static void pr_pull(FILE *fp,int indent,t_pull *pull)
{
int g;
PS("pull-geometry",EPULLGEOM(pull->eGeom));
pr_ivec(fp,indent,"pull-dim",pull->dim,DIM,TRUE);
PR("pull-r1",pull->cyl_r1);
PR("pull-r0",pull->cyl_r0);
PR("pull-constr-tol",pull->constr_tol);
PI("pull-nstxout",pull->nstxout);
PI("pull-nstfout",pull->nstfout);
PI("pull-ngrp",pull->ngrp);
for(g=0; g<pull->ngrp+1; g++)
pr_pullgrp(fp,indent,g,&pull->grp[g]);
}
void pr_qm_opts(FILE *fp,int indent,const char *title,t_grpopts *opts)
{
int i,m,j;
fprintf(fp,"%s:\n",title);
pr_int(fp,indent,"ngQM",opts->ngQM);
if (opts->ngQM > 0) {
pr_ivec(fp,indent,"QMmethod",opts->QMmethod,opts->ngQM,FALSE);
pr_ivec(fp,indent,"QMbasis",opts->QMbasis,opts->ngQM,FALSE);
pr_ivec(fp,indent,"QMcharge",opts->QMcharge,opts->ngQM,FALSE);
pr_ivec(fp,indent,"QMmult",opts->QMmult,opts->ngQM,FALSE);
pr_bvec(fp,indent,"bSH",opts->bSH,opts->ngQM,FALSE);
pr_ivec(fp,indent,"CASorbitals",opts->CASorbitals,opts->ngQM,FALSE);
pr_ivec(fp,indent,"CASelectrons",opts->CASelectrons,opts->ngQM,FALSE);
pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
pr_rvec(fp,indent,"SAon",opts->SAon,opts->ngQM,FALSE);
pr_ivec(fp,indent,"SAsteps",opts->SAsteps,opts->ngQM,FALSE);
pr_bvec(fp,indent,"bOPT",opts->bOPT,opts->ngQM,FALSE);
pr_bvec(fp,indent,"bTS",opts->bTS,opts->ngQM,FALSE);
}
}
void init_pppm(FILE *log,t_commrec *cr,t_nsborder *nsb,
bool bVerbose,bool bOld,rvec box,char *ghatfn,t_inputrec *ir)
{
int nx,ny,nz,m,porder;
ivec grids;
real r1,rc;
const real tol = 1e-5;
rvec spacing;
#ifdef WITHOUT_FFTW
fatal_error(0,"PPPM used, but GROMACS was compiled without FFTW support!\n");
#endif
if (cr != NULL) {
if (cr->nnodes > 1)
fprintf(log,"Initializing parallel PPPM.\n");
}
fprintf(log,"Will use the PPPM algorithm for long-range electrostatics\n");
if (!fexist(ghatfn)) {
beta[XX]=beta[YY]=beta[ZZ]= 1.85;
nx = ir->nkx;
ny = ir->nky;
nz = ir->nkz;
fprintf(log,"Generating Ghat function\n");
fprintf(log,"Grid size is %d x %d x %d\n",nx,ny,nz);
if ((nx < 4) || (ny < 4) || (nz < 4))
fatal_error(0,"Grid must be at least 4 points in all directions");
ghat = mk_rgrid(nx,ny,nz);
mk_ghat(NULL,nx,ny,nz,ghat,box,ir->rcoulomb_switch,ir->rcoulomb,TRUE,bOld);
if (bVerbose)
pr_scalar_gk("generghat.xvg",nx,ny,nz,box,ghat);
}
else {
fprintf(stderr,"Reading Ghat function from %s\n",ghatfn);
ghat = rd_ghat(log,ghatfn,grids,spacing,beta,&porder,&r1,&rc);
/* Check whether cut-offs correspond */
if ((fabs(r1-ir->rcoulomb_switch)>tol) || (fabs(rc-ir->rcoulomb)>tol)) {
fprintf(log,"rcoulomb_switch = %10.3e rcoulomb = %10.3e"
" r1 = %10.3e rc = %10.3e\n",
ir->rcoulomb_switch,ir->rcoulomb,r1,rc);
fflush(log);
fatal_error(0,"Cut-off lengths in tpb file and Ghat file %s "
"do not match\nCheck your log file!",ghatfn);
}
/* Check whether boxes correspond */
for(m=0; (m<DIM); m++)
if (fabs(box[m]-grids[m]*spacing[m]) > tol) {
pr_rvec(log,0,"box",box,DIM);
pr_rvec(log,0,"grid-spacing",spacing,DIM);
pr_ivec(log,0,"grid size",grids,DIM);
fflush(log);
fatal_error(0,"Box sizes in tpb file and Ghat file %s do not match\n"
"Check your log file!",ghatfn);
}
if (porder != 2)
fatal_error(0,"porder = %d, should be 2 in %s",porder,ghatfn);
nx = grids[XX];
ny = grids[YY];
nz = grids[ZZ];
if (bVerbose)
pr_scalar_gk("optimghat.xvg",nx,ny,nz,box,ghat);
}
/* Now setup the FFT things */
grid = mk_fftgrid(log,PAR(cr),nx,ny,nz,ir->bOptFFT);
}
void renum_atype(t_params plist[], gmx_mtop_t *mtop,
int *wall_atomtype,
gpp_atomtype_t ga, gmx_bool bVerbose)
{
int i, j, k, l, molt, mi, mj, nat, nrfp, ftype, ntype;
t_atoms *atoms;
t_param *nbsnew;
int *typelist;
real *new_radius;
real *new_vol;
real *new_surftens;
real *new_gb_radius;
real *new_S_hct;
int *new_atomnumber;
char ***new_atomname;
ntype = get_atomtype_ntypes(ga);
snew(typelist, ntype);
if (bVerbose)
{
fprintf(stderr, "renumbering atomtypes...\n");
}
/* Since the bonded interactions have been assigned now,
* we want to reduce the number of atom types by merging
* ones with identical nonbonded interactions, in addition
* to removing unused ones.
*
* With Generalized-Born electrostatics, or implicit solvent
* we also check that the atomtype radius, effective_volume
* and surface tension match.
*
* With QM/MM we also check that the atom numbers match
*/
/* Get nonbonded interaction type */
if (plist[F_LJ].nr > 0)
{
ftype = F_LJ;
}
else
{
ftype = F_BHAM;
}
/* Renumber atomtypes by first making a list of which ones are actually used.
* We provide the list of nonbonded parameters so search_atomtypes
* can determine if two types should be merged.
*/
nat = 0;
for (molt = 0; molt < mtop->nmoltype; molt++)
{
atoms = &mtop->moltype[molt].atoms;
for (i = 0; (i < atoms->nr); i++)
{
atoms->atom[i].type =
search_atomtypes(ga, &nat, typelist, atoms->atom[i].type,
plist[ftype].param, ftype);
atoms->atom[i].typeB =
search_atomtypes(ga, &nat, typelist, atoms->atom[i].typeB,
plist[ftype].param, ftype);
}
}
for (i = 0; i < 2; i++)
{
if (wall_atomtype[i] >= 0)
{
wall_atomtype[i] = search_atomtypes(ga, &nat, typelist, wall_atomtype[i],
plist[ftype].param, ftype);
}
}
snew(new_radius, nat);
snew(new_vol, nat);
snew(new_surftens, nat);
snew(new_atomnumber, nat);
snew(new_gb_radius, nat);
snew(new_S_hct, nat);
snew(new_atomname, nat);
/* We now have a list of unique atomtypes in typelist */
if (debug)
{
pr_ivec(debug, 0, "typelist", typelist, nat, TRUE);
}
/* Renumber nlist */
nbsnew = NULL;
snew(nbsnew, plist[ftype].nr);
nrfp = NRFP(ftype);
for (i = k = 0; (i < nat); i++)
{
mi = typelist[i];
for (j = 0; (j < nat); j++, k++)
{
mj = typelist[j];
for (l = 0; (l < nrfp); l++)
{
nbsnew[k].c[l] = plist[ftype].param[ntype*mi+mj].c[l];
}
}
new_radius[i] = get_atomtype_radius(mi, ga);
new_vol[i] = get_atomtype_vol(mi, ga);
new_surftens[i] = get_atomtype_surftens(mi, ga);
new_atomnumber[i] = get_atomtype_atomnumber(mi, ga);
new_gb_radius[i] = get_atomtype_gb_radius(mi, ga);
new_S_hct[i] = get_atomtype_S_hct(mi, ga);
new_atomname[i] = ga->atomname[mi];
}
for (i = 0; (i < nat*nat); i++)
{
for (l = 0; (l < nrfp); l++)
{
plist[ftype].param[i].c[l] = nbsnew[i].c[l];
}
}
plist[ftype].nr = i;
mtop->ffparams.atnr = nat;
sfree(ga->radius);
sfree(ga->vol);
sfree(ga->surftens);
sfree(ga->atomnumber);
sfree(ga->gb_radius);
sfree(ga->S_hct);
/* Dangling atomname pointers ? */
sfree(ga->atomname);
ga->radius = new_radius;
ga->vol = new_vol;
ga->surftens = new_surftens;
ga->atomnumber = new_atomnumber;
ga->gb_radius = new_gb_radius;
ga->S_hct = new_S_hct;
ga->atomname = new_atomname;
ga->nr = nat;
sfree(nbsnew);
sfree(typelist);
}
int gmx_pppm_init(FILE *log, t_commrec *cr,
const output_env_t oenv, gmx_bool bVerbose,
gmx_bool bOld, matrix box,
char *ghatfn, t_inputrec *ir,
gmx_bool bReproducible)
{
int nx,ny,nz,m,porder;
ivec grids;
real r1,rc;
const real tol = 1e-5;
rvec box_diag,spacing;
#ifdef DISABLE_PPPM
gmx_fatal(FARGS,"PPPM is not functional in the current version, we plan to implement PPPM through a small modification of the PME code.");
return -1;
#else
#ifdef GMX_WITHOUT_FFTW
gmx_fatal(FARGS,"PPPM used, but GROMACS was compiled without FFTW support!\n");
#endif
if (log) {
if (cr != NULL) {
if (cr->nnodes > 1)
fprintf(log,"Initializing parallel PPPM.\n");
}
fprintf(log,
"Will use the PPPM algorithm for long-range electrostatics\n");
}
for(m=0; m<DIM; m++)
box_diag[m] = box[m][m];
if (!gmx_fexist(ghatfn)) {
beta[XX]=beta[YY]=beta[ZZ]= 1.85;
nx = ir->nkx;
ny = ir->nky;
nz = ir->nkz;
if (log) {
fprintf(log,"Generating Ghat function\n");
fprintf(log,"Grid size is %d x %d x %d\n",nx,ny,nz);
}
if ((nx < 4) || (ny < 4) || (nz < 4))
gmx_fatal(FARGS,"Grid must be at least 4 points in all directions");
ghat = mk_rgrid(nx,ny,nz);
mk_ghat(NULL,nx,ny,nz,ghat,box_diag,
ir->rcoulomb_switch,ir->rcoulomb,TRUE,bOld);
if (bVerbose)
pr_scalar_gk("generghat.xvg",oenv,nx,ny,nz,box_diag,ghat);
}
else {
fprintf(stderr,"Reading Ghat function from %s\n",ghatfn);
ghat = rd_ghat(log,oenv,ghatfn,grids,spacing,beta,&porder,&r1,&rc);
/* Check whether cut-offs correspond */
if ((fabs(r1-ir->rcoulomb_switch)>tol) || (fabs(rc-ir->rcoulomb)>tol)) {
if (log) {
fprintf(log,"rcoulomb_switch = %10.3e rcoulomb = %10.3e"
" r1 = %10.3e rc = %10.3e\n",
ir->rcoulomb_switch,ir->rcoulomb,r1,rc);
fflush(log);
}
gmx_fatal(FARGS,"Cut-off lengths in tpb file and Ghat file %s "
"do not match\nCheck your log file!",ghatfn);
}
/* Check whether boxes correspond */
for(m=0; (m<DIM); m++)
if (fabs(box_diag[m]-grids[m]*spacing[m]) > tol) {
if (log) {
pr_rvec(log,0,"box",box_diag,DIM,TRUE);
pr_rvec(log,0,"grid-spacing",spacing,DIM,TRUE);
pr_ivec(log,0,"grid size",grids,DIM,TRUE);
fflush(log);
}
gmx_fatal(FARGS,"Box sizes in tpb file and Ghat file %s do not match\n"
"Check your log file!",ghatfn);
}
if (porder != 2)
gmx_fatal(FARGS,"porder = %d, should be 2 in %s",porder,ghatfn);
nx = grids[XX];
ny = grids[YY];
nz = grids[ZZ];
if (bVerbose)
pr_scalar_gk("optimghat.xvg",oenv,nx,ny,nz,box_diag,ghat);
}
/* Now setup the FFT things */
#ifdef GMX_MPI
cr->mpi_comm_mygroup=cr->mpi_comm_mysim;
#endif
grid = mk_fftgrid(nx,ny,nz,NULL,NULL,cr,bReproducible);
return 0;
#endif
}
