}
}
-void make_shake_sblock_serial(shakedata* shaked, const t_idef* idef, const t_mdatoms& md)
+void make_shake_sblock_serial(shakedata* shaked, InteractionDefinitions* idef, const t_mdatoms& md)
{
int i, j, m, ncons;
int bstart, bnr;
t_blocka sblocks;
t_sortblock* sb;
- t_iatom* iatom;
int* inv_sblock;
/* Since we are processing the local topology,
* the F_CONSTRNC ilist has been concatenated to the F_CONSTR ilist.
*/
- ncons = idef->il[F_CONSTR].nr / 3;
+ ncons = idef->il[F_CONSTR].size() / 3;
init_blocka(&sblocks);
sfree(sblocks.index); // To solve memory leak
- gen_sblocks(nullptr, 0, md.homenr, idef, &sblocks, FALSE);
+ gen_sblocks(nullptr, 0, md.homenr, *idef, &sblocks, FALSE);
/*
bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
* sort the constraints in order of the sblock number
* and the atom numbers, really sorting a segment of the array!
*/
- iatom = idef->il[F_CONSTR].iatoms;
+ int* iatom = idef->il[F_CONSTR].iatoms.data();
snew(sb, ncons);
for (i = 0; (i < ncons); i++, iatom += 3)
{
pr_sortblock(debug, "After sorting", ncons, sb);
}
- iatom = idef->il[F_CONSTR].iatoms;
+ iatom = idef->il[F_CONSTR].iatoms.data();
for (i = 0; (i < ncons); i++, iatom += 3)
{
for (m = 0; (m < 3); m++)
}
// TODO: Check if this code is useful. It might never be called.
-void make_shake_sblock_dd(shakedata* shaked, const t_ilist* ilcon, const gmx_domdec_t* dd)
+void make_shake_sblock_dd(shakedata* shaked, const InteractionList& ilcon, const gmx_domdec_t* dd)
{
- int ncons, c, cg;
- t_iatom* iatom;
+ int ncons, c, cg;
if (dd->ncg_home + 1 > shaked->sblock_nalloc)
{
srenew(shaked->sblock, shaked->sblock_nalloc);
}
- ncons = ilcon->nr / 3;
- iatom = ilcon->iatoms;
- shaked->nblocks = 0;
- cg = 0;
+ ncons = ilcon.size() / 3;
+ const int* iatom = ilcon.iatoms.data();
+ shaked->nblocks = 0;
+ cg = 0;
for (c = 0; c < ncons; c++)
{
if (c == 0 || iatom[1] >= cg + 1)
}
//! Applies SHAKE
-static int vec_shakef(FILE* fplog,
- shakedata* shaked,
- const real invmass[],
- int ncon,
- t_iparams ip[],
- t_iatom* iatom,
- real tol,
- const rvec x[],
- rvec prime[],
- real omega,
- bool bFEP,
- real lambda,
- real scaled_lagrange_multiplier[],
- real invdt,
- rvec* v,
- bool bCalcVir,
- tensor vir_r_m_dr,
- ConstraintVariable econq)
+static int vec_shakef(FILE* fplog,
+ shakedata* shaked,
+ const real invmass[],
+ int ncon,
+ ArrayRef<const t_iparams> ip,
+ const int* iatom,
+ real tol,
+ const rvec x[],
+ rvec prime[],
+ real omega,
+ bool bFEP,
+ real lambda,
+ real scaled_lagrange_multiplier[],
+ real invdt,
+ rvec* v,
+ bool bCalcVir,
+ tensor vir_r_m_dr,
+ ConstraintVariable econq)
{
- rvec* rij;
- real * half_of_reduced_mass, *distance_squared_tolerance, *constraint_distance_squared;
- int maxnit = 1000;
- int nit = 0, ll, i, j, d, d2, type;
- t_iatom* ia;
- real L1;
- real mm = 0., tmp;
- int error = 0;
- real constraint_distance;
+ rvec* rij;
+ real *half_of_reduced_mass, *distance_squared_tolerance, *constraint_distance_squared;
+ int maxnit = 1000;
+ int nit = 0, ll, i, j, d, d2, type;
+ real L1;
+ real mm = 0., tmp;
+ int error = 0;
+ real constraint_distance;
if (ncon > shaked->nalloc)
{
distance_squared_tolerance = shaked->distance_squared_tolerance;
constraint_distance_squared = shaked->constraint_distance_squared;
- L1 = 1.0 - lambda;
- ia = iatom;
+ L1 = 1.0 - lambda;
+ const int* ia = iatom;
for (ll = 0; (ll < ncon); ll++, ia += 3)
{
type = ia[0];
}
//! Check that constraints are satisfied.
-static void check_cons(FILE* log,
- int nc,
- const rvec x[],
- rvec prime[],
- rvec v[],
- t_iparams ip[],
- t_iatom* iatom,
- const real invmass[],
- ConstraintVariable econq)
+static void check_cons(FILE* log,
+ int nc,
+ const rvec x[],
+ rvec prime[],
+ rvec v[],
+ ArrayRef<const t_iparams> ip,
+ const int* iatom,
+ const real invmass[],
+ ConstraintVariable econq)
{
- t_iatom* ia;
- int ai, aj;
- int i;
- real d, dp;
- rvec dx, dv;
+ int ai, aj;
+ int i;
+ real d, dp;
+ rvec dx, dv;
GMX_ASSERT(v, "Input has to be non-null");
fprintf(log, " i mi j mj before after should be\n");
- ia = iatom;
+ const int* ia = iatom;
for (i = 0; (i < nc); i++, ia += 3)
{
ai = ia[1];
}
//! Applies SHAKE.
-static bool bshakef(FILE* log,
- shakedata* shaked,
- const real invmass[],
- const t_idef& idef,
- const t_inputrec& ir,
- const rvec x_s[],
- rvec prime[],
- t_nrnb* nrnb,
- real lambda,
- real* dvdlambda,
- real invdt,
- rvec* v,
- bool bCalcVir,
- tensor vir_r_m_dr,
- bool bDumpOnError,
- ConstraintVariable econq)
+static bool bshakef(FILE* log,
+ shakedata* shaked,
+ const real invmass[],
+ const InteractionDefinitions& idef,
+ const t_inputrec& ir,
+ const rvec x_s[],
+ rvec prime[],
+ t_nrnb* nrnb,
+ real lambda,
+ real* dvdlambda,
+ real invdt,
+ rvec* v,
+ bool bCalcVir,
+ tensor vir_r_m_dr,
+ bool bDumpOnError,
+ ConstraintVariable econq)
{
- t_iatom* iatoms;
- real * lam, dt_2, dvdl;
- int i, n0, ncon, blen, type, ll;
- int tnit = 0, trij = 0;
+ real *lam, dt_2, dvdl;
+ int i, n0, ncon, blen, type, ll;
+ int tnit = 0, trij = 0;
- ncon = idef.il[F_CONSTR].nr / 3;
+ ncon = idef.il[F_CONSTR].size() / 3;
for (ll = 0; ll < ncon; ll++)
{
// TODO Rewrite this block so that it is obvious that i, iatoms
// and lam are all iteration variables. Is this easier if the
// sblock data structure is organized differently?
- iatoms = &(idef.il[F_CONSTR].iatoms[shaked->sblock[0]]);
- lam = shaked->scaled_lagrange_multiplier;
+ const int* iatoms = &(idef.il[F_CONSTR].iatoms[shaked->sblock[0]]);
+ lam = shaked->scaled_lagrange_multiplier;
for (i = 0; (i < shaked->nblocks);)
{
blen = (shaked->sblock[i + 1] - shaked->sblock[i]);
{
if (ir.efep != efepNO)
{
- real bondA, bondB;
+ ArrayRef<const t_iparams> iparams = idef.iparams;
+
/* TODO This should probably use invdt, so that sd integrator scaling works properly */
dt_2 = 1 / gmx::square(ir.delta_t);
dvdl = 0;
/* The vector scaled_lagrange_multiplier[ll] contains the value -2 r_ll eta_ll
(eta_ll is the estimate of the Langrangian, definition on page 336 of Ryckaert et
al 1977), so the pre-factors are already present. */
- bondA = idef.iparams[type].constr.dA;
- bondB = idef.iparams[type].constr.dB;
+ const real bondA = iparams[type].constr.dA;
+ const real bondB = iparams[type].constr.dB;
dvdl += shaked->scaled_lagrange_multiplier[ll] * dt_2 * (bondB - bondA);
}
*dvdlambda += dvdl;
return TRUE;
}
-bool constrain_shake(FILE* log,
- shakedata* shaked,
- const real invmass[],
- const t_idef& idef,
- const t_inputrec& ir,
- const rvec x_s[],
- rvec xprime[],
- rvec vprime[],
- t_nrnb* nrnb,
- real lambda,
- real* dvdlambda,
- real invdt,
- rvec* v,
- bool bCalcVir,
- tensor vir_r_m_dr,
- bool bDumpOnError,
- ConstraintVariable econq)
+bool constrain_shake(FILE* log,
+ shakedata* shaked,
+ const real invmass[],
+ const InteractionDefinitions& idef,
+ const t_inputrec& ir,
+ const rvec x_s[],
+ rvec xprime[],
+ rvec vprime[],
+ t_nrnb* nrnb,
+ real lambda,
+ real* dvdlambda,
+ real invdt,
+ rvec* v,
+ bool bCalcVir,
+ tensor vir_r_m_dr,
+ bool bDumpOnError,
+ ConstraintVariable econq)
{
if (shaked->nblocks == 0)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff