int n_bonded_dx(const gmx_mtop_t *mtop, gmx_bool bExcl)
{
int mb, nmol, ftype, ndxb, ndx_excl;
int ndx;
const gmx_moltype_t *molt;
/* Count the number of pbc_rvec_sub calls required for bonded interactions.
* This number is also roughly proportional to the computational cost.
*/
ndx = 0;
ndx_excl = 0;
#if defined _ICC && __ICC == 1400 || defined __ICL && __ICL == 1400
#pragma novector /* Work-around for incorrect vectorization */
#endif
for (mb = 0; mb < mtop->nmolblock; mb++)
{
molt = &mtop->moltype[mtop->molblock[mb].type];
nmol = mtop->molblock[mb].nmol;
for (ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_BOND)
{
switch (ftype)
{
case F_POSRES:
case F_FBPOSRES:
ndxb = 1;
break;
case F_CONNBONDS:
ndxb = 0;
break;
default:
ndxb = NRAL(ftype) - 1;
break;
}
ndx += nmol*ndxb*molt->ilist[ftype].nr/(1 + NRAL(ftype));
}
}
if (bExcl)
{
ndx_excl += nmol*(molt->excls.nra - molt->atoms.nr)/2;
}
else
{
ndx_excl = 0;
}
}
if (debug)
{
fprintf(debug, "ndx bonded %d exclusions %d\n", ndx, ndx_excl);
}
ndx += ndx_excl;
return ndx;
}
static void enter_function(t_params *p, t_functype ftype, int comb, real reppow,
gmx_ffparams_t *ffparams, t_ilist *il,
int *maxtypes,
gmx_bool bNB, gmx_bool bAppend)
{
int k, type, nr, nral, delta, start;
start = ffparams->ntypes;
nr = p->nr;
for (k = 0; k < nr; k++)
{
if (*maxtypes <= ffparams->ntypes)
{
*maxtypes += 1000;
srenew(ffparams->functype, *maxtypes);
srenew(ffparams->iparams, *maxtypes);
if (debug)
{
fprintf(debug, "%s, line %d: srenewed idef->functype and idef->iparams to %d\n",
__FILE__, __LINE__, *maxtypes);
}
}
type = enter_params(ffparams, ftype, p->param[k].c, comb, reppow, start, bAppend);
/* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
if (!bNB && type >= 0)
{
nral = NRAL(ftype);
delta = nr*(nral+1);
srenew(il->iatoms, il->nr+delta);
append_interaction(il, type, nral, p->param[k].a);
}
}
}
static void cppar(t_param p[], int np, t_params plist[], int ftype)
{
int i, j, nral, nrfp;
t_params *ps;
ps = &plist[ftype];
nral = NRAL(ftype);
nrfp = NRFP(ftype);
/* Keep old stuff */
pr_alloc(np, ps);
for (i = 0; (i < np); i++)
{
for (j = 0; (j < nral); j++)
{
ps->param[ps->nr].a[j] = p[i].a[j];
}
for (j = 0; (j < nrfp); j++)
{
ps->param[ps->nr].c[j] = p[i].c[j];
}
for (j = 0; (j < MAXSLEN); j++)
{
ps->param[ps->nr].s[j] = p[i].s[j];
}
ps->nr++;
}
}
static int vsite_bond_nrcheck(int ftype)
{
int nrcheck;
if ((interaction_function[ftype].flags & (IF_BTYPE | IF_CONSTRAINT | IF_ATYPE)) || (ftype == F_IDIHS))
nrcheck = NRAL(ftype);
else
nrcheck = 0;
return nrcheck;
}
int gmx_mtop_ftype_count(const gmx_mtop_t *mtop,int ftype)
{
gmx_mtop_ilistloop_t iloop;
t_ilist *il;
int n,nmol;
n = 0;
iloop = gmx_mtop_ilistloop_init(mtop);
while (gmx_mtop_ilistloop_next(iloop,&il,&nmol))
{
n += nmol*il[ftype].nr/(1+NRAL(ftype));
}
return n;
}
gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop)
{
const gmx_moltype_t *molt;
const t_block *cgs;
const t_ilist *il;
int mb;
int nat, *at2cg, cg, a, ftype, i;
gmx_bool bInterCG;
bInterCG = FALSE;
for (mb = 0; mb < mtop->nmolblock && !bInterCG; mb++)
{
molt = &mtop->moltype[mtop->molblock[mb].type];
if (molt->ilist[F_CONSTR].nr > 0 ||
molt->ilist[F_CONSTRNC].nr > 0 ||
molt->ilist[F_SETTLE].nr > 0)
{
cgs = &molt->cgs;
snew(at2cg, molt->atoms.nr);
for (cg = 0; cg < cgs->nr; cg++)
{
for (a = cgs->index[cg]; a < cgs->index[cg+1]; a++)
{
at2cg[a] = cg;
}
}
for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
{
il = &molt->ilist[ftype];
for (i = 0; i < il->nr && !bInterCG; i += 1+NRAL(ftype))
{
if (at2cg[il->iatoms[i+1]] != at2cg[il->iatoms[i+2]])
{
bInterCG = TRUE;
}
}
}
sfree(at2cg);
}
}
return bInterCG;
}
static at2vsitecon_t *make_at2vsitecon(int natoms,t_params plist[])
{
gmx_bool *bVSI;
int ftype,i,j,ai,aj,nr;
at2vsitecon_t *at2vc;
snew(at2vc,natoms);
snew(bVSI,natoms);
for(ftype=0; (ftype<F_NRE); ftype++) {
if ((interaction_function[ftype].flags & IF_VSITE) && ftype != F_VSITEN) {
for(i=0; (i<plist[ftype].nr); i++) {
for(j=0; j<NRAL(ftype); j++)
bVSI[plist[ftype].param[i].a[j]] = TRUE;
}
}
}
for(ftype=0; (ftype<F_NRE); ftype++) {
if (interaction_function[ftype].flags & IF_CONSTRAINT) {
for(i=0; (i<plist[ftype].nr); i++) {
ai = plist[ftype].param[i].AI;
aj = plist[ftype].param[i].AJ;
if (bVSI[ai] && bVSI[aj]) {
/* Store forward direction */
nr = at2vc[ai].nr;
if (nr % 10 == 0)
srenew(at2vc[ai].aj,nr+10);
at2vc[ai].aj[nr] = aj;
at2vc[ai].nr++;
/* Store backward direction */
nr = at2vc[aj].nr;
if (nr % 10 == 0)
srenew(at2vc[aj].aj,nr+10);
at2vc[aj].aj[nr] = ai;
at2vc[aj].nr++;
}
}
}
}
sfree(bVSI);
return at2vc;
}
static at2vsitebond_t *make_at2vsitebond(int natoms,t_params plist[])
{
gmx_bool *bVSI;
int ftype,i,j,nrcheck,nr;
t_iatom *aa;
at2vsitebond_t *at2vb;
snew(at2vb,natoms);
snew(bVSI,natoms);
for(ftype=0; (ftype<F_NRE); ftype++) {
if ((interaction_function[ftype].flags & IF_VSITE) && ftype != F_VSITEN) {
for(i=0; (i<plist[ftype].nr); i++) {
for(j=0; j<NRAL(ftype); j++)
bVSI[plist[ftype].param[i].a[j]] = TRUE;
}
}
}
for(ftype=0; (ftype<F_NRE); ftype++) {
nrcheck = vsite_bond_nrcheck(ftype);
if (nrcheck > 0) {
for(i=0; (i<plist[ftype].nr); i++) {
aa = plist[ftype].param[i].a;
for(j=0; j<nrcheck; j++) {
if (bVSI[aa[j]]) {
nr = at2vb[aa[j]].nr;
if (nr % 10 == 0)
srenew(at2vb[aa[j]].vsbp,nr+10);
at2vb[aa[j]].vsbp[nr].ftype = ftype;
at2vb[aa[j]].vsbp[nr].param = &plist[ftype].param[i];
at2vb[aa[j]].nr++;
}
}
}
}
}
sfree(bVSI);
return at2vb;
}
static void enter_function(t_params *p, t_functype ftype, int comb, real reppow,
gmx_ffparams_t *ffparams, InteractionList *il,
bool bNB, bool bAppend)
{
int k, type, nr, nral, start;
start = ffparams->numTypes();
nr = p->nr;
for (k = 0; k < nr; k++)
{
type = enter_params(ffparams, ftype, p->param[k].c, comb, reppow, start, bAppend);
/* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
if (!bNB && type >= 0)
{
assert(il);
nral = NRAL(ftype);
append_interaction(il, type, nral, p->param[k].a);
}
}
}
static int *make_at2settle(int natoms, const t_ilist *ilist)
{
int *at2s;
int a, stride, s;
snew(at2s, natoms);
/* Set all to no settle */
for (a = 0; a < natoms; a++)
{
at2s[a] = -1;
}
stride = 1 + NRAL(F_SETTLE);
for (s = 0; s < ilist->nr; s += stride)
{
at2s[ilist->iatoms[s+1]] = s/stride;
at2s[ilist->iatoms[s+2]] = s/stride;
at2s[ilist->iatoms[s+3]] = s/stride;
}
return at2s;
}
static void ilistcat(int ftype,t_ilist *dest,t_ilist *src,int copies,
int dnum,int snum)
{
int nral,c,i,a;
nral = NRAL(ftype);
dest->nalloc = dest->nr + copies*src->nr;
srenew(dest->iatoms,dest->nalloc);
for(c=0; c<copies; c++)
{
for(i=0; i<src->nr; )
{
dest->iatoms[dest->nr++] = src->iatoms[i++];
for(a=0; a<nral; a++)
{
dest->iatoms[dest->nr++] = dnum + src->iatoms[i++];
}
}
dnum += snum;
}
}
//! Divides bonded interactions over threads
static void divide_bondeds_over_threads(t_idef *idef,
int nthread,
int max_nthread_uniform,
bool *haveBondeds)
{
ilist_data_t ild[F_NRE];
int ntype;
int f;
assert(nthread > 0);
idef->nthreads = nthread;
if (F_NRE*(nthread + 1) > idef->il_thread_division_nalloc)
{
idef->il_thread_division_nalloc = F_NRE*(nthread + 1);
snew(idef->il_thread_division, idef->il_thread_division_nalloc);
}
*haveBondeds = false;
ntype = 0;
for (f = 0; f < F_NRE; f++)
{
if (!ftype_is_bonded_potential(f))
{
continue;
}
if (idef->il[f].nr > 0)
{
*haveBondeds = true;
}
if (idef->il[f].nr == 0)
{
/* No interactions, avoid all the integer math below */
int t;
for (t = 0; t <= nthread; t++)
{
idef->il_thread_division[f*(nthread + 1) + t] = 0;
}
}
else if (nthread <= max_nthread_uniform || f == F_DISRES)
{
/* On up to 4 threads, load balancing the bonded work
* is more important than minimizing the reduction cost.
*/
int nat1, t;
/* nat1 = 1 + #atoms(ftype) which is the stride use for iatoms */
nat1 = 1 + NRAL(f);
for (t = 0; t <= nthread; t++)
{
int nr_t;
/* Divide equally over the threads */
nr_t = (((idef->il[f].nr/nat1)*t)/nthread)*nat1;
if (f == F_DISRES)
{
/* Ensure that distance restraint pairs with the same label
* end up on the same thread.
*/
while (nr_t > 0 && nr_t < idef->il[f].nr &&
idef->iparams[idef->il[f].iatoms[nr_t]].disres.label ==
idef->iparams[idef->il[f].iatoms[nr_t-nat1]].disres.label)
{
nr_t += nat1;
}
}
idef->il_thread_division[f*(nthread + 1) + t] = nr_t;
}
}
else
{
/* Add this ftype to the list to be distributed */
int nat;
nat = NRAL(f);
ild[ntype].ftype = f;
ild[ntype].il = &idef->il[f];
ild[ntype].nat = nat;
/* The first index for the thread division is always 0 */
idef->il_thread_division[f*(nthread + 1)] = 0;
ntype++;
}
}
if (ntype > 0)
{
divide_bondeds_by_locality(ntype, ild, nthread, idef);
}
if (debug)
{
int f;
fprintf(debug, "Division of bondeds over threads:\n");
for (f = 0; f < F_NRE; f++)
{
if (ftype_is_bonded_potential(f) && idef->il[f].nr > 0)
{
int t;
fprintf(debug, "%16s", interaction_function[f].name);
for (t = 0; t < nthread; t++)
{
fprintf(debug, " %4d",
(idef->il_thread_division[f*(nthread + 1) + t + 1] -
idef->il_thread_division[f*(nthread + 1) + t])/
(1 + NRAL(f)));
}
fprintf(debug, "\n");
}
}
}
}
static void get_verlet_buffer_atomtypes(const gmx_mtop_t *mtop,
verletbuf_atomtype_t **att_p,
int *natt_p,
int *n_nonlin_vsite)
{
verletbuf_atomtype_t *att;
int natt;
int mb, nmol, ft, i, a1, a2, a3, a;
const t_atoms *atoms;
const t_ilist *il;
const t_iparams *ip;
atom_nonbonded_kinetic_prop_t *prop;
real *vsite_m;
int n_nonlin_vsite_mol;
att = NULL;
natt = 0;
if (n_nonlin_vsite != NULL)
{
*n_nonlin_vsite = 0;
}
for (mb = 0; mb < mtop->nmolblock; mb++)
{
nmol = mtop->molblock[mb].nmol;
atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
/* Check for constraints, as they affect the kinetic energy.
* For virtual sites we need the masses and geometry of
* the constructing atoms to determine their velocity distribution.
*/
snew(prop, atoms->nr);
snew(vsite_m, atoms->nr);
for (ft = F_CONSTR; ft <= F_CONSTRNC; ft++)
{
il = &mtop->moltype[mtop->molblock[mb].type].ilist[ft];
for (i = 0; i < il->nr; i += 1+NRAL(ft))
{
ip = &mtop->ffparams.iparams[il->iatoms[i]];
a1 = il->iatoms[i+1];
a2 = il->iatoms[i+2];
if (atoms->atom[a2].m > prop[a1].con_mass)
{
prop[a1].con_mass = atoms->atom[a2].m;
prop[a1].con_len = ip->constr.dA;
}
if (atoms->atom[a1].m > prop[a2].con_mass)
{
prop[a2].con_mass = atoms->atom[a1].m;
prop[a2].con_len = ip->constr.dA;
}
}
}
il = &mtop->moltype[mtop->molblock[mb].type].ilist[F_SETTLE];
for (i = 0; i < il->nr; i += 1+NRAL(F_SETTLE))
{
ip = &mtop->ffparams.iparams[il->iatoms[i]];
a1 = il->iatoms[i+1];
a2 = il->iatoms[i+2];
a3 = il->iatoms[i+3];
/* Usually the mass of a1 (usually oxygen) is larger than a2/a3.
* If this is not the case, we overestimate the displacement,
* which leads to a larger buffer (ok since this is an exotic case).
*/
prop[a1].con_mass = atoms->atom[a2].m;
prop[a1].con_len = ip->settle.doh;
prop[a2].con_mass = atoms->atom[a1].m;
prop[a2].con_len = ip->settle.doh;
prop[a3].con_mass = atoms->atom[a1].m;
prop[a3].con_len = ip->settle.doh;
}
get_vsite_masses(&mtop->moltype[mtop->molblock[mb].type],
&mtop->ffparams,
vsite_m,
&n_nonlin_vsite_mol);
if (n_nonlin_vsite != NULL)
{
*n_nonlin_vsite += nmol*n_nonlin_vsite_mol;
}
for (a = 0; a < atoms->nr; a++)
{
if (atoms->atom[a].ptype == eptVSite)
{
prop[a].mass = vsite_m[a];
}
else
{
prop[a].mass = atoms->atom[a].m;
}
prop[a].type = atoms->atom[a].type;
prop[a].q = atoms->atom[a].q;
/* We consider an atom constrained, #DOF=2, when it is
* connected with constraints to (at least one) atom with
* a mass of more than 0.4x its own mass. This is not a critical
* parameter, since with roughly equal masses the unconstrained
* and constrained displacement will not differ much (and both
* overestimate the displacement).
*/
prop[a].bConstr = (prop[a].con_mass > 0.4*prop[a].mass);
add_at(&att, &natt, &prop[a], nmol);
}
sfree(vsite_m);
sfree(prop);
}
if (gmx_debug_at)
{
for (a = 0; a < natt; a++)
{
fprintf(debug, "type %d: m %5.2f t %d q %6.3f con %d con_m %5.3f con_l %5.3f n %d\n",
a, att[a].prop.mass, att[a].prop.type, att[a].prop.q,
att[a].prop.bConstr, att[a].prop.con_mass, att[a].prop.con_len,
att[a].n);
}
}
*att_p = att;
*natt_p = natt;
}
static void get_vsite_masses(const gmx_moltype_t *moltype,
const gmx_ffparams_t *ffparams,
real *vsite_m,
int *n_nonlin_vsite)
{
int ft, i;
const t_ilist *il;
*n_nonlin_vsite = 0;
/* Check for virtual sites, determine mass from constructing atoms */
for (ft = 0; ft < F_NRE; ft++)
{
if (IS_VSITE(ft))
{
il = &moltype->ilist[ft];
for (i = 0; i < il->nr; i += 1+NRAL(ft))
{
const t_iparams *ip;
real cam[5] = {0}, inv_mass, coeff, m_aj;
int a1, j, aj;
ip = &ffparams->iparams[il->iatoms[i]];
a1 = il->iatoms[i+1];
if (ft != F_VSITEN)
{
for (j = 1; j < NRAL(ft); j++)
{
cam[j] = moltype->atoms.atom[il->iatoms[i+1+j]].m;
if (cam[j] == 0)
{
cam[j] = vsite_m[il->iatoms[i+1+j]];
}
if (cam[j] == 0)
{
gmx_fatal(FARGS, "In molecule type '%s' %s construction involves atom %d, which is a virtual site of equal or high complexity. This is not supported.",
*moltype->name,
interaction_function[ft].longname,
il->iatoms[i+1+j]+1);
}
}
}
switch (ft)
{
case F_VSITE2:
/* Exact */
vsite_m[a1] = (cam[1]*cam[2])/(cam[2]*sqr(1-ip->vsite.a) + cam[1]*sqr(ip->vsite.a));
break;
case F_VSITE3:
/* Exact */
vsite_m[a1] = (cam[1]*cam[2]*cam[3])/(cam[2]*cam[3]*sqr(1-ip->vsite.a-ip->vsite.b) + cam[1]*cam[3]*sqr(ip->vsite.a) + cam[1]*cam[2]*sqr(ip->vsite.b));
break;
case F_VSITEN:
/* Exact */
inv_mass = 0;
for (j = 0; j < 3*ffparams->iparams[il->iatoms[i]].vsiten.n; j += 3)
{
aj = il->iatoms[i+j+2];
coeff = ffparams->iparams[il->iatoms[i+j]].vsiten.a;
if (moltype->atoms.atom[aj].ptype == eptVSite)
{
m_aj = vsite_m[aj];
}
else
{
m_aj = moltype->atoms.atom[aj].m;
}
if (m_aj <= 0)
{
gmx_incons("The mass of a vsiten constructing atom is <= 0");
}
inv_mass += coeff*coeff/m_aj;
}
vsite_m[a1] = 1/inv_mass;
/* Correct for loop increment of i */
i += j - 1 - NRAL(ft);
break;
default:
/* Use the mass of the lightest constructing atom.
* This is an approximation.
* If the distance of the virtual site to the
* constructing atom is less than all distances
* between constructing atoms, this is a safe
* over-estimate of the displacement of the vsite.
* This condition holds for all H mass replacement
* vsite constructions, except for SP2/3 groups.
* In SP3 groups one H will have a F_VSITE3
* construction, so even there the total drift
* estimate shouldn't be far off.
*/
assert(j >= 1);
vsite_m[a1] = cam[1];
for (j = 2; j < NRAL(ft); j++)
{
vsite_m[a1] = min(vsite_m[a1], cam[j]);
}
(*n_nonlin_vsite)++;
break;
}
if (gmx_debug_at)
{
fprintf(debug, "atom %4d %-20s mass %6.3f\n",
a1, interaction_function[ft].longname, vsite_m[a1]);
}
}
}
}
}
void count_bonded_distances(gmx_mtop_t *mtop, const t_inputrec *ir,
double *ndistance_c, double *ndistance_simd)
{
gmx_bool bExcl;
int nst_ener_or_vir;
double nonsimd_step_frac;
int mb, nmol, ftype;
gmx_moltype_t *molt;
double ndtot_c, ndtot_simd;
#ifdef GMX_SIMD_HAVE_REAL
gmx_bool bSimdBondeds = TRUE;
#else
gmx_bool bSimdBondeds = FALSE;
#endif
bExcl = (ir->cutoff_scheme == ecutsGROUP && IR_EXCL_FORCES(*ir)
&& !EEL_FULL(ir->coulombtype));
if (bSimdBondeds)
{
/* We only have SIMD versions of these bondeds without energy and
* without shift-forces, we take that into account here.
*/
if (ir->nstcalcenergy > 0)
{
nonsimd_step_frac = 1.0/ir->nstcalcenergy;
}
else
{
nonsimd_step_frac = 0;
}
if (ir->epc != epcNO && 1.0/ir->nstpcouple > nonsimd_step_frac)
{
nonsimd_step_frac = 1.0/ir->nstpcouple;
}
}
else
{
nonsimd_step_frac = 1;
}
/* Count the number of pbc_rvec_sub calls required for bonded interactions.
* This number is also roughly proportional to the computational cost.
*/
ndtot_c = 0;
ndtot_simd = 0;
#if defined _ICC && __ICC == 1400 || defined __ICL && __ICL == 1400
#pragma novector /* Work-around for incorrect vectorization */
#endif
for (mb = 0; mb < mtop->nmolblock; mb++)
{
molt = &mtop->moltype[mtop->molblock[mb].type];
nmol = mtop->molblock[mb].nmol;
for (ftype = 0; ftype < F_NRE; ftype++)
{
int nbonds;
if (interaction_function[ftype].flags & IF_BOND)
{
double nd_c, nd_simd;
nd_c = 0;
nd_simd = 0;
/* For all interactions, except for the three exceptions
* in the switch below, #distances = #atoms - 1.
*/
switch (ftype)
{
case F_POSRES:
case F_FBPOSRES:
nd_c = 1;
break;
case F_CONNBONDS:
break;
/* These bonded potentially use SIMD */
case F_ANGLES:
case F_PDIHS:
case F_RBDIHS:
nd_c = nonsimd_step_frac *(NRAL(ftype) - 1);
nd_simd = (1 - nonsimd_step_frac)*(NRAL(ftype) - 1);
break;
default:
nd_c = NRAL(ftype) - 1;
break;
}
nbonds = nmol*molt->ilist[ftype].nr/(1 + NRAL(ftype));
ndtot_c += nbonds*nd_c;
ndtot_simd += nbonds*nd_simd;
}
}
if (bExcl)
{
ndtot_c += nmol*(molt->excls.nra - molt->atoms.nr)/2;
}
}
if (debug)
{
fprintf(debug, "nr. of distance calculations in bondeds: C %.1f SIMD %.1f\n", ndtot_c, ndtot_simd);
}
if (ndistance_c != NULL)
{
*ndistance_c = ndtot_c;
}
if (ndistance_simd != NULL)
{
*ndistance_simd = ndtot_simd;
}
}
void print_bt(FILE *out, directive d, gpp_atomtype_t at,
int ftype, int fsubtype, t_params plist[],
gmx_bool bFullDih)
{
/* This dihp is a DIRTY patch because the dih-types do not use
* all four atoms to determine the type.
*/
const int dihp[2][2] = { { 1, 2 }, { 0, 3 } };
t_params *bt;
int i, j, f, nral, nrfp;
gmx_bool bDih = FALSE, bSwapParity;
bt = &(plist[ftype]);
if (!bt->nr)
{
return;
}
f = 0;
switch (ftype)
{
case F_G96ANGLES:
f = 1;
break;
case F_G96BONDS:
f = 1;
break;
case F_MORSE:
f = 2;
break;
case F_CUBICBONDS:
f = 3;
break;
case F_CONNBONDS:
f = 4;
break;
case F_HARMONIC:
f = 5;
break;
case F_CROSS_BOND_ANGLES:
f = 2;
break;
case F_CROSS_BOND_BONDS:
f = 3;
break;
case F_UREY_BRADLEY:
f = 4;
break;
case F_PDIHS:
case F_RBDIHS:
case F_FOURDIHS:
bDih = TRUE;
break;
case F_IDIHS:
f = 1;
bDih = TRUE;
break;
case F_CONSTRNC:
f = 1;
break;
case F_VSITE3FD:
f = 1;
break;
case F_VSITE3FAD:
f = 2;
break;
case F_VSITE3OUT:
f = 3;
break;
case F_VSITE4FDN:
f = 1;
break;
case F_CMAP:
f = 1;
break;
default:
bDih = FALSE;
}
if (bFullDih)
{
bDih = FALSE;
}
if (fsubtype)
{
f = fsubtype-1;
}
nral = NRAL(ftype);
nrfp = NRFP(ftype);
/* header */
fprintf(out, "[ %s ]\n", dir2str(d));
fprintf(out, "; ");
if (!bDih)
{
fprintf (out, "%3s %4s", "ai", "aj");
for (j = 2; (j < nral); j++)
{
fprintf (out, " %3c%c", 'a', 'i'+j);
}
}
else
{
for (j = 0; (j < 2); j++)
{
fprintf (out, "%3c%c", 'a', 'i'+dihp[f][j]);
}
}
fprintf (out, " funct");
for (j = 0; (j < nrfp); j++)
{
fprintf (out, " %12c%1d", 'c', j);
}
fprintf (out, "\n");
/* print bondtypes */
for (i = 0; (i < bt->nr); i++)
{
bSwapParity = (bt->param[i].C0 == NOTSET) && (bt->param[i].C1 == -1);
if (!bDih)
{
for (j = 0; (j < nral); j++)
{
fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[j], at));
}
}
else
{
for (j = 0; (j < 2); j++)
{
fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[dihp[f][j]], at));
}
}
fprintf (out, "%5d ", bSwapParity ? -f-1 : f+1);
if (bt->param[i].s[0])
{
fprintf(out, " %s", bt->param[i].s);
}
else
{
for (j = 0; (j < nrfp && (bt->param[i].c[j] != NOTSET)); j++)
{
fprintf (out, "%13.6e ", bt->param[i].c[j]);
}
}
fprintf (out, "\n");
}
fprintf (out, "\n");
fflush (out);
}
static void clean_vsite_angles(t_params *plist, t_pindex pindex[],
int cftype, int vsite_type[],
at2vsitecon_t *at2vc)
{
int i,j,parnr,k,l,m,n,nvsite,kept_i,vsnral,vsitetype;
atom_id atom,constr,at1,at2;
atom_id vsiteatoms[MAXATOMLIST];
gmx_bool bKeep,bUsed,bPresent,bAll3FAD,bFirstTwo;
t_params *ps;
ps = &(plist[cftype]);
vsnral=0;
kept_i=0;
for(i=0; (i<ps->nr); i++) { /* for all angles in the plist */
bKeep=FALSE;
bAll3FAD=TRUE;
/* check if all virtual sites are constructed from the same atoms */
nvsite=0;
for(k=0; (k<3) && !bKeep; k++) { /* for all atoms in the angle */
atom = ps->param[i].a[k];
if (vsite_type[atom]!=NOTSET) {
nvsite++;
bAll3FAD = bAll3FAD && (pindex[atom].ftype == F_VSITE3FAD);
if (nvsite==1) {
/* store construction atoms of first vsite */
vsnral=NRAL(pindex[atom].ftype)-1;
for(m=0; (m<vsnral); m++)
vsiteatoms[m]=
plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
} else
/* check if this vsite is constructed from the same atoms */
if (vsnral == NRAL(pindex[atom].ftype)-1 )
for(m=0; (m<vsnral) && !bKeep; m++) {
bPresent=FALSE;
constr=
plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
for(n=0; (n<vsnral) && !bPresent; n++)
if (constr == vsiteatoms[n])
bPresent=TRUE;
if (!bPresent)
bKeep=TRUE;
}
else
bKeep=TRUE;
}
}
/* keep all angles with no virtual sites in them or
with virtual sites with more than 3 constr. atoms */
if ( nvsite == 0 && vsnral > 3 )
bKeep=TRUE;
/* check if all non-vsite atoms are used in construction: */
bFirstTwo=TRUE;
for(k=0; (k<3) && !bKeep; k++) { /* for all atoms in the angle */
atom = ps->param[i].a[k];
if (vsite_type[atom]==NOTSET) {
bUsed=FALSE;
for(m=0; (m<vsnral) && !bUsed; m++)
if (atom == vsiteatoms[m]) {
bUsed=TRUE;
bFirstTwo = bFirstTwo && m<2;
}
if (!bUsed)
bKeep=TRUE;
}
}
if ( ! ( bAll3FAD && bFirstTwo ) )
/* check if all constructing atoms are constrained together */
for (m=0; m<vsnral && !bKeep; m++) { /* all constr. atoms */
at1 = vsiteatoms[m];
at2 = vsiteatoms[(m+1) % vsnral];
bPresent=FALSE;
for(j=0; j<at2vc[at1].nr; j++) {
if (at2vc[at1].aj[j] == at2)
bPresent = TRUE;
}
if (!bPresent)
bKeep=TRUE;
}
if ( bKeep ) {
/* now copy the angle to the new array */
memcpy(&(ps->param[kept_i]),
&(ps->param[i]),(size_t)sizeof(ps->param[0]));
kept_i++;
}
}
if (ps->nr != kept_i)
fprintf(stderr,"Removed %4d %15ss with virtual sites, %5d left\n",
ps->nr-kept_i, interaction_function[cftype].longname, kept_i);
ps->nr=kept_i;
}
int dd_make_local_constraints(gmx_domdec_t *dd,int at_start,
const gmx_mtop_t *mtop,
const int *cginfo,
gmx_constr_t constr,int nrec,
t_ilist *il_local)
{
gmx_domdec_constraints_t *dc;
t_ilist *ilc_local,*ils_local;
ind_req_t *ireq;
const t_blocka *at2con_mt;
const int **at2settle_mt;
gmx_hash_t ga2la_specat;
int at_end,i,j;
t_iatom *iap;
dc = dd->constraints;
ilc_local = &il_local[F_CONSTR];
ils_local = &il_local[F_SETTLE];
dc->ncon = 0;
ilc_local->nr = 0;
if (dd->constraint_comm)
{
at2con_mt = atom2constraints_moltype(constr);
ireq = &dd->constraint_comm->ireq[0];
ireq->n = 0;
}
else
{
at2con_mt = NULL;
ireq = NULL;
}
if (dd->bInterCGsettles)
{
at2settle_mt = atom2settle_moltype(constr);
ils_local->nr = 0;
}
else
{
/* Settle works inside charge groups, we assigned them already */
at2settle_mt = NULL;
}
if (at2settle_mt == NULL)
{
atoms_to_constraints(dd,mtop,cginfo,at2con_mt,nrec,
ilc_local,ireq);
}
else
{
int t0_set;
int thread;
/* Do the constraints, if present, on the first thread.
* Do the settles on all other threads.
*/
t0_set = ((at2con_mt != NULL && dc->nthread > 1) ? 1 : 0);
#pragma omp parallel for num_threads(dc->nthread) schedule(static)
for(thread=0; thread<dc->nthread; thread++)
{
if (at2con_mt && thread == 0)
{
atoms_to_constraints(dd,mtop,cginfo,at2con_mt,nrec,
ilc_local,ireq);
}
if (thread >= t0_set)
{
int cg0,cg1;
t_ilist *ilst;
ind_req_t *ireqt;
/* Distribute the settle check+assignments over
* dc->nthread or dc->nthread-1 threads.
*/
cg0 = (dd->ncg_home*(thread-t0_set ))/(dc->nthread-t0_set);
cg1 = (dd->ncg_home*(thread-t0_set+1))/(dc->nthread-t0_set);
if (thread == t0_set)
{
ilst = ils_local;
}
else
{
ilst = &dc->ils[thread];
}
ilst->nr = 0;
ireqt = &dd->constraint_comm->ireq[thread];
if (thread > 0)
{
ireqt->n = 0;
}
atoms_to_settles(dd,mtop,cginfo,at2settle_mt,
cg0,cg1,
ilst,ireqt);
}
}
/* Combine the generate settles and requested indices */
for(thread=1; thread<dc->nthread; thread++)
{
t_ilist *ilst;
ind_req_t *ireqt;
int ia;
if (thread > t0_set)
{
ilst = &dc->ils[thread];
if (ils_local->nr + ilst->nr > ils_local->nalloc)
{
ils_local->nalloc = over_alloc_large(ils_local->nr + ilst->nr);
srenew(ils_local->iatoms,ils_local->nalloc);
}
for(ia=0; ia<ilst->nr; ia++)
{
ils_local->iatoms[ils_local->nr+ia] = ilst->iatoms[ia];
}
ils_local->nr += ilst->nr;
}
ireqt = &dd->constraint_comm->ireq[thread];
if (ireq->n+ireqt->n > ireq->nalloc)
{
ireq->nalloc = over_alloc_large(ireq->n+ireqt->n);
srenew(ireq->ind,ireq->nalloc);
}
for(ia=0; ia<ireqt->n; ia++)
{
ireq->ind[ireq->n+ia] = ireqt->ind[ia];
}
ireq->n += ireqt->n;
}
if (debug)
{
fprintf(debug,"Settles: total %3d\n",ils_local->nr/4);
}
}
if (dd->constraint_comm) {
int nral1;
at_end =
setup_specat_communication(dd,ireq,dd->constraint_comm,
dd->constraints->ga2la,
at_start,2,
"constraint"," or lincs-order");
/* Fill in the missing indices */
ga2la_specat = dd->constraints->ga2la;
nral1 = 1 + NRAL(F_CONSTR);
for(i=0; i<ilc_local->nr; i+=nral1)
{
iap = ilc_local->iatoms + i;
for(j=1; j<nral1; j++)
{
if (iap[j] < 0)
{
iap[j] = gmx_hash_get_minone(ga2la_specat,-iap[j]-1);
}
}
}
nral1 = 1 + NRAL(F_SETTLE);
for(i=0; i<ils_local->nr; i+=nral1)
{
iap = ils_local->iatoms + i;
for(j=1; j<nral1; j++)
{
if (iap[j] < 0)
{
iap[j] = gmx_hash_get_minone(ga2la_specat,-iap[j]-1);
}
}
}
}
else
{
at_end = at_start;
}
return at_end;
}
void gmx_sort_ilist_fe(t_idef *idef, const real *qA, const real *qB)
{
int ftype, nral, i, ic, ib, a;
t_iparams *iparams;
t_ilist *ilist;
t_iatom *iatoms;
gmx_bool bPert;
t_iatom *iabuf;
int iabuf_nalloc;
if (qB == NULL)
{
qB = qA;
}
iabuf_nalloc = 0;
iabuf = NULL;
iparams = idef->iparams;
for (ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_BOND)
{
ilist = &idef->il[ftype];
iatoms = ilist->iatoms;
nral = NRAL(ftype);
ic = 0;
ib = 0;
i = 0;
while (i < ilist->nr)
{
/* Check if this interaction is perturbed */
if (ip_q_pert(ftype, iatoms+i, iparams, qA, qB))
{
/* Copy to the perturbed buffer */
if (ib + 1 + nral > iabuf_nalloc)
{
iabuf_nalloc = over_alloc_large(ib+1+nral);
srenew(iabuf, iabuf_nalloc);
}
for (a = 0; a < 1+nral; a++)
{
iabuf[ib++] = iatoms[i++];
}
}
else
{
/* Copy in place */
for (a = 0; a < 1+nral; a++)
{
iatoms[ic++] = iatoms[i++];
}
}
}
/* Now we now the number of non-perturbed interactions */
ilist->nr_nonperturbed = ic;
/* Copy the buffer with perturbed interactions to the ilist */
for (a = 0; a < ib; a++)
{
iatoms[ic++] = iabuf[a];
}
if (debug)
{
fprintf(debug, "%s non-pert %d pert %d\n",
interaction_function[ftype].longname,
ilist->nr_nonperturbed,
ilist->nr-ilist->nr_nonperturbed);
}
}
}
sfree(iabuf);
idef->ilsort = ilsortFE_SORTED;
}
void convert_params(int atnr, t_params nbtypes[],
t_molinfo *mi, t_molinfo *intermolecular_interactions,
int comb, double reppow, real fudgeQQ,
gmx_mtop_t *mtop)
{
int i;
unsigned long flags;
gmx_ffparams_t *ffp;
gmx_moltype_t *molt;
t_params *plist;
ffp = &mtop->ffparams;
ffp->atnr = atnr;
ffp->functype.clear();
ffp->iparams.clear();
ffp->reppow = reppow;
enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr,
TRUE, TRUE);
enter_function(&(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr,
TRUE, TRUE);
for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
{
molt = &mtop->moltype[mt];
for (i = 0; (i < F_NRE); i++)
{
molt->ilist[i].iatoms.clear();
plist = mi[mt].plist;
flags = interaction_function[i].flags;
if ((i != F_LJ) && (i != F_BHAM) && ((flags & IF_BOND) ||
(flags & IF_VSITE) ||
(flags & IF_CONSTRAINT)))
{
enter_function(&(plist[i]), static_cast<t_functype>(i), comb, reppow,
ffp, &molt->ilist[i],
FALSE, (i == F_POSRES || i == F_FBPOSRES));
}
}
}
mtop->bIntermolecularInteractions = FALSE;
if (intermolecular_interactions != nullptr)
{
/* Process the intermolecular interaction list */
mtop->intermolecular_ilist = gmx::compat::make_unique<InteractionLists>();
for (i = 0; (i < F_NRE); i++)
{
(*mtop->intermolecular_ilist)[i].iatoms.clear();
plist = intermolecular_interactions->plist;
if (plist[i].nr > 0)
{
flags = interaction_function[i].flags;
/* For intermolecular interactions we (currently)
* only support potentials.
* Constraints and virtual sites would be possible,
* but require a lot of extra (bug-prone) code.
*/
if (!(flags & IF_BOND))
{
gmx_fatal(FARGS, "The intermolecular_interaction section may only contain bonded potentials");
}
else if (NRAL(i) == 1) /* e.g. position restraints */
{
gmx_fatal(FARGS, "Single atom interactions don't make sense in the intermolecular_interaction section, you can put them in the moleculetype section");
}
else if (flags & IF_CHEMBOND)
{
gmx_fatal(FARGS, "The intermolecular_interaction can not contain chemically bonding interactions");
}
else
{
enter_function(&(plist[i]), static_cast<t_functype>(i), comb, reppow,
ffp, &(*mtop->intermolecular_ilist)[i],
FALSE, FALSE);
mtop->bIntermolecularInteractions = TRUE;
}
}
}
if (!mtop->bIntermolecularInteractions)
{
mtop->intermolecular_ilist.reset(nullptr);
}
}
ffp->fudgeQQ = fudgeQQ;
}
static void clean_vsite_dihs(t_params *plist, t_pindex pindex[],
int cftype, int vsite_type[])
{
int ftype,i,parnr,k,l,m,n,nvsite,kept_i,vsnral;
atom_id atom,constr;
atom_id vsiteatoms[3];
gmx_bool bKeep,bUsed,bPresent;
t_params *ps;
ps = &(plist[cftype]);
vsnral=0;
kept_i=0;
for(i=0; (i<ps->nr); i++) { /* for all dihedrals in the plist */
bKeep=FALSE;
/* check if all virtual sites are constructed from the same atoms */
nvsite=0;
for(k=0; (k<4) && !bKeep; k++) { /* for all atoms in the dihedral */
atom = ps->param[i].a[k];
if (vsite_type[atom]!=NOTSET) {
nvsite++;
if (nvsite==1) {
/* store construction atoms of first vsite */
vsnral=NRAL(pindex[atom].ftype)-1;
for(m=0; (m<vsnral); m++)
vsiteatoms[m]=
plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
if (debug) {
fprintf(debug,"dih w. vsite: %u %u %u %u\n",
ps->param[i].AI+1,ps->param[i].AJ+1,
ps->param[i].AK+1,ps->param[i].AL+1);
fprintf(debug,"vsite %u from: %u %u %u\n",
atom+1,vsiteatoms[0]+1,vsiteatoms[1]+1,vsiteatoms[2]+1);
}
} else
/* check if this vsite is constructed from the same atoms */
if (vsnral == NRAL(pindex[atom].ftype)-1 )
for(m=0; (m<vsnral) && !bKeep; m++) {
bPresent=FALSE;
constr=
plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
for(n=0; (n<vsnral) && !bPresent; n++)
if (constr == vsiteatoms[n])
bPresent=TRUE;
if (!bPresent)
bKeep=TRUE;
}
}
}
/* keep all dihedrals with no virtual sites in them */
if (nvsite==0)
bKeep=TRUE;
/* check if all atoms in dihedral are either virtual sites, or used in
construction of virtual sites. If so, keep it, if not throw away: */
for(k=0; (k<4) && !bKeep; k++) { /* for all atoms in the dihedral */
atom = ps->param[i].a[k];
if (vsite_type[atom]==NOTSET) {
bUsed=FALSE;
for(m=0; (m<vsnral) && !bUsed; m++)
if (atom == vsiteatoms[m])
bUsed=TRUE;
if (!bUsed) {
bKeep=TRUE;
if (debug) fprintf(debug,"unused atom in dih: %u\n",atom+1);
}
}
}
if ( bKeep ) {
memcpy(&(ps->param[kept_i]),
&(ps->param[i]),(size_t)sizeof(ps->param[0]));
kept_i++;
}
}
if (ps->nr != kept_i)
fprintf(stderr,"Removed %4d %15ss with virtual sites, %5d left\n",
ps->nr-kept_i, interaction_function[cftype].longname, kept_i);
ps->nr=kept_i;
}
int set_vsites(gmx_bool bVerbose, t_atoms *atoms, gpp_atomtype_t atype,
t_params plist[])
{
int i,j,ftype;
int nvsite,nrbond,nrang,nridih,nrset;
gmx_bool bFirst,bSet,bERROR;
at2vsitebond_t *at2vb;
t_mybonded *bonds;
t_mybonded *angles;
t_mybonded *idihs;
bFirst = TRUE;
bERROR = TRUE;
nvsite=0;
if (debug)
fprintf(debug, "\nCalculating parameters for virtual sites\n");
/* Make a reverse list to avoid ninteractions^2 operations */
at2vb = make_at2vsitebond(atoms->nr,plist);
for(ftype=0; (ftype<F_NRE); ftype++)
if ((interaction_function[ftype].flags & IF_VSITE) && ftype != F_VSITEN) {
nrset=0;
nvsite+=plist[ftype].nr;
for(i=0; (i<plist[ftype].nr); i++) {
/* check if all parameters are set */
bSet=TRUE;
for(j=0; j<NRFP(ftype) && bSet; j++)
bSet = plist[ftype].param[i].c[j]!=NOTSET;
if (debug) {
fprintf(debug,"bSet=%s ",bool_names[bSet]);
print_param(debug,ftype,i,&plist[ftype].param[i]);
}
if (!bSet) {
if (bVerbose && bFirst) {
fprintf(stderr,"Calculating parameters for virtual sites\n");
bFirst=FALSE;
}
nrbond=nrang=nridih=0;
bonds = NULL;
angles= NULL;
idihs = NULL;
nrset++;
/* now set the vsite parameters: */
get_bondeds(NRAL(ftype), plist[ftype].param[i].a, at2vb, plist,
&nrbond, &bonds, &nrang, &angles, &nridih, &idihs);
if (debug) {
fprintf(debug, "Found %d bonds, %d angles and %d idihs "
"for virtual site %u (%s)\n",nrbond,nrang,nridih,
plist[ftype].param[i].AI+1,
interaction_function[ftype].longname);
print_bad(debug, nrbond, bonds, nrang, angles, nridih, idihs);
} /* debug */
switch(ftype) {
case F_VSITE3:
bERROR =
calc_vsite3_param(atype, &(plist[ftype].param[i]), atoms,
nrbond, bonds, nrang, angles);
break;
case F_VSITE3FD:
bERROR =
calc_vsite3fd_param(&(plist[ftype].param[i]),
nrbond, bonds, nrang, angles);
break;
case F_VSITE3FAD:
bERROR =
calc_vsite3fad_param(&(plist[ftype].param[i]),
nrbond, bonds, nrang, angles);
break;
case F_VSITE3OUT:
bERROR =
calc_vsite3out_param(atype, &(plist[ftype].param[i]), atoms,
nrbond, bonds, nrang, angles);
break;
case F_VSITE4FD:
bERROR =
calc_vsite4fd_param(&(plist[ftype].param[i]),
nrbond, bonds, nrang, angles);
break;
case F_VSITE4FDN:
bERROR =
calc_vsite4fdn_param(&(plist[ftype].param[i]),
nrbond, bonds, nrang, angles);
break;
default:
gmx_fatal(FARGS,"Automatic parameter generation not supported "
"for %s atom %d",
interaction_function[ftype].longname,
plist[ftype].param[i].AI+1);
} /* switch */
if (bERROR)
gmx_fatal(FARGS,"Automatic parameter generation not supported "
"for %s atom %d for this bonding configuration",
interaction_function[ftype].longname,
plist[ftype].param[i].AI+1);
sfree(bonds);
sfree(angles);
sfree(idihs);
} /* if bSet */
} /* for i */
if (debug && plist[ftype].nr)
fprintf(stderr,"Calculated parameters for %d out of %d %s atoms\n",
nrset,plist[ftype].nr,interaction_function[ftype].longname);
} /* if IF_VSITE */
done_at2vsitebond(atoms->nr,at2vb);
return nvsite;
}
/*! \brief Looks up SETTLE constraints for a range of charge-groups */
static void atoms_to_settles(gmx_domdec_t *dd,
const gmx_mtop_t *mtop,
const int *cginfo,
const int **at2settle_mt,
int cg_start, int cg_end,
t_ilist *ils_local,
ind_req_t *ireq)
{
gmx_ga2la_t *ga2la;
gmx_mtop_atomlookup_t alook;
int settle;
int nral, sa;
int cg, a, a_gl, a_glsa, a_gls[3], a_locs[3];
int mb, molnr, a_mol, offset;
const gmx_molblock_t *molb;
const t_iatom *ia1;
gmx_bool a_home[3];
int nlocal;
gmx_bool bAssign;
ga2la = dd->ga2la;
alook = gmx_mtop_atomlookup_settle_init(mtop);
nral = NRAL(F_SETTLE);
for (cg = cg_start; cg < cg_end; cg++)
{
if (GET_CGINFO_SETTLE(cginfo[cg]))
{
for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
{
a_gl = dd->gatindex[a];
gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
molb = &mtop->molblock[mb];
settle = at2settle_mt[molb->type][a_mol];
if (settle >= 0)
{
offset = a_gl - a_mol;
ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms;
bAssign = FALSE;
nlocal = 0;
for (sa = 0; sa < nral; sa++)
{
a_glsa = offset + ia1[settle*(1+nral)+1+sa];
a_gls[sa] = a_glsa;
a_home[sa] = ga2la_get_home(ga2la, a_glsa, &a_locs[sa]);
if (a_home[sa])
{
if (nlocal == 0 && a_gl == a_glsa)
{
bAssign = TRUE;
}
nlocal++;
}
}
if (bAssign)
{
if (ils_local->nr+1+nral > ils_local->nalloc)
{
ils_local->nalloc = over_alloc_dd(ils_local->nr+1+nral);
srenew(ils_local->iatoms, ils_local->nalloc);
}
ils_local->iatoms[ils_local->nr++] = ia1[settle*4];
for (sa = 0; sa < nral; sa++)
{
if (ga2la_get_home(ga2la, a_gls[sa], &a_locs[sa]))
{
ils_local->iatoms[ils_local->nr++] = a_locs[sa];
}
else
{
ils_local->iatoms[ils_local->nr++] = -a_gls[sa] - 1;
/* Add this non-home atom to the list */
if (ireq->n+1 > ireq->nalloc)
{
ireq->nalloc = over_alloc_large(ireq->n+1);
srenew(ireq->ind, ireq->nalloc);
}
ireq->ind[ireq->n++] = a_gls[sa];
/* A check on double atom requests is
* not required for settle.
*/
}
}
}
}
}
}
}
gmx_mtop_atomlookup_destroy(alook);
}
static void clean_vsite_bonds(t_params *plist, t_pindex pindex[],
int cftype, int vsite_type[])
{
int ftype,i,j,parnr,k,l,m,n,nvsite,nOut,kept_i,vsnral,vsitetype;
int nconverted,nremoved;
atom_id atom,oatom,constr,at1,at2;
atom_id vsiteatoms[MAXATOMLIST];
gmx_bool bKeep,bRemove,bUsed,bPresent,bThisFD,bThisOUT,bAllFD,bFirstTwo;
t_params *ps;
if (cftype == F_CONNBONDS)
return;
ps = &(plist[cftype]);
vsnral=0;
kept_i=0;
nconverted=0;
nremoved=0;
nOut=0;
for(i=0; (i<ps->nr); i++) { /* for all bonds in the plist */
bKeep=FALSE;
bRemove=FALSE;
bAllFD=TRUE;
/* check if all virtual sites are constructed from the same atoms */
nvsite=0;
if(debug)
fprintf(debug,"constr %u %u:",ps->param[i].AI+1,ps->param[i].AJ+1);
for(k=0; (k<2) && !bKeep && !bRemove; k++) {
/* for all atoms in the bond */
atom = ps->param[i].a[k];
if (vsite_type[atom]!=NOTSET) {
if(debug) {
fprintf(debug," d%d[%d: %d %d %d]",k,atom+1,
plist[pindex[atom].ftype].param[pindex[atom].parnr].AJ+1,
plist[pindex[atom].ftype].param[pindex[atom].parnr].AK+1,
plist[pindex[atom].ftype].param[pindex[atom].parnr].AL+1);
}
nvsite++;
bThisFD = ( (pindex[atom].ftype == F_VSITE3FD ) ||
(pindex[atom].ftype == F_VSITE3FAD) ||
(pindex[atom].ftype == F_VSITE4FD ) ||
(pindex[atom].ftype == F_VSITE4FDN ) );
bThisOUT= ( (pindex[atom].ftype == F_VSITE3OUT) &&
(interaction_function[cftype].flags & IF_CONSTRAINT) );
bAllFD = bAllFD && bThisFD;
if (bThisFD || bThisOUT) {
if(debug)fprintf(debug," %s",bThisOUT?"out":"fd");
oatom = ps->param[i].a[1-k]; /* the other atom */
if ( vsite_type[oatom]==NOTSET &&
oatom==plist[pindex[atom].ftype].param[pindex[atom].parnr].AJ ){
/* if the other atom isn't a vsite, and it is AI */
bRemove=TRUE;
if (bThisOUT)
nOut++;
if(debug)fprintf(debug," D-AI");
}
}
if (!bRemove) {
if (nvsite==1) {
/* if this is the first vsite we encounter then
store construction atoms */
vsnral=NRAL(pindex[atom].ftype)-1;
for(m=0; (m<vsnral); m++)
vsiteatoms[m]=
plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
} else {
/* if it is not the first then
check if this vsite is constructed from the same atoms */
if (vsnral == NRAL(pindex[atom].ftype)-1 )
for(m=0; (m<vsnral) && !bKeep; m++) {
bPresent=FALSE;
constr=
plist[pindex[atom].ftype].param[pindex[atom].parnr].a[m+1];
for(n=0; (n<vsnral) && !bPresent; n++)
if (constr == vsiteatoms[n])
bPresent=TRUE;
if (!bPresent) {
bKeep=TRUE;
if(debug)fprintf(debug," !present");
}
}
else {
bKeep=TRUE;
if(debug)fprintf(debug," !same#at");
}
}
}
}
}
if (bRemove)
bKeep=FALSE;
else {
/* if we have no virtual sites in this bond, keep it */
if (nvsite==0) {
if (debug)fprintf(debug," no vsite");
bKeep=TRUE;
}
/* check if all non-vsite atoms are used in construction: */
bFirstTwo=TRUE;
for(k=0; (k<2) && !bKeep; k++) { /* for all atoms in the bond */
atom = ps->param[i].a[k];
if (vsite_type[atom]==NOTSET) {
bUsed=FALSE;
for(m=0; (m<vsnral) && !bUsed; m++)
if (atom == vsiteatoms[m]) {
bUsed=TRUE;
bFirstTwo = bFirstTwo && m<2;
}
if (!bUsed) {
bKeep=TRUE;
if(debug)fprintf(debug," !used");
}
}
}
if ( ! ( bAllFD && bFirstTwo ) )
/* check if all constructing atoms are constrained together */
for (m=0; m<vsnral && !bKeep; m++) { /* all constr. atoms */
at1 = vsiteatoms[m];
at2 = vsiteatoms[(m+1) % vsnral];
bPresent=FALSE;
for (ftype=0; ftype<F_NRE; ftype++)
if ( interaction_function[ftype].flags & IF_CONSTRAINT )
for (j=0; (j<plist[ftype].nr) && !bPresent; j++)
/* all constraints until one matches */
bPresent = ( ( (plist[ftype].param[j].AI == at1) &&
(plist[ftype].param[j].AJ == at2) ) ||
( (plist[ftype].param[j].AI == at2) &&
(plist[ftype].param[j].AJ == at1) ) );
if (!bPresent) {
bKeep=TRUE;
if(debug)fprintf(debug," !bonded");
}
}
}
if ( bKeep ) {
if(debug)fprintf(debug," keeping");
/* now copy the bond to the new array */
memcpy(&(ps->param[kept_i]),
&(ps->param[i]),(size_t)sizeof(ps->param[0]));
kept_i++;
} else if (IS_CHEMBOND(cftype)) {
srenew(plist[F_CONNBONDS].param,plist[F_CONNBONDS].nr+1);
memcpy(&(plist[F_CONNBONDS].param[plist[F_CONNBONDS].nr]),
&(ps->param[i]),(size_t)sizeof(plist[F_CONNBONDS].param[0]));
plist[F_CONNBONDS].nr++;
nconverted++;
} else
nremoved++;
if(debug)fprintf(debug,"\n");
}
if (nremoved)
fprintf(stderr,"Removed %4d %15ss with virtual sites, %5d left\n",
nremoved, interaction_function[cftype].longname, kept_i);
if (nconverted)
fprintf(stderr,"Converted %4d %15ss with virtual sites to connections, %5d left\n",
nconverted, interaction_function[cftype].longname, kept_i);
if (nOut)
fprintf(stderr,"Warning: removed %d %ss with vsite with %s construction\n"
" This vsite construction does not guarantee constant "
"bond-length\n"
" If the constructions were generated by pdb2gmx ignore "
"this warning\n",
nOut, interaction_function[cftype].longname,
interaction_function[F_VSITE3OUT].longname );
ps->nr=kept_i;
}
gmx_bool constrain(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
struct gmx_constr *constr,
t_idef *idef, t_inputrec *ir, gmx_ekindata_t *ekind,
t_commrec *cr,
gmx_int64_t step, int delta_step,
t_mdatoms *md,
rvec *x, rvec *xprime, rvec *min_proj,
gmx_bool bMolPBC, matrix box,
real lambda, real *dvdlambda,
rvec *v, tensor *vir,
t_nrnb *nrnb, int econq, gmx_bool bPscal,
real veta, real vetanew)
{
gmx_bool bOK, bDump;
int start, homenr, nrend;
int i, j, d;
int ncons, settle_error;
tensor vir_r_m_dr;
rvec *vstor;
real invdt, vir_fac, t;
t_ilist *settle;
int nsettle;
t_pbc pbc, *pbc_null;
char buf[22];
t_vetavars vetavar;
int nth, th;
if (econq == econqForceDispl && !EI_ENERGY_MINIMIZATION(ir->eI))
{
gmx_incons("constrain called for forces displacements while not doing energy minimization, can not do this while the LINCS and SETTLE constraint connection matrices are mass weighted");
}
bOK = TRUE;
bDump = FALSE;
start = 0;
homenr = md->homenr;
nrend = start+homenr;
/* set constants for pressure control integration */
init_vetavars(&vetavar, econq != econqCoord,
veta, vetanew, ir, ekind, bPscal);
if (ir->delta_t == 0)
{
invdt = 0;
}
else
{
invdt = 1/ir->delta_t;
}
if (ir->efep != efepNO && EI_DYNAMICS(ir->eI))
{
/* Set the constraint lengths for the step at which this configuration
* is meant to be. The invmasses should not be changed.
*/
lambda += delta_step*ir->fepvals->delta_lambda;
}
if (vir != NULL)
{
clear_mat(vir_r_m_dr);
}
where();
settle = &idef->il[F_SETTLE];
nsettle = settle->nr/(1+NRAL(F_SETTLE));
if (nsettle > 0)
{
nth = gmx_omp_nthreads_get(emntSETTLE);
}
else
{
nth = 1;
}
if (nth > 1 && constr->vir_r_m_dr_th == NULL)
{
snew(constr->vir_r_m_dr_th, nth);
snew(constr->settle_error, nth);
}
settle_error = -1;
/* We do not need full pbc when constraints do not cross charge groups,
* i.e. when dd->constraint_comm==NULL.
* Note that PBC for constraints is different from PBC for bondeds.
* For constraints there is both forward and backward communication.
*/
if (ir->ePBC != epbcNONE &&
(cr->dd || bMolPBC) && !(cr->dd && cr->dd->constraint_comm == NULL))
{
/* With pbc=screw the screw has been changed to a shift
* by the constraint coordinate communication routine,
* so that here we can use normal pbc.
*/
pbc_null = set_pbc_dd(&pbc, ir->ePBC, cr->dd, FALSE, box);
}
else
{
pbc_null = NULL;
}
/* Communicate the coordinates required for the non-local constraints
* for LINCS and/or SETTLE.
*/
if (cr->dd)
{
dd_move_x_constraints(cr->dd, box, x, xprime, econq == econqCoord);
}
if (constr->lincsd != NULL)
{
bOK = constrain_lincs(fplog, bLog, bEner, ir, step, constr->lincsd, md, cr,
x, xprime, min_proj,
box, pbc_null, lambda, dvdlambda,
invdt, v, vir != NULL, vir_r_m_dr,
econq, nrnb,
constr->maxwarn, &constr->warncount_lincs);
if (!bOK && constr->maxwarn >= 0)
{
if (fplog != NULL)
{
fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
econstr_names[econtLINCS], gmx_step_str(step, buf));
}
bDump = TRUE;
}
}
if (constr->nblocks > 0)
{
switch (econq)
{
case (econqCoord):
bOK = bshakef(fplog, constr->shaked,
md->invmass, constr->nblocks, constr->sblock,
idef, ir, x, xprime, nrnb,
constr->lagr, lambda, dvdlambda,
invdt, v, vir != NULL, vir_r_m_dr,
constr->maxwarn >= 0, econq, &vetavar);
break;
case (econqVeloc):
bOK = bshakef(fplog, constr->shaked,
md->invmass, constr->nblocks, constr->sblock,
idef, ir, x, min_proj, nrnb,
constr->lagr, lambda, dvdlambda,
invdt, NULL, vir != NULL, vir_r_m_dr,
constr->maxwarn >= 0, econq, &vetavar);
break;
default:
gmx_fatal(FARGS, "Internal error, SHAKE called for constraining something else than coordinates");
break;
}
if (!bOK && constr->maxwarn >= 0)
{
if (fplog != NULL)
{
fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
econstr_names[econtSHAKE], gmx_step_str(step, buf));
}
bDump = TRUE;
}
}
if (nsettle > 0)
{
int calcvir_atom_end;
if (vir == NULL)
{
calcvir_atom_end = 0;
}
else
{
calcvir_atom_end = md->homenr;
}
switch (econq)
{
case econqCoord:
#pragma omp parallel for num_threads(nth) schedule(static)
for (th = 0; th < nth; th++)
{
int start_th, end_th;
if (th > 0)
{
clear_mat(constr->vir_r_m_dr_th[th]);
}
start_th = (nsettle* th )/nth;
end_th = (nsettle*(th+1))/nth;
if (start_th >= 0 && end_th - start_th > 0)
{
csettle(constr->settled,
end_th-start_th,
settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
pbc_null,
x[0], xprime[0],
invdt, v ? v[0] : NULL, calcvir_atom_end,
th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
th == 0 ? &settle_error : &constr->settle_error[th],
&vetavar);
}
}
inc_nrnb(nrnb, eNR_SETTLE, nsettle);
if (v != NULL)
{
inc_nrnb(nrnb, eNR_CONSTR_V, nsettle*3);
}
if (vir != NULL)
{
inc_nrnb(nrnb, eNR_CONSTR_VIR, nsettle*3);
}
break;
case econqVeloc:
case econqDeriv:
case econqForce:
case econqForceDispl:
#pragma omp parallel for num_threads(nth) schedule(static)
for (th = 0; th < nth; th++)
{
int start_th, end_th;
if (th > 0)
{
clear_mat(constr->vir_r_m_dr_th[th]);
}
start_th = (nsettle* th )/nth;
end_th = (nsettle*(th+1))/nth;
if (start_th >= 0 && end_th - start_th > 0)
{
settle_proj(constr->settled, econq,
end_th-start_th,
settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
pbc_null,
x,
xprime, min_proj, calcvir_atom_end,
th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
&vetavar);
}
}
/* This is an overestimate */
inc_nrnb(nrnb, eNR_SETTLE, nsettle);
break;
case econqDeriv_FlexCon:
/* Nothing to do, since the are no flexible constraints in settles */
break;
default:
gmx_incons("Unknown constraint quantity for settle");
}
}
if (settle->nr > 0)
{
/* Combine virial and error info of the other threads */
for (i = 1; i < nth; i++)
{
m_add(vir_r_m_dr, constr->vir_r_m_dr_th[i], vir_r_m_dr);
settle_error = constr->settle_error[i];
}
if (econq == econqCoord && settle_error >= 0)
{
bOK = FALSE;
if (constr->maxwarn >= 0)
{
char buf[256];
sprintf(buf,
"\nstep " "%"GMX_PRId64 ": Water molecule starting at atom %d can not be "
"settled.\nCheck for bad contacts and/or reduce the timestep if appropriate.\n",
step, ddglatnr(cr->dd, settle->iatoms[settle_error*(1+NRAL(F_SETTLE))+1]));
if (fplog)
{
fprintf(fplog, "%s", buf);
}
fprintf(stderr, "%s", buf);
constr->warncount_settle++;
if (constr->warncount_settle > constr->maxwarn)
{
too_many_constraint_warnings(-1, constr->warncount_settle);
}
bDump = TRUE;
}
}
}
free_vetavars(&vetavar);
if (vir != NULL)
{
switch (econq)
{
case econqCoord:
vir_fac = 0.5/(ir->delta_t*ir->delta_t);
break;
case econqVeloc:
vir_fac = 0.5/ir->delta_t;
break;
case econqForce:
case econqForceDispl:
vir_fac = 0.5;
break;
default:
vir_fac = 0;
gmx_incons("Unsupported constraint quantity for virial");
}
if (EI_VV(ir->eI))
{
vir_fac *= 2; /* only constraining over half the distance here */
}
for (i = 0; i < DIM; i++)
{
for (j = 0; j < DIM; j++)
{
(*vir)[i][j] = vir_fac*vir_r_m_dr[i][j];
}
}
}
if (bDump)
{
dump_confs(fplog, step, constr->warn_mtop, start, homenr, cr, x, xprime, box);
}
if (econq == econqCoord)
{
if (ir->ePull == epullCONSTRAINT)
{
if (EI_DYNAMICS(ir->eI))
{
t = ir->init_t + (step + delta_step)*ir->delta_t;
}
else
{
t = ir->init_t;
}
set_pbc(&pbc, ir->ePBC, box);
pull_constraint(ir->pull, md, &pbc, cr, ir->delta_t, t, x, xprime, v, *vir);
}
if (constr->ed && delta_step > 0)
{
/* apply the essential dynamcs constraints here */
do_edsam(ir, step, cr, xprime, v, box, constr->ed);
}
}
return bOK;
}
int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil)
{
gmx_domdec_specat_comm_t *spac;
ind_req_t *ireq;
gmx_hash_t ga2la_specat;
int ftype, nral, i, j, a;
t_ilist *lilf;
t_iatom *iatoms;
int at_end;
spac = dd->vsite_comm;
ireq = &spac->ireq[0];
ga2la_specat = dd->ga2la_vsite;
ireq->n = 0;
/* Loop over all the home vsites */
for (ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_VSITE)
{
nral = NRAL(ftype);
lilf = &lil[ftype];
for (i = 0; i < lilf->nr; i += 1+nral)
{
iatoms = lilf->iatoms + i;
/* Check if we have the other atoms */
for (j = 1; j < 1+nral; j++)
{
if (iatoms[j] < 0)
{
/* This is not a home atom,
* we need to ask our neighbors.
*/
a = -iatoms[j] - 1;
/* Check to not ask for the same atom more than once */
if (gmx_hash_get_minone(dd->ga2la_vsite, a) == -1)
{
/* Add this non-home atom to the list */
if (ireq->n+1 > ireq->nalloc)
{
ireq->nalloc = over_alloc_large(ireq->n+1);
srenew(ireq->ind, ireq->nalloc);
}
ireq->ind[ireq->n++] = a;
/* Temporarily mark with -2,
* we get the index later.
*/
gmx_hash_set(ga2la_specat, a, -2);
}
}
}
}
}
}
at_end = setup_specat_communication(dd, ireq, dd->vsite_comm, ga2la_specat,
at_start, 1, "vsite", "");
/* Fill in the missing indices */
for (ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_VSITE)
{
nral = NRAL(ftype);
lilf = &lil[ftype];
for (i = 0; i < lilf->nr; i += 1+nral)
{
iatoms = lilf->iatoms + i;
for (j = 1; j < 1+nral; j++)
{
if (iatoms[j] < 0)
{
iatoms[j] = gmx_hash_get_minone(ga2la_specat, -iatoms[j]-1);
}
}
}
}
}
return at_end;
}
/*! \brief Looks up constraint for the local atoms */
static void atoms_to_constraints(gmx_domdec_t *dd,
const gmx_mtop_t *mtop,
const int *cginfo,
const t_blocka *at2con_mt, int nrec,
t_ilist *ilc_local,
ind_req_t *ireq)
{
const t_blocka *at2con;
gmx_ga2la_t *ga2la;
gmx_mtop_atomlookup_t alook;
int ncon1;
gmx_molblock_t *molb;
t_iatom *ia1, *ia2, *iap;
int nhome, cg, a, a_gl, a_mol, a_loc, b_lo, offset, mb, molnr, b_mol, i, con, con_offset;
gmx_domdec_constraints_t *dc;
gmx_domdec_specat_comm_t *dcc;
dc = dd->constraints;
dcc = dd->constraint_comm;
ga2la = dd->ga2la;
alook = gmx_mtop_atomlookup_init(mtop);
nhome = 0;
for (cg = 0; cg < dd->ncg_home; cg++)
{
if (GET_CGINFO_CONSTR(cginfo[cg]))
{
for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
{
a_gl = dd->gatindex[a];
gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
molb = &mtop->molblock[mb];
ncon1 = mtop->moltype[molb->type].ilist[F_CONSTR].nr/NRAL(F_SETTLE);
ia1 = mtop->moltype[molb->type].ilist[F_CONSTR].iatoms;
ia2 = mtop->moltype[molb->type].ilist[F_CONSTRNC].iatoms;
/* Calculate the global constraint number offset for the molecule.
* This is only required for the global index to make sure
* that we use each constraint only once.
*/
con_offset =
dc->molb_con_offset[mb] + molnr*dc->molb_ncon_mol[mb];
/* The global atom number offset for this molecule */
offset = a_gl - a_mol;
at2con = &at2con_mt[molb->type];
for (i = at2con->index[a_mol]; i < at2con->index[a_mol+1]; i++)
{
con = at2con->a[i];
iap = constr_iatomptr(ncon1, ia1, ia2, con);
if (a_mol == iap[1])
{
b_mol = iap[2];
}
else
{
b_mol = iap[1];
}
if (ga2la_get_home(ga2la, offset+b_mol, &a_loc))
{
/* Add this fully home constraint at the first atom */
if (a_mol < b_mol)
{
if (dc->ncon+1 > dc->con_nalloc)
{
dc->con_nalloc = over_alloc_large(dc->ncon+1);
srenew(dc->con_gl, dc->con_nalloc);
srenew(dc->con_nlocat, dc->con_nalloc);
}
dc->con_gl[dc->ncon] = con_offset + con;
dc->con_nlocat[dc->ncon] = 2;
if (ilc_local->nr + 3 > ilc_local->nalloc)
{
ilc_local->nalloc = over_alloc_dd(ilc_local->nr + 3);
srenew(ilc_local->iatoms, ilc_local->nalloc);
}
b_lo = a_loc;
ilc_local->iatoms[ilc_local->nr++] = iap[0];
ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? a : b_lo);
ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? b_lo : a );
dc->ncon++;
nhome++;
}
}
else
{
/* We need the nrec constraints coupled to this constraint,
* so we need to walk out of the home cell by nrec+1 atoms,
* since already atom bg is not locally present.
* Therefore we call walk_out with nrec recursions to go
* after this first call.
*/
walk_out(con, con_offset, b_mol, offset, nrec,
ncon1, ia1, ia2, at2con,
dd->ga2la, TRUE, dc, dcc, ilc_local, ireq);
}
}
}
}
}
gmx_mtop_atomlookup_destroy(alook);
if (debug)
{
fprintf(debug,
"Constraints: home %3d border %3d atoms: %3d\n",
nhome, dc->ncon-nhome,
dd->constraint_comm ? ireq->n : 0);
}
}
static void get_verlet_buffer_atomtypes(const gmx_mtop_t *mtop,
verletbuf_atomtype_t **att_p,
int *natt_p,
int *n_nonlin_vsite)
{
verletbuf_atomtype_t *att;
int natt;
int mb, nmol, ft, i, j, a1, a2, a3, a;
const t_atoms *atoms;
const t_ilist *il;
const t_atom *at;
const t_iparams *ip;
real *con_m, *vsite_m, cam[5];
att = NULL;
natt = 0;
if (n_nonlin_vsite != NULL)
{
*n_nonlin_vsite = 0;
}
for (mb = 0; mb < mtop->nmolblock; mb++)
{
nmol = mtop->molblock[mb].nmol;
atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
/* Check for constraints, as they affect the kinetic energy */
snew(con_m, atoms->nr);
snew(vsite_m, atoms->nr);
for (ft = F_CONSTR; ft <= F_CONSTRNC; ft++)
{
il = &mtop->moltype[mtop->molblock[mb].type].ilist[ft];
for (i = 0; i < il->nr; i += 1+NRAL(ft))
{
a1 = il->iatoms[i+1];
a2 = il->iatoms[i+2];
con_m[a1] += atoms->atom[a2].m;
con_m[a2] += atoms->atom[a1].m;
}
}
il = &mtop->moltype[mtop->molblock[mb].type].ilist[F_SETTLE];
for (i = 0; i < il->nr; i += 1+NRAL(F_SETTLE))
{
a1 = il->iatoms[i+1];
a2 = il->iatoms[i+2];
a3 = il->iatoms[i+3];
con_m[a1] += atoms->atom[a2].m + atoms->atom[a3].m;
con_m[a2] += atoms->atom[a1].m + atoms->atom[a3].m;
con_m[a3] += atoms->atom[a1].m + atoms->atom[a2].m;
}
/* Check for virtual sites, determine mass from constructing atoms */
for (ft = 0; ft < F_NRE; ft++)
{
if (IS_VSITE(ft))
{
il = &mtop->moltype[mtop->molblock[mb].type].ilist[ft];
for (i = 0; i < il->nr; i += 1+NRAL(ft))
{
ip = &mtop->ffparams.iparams[il->iatoms[i]];
a1 = il->iatoms[i+1];
for (j = 1; j < NRAL(ft); j++)
{
cam[j] = atoms->atom[il->iatoms[i+1+j]].m;
if (cam[j] == 0)
{
cam[j] = vsite_m[il->iatoms[i+1+j]];
}
if (cam[j] == 0)
{
gmx_fatal(FARGS, "In molecule type '%s' %s construction involves atom %d, which is a virtual site of equal or high complexity. This is not supported.",
*mtop->moltype[mtop->molblock[mb].type].name,
interaction_function[ft].longname,
il->iatoms[i+1+j]+1);
}
}
switch (ft)
{
case F_VSITE2:
/* Exact except for ignoring constraints */
vsite_m[a1] = (cam[2]*sqr(1-ip->vsite.a) + cam[1]*sqr(ip->vsite.a))/(cam[1]*cam[2]);
break;
case F_VSITE3:
/* Exact except for ignoring constraints */
vsite_m[a1] = (cam[2]*cam[3]*sqr(1-ip->vsite.a-ip->vsite.b) + cam[1]*cam[3]*sqr(ip->vsite.a) + cam[1]*cam[2]*sqr(ip->vsite.b))/(cam[1]*cam[2]*cam[3]);
break;
default:
/* Use the mass of the lightest constructing atom.
* This is an approximation.
* If the distance of the virtual site to the
* constructing atom is less than all distances
* between constructing atoms, this is a safe
* over-estimate of the displacement of the vsite.
* This condition holds for all H mass replacement
* replacement vsite constructions, except for SP2/3
* groups. In SP3 groups one H will have a F_VSITE3
* construction, so even there the total drift
* estimation shouldn't be far off.
*/
assert(j >= 1);
vsite_m[a1] = cam[1];
for (j = 2; j < NRAL(ft); j++)
{
vsite_m[a1] = min(vsite_m[a1], cam[j]);
}
if (n_nonlin_vsite != NULL)
{
*n_nonlin_vsite += nmol;
}
break;
}
}
}
}
for (a = 0; a < atoms->nr; a++)
{
at = &atoms->atom[a];
/* We consider an atom constrained, #DOF=2, when it is
* connected with constraints to one or more atoms with
* total mass larger than 1.5 that of the atom itself.
*/
add_at(&att, &natt,
at->m, at->type, at->q, con_m[a] > 1.5*at->m, nmol);
}
sfree(vsite_m);
sfree(con_m);
}
if (gmx_debug_at)
{
for (a = 0; a < natt; a++)
{
fprintf(debug, "type %d: m %5.2f t %d q %6.3f con %d n %d\n",
a, att[a].mass, att[a].type, att[a].q, att[a].con, att[a].n);
}
}
*att_p = att;
*natt_p = natt;
}
void convert_params(int atnr, t_params nbtypes[],
t_molinfo *mi, t_molinfo *intermolecular_interactions,
int comb, double reppow, real fudgeQQ,
gmx_mtop_t *mtop)
{
int i, maxtypes, mt;
unsigned long flags;
gmx_ffparams_t *ffp;
gmx_moltype_t *molt;
t_params *plist;
maxtypes = 0;
ffp = &mtop->ffparams;
ffp->ntypes = 0;
ffp->atnr = atnr;
ffp->functype = NULL;
ffp->iparams = NULL;
ffp->reppow = reppow;
enter_function(&(nbtypes[F_LJ]), (t_functype)F_LJ, comb, reppow, ffp, NULL,
&maxtypes, TRUE, TRUE);
enter_function(&(nbtypes[F_BHAM]), (t_functype)F_BHAM, comb, reppow, ffp, NULL,
&maxtypes, TRUE, TRUE);
for (mt = 0; mt < mtop->nmoltype; mt++)
{
molt = &mtop->moltype[mt];
for (i = 0; (i < F_NRE); i++)
{
molt->ilist[i].nr = 0;
molt->ilist[i].iatoms = NULL;
plist = mi[mt].plist;
flags = interaction_function[i].flags;
if ((i != F_LJ) && (i != F_BHAM) && ((flags & IF_BOND) ||
(flags & IF_VSITE) ||
(flags & IF_CONSTRAINT)))
{
enter_function(&(plist[i]), (t_functype)i, comb, reppow,
ffp, &molt->ilist[i],
&maxtypes, FALSE, (i == F_POSRES || i == F_FBPOSRES));
}
}
}
mtop->bIntermolecularInteractions = FALSE;
if (intermolecular_interactions != NULL)
{
/* Process the intermolecular interaction list */
snew(mtop->intermolecular_ilist, F_NRE);
for (i = 0; (i < F_NRE); i++)
{
mtop->intermolecular_ilist[i].nr = 0;
mtop->intermolecular_ilist[i].iatoms = NULL;
plist = intermolecular_interactions->plist;
if (plist[i].nr > 0)
{
flags = interaction_function[i].flags;
/* For intermolecular interactions we (currently)
* only support potentials.
* Constraints and virtual sites would be possible,
* but require a lot of extra (bug-prone) code.
*/
if (!(flags & IF_BOND))
{
gmx_fatal(FARGS, "The intermolecular_interaction section may only contain bonded potentials");
}
else if (NRAL(i) == 1) /* e.g. position restraints */
{
gmx_fatal(FARGS, "Single atom interactions don't make sense in the intermolecular_interaction section, you can put them in the moleculetype section");
}
else if (flags & IF_CHEMBOND)
{
gmx_fatal(FARGS, "The intermolecular_interaction can not contain chemically bonding interactions");
}
else
{
enter_function(&(plist[i]), (t_functype)i, comb, reppow,
ffp, &mtop->intermolecular_ilist[i],
&maxtypes, FALSE, FALSE);
mtop->bIntermolecularInteractions = TRUE;
}
}
}
if (!mtop->bIntermolecularInteractions)
{
sfree(mtop->intermolecular_ilist);
}
}
if (debug)
{
fprintf(debug, "%s, line %d: There are %d functypes in idef\n",
__FILE__, __LINE__, ffp->ntypes);
}
ffp->fudgeQQ = fudgeQQ;
}
int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
const struct gmx_mtop_t *mtop,
const int *cginfo,
gmx_constr_t constr, int nrec,
t_ilist *il_local)
{
gmx_domdec_constraints_t *dc;
t_ilist *ilc_local, *ils_local;
ind_req_t *ireq;
const t_blocka *at2con_mt;
const int **at2settle_mt;
gmx_hash_t *ga2la_specat;
int at_end, i, j;
t_iatom *iap;
// This code should not be called unless this condition is true,
// because that's the only time init_domdec_constraints is
// called...
GMX_RELEASE_ASSERT(dd->bInterCGcons || dd->bInterCGsettles, "dd_make_local_constraints called when there are no local constraints");
// ... and init_domdec_constraints always sets
// dd->constraint_comm...
GMX_RELEASE_ASSERT(dd->constraint_comm, "Invalid use of dd_make_local_constraints before construction of constraint_comm");
// ... which static analysis needs to be reassured about, because
// otherwise, when dd->bInterCGsettles is
// true. dd->constraint_comm is unilaterally dereferenced before
// the call to atoms_to_settles.
dc = dd->constraints;
ilc_local = &il_local[F_CONSTR];
ils_local = &il_local[F_SETTLE];
dc->ncon = 0;
ilc_local->nr = 0;
if (dd->constraint_comm)
{
at2con_mt = atom2constraints_moltype(constr);
ireq = &dd->constraint_comm->ireq[0];
ireq->n = 0;
}
else
{
// Currently unreachable
at2con_mt = NULL;
ireq = NULL;
}
if (dd->bInterCGsettles)
{
at2settle_mt = atom2settle_moltype(constr);
ils_local->nr = 0;
}
else
{
/* Settle works inside charge groups, we assigned them already */
at2settle_mt = NULL;
}
if (at2settle_mt == NULL)
{
atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec,
ilc_local, ireq);
}
else
{
int t0_set;
int thread;
/* Do the constraints, if present, on the first thread.
* Do the settles on all other threads.
*/
t0_set = ((at2con_mt != NULL && dc->nthread > 1) ? 1 : 0);
#pragma omp parallel for num_threads(dc->nthread) schedule(static)
for (thread = 0; thread < dc->nthread; thread++)
{
try
{
if (at2con_mt && thread == 0)
{
atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec,
ilc_local, ireq);
}
if (thread >= t0_set)
{
int cg0, cg1;
t_ilist *ilst;
ind_req_t *ireqt;
/* Distribute the settle check+assignments over
* dc->nthread or dc->nthread-1 threads.
*/
cg0 = (dd->ncg_home*(thread-t0_set ))/(dc->nthread-t0_set);
cg1 = (dd->ncg_home*(thread-t0_set+1))/(dc->nthread-t0_set);
if (thread == t0_set)
{
ilst = ils_local;
}
else
{
ilst = &dc->ils[thread];
}
ilst->nr = 0;
ireqt = &dd->constraint_comm->ireq[thread];
if (thread > 0)
{
ireqt->n = 0;
}
atoms_to_settles(dd, mtop, cginfo, at2settle_mt,
cg0, cg1,
ilst, ireqt);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
/* Combine the generate settles and requested indices */
for (thread = 1; thread < dc->nthread; thread++)
{
t_ilist *ilst;
ind_req_t *ireqt;
int ia;
if (thread > t0_set)
{
ilst = &dc->ils[thread];
if (ils_local->nr + ilst->nr > ils_local->nalloc)
{
ils_local->nalloc = over_alloc_large(ils_local->nr + ilst->nr);
srenew(ils_local->iatoms, ils_local->nalloc);
}
for (ia = 0; ia < ilst->nr; ia++)
{
ils_local->iatoms[ils_local->nr+ia] = ilst->iatoms[ia];
}
ils_local->nr += ilst->nr;
}
ireqt = &dd->constraint_comm->ireq[thread];
if (ireq->n+ireqt->n > ireq->nalloc)
{
ireq->nalloc = over_alloc_large(ireq->n+ireqt->n);
srenew(ireq->ind, ireq->nalloc);
}
for (ia = 0; ia < ireqt->n; ia++)
{
ireq->ind[ireq->n+ia] = ireqt->ind[ia];
}
ireq->n += ireqt->n;
}
if (debug)
{
fprintf(debug, "Settles: total %3d\n", ils_local->nr/4);
}
}
if (dd->constraint_comm)
{
int nral1;
at_end =
setup_specat_communication(dd, ireq, dd->constraint_comm,
dd->constraints->ga2la,
at_start, 2,
"constraint", " or lincs-order");
/* Fill in the missing indices */
ga2la_specat = dd->constraints->ga2la;
nral1 = 1 + NRAL(F_CONSTR);
for (i = 0; i < ilc_local->nr; i += nral1)
{
iap = ilc_local->iatoms + i;
for (j = 1; j < nral1; j++)
{
if (iap[j] < 0)
{
iap[j] = gmx_hash_get_minone(ga2la_specat, -iap[j]-1);
}
}
}
nral1 = 1 + NRAL(F_SETTLE);
for (i = 0; i < ils_local->nr; i += nral1)
{
iap = ils_local->iatoms + i;
for (j = 1; j < nral1; j++)
{
if (iap[j] < 0)
{
iap[j] = gmx_hash_get_minone(ga2la_specat, -iap[j]-1);
}
}
}
}
else
{
// Currently unreachable
at_end = at_start;
}
return at_end;
}
