void f_calc_vir(FILE *log,int i0,int i1,rvec x[],rvec f[],tensor vir,
t_graph *g,matrix box)
{
int start,end;
if (g && (g->nnodes > 0)) {
/* Calculate virial for bonded forces only when they belong to
* this node.
*/
start = max(i0,g->start);
end = min(i1,g->end+1);
#ifdef SAFE
lo_fcv2(start,end,x,f,vir,g->ishift,box,TRICLINIC(box));
#else
lo_fcv(start,end,0,x[0],f[0],vir,g->ishift[0],box[0],TRICLINIC(box));
#endif
/* If not all atoms are bonded, calculate their virial contribution
* anyway, without shifting back their coordinates.
* Note the nifty pointer arithmetic...
*/
if (start > i0)
calc_vir(log,start-i0,x + i0,f + i0,vir,FALSE,box);
if (end < i1)
calc_vir(log,i1-end,x + end,f + end,vir,FALSE,box);
}
else
calc_vir(log,i1-i0,x + i0,f + i0,vir,FALSE,box);
}
void f_calc_vir(int i0, int i1, rvec x[], rvec f[], tensor vir,
t_graph *g, matrix box)
{
int start, end;
if (g && (g->nnodes > 0))
{
/* Calculate virial for bonded forces only when they belong to
* this node.
*/
start = std::max(i0, g->at_start);
end = std::min(i1, g->at_end);
lo_fcv(start, end, x[0], f[0], vir, g->ishift[0], box[0], TRICLINIC(box));
/* If not all atoms are bonded, calculate their virial contribution
* anyway, without shifting back their coordinates.
* Note the nifty pointer arithmetic...
*/
if (start > i0)
{
calc_vir(start-i0, x + i0, f + i0, vir, FALSE, box);
}
if (end < i1)
{
calc_vir(i1-end, x + end, f + end, vir, FALSE, box);
}
}
else
{
calc_vir(i1-i0, x + i0, f + i0, vir, FALSE, box);
}
}
void write_espresso_conf_indexed(FILE *out, const char *title,
t_atoms *atoms, int nx, int *index,
rvec *x, rvec *v, matrix box)
{
int i, j;
fprintf(out, "# %s\n", title);
if (TRICLINIC(box))
{
gmx_warning("The Espresso format does not support triclinic unit-cells");
}
fprintf(out, "{variable {box_l %f %f %f}}\n", box[0][0], box[1][1], box[2][2]);
fprintf(out, "{particles {id pos type q%s}\n", v ? " v" : "");
for (i = 0; i < nx; i++)
{
if (index)
{
j = index[i];
}
else
{
j = i;
}
fprintf(out, "\t{%d %f %f %f %u %g",
j, x[j][XX], x[j][YY], x[j][ZZ],
atoms->atom[j].type, atoms->atom[j].q);
if (v)
{
fprintf(out, " %f %f %f", v[j][XX], v[j][YY], v[j][ZZ]);
}
fprintf(out, "}\n");
}
fprintf(out, "}\n");
}
void put_atoms_in_box(int ePBC, matrix box, int natoms, rvec x[])
{
int npbcdim, i, m, d;
if (ePBC == epbcSCREW)
{
gmx_fatal(FARGS, "Sorry, %s pbc is not yet supported", epbc_names[ePBC]);
}
if (ePBC == epbcXY)
{
npbcdim = 2;
}
else
{
npbcdim = 3;
}
if (TRICLINIC(box))
{
for (i = 0; (i < natoms); i++)
{
for (m = npbcdim-1; m >= 0; m--)
{
while (x[i][m] < 0)
{
for (d = 0; d <= m; d++)
{
x[i][d] += box[m][d];
}
}
while (x[i][m] >= box[m][m])
{
for (d = 0; d <= m; d++)
{
x[i][d] -= box[m][d];
}
}
}
}
}
else
{
for (i = 0; i < natoms; i++)
{
for (d = 0; d < npbcdim; d++)
{
while (x[i][d] < 0)
{
x[i][d] += box[d][d];
}
while (x[i][d] >= box[d][d])
{
x[i][d] -= box[d][d];
}
}
}
}
}
void visualize_box(FILE *out,int a0,int r0,matrix box,rvec gridsize)
{
int *edge;
rvec *vert,shift;
int nx,ny,nz,nbox,nat;
int i,j,x,y,z;
int rectedge[24] = { 0,1, 1,3, 3,2, 0,2, 0,4, 1,5, 3,7, 2,6, 4,5, 5,7, 7,6, 6,4 };
a0++;
r0++;
nx = (int)(gridsize[XX]+0.5);
ny = (int)(gridsize[YY]+0.5);
nz = (int)(gridsize[ZZ]+0.5);
nbox = nx*ny*nz;
if (TRICLINIC(box)) {
nat = nbox*NCUCVERT;
snew(vert,nat);
calc_compact_unitcell_vertices(ecenterDEF,box,vert);
j = 0;
for(z=0; z<nz; z++)
for(y=0; y<ny; y++)
for(x=0; x<nx; x++) {
for(i=0; i<DIM; i++)
shift[i] = x*box[0][i]+y*box[1][i]+z*box[2][i];
for(i=0; i<NCUCVERT; i++) {
rvec_add(vert[i],shift,vert[j]);
j++;
}
}
for(i=0; i<nat; i++) {
fprintf(out,pdbformat,"ATOM",a0+i,"C","BOX",'K'+i/NCUCVERT,r0+i,
10*vert[i][XX],10*vert[i][YY],10*vert[i][ZZ]);
fprintf(out,"\n");
}
edge = compact_unitcell_edges();
for(j=0; j<nbox; j++)
for(i=0; i<NCUCEDGE; i++)
fprintf(out,"CONECT%5d%5d\n",
a0 + j*NCUCVERT + edge[2*i],
a0 + j*NCUCVERT + edge[2*i+1]);
sfree(vert);
} else {
i=0;
for(z=0; z<=1; z++)
for(y=0; y<=1; y++)
for(x=0; x<=1; x++) {
fprintf(out,pdbformat,"ATOM",a0+i,"C","BOX",'K'+i/8,r0+i,
x*10*box[XX][XX],y*10*box[YY][YY],z*10*box[ZZ][ZZ]);
fprintf(out,"\n");
i++;
}
for(i=0; i<24; i+=2)
fprintf(out,"CONECT%5d%5d\n",a0+rectedge[i],a0+rectedge[i+1]);
}
}
void set_def (t_molwin *mw,int ePBC,matrix box)
{
mw->bShowHydrogen=TRUE;
mw->bond_type=eBFat;
mw->ePBC=ePBC;
mw->boxtype=esbRect;
mw->realbox=TRICLINIC(box) ? esbTri : esbRect;
}
void get_enx_state(char *fn, real t, gmx_groups_t *groups, t_inputrec *ir,
t_state *state)
{
/* Should match the names in mdebin.c */
static const char *boxvel_nm[] = {
"Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
"Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
};
static const char *pcouplmu_nm[] = {
"Pcoupl-Mu-XX", "Pcoupl-Mu-YY", "Pcoupl-Mu-ZZ",
"Pcoupl-Mu-YX", "Pcoupl-Mu-ZX", "Pcoupl-Mu-ZY"
};
int ind0[] = { XX,YY,ZZ,YY,ZZ,ZZ };
int ind1[] = { XX,YY,ZZ,XX,XX,YY };
int in,nre,nfr,i,ni,npcoupl;
char buf[STRLEN];
gmx_enxnm_t *enm;
t_enxframe *fr;
in = open_enx(fn,"r");
do_enxnms(in,&nre,&enm);
snew(fr,1);
nfr = 0;
while ((nfr==0 || fr->t != t) && do_enx(in,fr)) {
nfr++;
}
close_enx(in);
fprintf(stderr,"\n");
if (nfr == 0 || fr->t != t)
gmx_fatal(FARGS,"Could not find frame with time %f in '%s'",t,fn);
npcoupl = TRICLINIC(ir->compress) ? 6 : 3;
if (ir->epc == epcPARRINELLORAHMAN) {
clear_mat(state->boxv);
for(i=0; i<npcoupl; i++) {
state->boxv[ind0[i]][ind1[i]] =
find_energy(boxvel_nm[i],nre,enm,fr);
}
fprintf(stderr,"\nREAD %d BOX VELOCITIES FROM %s\n\n",npcoupl,fn);
}
if (ir->etc == etcNOSEHOOVER) {
for(i=0; i<state->ngtc; i++) {
ni = groups->grps[egcTC].nm_ind[i];
sprintf(buf,"Xi-%s",*(groups->grpname[ni]));
state->nosehoover_xi[i] = find_energy(buf,nre,enm,fr);
}
fprintf(stderr,"\nREAD %d NOSE-HOOVER Xi's FROM %s\n\n",state->ngtc,fn);
}
free_enxnms(nre,enm);
free_enxframe(fr);
sfree(fr);
}
void unshift_x(const t_graph *g, matrix box, rvec x[], const rvec x_s[])
{
ivec *is;
int g0, g1;
int j, tx, ty, tz;
if (g->bScrewPBC)
{
gmx_incons("screw pbc not implemented (yet) for unshift_x");
}
g0 = g->at_start;
g1 = g->at_end;
is = g->ishift;
for (j = g->at0; j < g0; j++)
{
copy_rvec(x_s[j], x[j]);
}
if (TRICLINIC(box))
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x[j][XX] = x_s[j][XX]-tx*box[XX][XX]-ty*box[YY][XX]-tz*box[ZZ][XX];
x[j][YY] = x_s[j][YY]-ty*box[YY][YY]-tz*box[ZZ][YY];
x[j][ZZ] = x_s[j][ZZ]-tz*box[ZZ][ZZ];
}
}
else
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x[j][XX] = x_s[j][XX]-tx*box[XX][XX];
x[j][YY] = x_s[j][YY]-ty*box[YY][YY];
x[j][ZZ] = x_s[j][ZZ]-tz*box[ZZ][ZZ];
}
}
for (j = g1; j < g->at1; j++)
{
copy_rvec(x_s[j], x[j]);
}
}
void shift_self(const t_graph *g, matrix box, rvec x[])
{
ivec *is;
int g0, g1;
int j, tx, ty, tz;
if (g->bScrewPBC)
{
gmx_incons("screw pbc not implemented for shift_self");
}
g0 = g->at_start;
g1 = g->at_end;
is = g->ishift;
#ifdef DEBUG
fprintf(stderr, "Shifting atoms %d to %d\n", g0, g0+gn);
#endif
if (TRICLINIC(box))
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x[j][XX] = x[j][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
x[j][YY] = x[j][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
x[j][ZZ] = x[j][ZZ]+tz*box[ZZ][ZZ];
}
}
else
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x[j][XX] = x[j][XX]+tx*box[XX][XX];
x[j][YY] = x[j][YY]+ty*box[YY][YY];
x[j][ZZ] = x[j][ZZ]+tz*box[ZZ][ZZ];
}
}
}
void unshift_self(const t_graph *g, matrix box, rvec x[])
{
ivec *is;
int g0, g1;
int j, tx, ty, tz;
if (g->bScrewPBC)
{
gmx_incons("screw pbc not implemented for unshift_self");
}
g0 = g->at_start;
g1 = g->at_end;
is = g->ishift;
if (TRICLINIC(box))
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x[j][XX] = x[j][XX]-tx*box[XX][XX]-ty*box[YY][XX]-tz*box[ZZ][XX];
x[j][YY] = x[j][YY]-ty*box[YY][YY]-tz*box[ZZ][YY];
x[j][ZZ] = x[j][ZZ]-tz*box[ZZ][ZZ];
}
}
else
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x[j][XX] = x[j][XX]-tx*box[XX][XX];
x[j][YY] = x[j][YY]-ty*box[YY][YY];
x[j][ZZ] = x[j][ZZ]-tz*box[ZZ][ZZ];
}
}
}
static void shift_positions_group(
const matrix box,
rvec x[], /* The positions [0..nr] */
ivec *is, /* The shifts [0..nr] */
int nr) /* The number of positions and shifts */
{
int i, tx, ty, tz;
/* Loop over the group's atoms */
if (TRICLINIC(box))
{
for (i = 0; i < nr; i++)
{
tx = is[i][XX];
ty = is[i][YY];
tz = is[i][ZZ];
x[i][XX] = x[i][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
x[i][YY] = x[i][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
x[i][ZZ] = x[i][ZZ]+tz*box[ZZ][ZZ];
}
}
else
{
for (i = 0; i < nr; i++)
{
tx = is[i][XX];
ty = is[i][YY];
tz = is[i][ZZ];
x[i][XX] = x[i][XX]+tx*box[XX][XX];
x[i][YY] = x[i][YY]+ty*box[YY][YY];
x[i][ZZ] = x[i][ZZ]+tz*box[ZZ][ZZ];
}
}
}
/*! \brief
* Sets ua a search grid for a given box.
*
* \param[in,out] d Grid information.
* \param[in] pbc Information about the box.
* \returns FALSE if grid search is not suitable.
*/
static gmx_bool
grid_set_box(gmx_ana_nbsearch_t *d, t_pbc *pbc)
{
int dd;
/* TODO: This check could be improved. */
if (0.5*pbc->max_cutoff2 < d->cutoff2)
{
return FALSE;
}
if (!grid_setup_cells(d, pbc))
{
return FALSE;
}
d->bTric = TRICLINIC(pbc->box);
if (d->bTric)
{
for (dd = 0; dd < DIM; ++dd)
{
svmul(1.0 / d->ncelldim[dd], pbc->box[dd], d->cellbox[dd]);
}
m_inv_ur0(d->cellbox, d->recipcell);
}
else
{
for (dd = 0; dd < DIM; ++dd)
{
d->cellbox[dd][dd] = pbc->box[dd][dd] / d->ncelldim[dd];
d->recipcell[dd][dd] = 1 / d->cellbox[dd][dd];
}
}
grid_init_cell_nblist(d, pbc);
return TRUE;
}
void shift_x(const t_graph *g, matrix box, const rvec x[], rvec x_s[])
{
ivec *is;
int g0, g1;
int j, tx, ty, tz;
GCHECK(g);
g0 = g->at_start;
g1 = g->at_end;
is = g->ishift;
for (j = g->at0; j < g0; j++)
{
copy_rvec(x[j], x_s[j]);
}
if (g->bScrewPBC)
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
if ((tx > 0 && tx % 2 == 1) ||
(tx < 0 && -tx %2 == 1))
{
x_s[j][XX] = x[j][XX] + tx*box[XX][XX];
x_s[j][YY] = box[YY][YY] + box[ZZ][YY] - x[j][YY];
x_s[j][ZZ] = box[ZZ][ZZ] - x[j][ZZ];
}
else
{
x_s[j][XX] = x[j][XX];
}
x_s[j][YY] = x[j][YY] + ty*box[YY][YY] + tz*box[ZZ][YY];
x_s[j][ZZ] = x[j][ZZ] + tz*box[ZZ][ZZ];
}
}
else if (TRICLINIC(box))
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x_s[j][XX] = x[j][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
x_s[j][YY] = x[j][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
x_s[j][ZZ] = x[j][ZZ]+tz*box[ZZ][ZZ];
}
}
else
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x_s[j][XX] = x[j][XX]+tx*box[XX][XX];
x_s[j][YY] = x[j][YY]+ty*box[YY][YY];
x_s[j][ZZ] = x[j][ZZ]+tz*box[ZZ][ZZ];
}
}
for (j = g1; j < g->at1; j++)
{
copy_rvec(x[j], x_s[j]);
}
}
static int mk_grey(egCol egc[], t_graph *g, int *AtomI,
int npbcdim, matrix box, const rvec x[], int *nerror)
{
int m, j, ng, ai, aj, g0;
rvec dx, hbox;
gmx_bool bTriclinic;
ivec is_aj;
t_pbc pbc;
for (m = 0; (m < DIM); m++)
{
hbox[m] = box[m][m]*0.5;
}
bTriclinic = TRICLINIC(box);
g0 = g->at_start;
ng = 0;
ai = g0 + *AtomI;
/* Loop over all the bonds */
for (j = 0; (j < g->nedge[ai-g0]); j++)
{
aj = g->edge[ai-g0][j];
/* If there is a white one, make it grey and set pbc */
if (g->bScrewPBC)
{
mk_1shift_screw(box, hbox, x[ai], x[aj], g->ishift[ai], is_aj);
}
else if (bTriclinic)
{
mk_1shift_tric(npbcdim, box, hbox, x[ai], x[aj], g->ishift[ai], is_aj);
}
else
{
mk_1shift(npbcdim, hbox, x[ai], x[aj], g->ishift[ai], is_aj);
}
if (egc[aj-g0] == egcolWhite)
{
if (aj - g0 < *AtomI)
{
*AtomI = aj - g0;
}
egc[aj-g0] = egcolGrey;
copy_ivec(is_aj, g->ishift[aj]);
ng++;
}
else if ((is_aj[XX] != g->ishift[aj][XX]) ||
(is_aj[YY] != g->ishift[aj][YY]) ||
(is_aj[ZZ] != g->ishift[aj][ZZ]))
{
if (gmx_debug_at)
{
set_pbc(&pbc, -1, box);
pbc_dx(&pbc, x[ai], x[aj], dx);
fprintf(debug, "mk_grey: shifts for atom %d due to atom %d\n"
"are (%d,%d,%d), should be (%d,%d,%d)\n"
"dx = (%g,%g,%g)\n",
aj+1, ai+1, is_aj[XX], is_aj[YY], is_aj[ZZ],
g->ishift[aj][XX], g->ishift[aj][YY], g->ishift[aj][ZZ],
dx[XX], dx[YY], dx[ZZ]);
}
(*nerror)++;
}
}
return ng;
}
void get_enx_state(const char *fn, real t, gmx_groups_t *groups, t_inputrec *ir,
t_state *state)
{
/* Should match the names in mdebin.c */
static const char *boxvel_nm[] = {
"Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
"Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
};
static const char *pcouplmu_nm[] = {
"Pcoupl-Mu-XX", "Pcoupl-Mu-YY", "Pcoupl-Mu-ZZ",
"Pcoupl-Mu-YX", "Pcoupl-Mu-ZX", "Pcoupl-Mu-ZY"
};
static const char *baro_nm[] = {
"Barostat"
};
int ind0[] = { XX,YY,ZZ,YY,ZZ,ZZ };
int ind1[] = { XX,YY,ZZ,XX,XX,YY };
int nre,nfr,i,j,ni,npcoupl;
char buf[STRLEN];
const char *bufi;
gmx_enxnm_t *enm=NULL;
t_enxframe *fr;
ener_file_t in;
in = open_enx(fn,"r");
do_enxnms(in,&nre,&enm);
snew(fr,1);
nfr = 0;
while ((nfr==0 || fr->t != t) && do_enx(in,fr)) {
nfr++;
}
close_enx(in);
fprintf(stderr,"\n");
if (nfr == 0 || fr->t != t)
gmx_fatal(FARGS,"Could not find frame with time %f in '%s'",t,fn);
npcoupl = TRICLINIC(ir->compress) ? 6 : 3;
if (ir->epc == epcPARRINELLORAHMAN) {
clear_mat(state->boxv);
for(i=0; i<npcoupl; i++) {
state->boxv[ind0[i]][ind1[i]] =
find_energy(boxvel_nm[i],nre,enm,fr);
}
fprintf(stderr,"\nREAD %d BOX VELOCITIES FROM %s\n\n",npcoupl,fn);
}
if (ir->etc == etcNOSEHOOVER)
{
for(i=0; i<state->ngtc; i++) {
ni = groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
for(j=0; (j<state->nhchainlength); j++)
{
sprintf(buf,"Xi-%d-%s",j,bufi);
state->nosehoover_xi[i] = find_energy(buf,nre,enm,fr);
sprintf(buf,"vXi-%d-%s",j,bufi);
state->nosehoover_vxi[i] = find_energy(buf,nre,enm,fr);
}
}
fprintf(stderr,"\nREAD %d NOSE-HOOVER Xi chains FROM %s\n\n",state->ngtc,fn);
if (IR_NPT_TROTTER(ir))
{
for(i=0; i<state->nnhpres; i++) {
bufi = baro_nm[0]; /* All barostat DOF's together for now */
for(j=0; (j<state->nhchainlength); j++)
{
sprintf(buf,"Xi-%d-%s",j,bufi);
state->nhpres_xi[i] = find_energy(buf,nre,enm,fr);
sprintf(buf,"vXi-%d-%s",j,bufi);
state->nhpres_vxi[i] = find_energy(buf,nre,enm,fr);
}
}
fprintf(stderr,"\nREAD %d NOSE-HOOVER BAROSTAT Xi chains FROM %s\n\n",state->nnhpres,fn);
}
}
free_enxnms(nre,enm);
free_enxframe(fr);
sfree(fr);
}
//! Do the real arithmetic for filling the pbc struct
static void low_set_pbc(t_pbc *pbc, int ePBC,
const ivec dd_pbc, const matrix box)
{
int order[3] = { 0, -1, 1 };
ivec bPBC;
const char *ptr;
pbc->ePBC = ePBC;
pbc->ndim_ePBC = ePBC2npbcdim(ePBC);
copy_mat(box, pbc->box);
pbc->max_cutoff2 = 0;
pbc->dim = -1;
pbc->ntric_vec = 0;
for (int i = 0; (i < DIM); i++)
{
pbc->fbox_diag[i] = box[i][i];
pbc->hbox_diag[i] = pbc->fbox_diag[i]*0.5;
pbc->mhbox_diag[i] = -pbc->hbox_diag[i];
}
ptr = check_box(ePBC, box);
if (ePBC == epbcNONE)
{
pbc->ePBCDX = epbcdxNOPBC;
}
else if (ptr)
{
fprintf(stderr, "Warning: %s\n", ptr);
pr_rvecs(stderr, 0, " Box", box, DIM);
fprintf(stderr, " Can not fix pbc.\n\n");
pbc->ePBCDX = epbcdxUNSUPPORTED;
}
else
{
if (ePBC == epbcSCREW && NULL != dd_pbc)
{
/* This combinated should never appear here */
gmx_incons("low_set_pbc called with screw pbc and dd_nc != NULL");
}
int npbcdim = 0;
for (int i = 0; i < DIM; i++)
{
if ((dd_pbc && dd_pbc[i] == 0) || (ePBC == epbcXY && i == ZZ))
{
bPBC[i] = 0;
}
else
{
bPBC[i] = 1;
npbcdim++;
}
}
switch (npbcdim)
{
case 1:
/* 1D pbc is not an mdp option and it is therefore only used
* with single shifts.
*/
pbc->ePBCDX = epbcdx1D_RECT;
for (int i = 0; i < DIM; i++)
{
if (bPBC[i])
{
pbc->dim = i;
}
}
GMX_ASSERT(pbc->dim < DIM, "Dimension for PBC incorrect");
for (int i = 0; i < pbc->dim; i++)
{
if (pbc->box[pbc->dim][i] != 0)
{
pbc->ePBCDX = epbcdx1D_TRIC;
}
}
break;
case 2:
pbc->ePBCDX = epbcdx2D_RECT;
for (int i = 0; i < DIM; i++)
{
if (!bPBC[i])
{
pbc->dim = i;
}
}
for (int i = 0; i < DIM; i++)
{
if (bPBC[i])
{
for (int j = 0; j < i; j++)
{
if (pbc->box[i][j] != 0)
{
pbc->ePBCDX = epbcdx2D_TRIC;
}
}
}
}
break;
case 3:
if (ePBC != epbcSCREW)
{
if (TRICLINIC(box))
{
pbc->ePBCDX = epbcdxTRICLINIC;
}
else
{
pbc->ePBCDX = epbcdxRECTANGULAR;
}
}
else
{
pbc->ePBCDX = (box[ZZ][YY] == 0 ? epbcdxSCREW_RECT : epbcdxSCREW_TRIC);
if (pbc->ePBCDX == epbcdxSCREW_TRIC)
{
fprintf(stderr,
"Screw pbc is not yet implemented for triclinic boxes.\n"
"Can not fix pbc.\n");
pbc->ePBCDX = epbcdxUNSUPPORTED;
}
}
break;
default:
gmx_fatal(FARGS, "Incorrect number of pbc dimensions with DD: %d",
npbcdim);
}
pbc->max_cutoff2 = max_cutoff2(ePBC, box);
if (pbc->ePBCDX == epbcdxTRICLINIC ||
pbc->ePBCDX == epbcdx2D_TRIC ||
pbc->ePBCDX == epbcdxSCREW_TRIC)
{
if (debug)
{
pr_rvecs(debug, 0, "Box", box, DIM);
fprintf(debug, "max cutoff %.3f\n", sqrt(pbc->max_cutoff2));
}
/* We will only need single shifts here */
for (int kk = 0; kk < 3; kk++)
{
int k = order[kk];
if (!bPBC[ZZ] && k != 0)
{
continue;
}
for (int jj = 0; jj < 3; jj++)
{
int j = order[jj];
if (!bPBC[YY] && j != 0)
{
continue;
}
for (int ii = 0; ii < 3; ii++)
{
int i = order[ii];
if (!bPBC[XX] && i != 0)
{
continue;
}
/* A shift is only useful when it is trilinic */
if (j != 0 || k != 0)
{
rvec trial;
rvec pos;
real d2old = 0;
real d2new = 0;
for (int d = 0; d < DIM; d++)
{
trial[d] = i*box[XX][d] + j*box[YY][d] + k*box[ZZ][d];
/* Choose the vector within the brick around 0,0,0 that
* will become the shortest due to shift try.
*/
if (d == pbc->dim)
{
trial[d] = 0;
pos[d] = 0;
}
else
{
if (trial[d] < 0)
{
pos[d] = std::min( pbc->hbox_diag[d], -trial[d]);
}
else
{
pos[d] = std::max(-pbc->hbox_diag[d], -trial[d]);
}
}
d2old += gmx::square(pos[d]);
d2new += gmx::square(pos[d] + trial[d]);
}
if (BOX_MARGIN*d2new < d2old)
{
/* Check if shifts with one box vector less do better */
gmx_bool bUse = TRUE;
for (int dd = 0; dd < DIM; dd++)
{
int shift = (dd == 0 ? i : (dd == 1 ? j : k));
if (shift)
{
real d2new_c = 0;
for (int d = 0; d < DIM; d++)
{
d2new_c += gmx::square(pos[d] + trial[d] - shift*box[dd][d]);
}
if (d2new_c <= BOX_MARGIN*d2new)
{
bUse = FALSE;
}
}
}
if (bUse)
{
/* Accept this shift vector. */
if (pbc->ntric_vec >= MAX_NTRICVEC)
{
fprintf(stderr, "\nWARNING: Found more than %d triclinic correction vectors, ignoring some.\n"
" There is probably something wrong with your box.\n", MAX_NTRICVEC);
pr_rvecs(stderr, 0, " Box", box, DIM);
}
else
{
copy_rvec(trial, pbc->tric_vec[pbc->ntric_vec]);
pbc->tric_shift[pbc->ntric_vec][XX] = i;
pbc->tric_shift[pbc->ntric_vec][YY] = j;
pbc->tric_shift[pbc->ntric_vec][ZZ] = k;
pbc->ntric_vec++;
if (debug)
{
fprintf(debug, " tricvec %2d = %2d %2d %2d %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
pbc->ntric_vec, i, j, k,
sqrt(d2old), sqrt(d2new),
trial[XX], trial[YY], trial[ZZ],
pos[XX], pos[YY], pos[ZZ]);
}
}
}
}
}
}
}
}
}
}
}
void force(FILE *fp, int step,
t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_nsborder *nsb,
t_commrec *cr, t_commrec *mcr,
t_nrnb *nrnb,
t_groups *grps, t_mdatoms *md,
int ngener, t_grpopts *opts,
rvec x[], rvec f[],
real epot[], t_fcdata *fcd,
bool bVerbose, matrix box,
real lambda, t_graph *graph,
t_block *excl, bool bNBFonly,
matrix lr_vir, rvec mu_tot,
real qsum, bool bGatherOnly)
{
int i,nit;
bool bDoEpot;
rvec box_size;
real Vlr,Vcorr=0;
/* Reset box */
for(i=0; (i<DIM); i++)
box_size[i]=box[i][i];
bDoEpot=((fr->nmol > 0) && (fr->nstcalc > 0) && (mod(step,fr->nstcalc)==0));
/* Reset epot... */
if (bDoEpot)
for(i=0; (i<fr->nmol); i++)
fr->mol_epot[i]=0.0;
debug_gmx();
/* Call the short range functions all in one go. */
do_fnbf(fp,cr,fr,x,f,md,
fr->bBHAM ? grps->estat.ee[egBHAM] : grps->estat.ee[egLJ],
grps->estat.ee[egCOUL],box_size,nrnb,
lambda,&epot[F_DVDL],FALSE,-1);
debug_gmx();
if (debug)
pr_rvecs(debug,0,"fshift after SR",fr->fshift,SHIFTS);
/* Shift the coordinates. Must be done before bonded forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no bonded forces have to be evaluated.
*/
if (debug && 0)
p_graph(debug,"DeBUGGGG",graph);
/* Check whether we need to do bondeds */
if (!bNBFonly) {
shift_self(graph,box,x);
if (debug && 0) {
fprintf(debug,"BBBBBBBBBBBBBBBB\n");
fprintf(debug,"%5d\n",graph->nnodes);
for(i=graph->start; (i<=graph->end); i++)
fprintf(debug,"%5d%5s%5s%5d%8.3f%8.3f%8.3f\n",
i,"A","B",i,x[i][XX],x[i][YY],x[i][ZZ]);
fprintf(debug,"%10.5f%10.5f%10.5f\n",
box[XX][XX],box[YY][YY],box[ZZ][ZZ]);
}
if (TRICLINIC(box))
inc_nrnb(nrnb,eNR_SHIFTX,2*graph->nnodes);
else
inc_nrnb(nrnb,eNR_SHIFTX,graph->nnodes);
debug_gmx();
}
if (EEL_LR(fr->eeltype)) {
switch (fr->eeltype) {
case eelPPPM:
Vlr = do_pppm(fp,FALSE,x,fr->f_pme,md->chargeT,
box_size,fr->phi,cr,nsb,nrnb);
break;
case eelPOISSON:
Vlr = do_poisson(fp,FALSE,ir,md->nr,x,fr->f_pme,md->chargeT,
box_size,fr->phi,cr,nrnb,&nit,TRUE);
break;
case eelPME:
Vlr = do_pme(fp,FALSE,ir,x,fr->f_pme,md->chargeT,
box,cr,nsb,nrnb,lr_vir,fr->ewaldcoeff,bGatherOnly);
break;
case eelEWALD:
Vlr = do_ewald(fp,FALSE,ir,x,fr->f_pme,md->chargeT,
box_size,cr,nsb,lr_vir,fr->ewaldcoeff);
break;
default:
Vlr = 0;
fatal_error(0,"No such electrostatics method implemented %s",
eel_names[fr->eeltype]);
}
if(fr->bEwald)
Vcorr =
ewald_LRcorrection(fp,nsb,cr,fr,md->chargeT,excl,x,box,mu_tot,qsum,
ir->ewald_geometry,ir->epsilon_surface,lr_vir);
else
Vcorr = shift_LRcorrection(fp,nsb,cr,fr,md->chargeT,excl,x,TRUE,box,lr_vir);
epot[F_LR] = Vlr + Vcorr;
if (debug)
fprintf(debug,"Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
Vlr,Vcorr,epot[F_LR]);
if (debug) {
pr_rvecs(debug,0,"lr_vir after corr",lr_vir,DIM);
pr_rvecs(debug,0,"fshift after LR Corrections",fr->fshift,SHIFTS);
}
}
debug_gmx();
if (debug)
print_nrnb(debug,nrnb);
debug_gmx();
if (!bNBFonly) {
calc_bonds(fp,cr,mcr,
idef,x,f,fr,graph,epot,nrnb,box,lambda,md,
opts->ngener,grps->estat.ee[egLJ14],grps->estat.ee[egCOUL14],
fcd,step,fr->bSepDVDL && do_per_step(step,ir->nstlog));
debug_gmx();
}
if (debug)
pr_rvecs(debug,0,"fshift after bondeds",fr->fshift,SHIFTS);
for(i=0; (i<F_EPOT); i++)
if (i != F_DISRES)
epot[F_EPOT]+=epot[i];
}
void put_charge_groups_in_box(FILE *fplog,int cg0,int cg1,
int ePBC,matrix box,t_block *cgs,
rvec pos[],rvec cg_cm[])
{
int npbcdim,icg,k,k0,k1,d,e;
rvec cg;
real nrcg,inv_ncg;
atom_id *cgindex;
gmx_bool bTric;
if (ePBC == epbcNONE)
gmx_incons("Calling put_charge_groups_in_box for a system without PBC");
#ifdef DEBUG
fprintf(fplog,"Putting cgs %d to %d in box\n",cg0,cg1);
#endif
cgindex = cgs->index;
if (ePBC == epbcXY)
npbcdim = 2;
else
npbcdim = 3;
bTric = TRICLINIC(box);
for(icg=cg0; (icg<cg1); icg++) {
/* First compute the center of geometry for this charge group */
k0 = cgindex[icg];
k1 = cgindex[icg+1];
nrcg = k1-k0;
if (nrcg == 1) {
copy_rvec(pos[k0],cg_cm[icg]);
} else {
inv_ncg = 1.0/nrcg;
clear_rvec(cg);
for(k=k0; (k<k1); k++) {
for(d=0; d<DIM; d++)
cg[d] += pos[k][d];
}
for(d=0; d<DIM; d++)
cg_cm[icg][d] = inv_ncg*cg[d];
}
/* Now check pbc for this cg */
if (bTric) {
for(d=npbcdim-1; d>=0; d--) {
while(cg_cm[icg][d] < 0) {
for(e=d; e>=0; e--) {
cg_cm[icg][e] += box[d][e];
for(k=k0; (k<k1); k++)
pos[k][e] += box[d][e];
}
}
while(cg_cm[icg][d] >= box[d][d]) {
for(e=d; e>=0; e--) {
cg_cm[icg][e] -= box[d][e];
for(k=k0; (k<k1); k++)
pos[k][e] -= box[d][e];
}
}
}
} else {
for(d=0; d<npbcdim; d++) {
while(cg_cm[icg][d] < 0) {
cg_cm[icg][d] += box[d][d];
for(k=k0; (k<k1); k++)
pos[k][d] += box[d][d];
}
while(cg_cm[icg][d] >= box[d][d]) {
cg_cm[icg][d] -= box[d][d];
for(k=k0; (k<k1); k++)
pos[k][d] -= box[d][d];
}
}
}
#ifdef DEBUG_PBC
for(d=0; (d<npbcdim); d++) {
if ((cg_cm[icg][d] < 0) || (cg_cm[icg][d] >= box[d][d]))
gmx_fatal(FARGS,"cg_cm[%d] = %15f %15f %15f\n"
"box = %15f %15f %15f\n",
icg,cg_cm[icg][XX],cg_cm[icg][YY],cg_cm[icg][ZZ],
box[XX][XX],box[YY][YY],box[ZZ][ZZ]);
}
#endif
}
}
static void low_set_pbc(t_pbc *pbc, int ePBC, ivec *dd_nc, matrix box)
{
int order[5] = {0, -1, 1, -2, 2};
int ii, jj, kk, i, j, k, d, dd, jc, kc, npbcdim, shift;
ivec bPBC;
real d2old, d2new, d2new_c;
rvec trial, pos;
gmx_bool bXY, bUse;
const char *ptr;
pbc->ndim_ePBC = ePBC2npbcdim(ePBC);
copy_mat(box, pbc->box);
pbc->bLimitDistance = FALSE;
pbc->max_cutoff2 = 0;
pbc->dim = -1;
for (i = 0; (i < DIM); i++)
{
pbc->fbox_diag[i] = box[i][i];
pbc->hbox_diag[i] = pbc->fbox_diag[i]*0.5;
pbc->mhbox_diag[i] = -pbc->hbox_diag[i];
}
ptr = check_box(ePBC, box);
if (ePBC == epbcNONE)
{
pbc->ePBCDX = epbcdxNOPBC;
}
else if (ptr)
{
fprintf(stderr, "Warning: %s\n", ptr);
pr_rvecs(stderr, 0, " Box", box, DIM);
fprintf(stderr, " Can not fix pbc.\n");
pbc->ePBCDX = epbcdxUNSUPPORTED;
pbc->bLimitDistance = TRUE;
pbc->limit_distance2 = 0;
}
else
{
if (ePBC == epbcSCREW && dd_nc)
{
/* This combinated should never appear here */
gmx_incons("low_set_pbc called with screw pbc and dd_nc != NULL");
}
npbcdim = 0;
for (i = 0; i < DIM; i++)
{
if ((dd_nc && (*dd_nc)[i] > 1) || (ePBC == epbcXY && i == ZZ))
{
bPBC[i] = 0;
}
else
{
bPBC[i] = 1;
npbcdim++;
}
}
switch (npbcdim)
{
case 1:
/* 1D pbc is not an mdp option and it is therefore only used
* with single shifts.
*/
pbc->ePBCDX = epbcdx1D_RECT;
for (i = 0; i < DIM; i++)
{
if (bPBC[i])
{
pbc->dim = i;
}
}
for (i = 0; i < pbc->dim; i++)
{
if (pbc->box[pbc->dim][i] != 0)
{
pbc->ePBCDX = epbcdx1D_TRIC;
}
}
break;
case 2:
pbc->ePBCDX = epbcdx2D_RECT;
for (i = 0; i < DIM; i++)
{
if (!bPBC[i])
{
pbc->dim = i;
}
}
for (i = 0; i < DIM; i++)
{
if (bPBC[i])
{
for (j = 0; j < i; j++)
{
if (pbc->box[i][j] != 0)
{
pbc->ePBCDX = epbcdx2D_TRIC;
}
}
}
}
break;
case 3:
if (ePBC != epbcSCREW)
{
if (TRICLINIC(box))
{
pbc->ePBCDX = epbcdxTRICLINIC;
}
else
{
pbc->ePBCDX = epbcdxRECTANGULAR;
}
}
else
{
pbc->ePBCDX = (box[ZZ][YY] == 0 ? epbcdxSCREW_RECT : epbcdxSCREW_TRIC);
if (pbc->ePBCDX == epbcdxSCREW_TRIC)
{
fprintf(stderr,
"Screw pbc is not yet implemented for triclinic boxes.\n"
"Can not fix pbc.\n");
pbc->ePBCDX = epbcdxUNSUPPORTED;
}
}
break;
default:
gmx_fatal(FARGS, "Incorrect number of pbc dimensions with DD: %d",
npbcdim);
}
pbc->max_cutoff2 = max_cutoff2(ePBC, box);
if (pbc->ePBCDX == epbcdxTRICLINIC ||
pbc->ePBCDX == epbcdx2D_TRIC ||
pbc->ePBCDX == epbcdxSCREW_TRIC)
{
if (debug)
{
pr_rvecs(debug, 0, "Box", box, DIM);
fprintf(debug, "max cutoff %.3f\n", sqrt(pbc->max_cutoff2));
}
pbc->ntric_vec = 0;
/* We will only use single shifts, but we will check a few
* more shifts to see if there is a limiting distance
* above which we can not be sure of the correct distance.
*/
for (kk = 0; kk < 5; kk++)
{
k = order[kk];
if (!bPBC[ZZ] && k != 0)
{
continue;
}
for (jj = 0; jj < 5; jj++)
{
j = order[jj];
if (!bPBC[YY] && j != 0)
{
continue;
}
for (ii = 0; ii < 3; ii++)
{
i = order[ii];
if (!bPBC[XX] && i != 0)
{
continue;
}
/* A shift is only useful when it is trilinic */
if (j != 0 || k != 0)
{
d2old = 0;
d2new = 0;
for (d = 0; d < DIM; d++)
{
trial[d] = i*box[XX][d] + j*box[YY][d] + k*box[ZZ][d];
/* Choose the vector within the brick around 0,0,0 that
* will become the shortest due to shift try.
*/
if (d == pbc->dim)
{
trial[d] = 0;
pos[d] = 0;
}
else
{
if (trial[d] < 0)
{
pos[d] = min( pbc->hbox_diag[d], -trial[d]);
}
else
{
pos[d] = max(-pbc->hbox_diag[d], -trial[d]);
}
}
d2old += sqr(pos[d]);
d2new += sqr(pos[d] + trial[d]);
}
if (BOX_MARGIN*d2new < d2old)
{
if (j < -1 || j > 1 || k < -1 || k > 1)
{
/* Check if there is a single shift vector
* that decreases this distance even more.
*/
jc = 0;
kc = 0;
if (j < -1 || j > 1)
{
jc = j/2;
}
if (k < -1 || k > 1)
{
kc = k/2;
}
d2new_c = 0;
for (d = 0; d < DIM; d++)
{
d2new_c += sqr(pos[d] + trial[d]
- jc*box[YY][d] - kc*box[ZZ][d]);
}
if (d2new_c > BOX_MARGIN*d2new)
{
/* Reject this shift vector, as there is no a priori limit
* to the number of shifts that decrease distances.
*/
if (!pbc->bLimitDistance || d2new < pbc->limit_distance2)
{
pbc->limit_distance2 = d2new;
}
pbc->bLimitDistance = TRUE;
}
}
else
{
/* Check if shifts with one box vector less do better */
bUse = TRUE;
for (dd = 0; dd < DIM; dd++)
{
shift = (dd == 0 ? i : (dd == 1 ? j : k));
if (shift)
{
d2new_c = 0;
for (d = 0; d < DIM; d++)
{
d2new_c += sqr(pos[d] + trial[d] - shift*box[dd][d]);
}
if (d2new_c <= BOX_MARGIN*d2new)
{
bUse = FALSE;
}
}
}
if (bUse)
{
/* Accept this shift vector. */
if (pbc->ntric_vec >= MAX_NTRICVEC)
{
fprintf(stderr, "\nWARNING: Found more than %d triclinic correction vectors, ignoring some.\n"
" There is probably something wrong with your box.\n", MAX_NTRICVEC);
pr_rvecs(stderr, 0, " Box", box, DIM);
}
else
{
copy_rvec(trial, pbc->tric_vec[pbc->ntric_vec]);
pbc->tric_shift[pbc->ntric_vec][XX] = i;
pbc->tric_shift[pbc->ntric_vec][YY] = j;
pbc->tric_shift[pbc->ntric_vec][ZZ] = k;
pbc->ntric_vec++;
}
}
}
if (debug)
{
fprintf(debug, " tricvec %2d = %2d %2d %2d %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
pbc->ntric_vec, i, j, k,
sqrt(d2old), sqrt(d2new),
trial[XX], trial[YY], trial[ZZ],
pos[XX], pos[YY], pos[ZZ]);
}
}
}
}
}
}
}
}
}
void do_force_lowlevel(FILE *fplog, gmx_large_int_t step,
t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_commrec *cr,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_mdatoms *md,
t_grpopts *opts,
rvec x[], history_t *hist,
rvec f[],
rvec f_longrange[],
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_mtop_t *mtop,
gmx_localtop_t *top,
gmx_genborn_t *born,
t_atomtypes *atype,
gmx_bool bBornRadii,
matrix box,
t_lambda *fepvals,
real *lambda,
t_graph *graph,
t_blocka *excl,
rvec mu_tot[],
int flags,
float *cycles_pme)
{
int i, j, status;
int donb_flags;
gmx_bool bDoEpot, bSepDVDL, bSB;
int pme_flags;
matrix boxs;
rvec box_size;
real Vsr, Vlr, Vcorr = 0;
t_pbc pbc;
real dvdgb;
char buf[22];
double clam_i, vlam_i;
real dvdl_dum[efptNR], dvdl, dvdl_nb[efptNR], lam_i[efptNR];
real dvdlsum;
#ifdef GMX_MPI
double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
#endif
#define PRINT_SEPDVDL(s, v, dvdlambda) if (bSepDVDL) {fprintf(fplog, sepdvdlformat, s, v, dvdlambda); }
GMX_MPE_LOG(ev_force_start);
set_pbc(&pbc, fr->ePBC, box);
/* reset free energy components */
for (i = 0; i < efptNR; i++)
{
dvdl_nb[i] = 0;
dvdl_dum[i] = 0;
}
/* Reset box */
for (i = 0; (i < DIM); i++)
{
box_size[i] = box[i][i];
}
bSepDVDL = (fr->bSepDVDL && do_per_step(step, ir->nstlog));
debug_gmx();
/* do QMMM first if requested */
if (fr->bQMMM)
{
enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr, md);
}
if (bSepDVDL)
{
fprintf(fplog, "Step %s: non-bonded V and dVdl for node %d:\n",
gmx_step_str(step, buf), cr->nodeid);
}
/* Call the short range functions all in one go. */
GMX_MPE_LOG(ev_do_fnbf_start);
#ifdef GMX_MPI
/*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
#define TAKETIME FALSE
if (TAKETIME)
{
MPI_Barrier(cr->mpi_comm_mygroup);
t0 = MPI_Wtime();
}
#endif
if (ir->nwall)
{
/* foreign lambda component for walls */
dvdl = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
enerd->grpp.ener[egLJSR], nrnb);
PRINT_SEPDVDL("Walls", 0.0, dvdl);
enerd->dvdl_lin[efptVDW] += dvdl;
}
/* If doing GB, reset dvda and calculate the Born radii */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsNONBONDED);
for (i = 0; i < born->nr; i++)
{
fr->dvda[i] = 0;
}
if (bBornRadii)
{
calc_gb_rad(cr, fr, ir, top, atype, x, &(fr->gblist), born, md, nrnb);
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
where();
/* We only do non-bonded calculation with group scheme here, the verlet
* calls are done from do_force_cutsVERLET(). */
if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
{
donb_flags = 0;
/* Add short-range interactions */
donb_flags |= GMX_NONBONDED_DO_SR;
if (flags & GMX_FORCE_FORCES)
{
donb_flags |= GMX_NONBONDED_DO_FORCE;
}
if (flags & GMX_FORCE_ENERGY)
{
donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
}
if (flags & GMX_FORCE_DO_LR)
{
donb_flags |= GMX_NONBONDED_DO_LR;
}
wallcycle_sub_start(wcycle, ewcsNONBONDED);
do_nonbonded(cr, fr, x, f, f_longrange, md, excl,
&enerd->grpp, box_size, nrnb,
lambda, dvdl_nb, -1, -1, donb_flags);
/* If we do foreign lambda and we have soft-core interactions
* we have to recalculate the (non-linear) energies contributions.
*/
if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
{
for (i = 0; i < enerd->n_lambda; i++)
{
for (j = 0; j < efptNR; j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
}
reset_foreign_enerdata(enerd);
do_nonbonded(cr, fr, x, f, f_longrange, md, excl,
&(enerd->foreign_grpp), box_size, nrnb,
lam_i, dvdl_dum, -1, -1,
(donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
sum_epot(&ir->opts, &(enerd->foreign_grpp), enerd->foreign_term);
enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
}
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
where();
}
/* If we are doing GB, calculate bonded forces and apply corrections
* to the solvation forces */
/* MRS: Eventually, many need to include free energy contribution here! */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsBONDED);
calc_gb_forces(cr, md, born, top, atype, x, f, fr, idef,
ir->gb_algorithm, ir->sa_algorithm, nrnb, bBornRadii, &pbc, graph, enerd);
wallcycle_sub_stop(wcycle, ewcsBONDED);
}
#ifdef GMX_MPI
if (TAKETIME)
{
t1 = MPI_Wtime();
fr->t_fnbf += t1-t0;
}
#endif
if (fepvals->sc_alpha != 0)
{
enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
}
else
{
enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
}
if (fepvals->sc_alpha != 0)
/* even though coulomb part is linear, we already added it, beacuse we
need to go through the vdw calculation anyway */
{
enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
}
else
{
enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
}
Vsr = 0;
if (bSepDVDL)
{
for (i = 0; i < enerd->grpp.nener; i++)
{
Vsr +=
(fr->bBHAM ?
enerd->grpp.ener[egBHAMSR][i] :
enerd->grpp.ener[egLJSR][i])
+ enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
}
dvdlsum = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
PRINT_SEPDVDL("VdW and Coulomb SR particle-p.", Vsr, dvdlsum);
}
debug_gmx();
GMX_MPE_LOG(ev_do_fnbf_finish);
if (debug)
{
pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
}
/* Shift the coordinates. Must be done before bonded forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no bonded forces have to be evaluated.
*/
/* Here sometimes we would not need to shift with NBFonly,
* but we do so anyhow for consistency of the returned coordinates.
*/
if (graph)
{
shift_self(graph, box, x);
if (TRICLINIC(box))
{
inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
}
else
{
inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
}
}
/* Check whether we need to do bondeds or correct for exclusions */
if (fr->bMolPBC &&
((flags & GMX_FORCE_BONDED)
|| EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype)))
{
/* Since all atoms are in the rectangular or triclinic unit-cell,
* only single box vector shifts (2 in x) are required.
*/
set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
}
debug_gmx();
if (flags & GMX_FORCE_BONDED)
{
GMX_MPE_LOG(ev_calc_bonds_start);
wallcycle_sub_start(wcycle, ewcsBONDED);
calc_bonds(fplog, cr->ms,
idef, x, hist, f, fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
flags,
fr->bSepDVDL && do_per_step(step, ir->nstlog), step);
/* Check if we have to determine energy differences
* at foreign lambda's.
*/
if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) &&
idef->ilsort != ilsortNO_FE)
{
if (idef->ilsort != ilsortFE_SORTED)
{
gmx_incons("The bonded interactions are not sorted for free energy");
}
for (i = 0; i < enerd->n_lambda; i++)
{
reset_foreign_enerdata(enerd);
for (j = 0; j < efptNR; j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
}
calc_bonds_lambda(fplog, idef, x, fr, &pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
fcd, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
sum_epot(&ir->opts, &(enerd->foreign_grpp), enerd->foreign_term);
enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
}
}
debug_gmx();
GMX_MPE_LOG(ev_calc_bonds_finish);
wallcycle_sub_stop(wcycle, ewcsBONDED);
}
where();
*cycles_pme = 0;
if (EEL_FULL(fr->eeltype))
{
bSB = (ir->nwall == 2);
if (bSB)
{
copy_mat(box, boxs);
svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
box_size[ZZ] *= ir->wall_ewald_zfac;
}
clear_mat(fr->vir_el_recip);
if (fr->bEwald)
{
Vcorr = 0;
dvdl = 0;
/* With the Verlet scheme exclusion forces are calculated
* in the non-bonded kernel.
*/
/* The TPI molecule does not have exclusions with the rest
* of the system and no intra-molecular PME grid contributions
* will be calculated in gmx_pme_calc_energy.
*/
if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
ir->ewald_geometry != eewg3D ||
ir->epsilon_surface != 0)
{
int nthreads, t;
wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
if (fr->n_tpi > 0)
{
gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
}
nthreads = gmx_omp_nthreads_get(emntBonded);
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (t = 0; t < nthreads; t++)
{
int s, e, i;
rvec *fnv;
tensor *vir;
real *Vcorrt, *dvdlt;
if (t == 0)
{
fnv = fr->f_novirsum;
vir = &fr->vir_el_recip;
Vcorrt = &Vcorr;
dvdlt = &dvdl;
}
else
{
fnv = fr->f_t[t].f;
vir = &fr->f_t[t].vir;
Vcorrt = &fr->f_t[t].Vcorr;
dvdlt = &fr->f_t[t].dvdl[efptCOUL];
for (i = 0; i < fr->natoms_force; i++)
{
clear_rvec(fnv[i]);
}
clear_mat(*vir);
}
*dvdlt = 0;
*Vcorrt =
ewald_LRcorrection(fplog,
fr->excl_load[t], fr->excl_load[t+1],
cr, t, fr,
md->chargeA,
md->nChargePerturbed ? md->chargeB : NULL,
ir->cutoff_scheme != ecutsVERLET,
excl, x, bSB ? boxs : box, mu_tot,
ir->ewald_geometry,
ir->epsilon_surface,
fnv, *vir,
lambda[efptCOUL], dvdlt);
}
if (nthreads > 1)
{
reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
fr->vir_el_recip,
&Vcorr, efptCOUL, &dvdl,
nthreads, fr->f_t);
}
wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
}
if (fr->n_tpi == 0)
{
Vcorr += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
&dvdl, fr->vir_el_recip);
}
PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr, dvdl);
enerd->dvdl_lin[efptCOUL] += dvdl;
}
status = 0;
Vlr = 0;
dvdl = 0;
switch (fr->eeltype)
{
case eelPME:
case eelPMESWITCH:
case eelPMEUSER:
case eelPMEUSERSWITCH:
case eelP3M_AD:
if (cr->duty & DUTY_PME)
{
assert(fr->n_tpi >= 0);
if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
{
pme_flags = GMX_PME_SPREAD_Q | GMX_PME_SOLVE;
if (flags & GMX_FORCE_FORCES)
{
pme_flags |= GMX_PME_CALC_F;
}
if (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY))
{
pme_flags |= GMX_PME_CALC_ENER_VIR;
}
if (fr->n_tpi > 0)
{
/* We don't calculate f, but we do want the potential */
pme_flags |= GMX_PME_CALC_POT;
}
wallcycle_start(wcycle, ewcPMEMESH);
status = gmx_pme_do(fr->pmedata,
md->start, md->homenr - fr->n_tpi,
x, fr->f_novirsum,
md->chargeA, md->chargeB,
bSB ? boxs : box, cr,
DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
nrnb, wcycle,
fr->vir_el_recip, fr->ewaldcoeff,
&Vlr, lambda[efptCOUL], &dvdl,
pme_flags);
*cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
/* We should try to do as little computation after
* this as possible, because parallel PME synchronizes
* the nodes, so we want all load imbalance of the rest
* of the force calculation to be before the PME call.
* DD load balancing is done on the whole time of
* the force call (without PME).
*/
}
if (fr->n_tpi > 0)
{
/* Determine the PME grid energy of the test molecule
* with the PME grid potential of the other charges.
*/
gmx_pme_calc_energy(fr->pmedata, fr->n_tpi,
x + md->homenr - fr->n_tpi,
md->chargeA + md->homenr - fr->n_tpi,
&Vlr);
}
PRINT_SEPDVDL("PME mesh", Vlr, dvdl);
}
break;
case eelEWALD:
Vlr = do_ewald(fplog, FALSE, ir, x, fr->f_novirsum,
md->chargeA, md->chargeB,
box_size, cr, md->homenr,
fr->vir_el_recip, fr->ewaldcoeff,
lambda[efptCOUL], &dvdl, fr->ewald_table);
PRINT_SEPDVDL("Ewald long-range", Vlr, dvdl);
break;
default:
gmx_fatal(FARGS, "No such electrostatics method implemented %s",
eel_names[fr->eeltype]);
}
if (status != 0)
{
gmx_fatal(FARGS, "Error %d in long range electrostatics routine %s",
status, EELTYPE(fr->eeltype));
}
/* Note that with separate PME nodes we get the real energies later */
enerd->dvdl_lin[efptCOUL] += dvdl;
enerd->term[F_COUL_RECIP] = Vlr + Vcorr;
if (debug)
{
fprintf(debug, "Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
Vlr, Vcorr, enerd->term[F_COUL_RECIP]);
pr_rvecs(debug, 0, "vir_el_recip after corr", fr->vir_el_recip, DIM);
pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
}
}
else
{
if (EEL_RF(fr->eeltype))
{
/* With the Verlet scheme exclusion forces are calculated
* in the non-bonded kernel.
*/
if (ir->cutoff_scheme != ecutsVERLET && fr->eeltype != eelRF_NEC)
{
dvdl = 0;
enerd->term[F_RF_EXCL] =
RF_excl_correction(fplog, fr, graph, md, excl, x, f,
fr->fshift, &pbc, lambda[efptCOUL], &dvdl);
}
enerd->dvdl_lin[efptCOUL] += dvdl;
PRINT_SEPDVDL("RF exclusion correction",
enerd->term[F_RF_EXCL], dvdl);
}
}
where();
debug_gmx();
if (debug)
{
print_nrnb(debug, nrnb);
}
debug_gmx();
#ifdef GMX_MPI
if (TAKETIME)
{
t2 = MPI_Wtime();
MPI_Barrier(cr->mpi_comm_mygroup);
t3 = MPI_Wtime();
fr->t_wait += t3-t2;
if (fr->timesteps == 11)
{
fprintf(stderr, "* PP load balancing info: node %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
cr->nodeid, gmx_step_str(fr->timesteps, buf),
100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
(fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
}
fr->timesteps++;
}
#endif
if (debug)
{
pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
}
GMX_MPE_LOG(ev_force_finish);
}
void init_md(t_commrec *cr,t_inputrec *ir,tensor box,real *t,real *t0,
real *lambda,real *lam0,real *SAfactor,
t_nrnb *mynrnb,bool *bTYZ,t_topology *top,
int nfile,t_filenm fnm[],char **traj,
char **xtc_traj,int *fp_ene,
FILE **fp_dgdl,t_mdebin **mdebin,t_groups *grps,
tensor force_vir,tensor pme_vir,
tensor shake_vir,t_mdatoms *mdatoms,rvec mu_tot,
bool *bNEMD,t_vcm **vcm,t_nsborder *nsb)
{
bool bBHAM,b14,bLR,bLJLR;
int i;
/* Initial values */
*t = *t0 = ir->init_t;
if (ir->efep != efepNO) {
*lambda = *lam0 = ir->init_lambda;
}
else {
*lambda = *lam0 = 0.0;
}
if (ir->bSimAnn) {
*SAfactor = 1.0 - *t0/ir->zero_temp_time;
if (*SAfactor < 0)
*SAfactor = 0;
} else
*SAfactor = 1.0;
init_nrnb(mynrnb);
/* Check Environment variables & other booleans */
#ifdef SPEC_CPU
*bTYZ = FALSE;
#else
*bTYZ=getenv("TYZ") != NULL;
#endif
set_pot_bools(ir,top,&bLR,&bLJLR,&bBHAM,&b14);
if (nfile != -1) {
/* Filenames */
*traj = ftp2fn(efTRN,nfile,fnm);
*xtc_traj = ftp2fn(efXTC,nfile,fnm);
#ifndef SPEC_CPU
if (MASTER(cr)) {
*fp_ene = open_enx(ftp2fn(efENX,nfile,fnm),"w");
if ((fp_dgdl != NULL) && ir->efep!=efepNO)
*fp_dgdl =
xvgropen(opt2fn("-dgdl",nfile,fnm),
"dG/d\\8l\\4","Time (ps)",
"dG/d\\8l\\4 (kJ mol\\S-1\\N nm\\S-2\\N \\8l\\4\\S-1\\N)");
} else
#endif
*fp_ene = -1;
*mdebin = init_mdebin(*fp_ene,grps,&(top->atoms),&(top->idef),
bLR,bLJLR,bBHAM,b14,ir->efep!=efepNO,ir->epc,
ir->eDispCorr,(TRICLINIC(ir->compress) || TRICLINIC(box)),
(ir->etc==etcNOSEHOOVER),cr);
}
/* Initiate variables */
clear_mat(force_vir);
clear_mat(pme_vir);
clear_mat(shake_vir);
clear_rvec(mu_tot);
/* Set initial values for invmass etc. */
init_mdatoms(mdatoms,*lambda,TRUE);
*vcm = init_vcm(stdlog,top,cr,mdatoms,START(nsb),HOMENR(nsb),ir->nstcomm);
debug_gmx();
*bNEMD = (ir->opts.ngacc > 1) || (norm(ir->opts.acc[0]) > 0);
if (ir->eI == eiSD)
init_sd_consts(ir->opts.ngtc,ir->opts.tau_t,ir->delta_t);
}
void do_force_lowlevel(t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_commrec *cr,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_mdatoms *md,
rvec x[], history_t *hist,
rvec f[],
rvec f_longrange[],
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_localtop_t *top,
gmx_genborn_t *born,
gmx_bool bBornRadii,
matrix box,
t_lambda *fepvals,
real *lambda,
t_graph *graph,
t_blocka *excl,
rvec mu_tot[],
int flags,
float *cycles_pme)
{
int i, j;
int donb_flags;
gmx_bool bSB;
int pme_flags;
matrix boxs;
rvec box_size;
t_pbc pbc;
real dvdl_dum[efptNR], dvdl_nb[efptNR];
#ifdef GMX_MPI
double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
#endif
set_pbc(&pbc, fr->ePBC, box);
/* reset free energy components */
for (i = 0; i < efptNR; i++)
{
dvdl_nb[i] = 0;
dvdl_dum[i] = 0;
}
/* Reset box */
for (i = 0; (i < DIM); i++)
{
box_size[i] = box[i][i];
}
debug_gmx();
/* do QMMM first if requested */
if (fr->bQMMM)
{
enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
}
/* Call the short range functions all in one go. */
#ifdef GMX_MPI
/*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
#define TAKETIME FALSE
if (TAKETIME)
{
MPI_Barrier(cr->mpi_comm_mygroup);
t0 = MPI_Wtime();
}
#endif
if (ir->nwall)
{
/* foreign lambda component for walls */
real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
enerd->grpp.ener[egLJSR], nrnb);
enerd->dvdl_lin[efptVDW] += dvdl_walls;
}
/* If doing GB, reset dvda and calculate the Born radii */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsNONBONDED);
for (i = 0; i < born->nr; i++)
{
fr->dvda[i] = 0;
}
if (bBornRadii)
{
calc_gb_rad(cr, fr, ir, top, x, &(fr->gblist), born, md, nrnb);
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
where();
/* We only do non-bonded calculation with group scheme here, the verlet
* calls are done from do_force_cutsVERLET(). */
if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
{
donb_flags = 0;
/* Add short-range interactions */
donb_flags |= GMX_NONBONDED_DO_SR;
/* Currently all group scheme kernels always calculate (shift-)forces */
if (flags & GMX_FORCE_FORCES)
{
donb_flags |= GMX_NONBONDED_DO_FORCE;
}
if (flags & GMX_FORCE_VIRIAL)
{
donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
}
if (flags & GMX_FORCE_ENERGY)
{
donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
}
if (flags & GMX_FORCE_DO_LR)
{
donb_flags |= GMX_NONBONDED_DO_LR;
}
wallcycle_sub_start(wcycle, ewcsNONBONDED);
do_nonbonded(fr, x, f, f_longrange, md, excl,
&enerd->grpp, nrnb,
lambda, dvdl_nb, -1, -1, donb_flags);
/* If we do foreign lambda and we have soft-core interactions
* we have to recalculate the (non-linear) energies contributions.
*/
if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
{
for (i = 0; i < enerd->n_lambda; i++)
{
real lam_i[efptNR];
for (j = 0; j < efptNR; j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
}
reset_foreign_enerdata(enerd);
do_nonbonded(fr, x, f, f_longrange, md, excl,
&(enerd->foreign_grpp), nrnb,
lam_i, dvdl_dum, -1, -1,
(donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
}
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
where();
}
/* If we are doing GB, calculate bonded forces and apply corrections
* to the solvation forces */
/* MRS: Eventually, many need to include free energy contribution here! */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsLISTED);
calc_gb_forces(cr, md, born, top, x, f, fr, idef,
ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
wallcycle_sub_stop(wcycle, ewcsLISTED);
}
#ifdef GMX_MPI
if (TAKETIME)
{
t1 = MPI_Wtime();
fr->t_fnbf += t1-t0;
}
#endif
if (fepvals->sc_alpha != 0)
{
enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
}
else
{
enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
}
if (fepvals->sc_alpha != 0)
/* even though coulomb part is linear, we already added it, beacuse we
need to go through the vdw calculation anyway */
{
enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
}
else
{
enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
}
debug_gmx();
if (debug)
{
pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
}
/* Shift the coordinates. Must be done before listed forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no listed forces have to be evaluated.
*
* The shifting and PBC code is deliberately not timed, since with
* the Verlet scheme it only takes non-zero time with triclinic
* boxes, and even then the time is around a factor of 100 less
* than the next smallest counter.
*/
/* Here sometimes we would not need to shift with NBFonly,
* but we do so anyhow for consistency of the returned coordinates.
*/
if (graph)
{
shift_self(graph, box, x);
if (TRICLINIC(box))
{
inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
}
else
{
inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
}
}
/* Check whether we need to do listed interactions or correct for exclusions */
if (fr->bMolPBC &&
((flags & GMX_FORCE_LISTED)
|| EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
{
/* TODO There are no electrostatics methods that require this
transformation, when using the Verlet scheme, so update the
above conditional. */
/* Since all atoms are in the rectangular or triclinic unit-cell,
* only single box vector shifts (2 in x) are required.
*/
set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
}
debug_gmx();
do_force_listed(wcycle, box, ir->fepvals, cr->ms,
idef, (const rvec *) x, hist, f, fr,
&pbc, graph, enerd, nrnb, lambda, md, fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
flags);
where();
*cycles_pme = 0;
clear_mat(fr->vir_el_recip);
clear_mat(fr->vir_lj_recip);
/* Do long-range electrostatics and/or LJ-PME, including related short-range
* corrections.
*/
if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
{
int status = 0;
real Vlr_q = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
bSB = (ir->nwall == 2);
if (bSB)
{
copy_mat(box, boxs);
svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
box_size[ZZ] *= ir->wall_ewald_zfac;
}
if (EEL_PME_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
{
real dvdl_long_range_correction_q = 0;
real dvdl_long_range_correction_lj = 0;
/* With the Verlet scheme exclusion forces are calculated
* in the non-bonded kernel.
*/
/* The TPI molecule does not have exclusions with the rest
* of the system and no intra-molecular PME grid
* contributions will be calculated in
* gmx_pme_calc_energy.
*/
if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
ir->ewald_geometry != eewg3D ||
ir->epsilon_surface != 0)
{
int nthreads, t;
wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
if (fr->n_tpi > 0)
{
gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
}
nthreads = gmx_omp_nthreads_get(emntBonded);
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (t = 0; t < nthreads; t++)
{
int i;
rvec *fnv;
tensor *vir_q, *vir_lj;
real *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
if (t == 0)
{
fnv = fr->f_novirsum;
vir_q = &fr->vir_el_recip;
vir_lj = &fr->vir_lj_recip;
Vcorrt_q = &Vcorr_q;
Vcorrt_lj = &Vcorr_lj;
dvdlt_q = &dvdl_long_range_correction_q;
dvdlt_lj = &dvdl_long_range_correction_lj;
}
else
{
fnv = fr->f_t[t].f;
vir_q = &fr->f_t[t].vir_q;
vir_lj = &fr->f_t[t].vir_lj;
Vcorrt_q = &fr->f_t[t].Vcorr_q;
Vcorrt_lj = &fr->f_t[t].Vcorr_lj;
dvdlt_q = &fr->f_t[t].dvdl[efptCOUL];
dvdlt_lj = &fr->f_t[t].dvdl[efptVDW];
for (i = 0; i < fr->natoms_force; i++)
{
clear_rvec(fnv[i]);
}
clear_mat(*vir_q);
clear_mat(*vir_lj);
}
*dvdlt_q = 0;
*dvdlt_lj = 0;
ewald_LRcorrection(fr->excl_load[t], fr->excl_load[t+1],
cr, t, fr,
md->chargeA, md->chargeB,
md->sqrt_c6A, md->sqrt_c6B,
md->sigmaA, md->sigmaB,
md->sigma3A, md->sigma3B,
md->nChargePerturbed || md->nTypePerturbed,
ir->cutoff_scheme != ecutsVERLET,
excl, x, bSB ? boxs : box, mu_tot,
ir->ewald_geometry,
ir->epsilon_surface,
fnv, *vir_q, *vir_lj,
Vcorrt_q, Vcorrt_lj,
lambda[efptCOUL], lambda[efptVDW],
dvdlt_q, dvdlt_lj);
}
if (nthreads > 1)
{
reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
fr->vir_el_recip, fr->vir_lj_recip,
&Vcorr_q, &Vcorr_lj,
&dvdl_long_range_correction_q,
&dvdl_long_range_correction_lj,
nthreads, fr->f_t);
}
wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
}
if (EEL_PME_EWALD(fr->eeltype) && fr->n_tpi == 0)
{
/* This is not in a subcounter because it takes a
negligible and constant-sized amount of time */
Vcorr_q += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
&dvdl_long_range_correction_q,
fr->vir_el_recip);
}
enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction_q;
enerd->dvdl_lin[efptVDW] += dvdl_long_range_correction_lj;
if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)) && (cr->duty & DUTY_PME))
{
/* Do reciprocal PME for Coulomb and/or LJ. */
assert(fr->n_tpi >= 0);
if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
{
pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
if (EEL_PME(fr->eeltype))
{
pme_flags |= GMX_PME_DO_COULOMB;
}
if (EVDW_PME(fr->vdwtype))
{
pme_flags |= GMX_PME_DO_LJ;
}
if (flags & GMX_FORCE_FORCES)
{
pme_flags |= GMX_PME_CALC_F;
}
if (flags & GMX_FORCE_VIRIAL)
{
pme_flags |= GMX_PME_CALC_ENER_VIR;
}
if (fr->n_tpi > 0)
{
/* We don't calculate f, but we do want the potential */
pme_flags |= GMX_PME_CALC_POT;
}
wallcycle_start(wcycle, ewcPMEMESH);
status = gmx_pme_do(fr->pmedata,
0, md->homenr - fr->n_tpi,
x, fr->f_novirsum,
md->chargeA, md->chargeB,
md->sqrt_c6A, md->sqrt_c6B,
md->sigmaA, md->sigmaB,
bSB ? boxs : box, cr,
DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
nrnb, wcycle,
fr->vir_el_recip, fr->ewaldcoeff_q,
fr->vir_lj_recip, fr->ewaldcoeff_lj,
&Vlr_q, &Vlr_lj,
lambda[efptCOUL], lambda[efptVDW],
&dvdl_long_range_q, &dvdl_long_range_lj, pme_flags);
*cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
if (status != 0)
{
gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
}
/* We should try to do as little computation after
* this as possible, because parallel PME synchronizes
* the nodes, so we want all load imbalance of the
* rest of the force calculation to be before the PME
* call. DD load balancing is done on the whole time
* of the force call (without PME).
*/
}
if (fr->n_tpi > 0)
{
if (EVDW_PME(ir->vdwtype))
{
gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
}
/* Determine the PME grid energy of the test molecule
* with the PME grid potential of the other charges.
*/
gmx_pme_calc_energy(fr->pmedata, fr->n_tpi,
x + md->homenr - fr->n_tpi,
md->chargeA + md->homenr - fr->n_tpi,
&Vlr_q);
}
}
}
if (!EEL_PME(fr->eeltype) && EEL_PME_EWALD(fr->eeltype))
{
Vlr_q = do_ewald(ir, x, fr->f_novirsum,
md->chargeA, md->chargeB,
box_size, cr, md->homenr,
fr->vir_el_recip, fr->ewaldcoeff_q,
lambda[efptCOUL], &dvdl_long_range_q, fr->ewald_table);
}
/* Note that with separate PME nodes we get the real energies later */
enerd->dvdl_lin[efptCOUL] += dvdl_long_range_q;
enerd->dvdl_lin[efptVDW] += dvdl_long_range_lj;
enerd->term[F_COUL_RECIP] = Vlr_q + Vcorr_q;
enerd->term[F_LJ_RECIP] = Vlr_lj + Vcorr_lj;
if (debug)
{
fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
Vlr_q, Vcorr_q, enerd->term[F_COUL_RECIP]);
pr_rvecs(debug, 0, "vir_el_recip after corr", fr->vir_el_recip, DIM);
pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
Vlr_lj, Vcorr_lj, enerd->term[F_LJ_RECIP]);
pr_rvecs(debug, 0, "vir_lj_recip after corr", fr->vir_lj_recip, DIM);
}
}
else
{
/* Is there a reaction-field exclusion correction needed? */
if (EEL_RF(fr->eeltype) && eelRF_NEC != fr->eeltype)
{
/* With the Verlet scheme, exclusion forces are calculated
* in the non-bonded kernel.
*/
if (ir->cutoff_scheme != ecutsVERLET)
{
real dvdl_rf_excl = 0;
enerd->term[F_RF_EXCL] =
RF_excl_correction(fr, graph, md, excl, x, f,
fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
}
}
}
where();
debug_gmx();
if (debug)
{
print_nrnb(debug, nrnb);
}
debug_gmx();
#ifdef GMX_MPI
if (TAKETIME)
{
t2 = MPI_Wtime();
MPI_Barrier(cr->mpi_comm_mygroup);
t3 = MPI_Wtime();
fr->t_wait += t3-t2;
if (fr->timesteps == 11)
{
char buf[22];
fprintf(stderr, "* PP load balancing info: rank %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
cr->nodeid, gmx_step_str(fr->timesteps, buf),
100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
(fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
}
fr->timesteps++;
}
#endif
if (debug)
{
pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
}
}
t_mdebin *init_mdebin(ener_file_t fp_ene,
const gmx_mtop_t *mtop,
const t_inputrec *ir,
FILE *fp_dhdl)
{
const char *ener_nm[F_NRE];
static const char *vir_nm[] = {
"Vir-XX", "Vir-XY", "Vir-XZ",
"Vir-YX", "Vir-YY", "Vir-YZ",
"Vir-ZX", "Vir-ZY", "Vir-ZZ"
};
static const char *sv_nm[] = {
"ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
"ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
"ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
};
static const char *fv_nm[] = {
"ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
"ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
"ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
};
static const char *pres_nm[] = {
"Pres-XX","Pres-XY","Pres-XZ",
"Pres-YX","Pres-YY","Pres-YZ",
"Pres-ZX","Pres-ZY","Pres-ZZ"
};
static const char *surft_nm[] = {
"#Surf*SurfTen"
};
static const char *mu_nm[] = {
"Mu-X", "Mu-Y", "Mu-Z"
};
static const char *vcos_nm[] = {
"2CosZ*Vel-X"
};
static const char *visc_nm[] = {
"1/Viscosity"
};
static const char *baro_nm[] = {
"Barostat"
};
char **grpnms;
const gmx_groups_t *groups;
char **gnm;
char buf[256];
const char *bufi;
t_mdebin *md;
int i,j,ni,nj,n,nh,k,kk,ncon,nset;
gmx_bool bBHAM,bNoseHoover,b14;
snew(md,1);
if (EI_DYNAMICS(ir->eI))
{
md->delta_t = ir->delta_t;
}
else
{
md->delta_t = 0;
}
groups = &mtop->groups;
bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0);
ncon = gmx_mtop_ftype_count(mtop,F_CONSTR);
nset = gmx_mtop_ftype_count(mtop,F_SETTLE);
md->bConstr = (ncon > 0 || nset > 0);
md->bConstrVir = FALSE;
if (md->bConstr) {
if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
if (ir->eI == eiSD2)
md->nCrmsd = 2;
else
md->nCrmsd = 1;
}
md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
} else {
md->nCrmsd = 0;
}
/* Energy monitoring */
for(i=0;i<egNR;i++)
{
md->bEInd[i]=FALSE;
}
#ifndef GMX_OPENMM
for(i=0; i<F_NRE; i++)
{
md->bEner[i] = FALSE;
if (i == F_LJ)
md->bEner[i] = !bBHAM;
else if (i == F_BHAM)
md->bEner[i] = bBHAM;
else if (i == F_EQM)
md->bEner[i] = ir->bQMMM;
else if (i == F_COUL_LR)
md->bEner[i] = (ir->rcoulomb > ir->rlist);
else if (i == F_LJ_LR)
md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
else if (i == F_BHAM_LR)
md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
else if (i == F_RF_EXCL)
md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC);
else if (i == F_COUL_RECIP)
md->bEner[i] = EEL_FULL(ir->coulombtype);
else if (i == F_LJ14)
md->bEner[i] = b14;
else if (i == F_COUL14)
md->bEner[i] = b14;
else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
md->bEner[i] = FALSE;
else if ((i == F_DVDL) || (i == F_DKDL))
md->bEner[i] = (ir->efep != efepNO);
else if (i == F_DHDL_CON)
md->bEner[i] = (ir->efep != efepNO && md->bConstr);
else if ((interaction_function[i].flags & IF_VSITE) ||
(i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
md->bEner[i] = FALSE;
else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM))
md->bEner[i] = TRUE;
else if ((i == F_GBPOL) && ir->implicit_solvent==eisGBSA)
md->bEner[i] = TRUE;
else if ((i == F_NPSOLVATION) && ir->implicit_solvent==eisGBSA && (ir->sa_algorithm != esaNO))
md->bEner[i] = TRUE;
else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
md->bEner[i] = FALSE;
else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
md->bEner[i] = EI_DYNAMICS(ir->eI);
else if (i==F_VTEMP)
md->bEner[i] = (EI_DYNAMICS(ir->eI) && getenv("GMX_VIRIAL_TEMPERATURE"));
else if (i == F_DISPCORR || i == F_PDISPCORR)
md->bEner[i] = (ir->eDispCorr != edispcNO);
else if (i == F_DISRESVIOL)
md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
else if (i == F_ORIRESDEV)
md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
else if (i == F_CONNBONDS)
md->bEner[i] = FALSE;
else if (i == F_COM_PULL)
md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F);
else if (i == F_ECONSERVED)
md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
(ir->epc == epcNO || ir->epc==epcMTTK));
else
md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
}
#else
/* OpenMM always produces only the following 4 energy terms */
md->bEner[F_EPOT] = TRUE;
md->bEner[F_EKIN] = TRUE;
md->bEner[F_ETOT] = TRUE;
md->bEner[F_TEMP] = TRUE;
#endif
md->f_nre=0;
for(i=0; i<F_NRE; i++)
{
if (md->bEner[i])
{
/* FIXME: The constness should not be cast away */
/*ener_nm[f_nre]=(char *)interaction_function[i].longname;*/
ener_nm[md->f_nre]=interaction_function[i].longname;
md->f_nre++;
}
}
md->epc = ir->epc;
for (i=0;i<DIM;i++)
{
for (j=0;j<DIM;j++)
{
md->ref_p[i][j] = ir->ref_p[i][j];
}
}
md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
md->bDynBox = DYNAMIC_BOX(*ir);
md->etc = ir->etc;
md->bNHC_trotter = IR_NVT_TROTTER(ir);
md->bMTTK = IR_NPT_TROTTER(ir);
md->ebin = mk_ebin();
/* Pass NULL for unit to let get_ebin_space determine the units
* for interaction_function[i].longname
*/
md->ie = get_ebin_space(md->ebin,md->f_nre,ener_nm,NULL);
if (md->nCrmsd)
{
/* This should be called directly after the call for md->ie,
* such that md->iconrmsd follows directly in the list.
*/
md->iconrmsd = get_ebin_space(md->ebin,md->nCrmsd,conrmsd_nm,"");
}
if (md->bDynBox)
{
md->ib = get_ebin_space(md->ebin,
md->bTricl ? NTRICLBOXS : NBOXS,
md->bTricl ? tricl_boxs_nm : boxs_nm,
unit_length);
md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
}
if (md->bConstrVir)
{
md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm,unit_energy);
md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm,unit_energy);
}
md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm,unit_energy);
md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm,unit_pres_bar);
md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm,
unit_surft_bar);
if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
{
md->ipc = get_ebin_space(md->ebin,md->bTricl ? 6 : 3,
boxvel_nm,unit_vel);
}
md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D);
if (ir->cos_accel != 0)
{
md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel);
md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm,
unit_invvisc_SI);
}
/* Energy monitoring */
for(i=0;i<egNR;i++)
{
md->bEInd[i] = FALSE;
}
md->bEInd[egCOULSR] = TRUE;
md->bEInd[egLJSR ] = TRUE;
if (ir->rcoulomb > ir->rlist)
{
md->bEInd[egCOULLR] = TRUE;
}
if (!bBHAM)
{
if (ir->rvdw > ir->rlist)
{
md->bEInd[egLJLR] = TRUE;
}
}
else
{
md->bEInd[egLJSR] = FALSE;
md->bEInd[egBHAMSR] = TRUE;
if (ir->rvdw > ir->rlist)
{
md->bEInd[egBHAMLR] = TRUE;
}
}
if (b14)
{
md->bEInd[egLJ14] = TRUE;
md->bEInd[egCOUL14] = TRUE;
}
md->nEc=0;
for(i=0; (i<egNR); i++)
{
if (md->bEInd[i])
{
md->nEc++;
}
}
n=groups->grps[egcENER].nr;
md->nEg=n;
md->nE=(n*(n+1))/2;
snew(md->igrp,md->nE);
if (md->nE > 1)
{
n=0;
snew(gnm,md->nEc);
for(k=0; (k<md->nEc); k++)
{
snew(gnm[k],STRLEN);
}
for(i=0; (i<groups->grps[egcENER].nr); i++)
{
ni=groups->grps[egcENER].nm_ind[i];
for(j=i; (j<groups->grps[egcENER].nr); j++)
{
nj=groups->grps[egcENER].nm_ind[j];
for(k=kk=0; (k<egNR); k++)
{
if (md->bEInd[k])
{
sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
*(groups->grpname[ni]),*(groups->grpname[nj]));
kk++;
}
}
md->igrp[n]=get_ebin_space(md->ebin,md->nEc,
(const char **)gnm,unit_energy);
n++;
}
}
for(k=0; (k<md->nEc); k++)
{
sfree(gnm[k]);
}
sfree(gnm);
if (n != md->nE)
{
gmx_incons("Number of energy terms wrong");
}
}
md->nTC=groups->grps[egcTC].nr;
md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
if (md->bMTTK)
{
md->nTCP = 1; /* assume only one possible coupling system for barostat
for now */
}
else
{
md->nTCP = 0;
}
if (md->etc == etcNOSEHOOVER) {
if (md->bNHC_trotter) {
md->mde_n = 2*md->nNHC*md->nTC;
}
else
{
md->mde_n = 2*md->nTC;
}
if (md->epc == epcMTTK)
{
md->mdeb_n = 2*md->nNHC*md->nTCP;
}
} else {
md->mde_n = md->nTC;
md->mdeb_n = 0;
}
snew(md->tmp_r,md->mde_n);
snew(md->tmp_v,md->mde_n);
snew(md->grpnms,md->mde_n);
grpnms = md->grpnms;
for(i=0; (i<md->nTC); i++)
{
ni=groups->grps[egcTC].nm_ind[i];
sprintf(buf,"T-%s",*(groups->grpname[ni]));
grpnms[i]=strdup(buf);
}
md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
unit_temp_K);
bNoseHoover = (getenv("GMX_NOSEHOOVER_CHAINS") != NULL); /* whether to print Nose-Hoover chains */
if (md->etc == etcNOSEHOOVER)
{
if (bNoseHoover)
{
if (md->bNHC_trotter)
{
for(i=0; (i<md->nTC); i++)
{
ni=groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
for(j=0; (j<md->nNHC); j++)
{
sprintf(buf,"Xi-%d-%s",j,bufi);
grpnms[2*(i*md->nNHC+j)]=strdup(buf);
sprintf(buf,"vXi-%d-%s",j,bufi);
grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
}
}
md->itc=get_ebin_space(md->ebin,md->mde_n,
(const char **)grpnms,unit_invtime);
if (md->bMTTK)
{
for(i=0; (i<md->nTCP); i++)
{
bufi = baro_nm[0]; /* All barostat DOF's together for now. */
for(j=0; (j<md->nNHC); j++)
{
sprintf(buf,"Xi-%d-%s",j,bufi);
grpnms[2*(i*md->nNHC+j)]=strdup(buf);
sprintf(buf,"vXi-%d-%s",j,bufi);
grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
}
}
md->itcb=get_ebin_space(md->ebin,md->mdeb_n,
(const char **)grpnms,unit_invtime);
}
}
else
{
for(i=0; (i<md->nTC); i++)
{
ni=groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
sprintf(buf,"Xi-%s",bufi);
grpnms[2*i]=strdup(buf);
sprintf(buf,"vXi-%s",bufi);
grpnms[2*i+1]=strdup(buf);
}
md->itc=get_ebin_space(md->ebin,md->mde_n,
(const char **)grpnms,unit_invtime);
}
}
}
else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
md->etc == etcVRESCALE)
{
for(i=0; (i<md->nTC); i++)
{
ni=groups->grps[egcTC].nm_ind[i];
sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
grpnms[i]=strdup(buf);
}
md->itc=get_ebin_space(md->ebin,md->mde_n,(const char **)grpnms,"");
}
sfree(grpnms);
md->nU=groups->grps[egcACC].nr;
if (md->nU > 1)
{
snew(grpnms,3*md->nU);
for(i=0; (i<md->nU); i++)
{
ni=groups->grps[egcACC].nm_ind[i];
sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
grpnms[3*i+XX]=strdup(buf);
sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
grpnms[3*i+YY]=strdup(buf);
sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
grpnms[3*i+ZZ]=strdup(buf);
}
md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel);
sfree(grpnms);
}
if ( fp_ene )
{
do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
}
md->print_grpnms=NULL;
/* check whether we're going to write dh histograms */
md->dhc=NULL;
if (ir->separate_dhdl_file == sepdhdlfileNO )
{
int i;
snew(md->dhc, 1);
mde_delta_h_coll_init(md->dhc, ir);
md->fp_dhdl = NULL;
}
else
{
md->fp_dhdl = fp_dhdl;
}
md->dhdl_derivatives = (ir->dhdl_derivatives==dhdlderivativesYES);
return md;
}
void do_force_lowlevel(t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_commrec *cr,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_mdatoms *md,
rvec x[], history_t *hist,
rvec f[],
rvec f_longrange[],
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_localtop_t *top,
gmx_genborn_t *born,
gmx_bool bBornRadii,
matrix box,
t_lambda *fepvals,
real *lambda,
t_graph *graph,
t_blocka *excl,
rvec mu_tot[],
int flags,
float *cycles_pme)
{
int i, j;
int donb_flags;
gmx_bool bSB;
int pme_flags;
matrix boxs;
rvec box_size;
t_pbc pbc;
real dvdl_dum[efptNR], dvdl_nb[efptNR];
#ifdef GMX_MPI
double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
#endif
set_pbc(&pbc, fr->ePBC, box);
/* reset free energy components */
for (i = 0; i < efptNR; i++)
{
dvdl_nb[i] = 0;
dvdl_dum[i] = 0;
}
/* Reset box */
for (i = 0; (i < DIM); i++)
{
box_size[i] = box[i][i];
}
debug_gmx();
/* do QMMM first if requested */
if (fr->bQMMM)
{
enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
}
/* Call the short range functions all in one go. */
#ifdef GMX_MPI
/*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
#define TAKETIME FALSE
if (TAKETIME)
{
MPI_Barrier(cr->mpi_comm_mygroup);
t0 = MPI_Wtime();
}
#endif
if (ir->nwall)
{
/* foreign lambda component for walls */
real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
enerd->grpp.ener[egLJSR], nrnb);
enerd->dvdl_lin[efptVDW] += dvdl_walls;
}
/* If doing GB, reset dvda and calculate the Born radii */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsNONBONDED);
for (i = 0; i < born->nr; i++)
{
fr->dvda[i] = 0;
}
if (bBornRadii)
{
calc_gb_rad(cr, fr, ir, top, x, &(fr->gblist), born, md, nrnb);
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
where();
/* We only do non-bonded calculation with group scheme here, the verlet
* calls are done from do_force_cutsVERLET(). */
if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
{
donb_flags = 0;
/* Add short-range interactions */
donb_flags |= GMX_NONBONDED_DO_SR;
/* Currently all group scheme kernels always calculate (shift-)forces */
if (flags & GMX_FORCE_FORCES)
{
donb_flags |= GMX_NONBONDED_DO_FORCE;
}
if (flags & GMX_FORCE_VIRIAL)
{
donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
}
if (flags & GMX_FORCE_ENERGY)
{
donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
}
if (flags & GMX_FORCE_DO_LR)
{
donb_flags |= GMX_NONBONDED_DO_LR;
}
wallcycle_sub_start(wcycle, ewcsNONBONDED);
do_nonbonded(fr, x, f, f_longrange, md, excl,
&enerd->grpp, nrnb,
lambda, dvdl_nb, -1, -1, donb_flags);
/* If we do foreign lambda and we have soft-core interactions
* we have to recalculate the (non-linear) energies contributions.
*/
if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
{
for (i = 0; i < enerd->n_lambda; i++)
{
real lam_i[efptNR];
for (j = 0; j < efptNR; j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
}
reset_foreign_enerdata(enerd);
do_nonbonded(fr, x, f, f_longrange, md, excl,
&(enerd->foreign_grpp), nrnb,
lam_i, dvdl_dum, -1, -1,
(donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
}
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
where();
}
/* If we are doing GB, calculate bonded forces and apply corrections
* to the solvation forces */
/* MRS: Eventually, many need to include free energy contribution here! */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsLISTED);
calc_gb_forces(cr, md, born, top, x, f, fr, idef,
ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
wallcycle_sub_stop(wcycle, ewcsLISTED);
}
#ifdef GMX_MPI
if (TAKETIME)
{
t1 = MPI_Wtime();
fr->t_fnbf += t1-t0;
}
#endif
if (fepvals->sc_alpha != 0)
{
enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
}
else
{
enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
}
if (fepvals->sc_alpha != 0)
/* even though coulomb part is linear, we already added it, beacuse we
need to go through the vdw calculation anyway */
{
enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
}
else
{
enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
}
debug_gmx();
if (debug)
{
pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
}
/* Shift the coordinates. Must be done before listed forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no listed forces have to be evaluated.
*
* The shifting and PBC code is deliberately not timed, since with
* the Verlet scheme it only takes non-zero time with triclinic
* boxes, and even then the time is around a factor of 100 less
* than the next smallest counter.
*/
/* Here sometimes we would not need to shift with NBFonly,
* but we do so anyhow for consistency of the returned coordinates.
*/
if (graph)
{
shift_self(graph, box, x);
if (TRICLINIC(box))
{
inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
}
else
{
inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
}
}
/* Check whether we need to do listed interactions or correct for exclusions */
if (fr->bMolPBC &&
((flags & GMX_FORCE_LISTED)
|| EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
{
/* TODO There are no electrostatics methods that require this
transformation, when using the Verlet scheme, so update the
above conditional. */
/* Since all atoms are in the rectangular or triclinic unit-cell,
* only single box vector shifts (2 in x) are required.
*/
set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
}
debug_gmx();
do_force_listed(wcycle, box, ir->fepvals, cr->ms,
idef, (const rvec *) x, hist, f, fr,
&pbc, graph, enerd, nrnb, lambda, md, fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
flags);
where();
*cycles_pme = 0;
clear_mat(fr->vir_el_recip);
clear_mat(fr->vir_lj_recip);
/* Do long-range electrostatics and/or LJ-PME, including related short-range
* corrections.
*/
if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
{
int status = 0;
real Vlr_q = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
bSB = (ir->nwall == 2);
if (bSB)
{
copy_mat(box, boxs);
svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
box_size[ZZ] *= ir->wall_ewald_zfac;
}
if (EEL_PME_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
{
real dvdl_long_range_correction_q = 0;
real dvdl_long_range_correction_lj = 0;
/* With the Verlet scheme exclusion forces are calculated
* in the non-bonded kernel.
*/
/* The TPI molecule does not have exclusions with the rest
* of the system and no intra-molecular PME grid
* contributions will be calculated in
* gmx_pme_calc_energy.
*/
if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
ir->ewald_geometry != eewg3D ||
ir->epsilon_surface != 0)
{
int nthreads, t;
wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
if (fr->n_tpi > 0)
{
gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
}
nthreads = fr->nthread_ewc;
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (t = 0; t < nthreads; t++)
{
try
{
tensor *vir_q, *vir_lj;
real *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
if (t == 0)
{
vir_q = &fr->vir_el_recip;
vir_lj = &fr->vir_lj_recip;
Vcorrt_q = &Vcorr_q;
Vcorrt_lj = &Vcorr_lj;
dvdlt_q = &dvdl_long_range_correction_q;
dvdlt_lj = &dvdl_long_range_correction_lj;
}
else
{
vir_q = &fr->ewc_t[t].vir_q;
vir_lj = &fr->ewc_t[t].vir_lj;
Vcorrt_q = &fr->ewc_t[t].Vcorr_q;
Vcorrt_lj = &fr->ewc_t[t].Vcorr_lj;
dvdlt_q = &fr->ewc_t[t].dvdl[efptCOUL];
dvdlt_lj = &fr->ewc_t[t].dvdl[efptVDW];
clear_mat(*vir_q);
clear_mat(*vir_lj);
}
*dvdlt_q = 0;
*dvdlt_lj = 0;
/* Threading is only supported with the Verlet cut-off
* scheme and then only single particle forces (no
* exclusion forces) are calculated, so we can store
* the forces in the normal, single fr->f_novirsum array.
*/
ewald_LRcorrection(fr->excl_load[t], fr->excl_load[t+1],
cr, t, fr,
md->chargeA, md->chargeB,
md->sqrt_c6A, md->sqrt_c6B,
md->sigmaA, md->sigmaB,
md->sigma3A, md->sigma3B,
md->nChargePerturbed || md->nTypePerturbed,
ir->cutoff_scheme != ecutsVERLET,
excl, x, bSB ? boxs : box, mu_tot,
ir->ewald_geometry,
ir->epsilon_surface,
fr->f_novirsum, *vir_q, *vir_lj,
Vcorrt_q, Vcorrt_lj,
lambda[efptCOUL], lambda[efptVDW],
dvdlt_q, dvdlt_lj);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
if (nthreads > 1)
{
reduce_thread_energies(fr->vir_el_recip, fr->vir_lj_recip,
&Vcorr_q, &Vcorr_lj,
&dvdl_long_range_correction_q,
&dvdl_long_range_correction_lj,
nthreads, fr->ewc_t);
}
wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
}
void sas_plot(int nfile,t_filenm fnm[],real solsize,int ndots,
real qcut,gmx_bool bSave,real minarea,gmx_bool bPBC,
real dgs_default,gmx_bool bFindex, const output_env_t oenv)
{
FILE *fp,*fp2,*fp3=NULL,*vp;
const char *flegend[] = { "Hydrophobic", "Hydrophilic",
"Total", "D Gsolv" };
const char *vlegend[] = { "Volume (nm\\S3\\N)", "Density (g/l)" };
const char *or_and_oa_legend[] = { "Average (nm\\S2\\N)", "Standard deviation (nm\\S2\\N)" };
const char *vfile;
real t;
gmx_atomprop_t aps=NULL;
gmx_rmpbc_t gpbc=NULL;
t_trxstatus *status;
int ndefault;
int i,j,ii,nfr,natoms,flag,nsurfacedots,res;
rvec *xtop,*x;
matrix topbox,box;
t_topology top;
char title[STRLEN];
int ePBC;
gmx_bool bTop;
t_atoms *atoms;
gmx_bool *bOut,*bPhobic;
gmx_bool bConnelly;
gmx_bool bResAt,bITP,bDGsol;
real *radius,*dgs_factor=NULL,*area=NULL,*surfacedots=NULL;
real at_area,*atom_area=NULL,*atom_area2=NULL;
real *res_a=NULL,*res_area=NULL,*res_area2=NULL;
real totarea,totvolume,totmass=0,density,harea,tarea,fluc2;
atom_id **index,*findex;
int *nx,nphobic,npcheck,retval;
char **grpname,*fgrpname;
real dgsolv;
bITP = opt2bSet("-i",nfile,fnm);
bResAt = opt2bSet("-or",nfile,fnm) || opt2bSet("-oa",nfile,fnm) || bITP;
bTop = read_tps_conf(ftp2fn(efTPS,nfile,fnm),title,&top,&ePBC,
&xtop,NULL,topbox,FALSE);
atoms = &(top.atoms);
if (!bTop) {
fprintf(stderr,"No tpr file, will not compute Delta G of solvation\n");
bDGsol = FALSE;
} else {
bDGsol = strcmp(*(atoms->atomtype[0]),"?") != 0;
if (!bDGsol) {
fprintf(stderr,"Warning: your tpr file is too old, will not compute "
"Delta G of solvation\n");
} else {
printf("In case you use free energy of solvation predictions:\n");
please_cite(stdout,"Eisenberg86a");
}
}
aps = gmx_atomprop_init();
if ((natoms=read_first_x(oenv,&status,ftp2fn(efTRX,nfile,fnm),
&t,&x,box))==0)
gmx_fatal(FARGS,"Could not read coordinates from statusfile\n");
if ((ePBC != epbcXYZ) || (TRICLINIC(box))) {
fprintf(stderr,"\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
"Analysis based on vacuum simulations (with the possibility of evaporation)\n"
"will certainly crash the analysis.\n\n");
}
snew(nx,2);
snew(index,2);
snew(grpname,2);
fprintf(stderr,"Select a group for calculation of surface and a group for output:\n");
get_index(atoms,ftp2fn_null(efNDX,nfile,fnm),2,nx,index,grpname);
if (bFindex) {
fprintf(stderr,"Select a group of hydrophobic atoms:\n");
get_index(atoms,ftp2fn_null(efNDX,nfile,fnm),1,&nphobic,&findex,&fgrpname);
}
snew(bOut,natoms);
for(i=0; i<nx[1]; i++)
bOut[index[1][i]] = TRUE;
/* Now compute atomic readii including solvent probe size */
snew(radius,natoms);
snew(bPhobic,nx[0]);
if (bResAt) {
snew(atom_area,nx[0]);
snew(atom_area2,nx[0]);
snew(res_a,atoms->nres);
snew(res_area,atoms->nres);
snew(res_area2,atoms->nres);
}
if (bDGsol)
snew(dgs_factor,nx[0]);
/* Get a Van der Waals radius for each atom */
ndefault = 0;
for(i=0; (i<natoms); i++) {
if (!gmx_atomprop_query(aps,epropVDW,
*(atoms->resinfo[atoms->atom[i].resind].name),
*(atoms->atomname[i]),&radius[i]))
ndefault++;
/* radius[i] = calc_radius(*(top->atoms.atomname[i])); */
radius[i] += solsize;
}
if (ndefault > 0)
fprintf(stderr,"WARNING: could not find a Van der Waals radius for %d atoms\n",ndefault);
/* Determine which atom is counted as hydrophobic */
if (bFindex) {
npcheck = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
for(j=0; (j<nphobic); j++) {
if (findex[j] == ii) {
bPhobic[i] = TRUE;
if (bOut[ii])
npcheck++;
}
}
}
if (npcheck != nphobic)
gmx_fatal(FARGS,"Consistency check failed: not all %d atoms in the hydrophobic index\n"
"found in the normal index selection (%d atoms)",nphobic,npcheck);
}
else
nphobic = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
if (!bFindex) {
bPhobic[i] = fabs(atoms->atom[ii].q) <= qcut;
if (bPhobic[i] && bOut[ii])
nphobic++;
}
if (bDGsol)
if (!gmx_atomprop_query(aps,epropDGsol,
*(atoms->resinfo[atoms->atom[ii].resind].name),
*(atoms->atomtype[ii]),&(dgs_factor[i])))
dgs_factor[i] = dgs_default;
if (debug)
fprintf(debug,"Atom %5d %5s-%5s: q= %6.3f, r= %6.3f, dgsol= %6.3f, hydrophobic= %s\n",
ii+1,*(atoms->resinfo[atoms->atom[ii].resind].name),
*(atoms->atomname[ii]),
atoms->atom[ii].q,radius[ii]-solsize,dgs_factor[i],
BOOL(bPhobic[i]));
}
fprintf(stderr,"%d out of %d atoms were classified as hydrophobic\n",
nphobic,nx[1]);
fp=xvgropen(opt2fn("-o",nfile,fnm),"Solvent Accessible Surface","Time (ps)",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp,asize(flegend) - (bDGsol ? 0 : 1),flegend,oenv);
vfile = opt2fn_null("-tv",nfile,fnm);
if (vfile) {
if (!bTop) {
gmx_fatal(FARGS,"Need a tpr file for option -tv");
}
vp=xvgropen(vfile,"Volume and Density","Time (ps)","",oenv);
xvgr_legend(vp,asize(vlegend),vlegend,oenv);
totmass = 0;
ndefault = 0;
for(i=0; (i<nx[0]); i++) {
real mm;
ii = index[0][i];
/*
if (!query_atomprop(atomprop,epropMass,
*(top->atoms.resname[top->atoms.atom[ii].resnr]),
*(top->atoms.atomname[ii]),&mm))
ndefault++;
totmass += mm;
*/
totmass += atoms->atom[ii].m;
}
if (ndefault)
fprintf(stderr,"WARNING: Using %d default masses for density calculation, which most likely are inaccurate\n",ndefault);
}
else
vp = NULL;
gmx_atomprop_destroy(aps);
if (bPBC)
gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
nfr=0;
do {
if (bPBC)
gmx_rmpbc(gpbc,natoms,box,x);
bConnelly = (nfr==0 && opt2bSet("-q",nfile,fnm));
if (bConnelly) {
if (!bTop)
gmx_fatal(FARGS,"Need a tpr file for Connelly plot");
flag = FLAG_ATOM_AREA | FLAG_DOTS;
} else {
flag = FLAG_ATOM_AREA;
}
if (vp) {
flag = flag | FLAG_VOLUME;
}
if (debug)
write_sto_conf("check.pdb","pbc check",atoms,x,NULL,ePBC,box);
retval = nsc_dclm_pbc(x,radius,nx[0],ndots,flag,&totarea,
&area,&totvolume,&surfacedots,&nsurfacedots,
index[0],ePBC,bPBC ? box : NULL);
if (retval)
gmx_fatal(FARGS,"Something wrong in nsc_dclm_pbc");
if (bConnelly)
connelly_plot(ftp2fn(efPDB,nfile,fnm),
nsurfacedots,surfacedots,x,atoms,
&(top.symtab),ePBC,box,bSave);
harea = 0;
tarea = 0;
dgsolv = 0;
if (bResAt)
for(i=0; i<atoms->nres; i++)
res_a[i] = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
if (bOut[ii]) {
at_area = area[i];
if (bResAt) {
atom_area[i] += at_area;
atom_area2[i] += sqr(at_area);
res_a[atoms->atom[ii].resind] += at_area;
}
tarea += at_area;
if (bDGsol)
dgsolv += at_area*dgs_factor[i];
if (bPhobic[i])
harea += at_area;
}
}
if (bResAt)
for(i=0; i<atoms->nres; i++) {
res_area[i] += res_a[i];
res_area2[i] += sqr(res_a[i]);
}
fprintf(fp,"%10g %10g %10g %10g",t,harea,tarea-harea,tarea);
if (bDGsol)
fprintf(fp," %10g\n",dgsolv);
else
fprintf(fp,"\n");
/* Print volume */
if (vp) {
density = totmass*AMU/(totvolume*NANO*NANO*NANO);
fprintf(vp,"%12.5e %12.5e %12.5e\n",t,totvolume,density);
}
if (area) {
sfree(area);
area = NULL;
}
if (surfacedots) {
sfree(surfacedots);
surfacedots = NULL;
}
nfr++;
} while (read_next_x(oenv,status,&t,natoms,x,box));
if (bPBC)
gmx_rmpbc_done(gpbc);
fprintf(stderr,"\n");
close_trj(status);
ffclose(fp);
if (vp)
ffclose(vp);
/* if necessary, print areas per atom to file too: */
if (bResAt) {
for(i=0; i<atoms->nres; i++) {
res_area[i] /= nfr;
res_area2[i] /= nfr;
}
for(i=0; i<nx[0]; i++) {
atom_area[i] /= nfr;
atom_area2[i] /= nfr;
}
fprintf(stderr,"Printing out areas per atom\n");
fp = xvgropen(opt2fn("-or",nfile,fnm),"Area per residue over the trajectory","Residue",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp, asize(or_and_oa_legend),or_and_oa_legend,oenv);
fp2 = xvgropen(opt2fn("-oa",nfile,fnm),"Area per atom over the trajectory","Atom #",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp2, asize(or_and_oa_legend),or_and_oa_legend,oenv);
if (bITP) {
fp3 = ftp2FILE(efITP,nfile,fnm,"w");
fprintf(fp3,"[ position_restraints ]\n"
"#define FCX 1000\n"
"#define FCY 1000\n"
"#define FCZ 1000\n"
"; Atom Type fx fy fz\n");
}
for(i=0; i<nx[0]; i++) {
ii = index[0][i];
res = atoms->atom[ii].resind;
if (i==nx[0]-1 || res!=atoms->atom[index[0][i+1]].resind) {
fluc2 = res_area2[res]-sqr(res_area[res]);
if (fluc2 < 0)
fluc2 = 0;
fprintf(fp,"%10d %10g %10g\n",
atoms->resinfo[res].nr,res_area[res],sqrt(fluc2));
}
fluc2 = atom_area2[i]-sqr(atom_area[i]);
if (fluc2 < 0)
fluc2 = 0;
fprintf(fp2,"%d %g %g\n",index[0][i]+1,atom_area[i],sqrt(fluc2));
if (bITP && (atom_area[i] > minarea))
fprintf(fp3,"%5d 1 FCX FCX FCZ\n",ii+1);
}
if (bITP)
ffclose(fp3);
ffclose(fp);
}
/* Be a good citizen, keep our memory free! */
sfree(x);
sfree(nx);
for(i=0;i<2;i++)
{
sfree(index[i]);
sfree(grpname[i]);
}
sfree(bOut);
sfree(radius);
sfree(bPhobic);
if(bResAt)
{
sfree(atom_area);
sfree(atom_area2);
sfree(res_a);
sfree(res_area);
sfree(res_area2);
}
if(bDGsol)
{
sfree(dgs_factor);
}
}
int gmx_editconf(int argc, char *argv[])
{
const char
*desc[] =
{
"editconf converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
"or [TT].pdb[tt].",
"[PAR]",
"The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
"[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
"will center the system in the box, unless [TT]-noc[tt] is used.",
"[PAR]",
"Option [TT]-bt[tt] determines the box type: [TT]triclinic[tt] is a",
"triclinic box, [TT]cubic[tt] is a rectangular box with all sides equal",
"[TT]dodecahedron[tt] represents a rhombic dodecahedron and",
"[TT]octahedron[tt] is a truncated octahedron.",
"The last two are special cases of a triclinic box.",
"The length of the three box vectors of the truncated octahedron is the",
"shortest distance between two opposite hexagons.",
"The volume of a dodecahedron is 0.71 and that of a truncated octahedron",
"is 0.77 of that of a cubic box with the same periodic image distance.",
"[PAR]",
"Option [TT]-box[tt] requires only",
"one value for a cubic box, dodecahedron and a truncated octahedron.",
"[PAR]",
"With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the x, y",
"and z directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
"[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
"to the diameter of the system (largest distance between atoms) plus twice",
"the specified distance.",
"[PAR]",
"Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
"a triclinic box and can not be used with option [TT]-d[tt].",
"[PAR]",
"When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
"can be selected for calculating the size and the geometric center,",
"otherwise the whole system is used.",
"[PAR]",
"[TT]-rotate[tt] rotates the coordinates and velocities.",
"[PAR]",
"[TT]-princ[tt] aligns the principal axes of the system along the",
"coordinate axes, this may allow you to decrease the box volume,",
"but beware that molecules can rotate significantly in a nanosecond.",
"[PAR]",
"Scaling is applied before any of the other operations are",
"performed. Boxes and coordinates can be scaled to give a certain density (option",
"[TT]-density[tt]). Note that this may be inaccurate in case a gro",
"file is given as input. A special feature of the scaling option, when the",
"factor -1 is given in one dimension, one obtains a mirror image,",
"mirrored in one of the plains, when one uses -1 in three dimensions",
"a point-mirror image is obtained.[PAR]",
"Groups are selected after all operations have been applied.[PAR]",
"Periodicity can be removed in a crude manner.",
"It is important that the box sizes at the bottom of your input file",
"are correct when the periodicity is to be removed.",
"[PAR]",
"When writing [TT].pdb[tt] files, B-factors can be",
"added with the [TT]-bf[tt] option. B-factors are read",
"from a file with with following format: first line states number of",
"entries in the file, next lines state an index",
"followed by a B-factor. The B-factors will be attached per residue",
"unless an index is larger than the number of residues or unless the",
"[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
"be added instead of B-factors. [TT]-legend[tt] will produce",
"a row of CA atoms with B-factors ranging from the minimum to the",
"maximum value found, effectively making a legend for viewing.",
"[PAR]",
"With the option -mead a special pdb (pqr) file for the MEAD electrostatics",
"program (Poisson-Boltzmann solver) can be made. A further prerequisite",
"is that the input file is a run input file.",
"The B-factor field is then filled with the Van der Waals radius",
"of the atoms while the occupancy field will hold the charge.",
"[PAR]",
"The option -grasp is similar, but it puts the charges in the B-factor",
"and the radius in the occupancy.",
"[PAR]",
"Option [TT]-align[tt] allows alignment",
"of the principal axis of a specified group against the given vector, ",
"with an optional center of rotation specified by [TT]-aligncenter[tt].",
"[PAR]",
"Finally with option [TT]-label[tt] editconf can add a chain identifier",
"to a pdb file, which can be useful for analysis with e.g. rasmol.",
"[PAR]",
"To convert a truncated octrahedron file produced by a package which uses",
"a cubic box with the corners cut off (such as Gromos) use:[BR]",
"[TT]editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out>[tt][BR]",
"where [TT]veclen[tt] is the size of the cubic box times sqrt(3)/2." };
const char *bugs[] =
{
"For complex molecules, the periodicity removal routine may break down, ",
"in that case you can use trjconv." };
static real dist = 0.0, rbox = 0.0, to_diam = 0.0;
static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
FALSE, bCONECT = FALSE;
static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead =
FALSE, bGrasp = FALSE, bSig56 = FALSE;
static rvec scale =
{ 1, 1, 1 }, newbox =
{ 0, 0, 0 }, newang =
{ 90, 90, 90 };
static real rho = 1000.0, rvdw = 0.12;
static rvec center =
{ 0, 0, 0 }, translation =
{ 0, 0, 0 }, rotangles =
{ 0, 0, 0 }, aligncenter =
{ 0, 0, 0 }, targetvec =
{ 0, 0, 0 };
static const char *btype[] =
{ NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },
*label = "A";
static rvec visbox =
{ 0, 0, 0 };
t_pargs
pa[] =
{
{ "-ndef", FALSE, etBOOL,
{ &bNDEF }, "Choose output from default index groups" },
{ "-visbox", FALSE, etRVEC,
{ visbox },
"HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
{ "-bt", FALSE, etENUM,
{ btype }, "Box type for -box and -d" },
{ "-box", FALSE, etRVEC,
{ newbox }, "Box vector lengths (a,b,c)" },
{ "-angles", FALSE, etRVEC,
{ newang }, "Angles between the box vectors (bc,ac,ab)" },
{ "-d", FALSE, etREAL,
{ &dist }, "Distance between the solute and the box" },
{ "-c", FALSE, etBOOL,
{ &bCenter },
"Center molecule in box (implied by -box and -d)" },
{ "-center", FALSE, etRVEC,
{ center }, "Coordinates of geometrical center" },
{ "-aligncenter", FALSE, etRVEC,
{ aligncenter }, "Center of rotation for alignment" },
{ "-align", FALSE, etRVEC,
{ targetvec },
"Align to target vector" },
{ "-translate", FALSE, etRVEC,
{ translation }, "Translation" },
{ "-rotate", FALSE, etRVEC,
{ rotangles },
"Rotation around the X, Y and Z axes in degrees" },
{ "-princ", FALSE, etBOOL,
{ &bOrient },
"Orient molecule(s) along their principal axes" },
{ "-scale", FALSE, etRVEC,
{ scale }, "Scaling factor" },
{ "-density", FALSE, etREAL,
{ &rho },
"Density (g/l) of the output box achieved by scaling" },
{ "-pbc", FALSE, etBOOL,
{ &bRMPBC },
"Remove the periodicity (make molecule whole again)" },
{ "-grasp", FALSE, etBOOL,
{ &bGrasp },
"Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field" },
{
"-rvdw", FALSE, etREAL,
{ &rvdw },
"Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file" },
{ "-sig56", FALSE, etREAL,
{ &bSig56 },
"Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 " },
{
"-vdwread", FALSE, etBOOL,
{ &bReadVDW },
"Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field" },
{ "-atom", FALSE, etBOOL,
{ &peratom }, "Force B-factor attachment per atom" },
{ "-legend", FALSE, etBOOL,
{ &bLegend }, "Make B-factor legend" },
{ "-label", FALSE, etSTR,
{ &label }, "Add chain label for all residues" },
{
"-conect", FALSE, etBOOL,
{ &bCONECT },
"Add CONECT records to a pdb file when written. Can only be done when a topology is present" } };
#define NPA asize(pa)
FILE *out;
const char *infile, *outfile;
char title[STRLEN];
int outftp, inftp, natom, i, j, n_bfac, itype, ntype;
double *bfac = NULL, c6, c12;
int *bfac_nr = NULL;
t_topology *top = NULL;
t_atoms atoms;
char *grpname, *sgrpname, *agrpname;
int isize, ssize, tsize, asize;
atom_id *index, *sindex, *tindex, *aindex;
rvec *x, *v, gc, min, max, size;
int ePBC;
matrix box,rotmatrix,trans;
rvec princd,tmpvec;
gmx_bool bIndex, bSetSize, bSetAng, bCubic, bDist, bSetCenter, bAlign;
gmx_bool bHaveV, bScale, bRho, bTranslate, bRotate, bCalcGeom, bCalcDiam;
real xs, ys, zs, xcent, ycent, zcent, diam = 0, mass = 0, d, vdw;
gmx_atomprop_t aps;
gmx_conect conect;
output_env_t oenv;
t_filenm fnm[] =
{
{ efSTX, "-f", NULL, ffREAD },
{ efNDX, "-n", NULL, ffOPTRD },
{ efSTO, NULL, NULL, ffOPTWR },
{ efPQR, "-mead", "mead", ffOPTWR },
{ efDAT, "-bf", "bfact", ffOPTRD } };
#define NFILE asize(fnm)
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
asize(desc), desc, asize(bugs), bugs, &oenv);
bIndex = opt2bSet("-n", NFILE, fnm) || bNDEF;
bMead = opt2bSet("-mead", NFILE, fnm);
bSetSize = opt2parg_bSet("-box", NPA, pa);
bSetAng = opt2parg_bSet("-angles", NPA, pa);
bSetCenter = opt2parg_bSet("-center", NPA, pa);
bDist = opt2parg_bSet("-d", NPA, pa);
bAlign = opt2parg_bSet("-align", NPA, pa);
/* Only automatically turn on centering without -noc */
if ((bDist || bSetSize || bSetCenter) && !opt2parg_bSet("-c", NPA, pa))
{
bCenter = TRUE;
}
bScale = opt2parg_bSet("-scale", NPA, pa);
bRho = opt2parg_bSet("-density", NPA, pa);
bTranslate = opt2parg_bSet("-translate", NPA, pa);
bRotate = opt2parg_bSet("-rotate", NPA, pa);
if (bScale && bRho)
fprintf(stderr, "WARNING: setting -density overrides -scale\n");
bScale = bScale || bRho;
bCalcGeom = bCenter || bRotate || bOrient || bScale;
bCalcDiam = btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o';
infile = ftp2fn(efSTX, NFILE, fnm);
if (bMead)
outfile = ftp2fn(efPQR, NFILE, fnm);
else
outfile = ftp2fn(efSTO, NFILE, fnm);
outftp = fn2ftp(outfile);
inftp = fn2ftp(infile);
aps = gmx_atomprop_init();
if (bMead && bGrasp)
{
printf("Incompatible options -mead and -grasp. Turning off -grasp\n");
bGrasp = FALSE;
}
if (bGrasp && (outftp != efPDB))
gmx_fatal(FARGS, "Output file should be a .pdb file"
" when using the -grasp option\n");
if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
(fn2ftp(infile) == efTPA) ||
(fn2ftp(infile) == efTPB)))
gmx_fatal(FARGS,"Input file should be a .tp[abr] file"
" when using the -mead option\n");
get_stx_coordnum(infile,&natom);
init_t_atoms(&atoms,natom,TRUE);
snew(x,natom);
snew(v,natom);
read_stx_conf(infile,title,&atoms,x,v,&ePBC,box);
if (fn2ftp(infile) == efPDB)
{
get_pdb_atomnumber(&atoms,aps);
}
printf("Read %d atoms\n",atoms.nr);
/* Get the element numbers if available in a pdb file */
if (fn2ftp(infile) == efPDB)
get_pdb_atomnumber(&atoms,aps);
if (ePBC != epbcNONE)
{
real vol = det(box);
printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
vol,100*((int)(vol*4.5)));
}
if (bMead || bGrasp || bCONECT)
top = read_top(infile,NULL);
if (bMead || bGrasp)
{
if (atoms.nr != top->atoms.nr)
gmx_fatal(FARGS,"Atom numbers don't match (%d vs. %d)",atoms.nr,top->atoms.nr);
snew(atoms.pdbinfo,top->atoms.nr);
ntype = top->idef.atnr;
for(i=0; (i<atoms.nr); i++) {
/* Determine the Van der Waals radius from the force field */
if (bReadVDW) {
if (!gmx_atomprop_query(aps,epropVDW,
*top->atoms.resinfo[top->atoms.atom[i].resind].name,
*top->atoms.atomname[i],&vdw))
vdw = rvdw;
}
else {
itype = top->atoms.atom[i].type;
c12 = top->idef.iparams[itype*ntype+itype].lj.c12;
c6 = top->idef.iparams[itype*ntype+itype].lj.c6;
if ((c6 != 0) && (c12 != 0)) {
real sig6;
if (bSig56)
sig6 = 2*c12/c6;
else
sig6 = c12/c6;
vdw = 0.5*pow(sig6,1.0/6.0);
}
else
vdw = rvdw;
}
/* Factor of 10 for nm -> Angstroms */
vdw *= 10;
if (bMead) {
atoms.pdbinfo[i].occup = top->atoms.atom[i].q;
atoms.pdbinfo[i].bfac = vdw;
}
else {
atoms.pdbinfo[i].occup = vdw;
atoms.pdbinfo[i].bfac = top->atoms.atom[i].q;
}
}
}
bHaveV=FALSE;
for (i=0; (i<natom) && !bHaveV; i++)
for (j=0; (j<DIM) && !bHaveV; j++)
bHaveV=bHaveV || (v[i][j]!=0);
printf("%selocities found\n",bHaveV?"V":"No v");
if (visbox[0] > 0) {
if (bIndex)
gmx_fatal(FARGS,"Sorry, can not visualize box with index groups");
if (outftp != efPDB)
gmx_fatal(FARGS,"Sorry, can only visualize box with a pdb file");
} else if (visbox[0] == -1)
visualize_images("images.pdb",ePBC,box);
/* remove pbc */
if (bRMPBC)
rm_gropbc(&atoms,x,box);
if (bCalcGeom) {
if (bIndex) {
fprintf(stderr,"\nSelect a group for determining the system size:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
diam=calc_geom(ssize,sindex,x,gc,min,max,bCalcDiam);
rvec_sub(max, min, size);
printf(" system size :%7.3f%7.3f%7.3f (nm)\n",
size[XX], size[YY], size[ZZ]);
if (bCalcDiam)
printf(" diameter :%7.3f (nm)\n",diam);
printf(" center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
printf(" box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf(" box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf(" box volume :%7.2f (nm^3)\n",det(box));
}
if (bRho || bOrient || bAlign)
mass = calc_mass(&atoms,!fn2bTPX(infile),aps);
if (bOrient) {
atom_id *index;
char *grpnames;
/* Get a group for principal component analysis */
fprintf(stderr,"\nSelect group for the determining the orientation\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpnames);
/* Orient the principal axes along the coordinate axes */
orient_princ(&atoms,isize,index,natom,x,bHaveV ? v : NULL, NULL);
sfree(index);
sfree(grpnames);
}
if ( bScale ) {
/* scale coordinates and box */
if (bRho) {
/* Compute scaling constant */
real vol,dens;
vol = det(box);
dens = (mass*AMU)/(vol*NANO*NANO*NANO);
fprintf(stderr,"Volume of input %g (nm^3)\n",vol);
fprintf(stderr,"Mass of input %g (a.m.u.)\n",mass);
fprintf(stderr,"Density of input %g (g/l)\n",dens);
if (vol==0 || mass==0)
gmx_fatal(FARGS,"Cannot scale density with "
"zero mass (%g) or volume (%g)\n",mass,vol);
scale[XX] = scale[YY] = scale[ZZ] = pow(dens/rho,1.0/3.0);
fprintf(stderr,"Scaling all box vectors by %g\n",scale[XX]);
}
scale_conf(atoms.nr,x,box,scale);
}
if (bAlign) {
if (bIndex) {
fprintf(stderr,"\nSelect a group that you want to align:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&asize,&aindex,&agrpname);
} else {
asize = atoms.nr;
snew(aindex,asize);
for (i=0;i<asize;i++)
aindex[i]=i;
}
printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n",asize,natom,
targetvec[XX],targetvec[YY],targetvec[ZZ],
aligncenter[XX],aligncenter[YY],aligncenter[ZZ]);
/*subtract out pivot point*/
for(i=0; i<asize; i++)
rvec_dec(x[aindex[i]],aligncenter);
/*now determine transform and rotate*/
/*will this work?*/
principal_comp(asize,aindex,atoms.atom,x, trans,princd);
unitv(targetvec,targetvec);
printf("Using %g %g %g as principal axis\n", trans[0][2],trans[1][2],trans[2][2]);
tmpvec[XX]=trans[0][2]; tmpvec[YY]=trans[1][2]; tmpvec[ZZ]=trans[2][2];
calc_rotmatrix(tmpvec, targetvec, rotmatrix);
/* rotmatrix finished */
for (i=0;i<asize;++i)
{
mvmul(rotmatrix,x[aindex[i]],tmpvec);
copy_rvec(tmpvec,x[aindex[i]]);
}
/*add pivot point back*/
for(i=0; i<asize; i++)
rvec_inc(x[aindex[i]],aligncenter);
if (!bIndex)
sfree(aindex);
}
if (bTranslate) {
if (bIndex) {
fprintf(stderr,"\nSelect a group that you want to translate:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
printf("Translating %d atoms (out of %d) by %g %g %g nm\n",ssize,natom,
translation[XX],translation[YY],translation[ZZ]);
if (sindex) {
for(i=0; i<ssize; i++)
rvec_inc(x[sindex[i]],translation);
}
else {
for(i=0; i<natom; i++)
rvec_inc(x[i],translation);
}
}
if (bRotate) {
/* Rotate */
printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n",rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<DIM; i++)
rotangles[i] *= DEG2RAD;
rotate_conf(natom,x,v,rotangles[XX],rotangles[YY],rotangles[ZZ]);
}
if (bCalcGeom) {
/* recalc geometrical center and max and min coordinates and size */
calc_geom(ssize,sindex,x,gc,min,max,FALSE);
rvec_sub(max, min, size);
if (bScale || bOrient || bRotate)
printf("new system size : %6.3f %6.3f %6.3f\n",
size[XX],size[YY],size[ZZ]);
}
if (bSetSize || bDist || (btype[0][0]=='t' && bSetAng)) {
ePBC = epbcXYZ;
if (!(bSetSize || bDist))
for (i=0; i<DIM; i++)
newbox[i] = norm(box[i]);
clear_mat(box);
/* calculate new boxsize */
switch(btype[0][0]){
case 't':
if (bDist)
for(i=0; i<DIM; i++)
newbox[i] = size[i]+2*dist;
if (!bSetAng) {
box[XX][XX] = newbox[XX];
box[YY][YY] = newbox[YY];
box[ZZ][ZZ] = newbox[ZZ];
} else {
matrix_convert(box,newbox,newang);
}
break;
case 'c':
case 'd':
case 'o':
if (bSetSize)
d = newbox[0];
else
d = diam+2*dist;
if (btype[0][0] == 'c')
for(i=0; i<DIM; i++)
box[i][i] = d;
else if (btype[0][0] == 'd') {
box[XX][XX] = d;
box[YY][YY] = d;
box[ZZ][XX] = d/2;
box[ZZ][YY] = d/2;
box[ZZ][ZZ] = d*sqrt(2)/2;
} else {
box[XX][XX] = d;
box[YY][XX] = d/3;
box[YY][YY] = d*sqrt(2)*2/3;
box[ZZ][XX] = -d/3;
box[ZZ][YY] = d*sqrt(2)/3;
box[ZZ][ZZ] = d*sqrt(6)/3;
}
break;
}
}
/* calculate new coords for geometrical center */
if (!bSetCenter)
calc_box_center(ecenterDEF,box,center);
/* center molecule on 'center' */
if (bCenter)
center_conf(natom,x,center,gc);
/* print some */
if (bCalcGeom) {
calc_geom(ssize,sindex,x, gc, min, max, FALSE);
printf("new center :%7.3f%7.3f%7.3f (nm)\n",gc[XX],gc[YY],gc[ZZ]);
}
if (bOrient || bScale || bDist || bSetSize) {
printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf("new box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf("new box volume :%7.2f (nm^3)\n",det(box));
}
if (check_box(epbcXYZ,box))
printf("\nWARNING: %s\n",check_box(epbcXYZ,box));
if (bDist && btype[0][0]=='t')
{
if(TRICLINIC(box))
{
printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
"distance from the solute to a box surface along the corresponding normal\n"
"vector might be somewhat smaller than your specified value %f.\n"
"You can check the actual value with g_mindist -pi\n",dist);
}
else
{
printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
"If the molecule rotates the actual distance will be smaller. You might want\n"
"to use a cubic box instead, or why not try a dodecahedron today?\n");
}
}
if (bCONECT && (outftp == efPDB) && (inftp == efTPR))
conect = gmx_conect_generate(top);
else
conect = NULL;
if (bIndex) {
fprintf(stderr,"\nSelect a group for output:\n");
get_index(&atoms,opt2fn_null("-n",NFILE,fnm),
1,&isize,&index,&grpname);
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
if (opt2bSet("-bf",NFILE,fnm) || bLegend)
{
gmx_fatal(FARGS,"Sorry, cannot do bfactors with an index group.");
}
if (outftp == efPDB)
{
out=ffopen(outfile,"w");
write_pdbfile_indexed(out,title,&atoms,x,ePBC,box,' ',1,isize,index,conect,TRUE);
ffclose(out);
}
else
{
write_sto_conf_indexed(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box,isize,index);
}
}
else {
if ((outftp == efPDB) || (outftp == efPQR)) {
out=ffopen(outfile,"w");
if (bMead) {
set_pdb_wide_format(TRUE);
fprintf(out,"REMARK "
"The B-factors in this file hold atomic radii\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic charges\n");
}
else if (bGrasp) {
fprintf(out,"GRASP PDB FILE\nFORMAT NUMBER=1\n");
fprintf(out,"REMARK "
"The B-factors in this file hold atomic charges\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic radii\n");
}
else if (opt2bSet("-bf",NFILE,fnm)) {
read_bfac(opt2fn("-bf",NFILE,fnm),&n_bfac,&bfac,&bfac_nr);
set_pdb_conf_bfac(atoms.nr,atoms.nres,&atoms,
n_bfac,bfac,bfac_nr,peratom);
}
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
write_pdbfile(out,title,&atoms,x,ePBC,box,' ',-1,conect,TRUE);
if (bLegend)
pdb_legend(out,atoms.nr,atoms.nres,&atoms,x);
if (visbox[0] > 0)
visualize_box(out,bLegend ? atoms.nr+12 : atoms.nr,
bLegend? atoms.nres=12 : atoms.nres,box,visbox);
ffclose(out);
}
else
write_sto_conf(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box);
}
gmx_atomprop_destroy(aps);
do_view(oenv,outfile,NULL);
thanx(stderr);
return 0;
}
void do_force_lowlevel(FILE *fplog, gmx_large_int_t step,
t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_commrec *cr,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_mdatoms *md,
t_grpopts *opts,
rvec x[], history_t *hist,
rvec f[],
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_mtop_t *mtop,
gmx_localtop_t *top,
gmx_genborn_t *born,
t_atomtypes *atype,
gmx_bool bBornRadii,
matrix box,
real lambda,
t_graph *graph,
t_blocka *excl,
rvec mu_tot[],
int flags,
float *cycles_pme)
{
int i,status;
int donb_flags;
gmx_bool bDoEpot,bSepDVDL,bSB;
int pme_flags;
matrix boxs;
rvec box_size;
real dvdlambda,Vsr,Vlr,Vcorr=0,vdip,vcharge;
t_pbc pbc;
real dvdgb;
char buf[22];
gmx_enerdata_t ed_lam;
double lam_i;
real dvdl_dum;
#ifdef GMX_MPI
double t0=0.0,t1,t2,t3; /* time measurement for coarse load balancing */
#endif
#define PRINT_SEPDVDL(s,v,dvdl) if (bSepDVDL) fprintf(fplog,sepdvdlformat,s,v,dvdl);
GMX_MPE_LOG(ev_force_start);
set_pbc(&pbc,fr->ePBC,box);
/* Reset box */
for(i=0; (i<DIM); i++)
{
box_size[i]=box[i][i];
}
bSepDVDL=(fr->bSepDVDL && do_per_step(step,ir->nstlog));
debug_gmx();
/* do QMMM first if requested */
if(fr->bQMMM)
{
enerd->term[F_EQM] = calculate_QMMM(cr,x,f,fr,md);
}
if (bSepDVDL)
{
fprintf(fplog,"Step %s: non-bonded V and dVdl for node %d:\n",
gmx_step_str(step,buf),cr->nodeid);
}
/* Call the short range functions all in one go. */
GMX_MPE_LOG(ev_do_fnbf_start);
dvdlambda = 0;
#ifdef GMX_MPI
/*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
#define TAKETIME FALSE
if (TAKETIME)
{
MPI_Barrier(cr->mpi_comm_mygroup);
t0=MPI_Wtime();
}
#endif
if (ir->nwall)
{
dvdlambda = do_walls(ir,fr,box,md,x,f,lambda,
enerd->grpp.ener[egLJSR],nrnb);
PRINT_SEPDVDL("Walls",0.0,dvdlambda);
enerd->dvdl_lin += dvdlambda;
}
/* If doing GB, reset dvda and calculate the Born radii */
if (ir->implicit_solvent)
{
/* wallcycle_start(wcycle,ewcGB); */
for(i=0; i<born->nr; i++)
{
fr->dvda[i]=0;
}
if(bBornRadii)
{
calc_gb_rad(cr,fr,ir,top,atype,x,&(fr->gblist),born,md,nrnb);
}
/* wallcycle_stop(wcycle, ewcGB); */
}
where();
donb_flags = 0;
if (flags & GMX_FORCE_FORCES)
{
donb_flags |= GMX_DONB_FORCES;
}
do_nonbonded(cr,fr,x,f,md,excl,
fr->bBHAM ?
enerd->grpp.ener[egBHAMSR] :
enerd->grpp.ener[egLJSR],
enerd->grpp.ener[egCOULSR],
enerd->grpp.ener[egGB],box_size,nrnb,
lambda,&dvdlambda,-1,-1,donb_flags);
/* If we do foreign lambda and we have soft-core interactions
* we have to recalculate the (non-linear) energies contributions.
*/
if (ir->n_flambda > 0 && (flags & GMX_FORCE_DHDL) && ir->sc_alpha != 0)
{
init_enerdata(mtop->groups.grps[egcENER].nr,ir->n_flambda,&ed_lam);
for(i=0; i<enerd->n_lambda; i++)
{
lam_i = (i==0 ? lambda : ir->flambda[i-1]);
dvdl_dum = 0;
reset_enerdata(&ir->opts,fr,TRUE,&ed_lam,FALSE);
do_nonbonded(cr,fr,x,f,md,excl,
fr->bBHAM ?
ed_lam.grpp.ener[egBHAMSR] :
ed_lam.grpp.ener[egLJSR],
ed_lam.grpp.ener[egCOULSR],
enerd->grpp.ener[egGB], box_size,nrnb,
lam_i,&dvdl_dum,-1,-1,
GMX_DONB_FOREIGNLAMBDA);
sum_epot(&ir->opts,&ed_lam);
enerd->enerpart_lambda[i] += ed_lam.term[F_EPOT];
}
destroy_enerdata(&ed_lam);
}
where();
/* If we are doing GB, calculate bonded forces and apply corrections
* to the solvation forces */
if (ir->implicit_solvent) {
calc_gb_forces(cr,md,born,top,atype,x,f,fr,idef,
ir->gb_algorithm,ir->sa_algorithm,nrnb,bBornRadii,&pbc,graph,enerd);
}
#ifdef GMX_MPI
if (TAKETIME)
{
t1=MPI_Wtime();
fr->t_fnbf += t1-t0;
}
#endif
if (ir->sc_alpha != 0)
{
enerd->dvdl_nonlin += dvdlambda;
}
else
{
enerd->dvdl_lin += dvdlambda;
}
Vsr = 0;
if (bSepDVDL)
{
for(i=0; i<enerd->grpp.nener; i++)
{
Vsr +=
(fr->bBHAM ?
enerd->grpp.ener[egBHAMSR][i] :
enerd->grpp.ener[egLJSR][i])
+ enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
}
}
PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",Vsr,dvdlambda);
debug_gmx();
GMX_MPE_LOG(ev_do_fnbf_finish);
if (debug)
{
pr_rvecs(debug,0,"fshift after SR",fr->fshift,SHIFTS);
}
/* Shift the coordinates. Must be done before bonded forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no bonded forces have to be evaluated.
*/
/* Here sometimes we would not need to shift with NBFonly,
* but we do so anyhow for consistency of the returned coordinates.
*/
if (graph)
{
shift_self(graph,box,x);
if (TRICLINIC(box))
{
inc_nrnb(nrnb,eNR_SHIFTX,2*graph->nnodes);
}
else
{
inc_nrnb(nrnb,eNR_SHIFTX,graph->nnodes);
}
}
/* Check whether we need to do bondeds or correct for exclusions */
if (fr->bMolPBC &&
((flags & GMX_FORCE_BONDED)
|| EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype)))
{
/* Since all atoms are in the rectangular or triclinic unit-cell,
* only single box vector shifts (2 in x) are required.
*/
set_pbc_dd(&pbc,fr->ePBC,cr->dd,TRUE,box);
}
debug_gmx();
if (flags & GMX_FORCE_BONDED)
{
GMX_MPE_LOG(ev_calc_bonds_start);
calc_bonds(fplog,cr->ms,
idef,x,hist,f,fr,&pbc,graph,enerd,nrnb,lambda,md,fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
fr->bSepDVDL && do_per_step(step,ir->nstlog),step);
/* Check if we have to determine energy differences
* at foreign lambda's.
*/
if (ir->n_flambda > 0 && (flags & GMX_FORCE_DHDL) &&
idef->ilsort != ilsortNO_FE)
{
if (idef->ilsort != ilsortFE_SORTED)
{
gmx_incons("The bonded interactions are not sorted for free energy");
}
init_enerdata(mtop->groups.grps[egcENER].nr,ir->n_flambda,&ed_lam);
for(i=0; i<enerd->n_lambda; i++)
{
lam_i = (i==0 ? lambda : ir->flambda[i-1]);
dvdl_dum = 0;
reset_enerdata(&ir->opts,fr,TRUE,&ed_lam,FALSE);
calc_bonds_lambda(fplog,
idef,x,fr,&pbc,graph,&ed_lam,nrnb,lam_i,md,
fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
sum_epot(&ir->opts,&ed_lam);
enerd->enerpart_lambda[i] += ed_lam.term[F_EPOT];
}
destroy_enerdata(&ed_lam);
}
debug_gmx();
GMX_MPE_LOG(ev_calc_bonds_finish);
}
where();
*cycles_pme = 0;
if (EEL_FULL(fr->eeltype))
{
bSB = (ir->nwall == 2);
if (bSB)
{
copy_mat(box,boxs);
svmul(ir->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
box_size[ZZ] *= ir->wall_ewald_zfac;
}
clear_mat(fr->vir_el_recip);
if (fr->bEwald)
{
if (fr->n_tpi == 0)
{
dvdlambda = 0;
Vcorr = ewald_LRcorrection(fplog,md->start,md->start+md->homenr,
cr,fr,
md->chargeA,
md->nChargePerturbed ? md->chargeB : NULL,
excl,x,bSB ? boxs : box,mu_tot,
ir->ewald_geometry,
ir->epsilon_surface,
lambda,&dvdlambda,&vdip,&vcharge);
PRINT_SEPDVDL("Ewald excl./charge/dip. corr.",Vcorr,dvdlambda);
enerd->dvdl_lin += dvdlambda;
}
else
{
if (ir->ewald_geometry != eewg3D || ir->epsilon_surface != 0)
{
gmx_fatal(FARGS,"TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
}
/* The TPI molecule does not have exclusions with the rest
* of the system and no intra-molecular PME grid contributions
* will be calculated in gmx_pme_calc_energy.
*/
Vcorr = 0;
}
}
else
{
Vcorr = shift_LRcorrection(fplog,md->start,md->homenr,cr,fr,
md->chargeA,excl,x,TRUE,box,
fr->vir_el_recip);
}
dvdlambda = 0;
status = 0;
switch (fr->eeltype)
{
case eelPPPM:
status = gmx_pppm_do(fplog,fr->pmedata,FALSE,x,fr->f_novirsum,
md->chargeA,
box_size,fr->phi,cr,md->start,md->homenr,
nrnb,ir->pme_order,&Vlr);
break;
case eelPME:
case eelPMESWITCH:
case eelPMEUSER:
case eelPMEUSERSWITCH:
if (cr->duty & DUTY_PME)
{
if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
{
pme_flags = GMX_PME_SPREAD_Q | GMX_PME_SOLVE;
if (flags & GMX_FORCE_FORCES)
{
pme_flags |= GMX_PME_CALC_F;
}
if (flags & GMX_FORCE_VIRIAL)
{
pme_flags |= GMX_PME_CALC_ENER_VIR;
}
if (fr->n_tpi > 0)
{
/* We don't calculate f, but we do want the potential */
pme_flags |= GMX_PME_CALC_POT;
}
wallcycle_start(wcycle,ewcPMEMESH);
status = gmx_pme_do(fr->pmedata,
md->start,md->homenr - fr->n_tpi,
x,fr->f_novirsum,
md->chargeA,md->chargeB,
bSB ? boxs : box,cr,
DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
nrnb,wcycle,
fr->vir_el_recip,fr->ewaldcoeff,
&Vlr,lambda,&dvdlambda,
pme_flags);
*cycles_pme = wallcycle_stop(wcycle,ewcPMEMESH);
/* We should try to do as little computation after
* this as possible, because parallel PME synchronizes
* the nodes, so we want all load imbalance of the rest
* of the force calculation to be before the PME call.
* DD load balancing is done on the whole time of
* the force call (without PME).
*/
}
if (fr->n_tpi > 0)
{
/* Determine the PME grid energy of the test molecule
* with the PME grid potential of the other charges.
*/
gmx_pme_calc_energy(fr->pmedata,fr->n_tpi,
x + md->homenr - fr->n_tpi,
md->chargeA + md->homenr - fr->n_tpi,
&Vlr);
}
PRINT_SEPDVDL("PME mesh",Vlr,dvdlambda);
}
else
{
/* Energies and virial are obtained later from the PME nodes */
/* but values have to be zeroed out here */
Vlr=0.0;
}
break;
case eelEWALD:
Vlr = do_ewald(fplog,FALSE,ir,x,fr->f_novirsum,
md->chargeA,md->chargeB,
box_size,cr,md->homenr,
fr->vir_el_recip,fr->ewaldcoeff,
lambda,&dvdlambda,fr->ewald_table);
PRINT_SEPDVDL("Ewald long-range",Vlr,dvdlambda);
break;
default:
Vlr = 0;
gmx_fatal(FARGS,"No such electrostatics method implemented %s",
eel_names[fr->eeltype]);
}
if (status != 0)
{
gmx_fatal(FARGS,"Error %d in long range electrostatics routine %s",
status,EELTYPE(fr->eeltype));
}
enerd->dvdl_lin += dvdlambda;
enerd->term[F_COUL_RECIP] = Vlr + Vcorr;
if (debug)
{
fprintf(debug,"Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
Vlr,Vcorr,enerd->term[F_COUL_RECIP]);
pr_rvecs(debug,0,"vir_el_recip after corr",fr->vir_el_recip,DIM);
pr_rvecs(debug,0,"fshift after LR Corrections",fr->fshift,SHIFTS);
}
}
else
{
if (EEL_RF(fr->eeltype))
{
dvdlambda = 0;
if (fr->eeltype != eelRF_NEC)
{
enerd->term[F_RF_EXCL] =
RF_excl_correction(fplog,fr,graph,md,excl,x,f,
fr->fshift,&pbc,lambda,&dvdlambda);
}
enerd->dvdl_lin += dvdlambda;
PRINT_SEPDVDL("RF exclusion correction",
enerd->term[F_RF_EXCL],dvdlambda);
}
}
where();
debug_gmx();
if (debug)
{
print_nrnb(debug,nrnb);
}
debug_gmx();
#ifdef GMX_MPI
if (TAKETIME)
{
t2=MPI_Wtime();
MPI_Barrier(cr->mpi_comm_mygroup);
t3=MPI_Wtime();
fr->t_wait += t3-t2;
if (fr->timesteps == 11)
{
fprintf(stderr,"* PP load balancing info: node %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
cr->nodeid, gmx_step_str(fr->timesteps,buf),
100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
(fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
}
fr->timesteps++;
}
#endif
if (debug)
{
pr_rvecs(debug,0,"fshift after bondeds",fr->fshift,SHIFTS);
}
GMX_MPE_LOG(ev_force_finish);
}
t_mdebin *init_mdebin(ener_file_t fp_ene,
const gmx_mtop_t *mtop,
const t_inputrec *ir,
FILE *fp_dhdl)
{
const char *ener_nm[F_NRE];
static const char *vir_nm[] = {
"Vir-XX", "Vir-XY", "Vir-XZ",
"Vir-YX", "Vir-YY", "Vir-YZ",
"Vir-ZX", "Vir-ZY", "Vir-ZZ"
};
static const char *sv_nm[] = {
"ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
"ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
"ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
};
static const char *fv_nm[] = {
"ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
"ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
"ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
};
static const char *pres_nm[] = {
"Pres-XX", "Pres-XY", "Pres-XZ",
"Pres-YX", "Pres-YY", "Pres-YZ",
"Pres-ZX", "Pres-ZY", "Pres-ZZ"
};
static const char *surft_nm[] = {
"#Surf*SurfTen"
};
static const char *mu_nm[] = {
"Mu-X", "Mu-Y", "Mu-Z"
};
static const char *vcos_nm[] = {
"2CosZ*Vel-X"
};
static const char *visc_nm[] = {
"1/Viscosity"
};
static const char *baro_nm[] = {
"Barostat"
};
char **grpnms;
const gmx_groups_t *groups;
char **gnm;
char buf[256];
const char *bufi;
t_mdebin *md;
int i, j, ni, nj, n, k, kk, ncon, nset;
gmx_bool bBHAM, b14;
snew(md, 1);
if (EI_DYNAMICS(ir->eI))
{
md->delta_t = ir->delta_t;
}
else
{
md->delta_t = 0;
}
groups = &mtop->groups;
bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
b14 = (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0);
ncon = gmx_mtop_ftype_count(mtop, F_CONSTR);
nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
md->bConstr = (ncon > 0 || nset > 0);
md->bConstrVir = FALSE;
if (md->bConstr)
{
if (ncon > 0 && ir->eConstrAlg == econtLINCS)
{
md->nCrmsd = 1;
}
md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
}
else
{
md->nCrmsd = 0;
}
/* Energy monitoring */
for (i = 0; i < egNR; i++)
{
md->bEInd[i] = FALSE;
}
for (i = 0; i < F_NRE; i++)
{
md->bEner[i] = FALSE;
if (i == F_LJ)
{
md->bEner[i] = !bBHAM;
}
else if (i == F_BHAM)
{
md->bEner[i] = bBHAM;
}
else if (i == F_EQM)
{
md->bEner[i] = ir->bQMMM;
}
else if (i == F_RF_EXCL)
{
md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->cutoff_scheme == ecutsGROUP);
}
else if (i == F_COUL_RECIP)
{
md->bEner[i] = EEL_FULL(ir->coulombtype);
}
else if (i == F_LJ_RECIP)
{
md->bEner[i] = EVDW_PME(ir->vdwtype);
}
else if (i == F_LJ14)
{
md->bEner[i] = b14;
}
else if (i == F_COUL14)
{
md->bEner[i] = b14;
}
else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
{
md->bEner[i] = FALSE;
}
else if ((i == F_DVDL_COUL && ir->fepvals->separate_dvdl[efptCOUL]) ||
(i == F_DVDL_VDW && ir->fepvals->separate_dvdl[efptVDW]) ||
(i == F_DVDL_BONDED && ir->fepvals->separate_dvdl[efptBONDED]) ||
(i == F_DVDL_RESTRAINT && ir->fepvals->separate_dvdl[efptRESTRAINT]) ||
(i == F_DKDL && ir->fepvals->separate_dvdl[efptMASS]) ||
(i == F_DVDL && ir->fepvals->separate_dvdl[efptFEP]))
{
md->bEner[i] = (ir->efep != efepNO);
}
else if ((interaction_function[i].flags & IF_VSITE) ||
(i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
{
md->bEner[i] = FALSE;
}
else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i == F_EQM))
{
md->bEner[i] = TRUE;
}
else if ((i == F_GBPOL) && ir->implicit_solvent == eisGBSA)
{
md->bEner[i] = TRUE;
}
else if ((i == F_NPSOLVATION) && ir->implicit_solvent == eisGBSA && (ir->sa_algorithm != esaNO))
{
md->bEner[i] = TRUE;
}
else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
{
md->bEner[i] = FALSE;
}
else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
{
md->bEner[i] = EI_DYNAMICS(ir->eI);
}
else if (i == F_DISPCORR || i == F_PDISPCORR)
{
md->bEner[i] = (ir->eDispCorr != edispcNO);
}
else if (i == F_DISRESVIOL)
{
md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_DISRES) > 0);
}
else if (i == F_ORIRESDEV)
{
md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
}
else if (i == F_CONNBONDS)
{
md->bEner[i] = FALSE;
}
else if (i == F_COM_PULL)
{
md->bEner[i] = (ir->bPull && pull_have_potential(ir->pull_work));
}
else if (i == F_ECONSERVED)
{
md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
(ir->epc == epcNO || ir->epc == epcMTTK));
}
else
{
md->bEner[i] = (gmx_mtop_ftype_count(mtop, i) > 0);
}
}
md->f_nre = 0;
for (i = 0; i < F_NRE; i++)
{
if (md->bEner[i])
{
ener_nm[md->f_nre] = interaction_function[i].longname;
md->f_nre++;
}
}
md->epc = ir->epc;
md->bDiagPres = !TRICLINIC(ir->ref_p);
md->ref_p = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
md->bDynBox = inputrecDynamicBox(ir);
md->etc = ir->etc;
md->bNHC_trotter = inputrecNvtTrotter(ir);
md->bPrintNHChains = ir->bPrintNHChains;
md->bMTTK = (inputrecNptTrotter(ir) || inputrecNphTrotter(ir));
md->bMu = inputrecNeedMutot(ir);
md->ebin = mk_ebin();
/* Pass NULL for unit to let get_ebin_space determine the units
* for interaction_function[i].longname
*/
md->ie = get_ebin_space(md->ebin, md->f_nre, ener_nm, NULL);
if (md->nCrmsd)
{
/* This should be called directly after the call for md->ie,
* such that md->iconrmsd follows directly in the list.
*/
md->iconrmsd = get_ebin_space(md->ebin, md->nCrmsd, conrmsd_nm, "");
}
if (md->bDynBox)
{
md->ib = get_ebin_space(md->ebin,
md->bTricl ? NTRICLBOXS : NBOXS,
md->bTricl ? tricl_boxs_nm : boxs_nm,
unit_length);
md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
if (md->bDiagPres)
{
md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
}
}
if (md->bConstrVir)
{
md->isvir = get_ebin_space(md->ebin, asize(sv_nm), sv_nm, unit_energy);
md->ifvir = get_ebin_space(md->ebin, asize(fv_nm), fv_nm, unit_energy);
}
md->ivir = get_ebin_space(md->ebin, asize(vir_nm), vir_nm, unit_energy);
md->ipres = get_ebin_space(md->ebin, asize(pres_nm), pres_nm, unit_pres_bar);
md->isurft = get_ebin_space(md->ebin, asize(surft_nm), surft_nm,
unit_surft_bar);
if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
{
md->ipc = get_ebin_space(md->ebin, md->bTricl ? 6 : 3,
boxvel_nm, unit_vel);
}
if (md->bMu)
{
md->imu = get_ebin_space(md->ebin, asize(mu_nm), mu_nm, unit_dipole_D);
}
if (ir->cos_accel != 0)
{
md->ivcos = get_ebin_space(md->ebin, asize(vcos_nm), vcos_nm, unit_vel);
md->ivisc = get_ebin_space(md->ebin, asize(visc_nm), visc_nm,
unit_invvisc_SI);
}
/* Energy monitoring */
for (i = 0; i < egNR; i++)
{
md->bEInd[i] = FALSE;
}
md->bEInd[egCOULSR] = TRUE;
md->bEInd[egLJSR ] = TRUE;
if (bBHAM)
{
md->bEInd[egLJSR] = FALSE;
md->bEInd[egBHAMSR] = TRUE;
}
if (b14)
{
md->bEInd[egLJ14] = TRUE;
md->bEInd[egCOUL14] = TRUE;
}
md->nEc = 0;
for (i = 0; (i < egNR); i++)
{
if (md->bEInd[i])
{
md->nEc++;
}
}
n = groups->grps[egcENER].nr;
md->nEg = n;
md->nE = (n*(n+1))/2;
snew(md->igrp, md->nE);
if (md->nE > 1)
{
n = 0;
snew(gnm, md->nEc);
for (k = 0; (k < md->nEc); k++)
{
snew(gnm[k], STRLEN);
}
for (i = 0; (i < groups->grps[egcENER].nr); i++)
{
ni = groups->grps[egcENER].nm_ind[i];
for (j = i; (j < groups->grps[egcENER].nr); j++)
{
nj = groups->grps[egcENER].nm_ind[j];
for (k = kk = 0; (k < egNR); k++)
{
if (md->bEInd[k])
{
sprintf(gnm[kk], "%s:%s-%s", egrp_nm[k],
*(groups->grpname[ni]), *(groups->grpname[nj]));
kk++;
}
}
md->igrp[n] = get_ebin_space(md->ebin, md->nEc,
(const char **)gnm, unit_energy);
n++;
}
}
for (k = 0; (k < md->nEc); k++)
{
sfree(gnm[k]);
}
sfree(gnm);
if (n != md->nE)
{
gmx_incons("Number of energy terms wrong");
}
}
md->nTC = groups->grps[egcTC].nr;
md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
if (md->bMTTK)
{
md->nTCP = 1; /* assume only one possible coupling system for barostat
for now */
}
else
{
md->nTCP = 0;
}
if (md->etc == etcNOSEHOOVER)
{
if (md->bNHC_trotter)
{
md->mde_n = 2*md->nNHC*md->nTC;
}
else
{
md->mde_n = 2*md->nTC;
}
if (md->epc == epcMTTK)
{
md->mdeb_n = 2*md->nNHC*md->nTCP;
}
}
else
{
md->mde_n = md->nTC;
md->mdeb_n = 0;
}
snew(md->tmp_r, md->mde_n);
snew(md->tmp_v, md->mde_n);
snew(md->grpnms, md->mde_n);
grpnms = md->grpnms;
for (i = 0; (i < md->nTC); i++)
{
ni = groups->grps[egcTC].nm_ind[i];
sprintf(buf, "T-%s", *(groups->grpname[ni]));
grpnms[i] = gmx_strdup(buf);
}
md->itemp = get_ebin_space(md->ebin, md->nTC, (const char **)grpnms,
unit_temp_K);
if (md->etc == etcNOSEHOOVER)
{
if (md->bPrintNHChains)
{
if (md->bNHC_trotter)
{
for (i = 0; (i < md->nTC); i++)
{
ni = groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
for (j = 0; (j < md->nNHC); j++)
{
sprintf(buf, "Xi-%d-%s", j, bufi);
grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
}
}
md->itc = get_ebin_space(md->ebin, md->mde_n,
(const char **)grpnms, unit_invtime);
if (md->bMTTK)
{
for (i = 0; (i < md->nTCP); i++)
{
bufi = baro_nm[0]; /* All barostat DOF's together for now. */
for (j = 0; (j < md->nNHC); j++)
{
sprintf(buf, "Xi-%d-%s", j, bufi);
grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
}
}
md->itcb = get_ebin_space(md->ebin, md->mdeb_n,
(const char **)grpnms, unit_invtime);
}
}
else
{
for (i = 0; (i < md->nTC); i++)
{
ni = groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
sprintf(buf, "Xi-%s", bufi);
grpnms[2*i] = gmx_strdup(buf);
sprintf(buf, "vXi-%s", bufi);
grpnms[2*i+1] = gmx_strdup(buf);
}
md->itc = get_ebin_space(md->ebin, md->mde_n,
(const char **)grpnms, unit_invtime);
}
}
}
else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
md->etc == etcVRESCALE)
{
for (i = 0; (i < md->nTC); i++)
{
ni = groups->grps[egcTC].nm_ind[i];
sprintf(buf, "Lamb-%s", *(groups->grpname[ni]));
grpnms[i] = gmx_strdup(buf);
}
md->itc = get_ebin_space(md->ebin, md->mde_n, (const char **)grpnms, "");
}
sfree(grpnms);
md->nU = groups->grps[egcACC].nr;
if (md->nU > 1)
{
snew(grpnms, 3*md->nU);
for (i = 0; (i < md->nU); i++)
{
ni = groups->grps[egcACC].nm_ind[i];
sprintf(buf, "Ux-%s", *(groups->grpname[ni]));
grpnms[3*i+XX] = gmx_strdup(buf);
sprintf(buf, "Uy-%s", *(groups->grpname[ni]));
grpnms[3*i+YY] = gmx_strdup(buf);
sprintf(buf, "Uz-%s", *(groups->grpname[ni]));
grpnms[3*i+ZZ] = gmx_strdup(buf);
}
md->iu = get_ebin_space(md->ebin, 3*md->nU, (const char **)grpnms, unit_vel);
sfree(grpnms);
}
if (fp_ene)
{
do_enxnms(fp_ene, &md->ebin->nener, &md->ebin->enm);
}
md->print_grpnms = NULL;
/* check whether we're going to write dh histograms */
md->dhc = NULL;
if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO)
{
/* Currently dh histograms are only written with dynamics */
if (EI_DYNAMICS(ir->eI))
{
snew(md->dhc, 1);
mde_delta_h_coll_init(md->dhc, ir);
}
md->fp_dhdl = NULL;
snew(md->dE, ir->fepvals->n_lambda);
}
else
{
md->fp_dhdl = fp_dhdl;
snew(md->dE, ir->fepvals->n_lambda);
}
if (ir->bSimTemp)
{
int i;
snew(md->temperatures, ir->fepvals->n_lambda);
for (i = 0; i < ir->fepvals->n_lambda; i++)
{
md->temperatures[i] = ir->simtempvals->temperatures[i];
}
}
return md;
}
t_mdebin *init_mdebin(int fp_ene,
const gmx_mtop_t *mtop,
const t_inputrec *ir)
{
char *ener_nm[F_NRE];
static char *vir_nm[] = {
"Vir-XX", "Vir-XY", "Vir-XZ",
"Vir-YX", "Vir-YY", "Vir-YZ",
"Vir-ZX", "Vir-ZY", "Vir-ZZ"
};
static char *sv_nm[] = {
"ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
"ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
"ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
};
static char *fv_nm[] = {
"ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
"ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
"ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
};
static char *pres_nm[] = {
"Pres-XX (bar)","Pres-XY (bar)","Pres-XZ (bar)",
"Pres-YX (bar)","Pres-YY (bar)","Pres-YZ (bar)",
"Pres-ZX (bar)","Pres-ZY (bar)","Pres-ZZ (bar)"
};
static char *surft_nm[] = {
"#Surf*SurfTen"
};
static char *mu_nm[] = {
"Mu-X", "Mu-Y", "Mu-Z"
};
static char *vcos_nm[] = {
"2CosZ*Vel-X"
};
static char *visc_nm[] = {
"1/Viscosity (SI)"
};
static char **grpnms;
const gmx_groups_t *groups;
char **gnm;
char buf[256];
t_mdebin *md;
int i,j,ni,nj,n,k,kk,ncon,nset;
bool bBHAM,b14;
f_nre = 0; // otherwise, multiple calls to mdrunner_integrate are not possible!NnCrmsd;
groups = &mtop->groups;
bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0);
ncon = gmx_mtop_ftype_count(mtop,F_CONSTR);
nset = gmx_mtop_ftype_count(mtop,F_SETTLE);
bConstr = (ncon > 0 || nset > 0);
bConstrVir = FALSE;
if (bConstr) {
if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
if (ir->eI == eiSD2)
nCrmsd = 2;
else
nCrmsd = 1;
}
bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
} else {
nCrmsd = 0;
}
for(i=0; i<F_NRE; i++) {
bEner[i] = FALSE;
if (i == F_LJ)
bEner[i] = !bBHAM;
else if (i == F_BHAM)
bEner[i] = bBHAM;
else if (i == F_EQM)
bEner[i] = ir->bQMMM;
else if (i == F_COUL_LR)
bEner[i] = (ir->rcoulomb > ir->rlist);
else if (i == F_LJ_LR)
bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
else if (i == F_BHAM_LR)
bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
else if (i == F_RF_EXCL)
bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC);
else if (i == F_COUL_RECIP)
bEner[i] = EEL_FULL(ir->coulombtype);
else if (i == F_LJ14)
bEner[i] = b14;
else if (i == F_COUL14)
bEner[i] = b14;
else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
bEner[i] = FALSE;
else if ((i == F_DVDL) || (i == F_DKDL))
bEner[i] = (ir->efep != efepNO);
else if (i == F_DGDL_CON)
bEner[i] = (ir->efep != efepNO && bConstr);
else if ((interaction_function[i].flags & IF_VSITE) ||
(i == F_CONSTR) || (i == F_SETTLE))
bEner[i] = FALSE;
else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM))
bEner[i] = TRUE;
else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
bEner[i] = EI_DYNAMICS(ir->eI);
else if (i == F_DISPCORR)
bEner[i] = (ir->eDispCorr != edispcNO);
else if (i == F_DISRESVIOL)
bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
else if (i == F_ORIRESDEV)
bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
else if (i == F_CONNBONDS)
bEner[i] = FALSE;
else if (i == F_COM_PULL)
bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F);
else if (i == F_ECONSERVED)
bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
ir->epc == epcNO);
else
bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
}
for(i=0; i<F_NRE; i++)
if (bEner[i]) {
ener_nm[f_nre]=interaction_function[i].longname;
f_nre++;
}
epc = ir->epc;
bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
bDynBox = DYNAMIC_BOX(*ir);
etc = ir->etc;
/* Energy monitoring */
snew(md,1);
md->ebin = mk_ebin();
md->ie = get_ebin_space(md->ebin,f_nre,ener_nm);
if (nCrmsd) {
/* This should be called directly after the call for md->ie,
* such that md->iconrmsd follows directly in the list.
*/
md->iconrmsd = get_ebin_space(md->ebin,nCrmsd,conrmsd_nm);
}
if (bDynBox)
md->ib = get_ebin_space(md->ebin, bTricl ? NTRICLBOXS :
NBOXS, bTricl ? tricl_boxs_nm : boxs_nm);
if (bConstrVir) {
md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm);
md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm);
}
md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm);
md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm);
md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm);
if (epc == epcPARRINELLORAHMAN) {
md->ipc = get_ebin_space(md->ebin,bTricl ? 6 : 3,boxvel_nm);
}
md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm);
if (ir->cos_accel != 0) {
md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm);
md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm);
}
if (ir->rcoulomb > ir->rlist)
bEInd[egCOULLR] = TRUE;
if (!bBHAM) {
if (ir->rvdw > ir->rlist)
bEInd[egLJLR] = TRUE;
} else {
bEInd[egLJSR] = FALSE;
bEInd[egBHAMSR] = TRUE;
if (ir->rvdw > ir->rlist)
bEInd[egBHAMLR] = TRUE;
}
if (b14) {
bEInd[egLJ14] = TRUE;
bEInd[egCOUL14] = TRUE;
}
md->nEc=0;
for(i=0; (i<egNR); i++)
if (bEInd[i])
md->nEc++;
n=groups->grps[egcENER].nr;
md->nEg=n;
md->nE=(n*(n+1))/2;
snew(md->igrp,md->nE);
if (md->nE > 1) {
n=0;
snew(gnm,md->nEc);
for(k=0; (k<md->nEc); k++)
snew(gnm[k],STRLEN);
for(i=0; (i<groups->grps[egcENER].nr); i++) {
ni=groups->grps[egcENER].nm_ind[i];
for(j=i; (j<groups->grps[egcENER].nr); j++) {
nj=groups->grps[egcENER].nm_ind[j];
for(k=kk=0; (k<egNR); k++) {
if (bEInd[k]) {
sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
*(groups->grpname[ni]),*(groups->grpname[nj]));
kk++;
}
}
md->igrp[n]=get_ebin_space(md->ebin,md->nEc,gnm);
n++;
}
}
for(k=0; (k<md->nEc); k++)
sfree(gnm[k]);
sfree(gnm);
if (n != md->nE)
gmx_incons("Number of energy terms wrong");
}
md->nTC=groups->grps[egcTC].nr;
snew(grpnms,md->nTC);
for(i=0; (i<md->nTC); i++) {
ni=groups->grps[egcTC].nm_ind[i];
sprintf(buf,"T-%s",*(groups->grpname[ni]));
grpnms[i]=strdup(buf);
}
md->itemp=get_ebin_space(md->ebin,md->nTC,grpnms);
sfree(*grpnms);
if (etc == etcNOSEHOOVER) {
for(i=0; (i<md->nTC); i++) {
ni=groups->grps[egcTC].nm_ind[i];
sprintf(buf,"Xi-%s",*(groups->grpname[ni]));
grpnms[i]=strdup(buf);
}
md->itc=get_ebin_space(md->ebin,md->nTC,grpnms);
sfree(*grpnms);
} else if (etc == etcBERENDSEN || etc == etcYES || etc == etcVRESCALE) {
for(i=0; (i<md->nTC); i++) {
ni=groups->grps[egcTC].nm_ind[i];
sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
grpnms[i]=strdup(buf);
}
md->itc=get_ebin_space(md->ebin,md->nTC,grpnms);
sfree(*grpnms);
}
sfree(grpnms);
md->nU=groups->grps[egcACC].nr;
if (md->nU > 1) {
snew(grpnms,3*md->nU);
for(i=0; (i<md->nU); i++) {
ni=groups->grps[egcACC].nm_ind[i];
sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
grpnms[3*i+XX]=strdup(buf);
sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
grpnms[3*i+YY]=strdup(buf);
sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
grpnms[3*i+ZZ]=strdup(buf);
}
md->iu=get_ebin_space(md->ebin,3*md->nU,grpnms);
sfree(*grpnms);
sfree(grpnms);
}
if (fp_ene != -1)
do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
return md;
}