */
t_edvecs vecs; /* eigenvectors */
real slope; /* minimal slope in acceptance radexp */
- gmx_bool bNeedDoEdsam; /* if any of the options mon, linfix, ...
+ gmx_bool bNeedDoEdsam; /* if any of the options mon, linfix, ...
* is used (i.e. apart from flooding) */
t_edflood flood; /* parameters especially for flooding */
struct t_ed_buffer *buf; /* handle to local buffers */
const char *edonam; /* output */
FILE *edo; /* output file pointer */
t_edpar *edpar;
- gmx_bool bFirst;
- gmx_bool bStartFromCpt;
+ gmx_bool bFirst;
+ gmx_bool bStartFromCpt;
} t_gmx_edsam;
ivec *extra_shifts_xcoll; /* xcoll shift changes since last NS step */
ivec *shifts_xc_ref; /* Shifts for xc_ref */
ivec *extra_shifts_xc_ref; /* xc_ref shift changes since last NS step */
- gmx_bool bUpdateShifts; /* TRUE in NS steps to indicate that the
+ gmx_bool bUpdateShifts; /* TRUE in NS steps to indicate that the
ED shifts for this ED dataset need to
be updated */
};
for(i=0; (i < tvec->neig); i++)
{
fgets2 (line,STRLEN,in);
- if (bReadRefproj) /* only when using flooding as harmonic restraint */
+ if (bReadRefproj) /* ONLY when using flooding as harmonic restraint */
{
nscan = sscanf(line,"%d%lf%lf%lf",&idum,&rdum,&refproj_dum,&refprojslope_dum);
- if (4 == nscan)
+ /* Zero out values which were not scanned */
+ switch(nscan)
{
- fprintf(stdout, "ED: Will add %15.8e to the reference projection of eigenvector %d at each time step.\n",
- refprojslope_dum, i);
+ case 4:
+ /* Every 4 values read */
+ break;
+ case 3:
+ /* No value for slope, set to 0 */
+ refprojslope_dum = 0.0;
+ break;
+ case 2:
+ /* No values for reference projection and slope, set to 0 */
+ refproj_dum = 0.0;
+ refprojslope_dum = 0.0;
+ break;
+ default:
+ gmx_fatal(FARGS,"Expected 2 - 4 (not %d) values for flooding vec: <nr> <spring const> <refproj> <refproj-slope>\n", nscan);
+ break;
}
- else
- {
- refprojslope_dum = 0.0;
- if (nscan != 3)
- {
- /* Neither 3, nor 4 values found */
- gmx_fatal(FARGS,"Expected 4 (not %d) values for flooding vec: <nr> <spring const> <refproj> <refproj-slope>\n",
- nscan);
- }
- }
- tvec->ieig[i]=idum;
- tvec->stpsz[i]=rdum;
tvec->refproj[i]=refproj_dum;
tvec->refproj0[i]=refproj_dum;
tvec->refprojslope[i]=refprojslope_dum;
}
- else
+ else /* Normal flooding */
{
nscan = sscanf(line,"%d%lf",&idum,&rdum);
if (nscan != 2)
gmx_fatal(FARGS,"Expected 2 values for flooding vec: <nr> <stpsz>\n");
- tvec->ieig[i]=idum;
- tvec->stpsz[i]=rdum;
}
- }
+ tvec->ieig[i]=idum;
+ tvec->stpsz[i]=rdum;
+ } /* end of loop over eigenvectors */
+
for(i=0; (i < tvec->neig); i++)
{
snew(tvec->vec[i],nr);
if (readmagic != magic)
{
if (readmagic==666 || readmagic==667 || readmagic==668)
- gmx_fatal(FARGS,"wrong magic number: Use newest version of make_edi to produce edi file");
+ gmx_fatal(FARGS,"Wrong magic number: Use newest version of make_edi to produce edi file");
else
gmx_fatal(FARGS,"Wrong magic number %d in %s",readmagic,ed->edinam);
}
fprintf(ed->edo," contracting radius = %f\n", calc_radius(&edi->vecs.radcon));
}
}
- else
- {
- fprintf(ed->edo, " NOTE: none of the ED options mon/linfix/linacc/radfix/radacc/radcon were chosen for dataset #%d!\n", nr_edi);
- }
}
/* Returns if any constraints are switched on */
/* process target structure, if required */
if (edi->star.nr > 0)
{
+ fprintf(stderr, "ED: Fitting target structure to reference structure\n");
/* get translation & rotation for fit of target structure to reference structure */
fit_to_reference(edi->star.x, fit_transvec, fit_rotmat, edi);
/* do the fit */
rad_project(edi, xstart, &edi->vecs.radcon, cr);
/* process structure that will serve as origin of expansion circle */
+ if (eEDflood == ed->eEDtype)
+ fprintf(stderr, "ED: Setting center of flooding potential (0 = average structure)\n");
if (edi->sori.nr > 0)
{
+ fprintf(stderr, "ED: Fitting origin structure to reference structure\n");
/* fit this structure to reference structure */
fit_to_reference(edi->sori.x, fit_transvec, fit_rotmat, edi);
/* do the fit */
rad_project(edi, edi->sori.x, &edi->vecs.radfix, cr);
if (ed->eEDtype == eEDflood)
{
+ fprintf(stderr, "ED: The ORIGIN structure will define the flooding potential center.\n");
/* Set center of flooding potential to the ORIGIN structure */
rad_project(edi, edi->sori.x, &edi->flood.vecs, cr);
}
}
- else
+ else /* No origin structure given */
{
rad_project(edi, xstart, &edi->vecs.radacc, cr);
rad_project(edi, xstart, &edi->vecs.radfix, cr);
if (ed->eEDtype == eEDflood)
{
- /* Set center of flooding potential to the center of the covariance matrix,
- * i.e. the average structure, i.e. zero in the projected system */
- for (i=0; i<edi->flood.vecs.neig; i++)
+ if (edi->flood.bHarmonic)
+ {
+ fprintf(stderr, "ED: A (possibly changing) ref. projection will define the flooding potential center.\n");
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ edi->flood.vecs.refproj[i] = edi->flood.vecs.refproj0[i];
+ }
+ else
{
- if (!edi->flood.bHarmonic)
+ fprintf(stderr, "ED: The AVERAGE structure will define the flooding potential center.\n");
+ /* Set center of flooding potential to the center of the covariance matrix,
+ * i.e. the average structure, i.e. zero in the projected system */
+ for (i=0; i<edi->flood.vecs.neig; i++)
edi->flood.vecs.refproj[i] = 0.0;
}
}
}
+ /* For convenience, output the center of the flooding potential for the eigenvectors */
+ if (eEDflood == ed->eEDtype)
+ {
+ for (i=0; i<edi->flood.vecs.neig; i++)
+ {
+ fprintf(stdout, "ED: EV %d flooding potential center: %11.4e (adding %11.4e/timestep)\n",
+ i, edi->flood.vecs.refproj[i], edi->flood.vecs.refprojslope[i]);
+ }
+ }
/* set starting projections for linsam */
rad_project(edi, xstart, &edi->vecs.linacc, cr);
struct t_do_edsam *buf;
t_edpar *edi;
real rmsdev=-1; /* RMSD from reference structure prior to applying the constraints */
- gmx_bool bSuppress=FALSE; /* Write .edo file on master? */
+ gmx_bool bSuppress=FALSE; /* Write .edo file on master? */
/* Check if ED sampling has to be performed */
typedef struct
{
real deltaF0;
- gmx_bool bHarmonic;
+ gmx_bool bHarmonic;
real tau;
real deltaF;
real kT;
typedef struct edipar
{
int nini; /* total Nr of atoms */
- gmx_bool fitmas; /* true if trans fit with cm */
- gmx_bool pcamas; /* true if mass-weighted PCA */
+ gmx_bool fitmas; /* true if trans fit with cm */
+ gmx_bool pcamas; /* true if mass-weighted PCA */
int presteps; /* number of steps to run without any
* perturbations ... just monitoring */
int outfrq; /* freq (in steps) of writing to edo */
else {*/
/* make space for coordinates and velocities */
init_t_atoms(&confat,natoms,FALSE);
- printf("init_t\n");
snew(*x,natoms);
read_stx_conf(confin,title,&confat,*x,NULL,NULL,box);
return natoms;
/* print the interpreted list of eigenvectors - to give some feedback*/
for (ev_class=0; ev_class<evEND; ++ev_class) {
- printf("list %s consist of the indices:",evOptions[ev_class]);
+ printf("Eigenvector list %7s consists of the indices: ",evOptions[ev_class]);
i=0;
while(listen[ev_class][i])
printf("%d ",listen[ev_class][i++]);
make_t_edx(&edi_params.sav,natoms,xav1,index);
- /*store target positions in edi_params*/
- if (opt2bSet("-tar",NFILE,fnm)) {
- get_structure(atoms,indexfile,TargetFile,&edi_params.star,nfit,
- ifit,natoms,index);
- } else
+ /* Store target positions in edi_params */
+ if (opt2bSet("-tar",NFILE,fnm))
+ {
+ if (0 != listen[evFLOOD][0])
+ {
+ fprintf(stderr, "\nNote: Providing a TARGET structure has no effect when using flooding.\n"
+ " You may want to use -ori to define the flooding potential center.\n\n");
+ }
+ get_structure(atoms,indexfile,TargetFile,&edi_params.star,nfit,ifit,natoms,index);
+ }
+ else
+ {
make_t_edx(&edi_params.star,0,NULL,index);
- /*store origin positions*/
- if (opt2bSet("-ori",NFILE,fnm)) {
- get_structure(atoms,indexfile,OriginFile,&edi_params.sori,nfit,
- ifit,natoms,index);
- } else
+ }
+
+ /* Store origin positions */
+ if (opt2bSet("-ori",NFILE,fnm))
+ {
+ get_structure(atoms,indexfile,OriginFile,&edi_params.sori,nfit,ifit,natoms,index);
+ }
+ else
+ {
make_t_edx(&edi_params.sori,0,NULL,index);
-
- /*write edi-file*/
+ }
+
+ /* Write edi-file */
write_the_whole_thing(ffopen(EdiFile,"w"), &edi_params, eigvec1,nvec1, listen, evStepList);
thanx(stderr);
+
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff