using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
-typedef struct {
+struct gmx_sd_const_t {
double em;
-} gmx_sd_const_t;
+};
-typedef struct {
+struct gmx_sd_sigma_t {
real V;
-} gmx_sd_sigma_t;
+};
struct gmx_stochd_t
{
std::vector<bool> randomize_group;
std::vector<real> boltzfac;
- gmx_stochd_t(const t_inputrec *ir);
+ explicit gmx_stochd_t(const t_inputrec *ir);
};
-struct gmx_update_t
+//! pImpled implementation for Update
+class Update::Impl
{
- std::unique_ptr<gmx_stochd_t> sd;
- /* xprime for constraint algorithms */
- PaddedVector<gmx::RVec> xp;
+ public:
+ //! Constructor
+ Impl(const t_inputrec *ir, BoxDeformation *boxDeformation);
+ //! Destructor
+ ~Impl() = default;
+ //! stochastic dynamics struct
+ std::unique_ptr<gmx_stochd_t> sd;
+ //! xprime for constraint algorithms
+ PaddedVector<RVec> xp;
+ //! Box deformation handler (or nullptr if inactive).
+ BoxDeformation *deform = nullptr;
+};
- /* Variables for the deform algorithm */
- int64_t deformref_step;
- matrix deformref_box;
+Update::Update(const t_inputrec *ir, BoxDeformation *boxDeformation)
+ : impl_(new Impl(ir, boxDeformation))
+{};
- //! Box deformation handler (or nullptr if inactive).
- gmx::BoxDeformation *deform;
-};
+Update::~Update()
+{};
+
+gmx_stochd_t* Update::sd() const
+{
+ return impl_->sd.get();
+}
+
+PaddedVector<RVec> * Update::xp()
+{
+ return &impl_->xp;
+}
+
+BoxDeformation * Update::deform() const
+{
+ return impl_->deform;
+}
static bool isTemperatureCouplingStep(int64_t step, const t_inputrec *ir)
{
}
}
-void update_temperature_constants(gmx_update_t *upd, const t_inputrec *ir)
+void update_temperature_constants(gmx_stochd_t *sd, const t_inputrec *ir)
{
if (ir->eI == eiBD)
{
{
for (int gt = 0; gt < ir->opts.ngtc; gt++)
{
- upd->sd->bd_rf[gt] = std::sqrt(2.0*BOLTZ*ir->opts.ref_t[gt]/(ir->bd_fric*ir->delta_t));
+ sd->bd_rf[gt] = std::sqrt(2.0*BOLTZ*ir->opts.ref_t[gt]/(ir->bd_fric*ir->delta_t));
}
}
else
{
for (int gt = 0; gt < ir->opts.ngtc; gt++)
{
- upd->sd->bd_rf[gt] = std::sqrt(2.0*BOLTZ*ir->opts.ref_t[gt]);
+ sd->bd_rf[gt] = std::sqrt(2.0*BOLTZ*ir->opts.ref_t[gt]);
}
}
}
{
real kT = BOLTZ*ir->opts.ref_t[gt];
/* The mass is accounted for later, since this differs per atom */
- upd->sd->sdsig[gt].V = std::sqrt(kT*(1 - upd->sd->sdc[gt].em*upd->sd->sdc[gt].em));
+ sd->sdsig[gt].V = std::sqrt(kT*(1 - sd->sdc[gt].em * sd->sdc[gt].em));
}
}
}
-gmx_update_t *init_update(const t_inputrec *ir,
- gmx::BoxDeformation *deform)
+Update::Impl::Impl(const t_inputrec *ir, BoxDeformation *boxDeformation)
{
- gmx_update_t *upd = new(gmx_update_t);
-
- upd->sd = gmx::compat::make_unique<gmx_stochd_t>(ir);
-
- update_temperature_constants(upd, ir);
-
- upd->xp.resizeWithPadding(0);
-
- upd->deform = deform;
-
- return upd;
+ sd = gmx::compat::make_unique<gmx_stochd_t>(ir);
+ update_temperature_constants(sd.get(), ir);
+ xp.resizeWithPadding(0);
+ deform = boxDeformation;
}
-void update_realloc(gmx_update_t *upd, int natoms)
+void Update::setNumAtoms(int nAtoms)
{
- GMX_ASSERT(upd, "upd must be allocated before its fields can be reallocated");
- upd->xp.resizeWithPadding(natoms);
+ impl_->xp.resizeWithPadding(nAtoms);
}
/*! \brief Sets the SD update type */
}
}
-void constrain_coordinates(int64_t step,
- real *dvdlambda, /* the contribution to be added to the bonded interactions */
- t_state *state,
- tensor vir_part,
- gmx_update_t *upd,
- gmx::Constraints *constr,
- gmx_bool bCalcVir,
- bool do_log,
- bool do_ene)
+void constrain_coordinates(int64_t step,
+ real *dvdlambda, /* the contribution to be added to the bonded interactions */
+ t_state *state,
+ tensor vir_part,
+ Update *upd,
+ gmx::Constraints *constr,
+ gmx_bool bCalcVir,
+ bool do_log,
+ bool do_ene)
{
if (!constr)
{
/* Constrain the coordinates upd->xp */
constr->apply(do_log, do_ene,
step, 1, 1.0,
- state->x.rvec_array(), upd->xp.rvec_array(), nullptr,
+ state->x.rvec_array(), upd->xp()->rvec_array(), nullptr,
state->box,
state->lambda[efptBONDED], dvdlambda,
as_rvec_array(state->v.data()), bCalcVir ? &vir_con : nullptr, ConstraintVariable::Positions);
}
void
-update_sd_second_half(int64_t step,
- real *dvdlambda, /* the contribution to be added to the bonded interactions */
- const t_inputrec *inputrec, /* input record and box stuff */
- const t_mdatoms *md,
- t_state *state,
- const t_commrec *cr,
- t_nrnb *nrnb,
- gmx_wallcycle_t wcycle,
- gmx_update_t *upd,
- gmx::Constraints *constr,
- bool do_log,
- bool do_ene)
+update_sd_second_half(int64_t step,
+ real *dvdlambda, /* the contribution to be added to the bonded interactions */
+ const t_inputrec *inputrec, /* input record and box stuff */
+ const t_mdatoms *md,
+ t_state *state,
+ const t_commrec *cr,
+ t_nrnb *nrnb,
+ gmx_wallcycle_t wcycle,
+ Update *upd,
+ gmx::Constraints *constr,
+ bool do_log,
+ bool do_ene)
{
if (!constr)
{
getThreadAtomRange(nth, th, homenr, &start_th, &end_th);
doSDUpdateGeneral<SDUpdate::FrictionAndNoiseOnly>
- (*upd->sd,
+ (*upd->sd(),
start_th, end_th, dt,
inputrec->opts.acc, inputrec->opts.nFreeze,
md->invmass, md->ptype,
md->cFREEZE, nullptr, md->cTC,
- state->x.rvec_array(), upd->xp.rvec_array(),
+ state->x.rvec_array(), upd->xp()->rvec_array(),
state->v.rvec_array(), nullptr,
step, inputrec->ld_seed,
DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr);
/* Constrain the coordinates upd->xp for half a time step */
constr->apply(do_log, do_ene,
step, 1, 0.5,
- state->x.rvec_array(), upd->xp.rvec_array(), nullptr,
+ state->x.rvec_array(), upd->xp()->rvec_array(), nullptr,
state->box,
state->lambda[efptBONDED], dvdlambda,
as_rvec_array(state->v.data()), nullptr, ConstraintVariable::Positions);
}
}
-void finish_update(const t_inputrec *inputrec, /* input record and box stuff */
- const t_mdatoms *md,
- t_state *state,
- const t_graph *graph,
- t_nrnb *nrnb,
- gmx_wallcycle_t wcycle,
- gmx_update_t *upd,
- const gmx::Constraints *constr)
+void finish_update(const t_inputrec *inputrec, /* input record and box stuff */
+ const t_mdatoms *md,
+ t_state *state,
+ const t_graph *graph,
+ t_nrnb *nrnb,
+ gmx_wallcycle_t wcycle,
+ Update *upd,
+ const gmx::Constraints *constr)
{
int homenr = md->homenr;
}
if (partialFreezeAndConstraints)
{
- auto xp = makeArrayRef(upd->xp).subArray(0, homenr);
+ auto xp = makeArrayRef(*upd->xp()).subArray(0, homenr);
auto x = makeConstArrayRef(state->x).subArray(0, homenr);
for (int i = 0; i < homenr; i++)
{
if (graph && (graph->nnodes > 0))
{
- unshift_x(graph, state->box, state->x.rvec_array(), upd->xp.rvec_array());
+ unshift_x(graph, state->box, state->x.rvec_array(), upd->xp()->rvec_array());
if (TRICLINIC(state->box))
{
inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
}
else
{
- auto xp = makeConstArrayRef(upd->xp).subArray(0, homenr);
+ auto xp = makeConstArrayRef(*upd->xp()).subArray(0, homenr);
auto x = makeArrayRef(state->x).subArray(0, homenr);
#ifndef __clang_analyzer__
int gmx_unused nth = gmx_omp_nthreads_get(emntUpdate);
const matrix parrinellorahmanMu,
t_state *state,
t_nrnb *nrnb,
- gmx_update_t *upd)
+ Update *upd)
{
int start = 0;
int homenr = md->homenr;
break;
}
- if (upd->deform)
+ if (upd->deform())
{
auto localX = makeArrayRef(state->x).subArray(start, homenr);
- upd->deform->apply(localX, state->box, step);
+ upd->deform()->apply(localX, state->box, step);
}
}
const t_fcdata *fcd,
const gmx_ekindata_t *ekind,
const matrix M,
- gmx_update_t *upd,
+ Update *upd,
int UpdatePart,
const t_commrec *cr, /* these shouldn't be here -- need to think about it */
const gmx::Constraints *constr)
getThreadAtomRange(nth, th, homenr, &start_th, &end_th);
const rvec *x_rvec = state->x.rvec_array();
- rvec *xp_rvec = upd->xp.rvec_array();
+ rvec *xp_rvec = upd->xp()->rvec_array();
rvec *v_rvec = state->v.rvec_array();
const rvec *f_rvec = as_rvec_array(f.unpaddedArrayRef().data());
{
// With constraints, the SD update is done in 2 parts
doSDUpdateGeneral<SDUpdate::ForcesOnly>
- (*upd->sd,
+ (*upd->sd(),
start_th, end_th, dt,
inputrec->opts.acc, inputrec->opts.nFreeze,
md->invmass, md->ptype,
else
{
doSDUpdateGeneral<SDUpdate::Combined>
- (*upd->sd,
+ (*upd->sd(),
start_th, end_th, dt,
inputrec->opts.acc, inputrec->opts.nFreeze,
md->invmass, md->ptype,
md->cFREEZE, md->cTC,
x_rvec, xp_rvec, v_rvec, f_rvec,
inputrec->bd_fric,
- upd->sd->bd_rf.data(),
+ upd->sd()->bd_rf.data(),
step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr);
break;
case (eiVV):
extern gmx_bool update_randomize_velocities(const t_inputrec *ir, int64_t step, const t_commrec *cr,
const t_mdatoms *md,
gmx::ArrayRef<gmx::RVec> v,
- const gmx_update_t *upd,
+ const Update *upd,
const gmx::Constraints *constr)
{
if ((ir->etc == etcANDERSEN) || do_per_step(step, roundToInt(1.0/rate)))
{
andersen_tcoupl(ir, step, cr, md, v, rate,
- upd->sd->randomize_group,
- upd->sd->boltzfac);
+ upd->sd()->randomize_group,
+ upd->sd()->boltzfac);
return TRUE;
}
return FALSE;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff