/* The source code in this file should be thread-safe.
Please keep it that way. */
-history_t::history_t() : disre_initf(0),
- ndisrepairs(0),
- disre_rm3tav(nullptr),
- orire_initf(0),
- norire_Dtav(0),
- orire_Dtav(nullptr)
-{
-};
-
-ekinstate_t::ekinstate_t() : bUpToDate(FALSE),
- ekin_n(0),
- ekinh(nullptr),
- ekinf(nullptr),
- ekinh_old(nullptr),
- ekin_total(),
-
- dekindl(0),
- mvcos(0)
+history_t::history_t() :
+ disre_initf(0),
+ ndisrepairs(0),
+ disre_rm3tav(nullptr),
+ orire_initf(0),
+ norire_Dtav(0),
+ orire_Dtav(nullptr){};
+
+ekinstate_t::ekinstate_t() :
+ bUpToDate(FALSE),
+ ekin_n(0),
+ ekinh(nullptr),
+ ekinf(nullptr),
+ ekinh_old(nullptr),
+ ekin_total(),
+
+ dekindl(0),
+ mvcos(0)
{
clear_mat(ekin_total);
};
-void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
+void init_gtc_state(t_state* state, int ngtc, int nnhpres, int nhchainlength)
{
state->ngtc = ngtc;
state->nnhpres = nnhpres;
state->nhchainlength = nhchainlength;
- state->nosehoover_xi.resize(state->nhchainlength*state->ngtc, 0);
- state->nosehoover_vxi.resize(state->nhchainlength*state->ngtc, 0);
+ state->nosehoover_xi.resize(state->nhchainlength * state->ngtc, 0);
+ state->nosehoover_vxi.resize(state->nhchainlength * state->ngtc, 0);
state->therm_integral.resize(state->ngtc, 0);
state->baros_integral = 0.0;
- state->nhpres_xi.resize(state->nhchainlength*nnhpres, 0);
- state->nhpres_vxi.resize(state->nhchainlength*nnhpres, 0);
+ state->nhpres_xi.resize(state->nhchainlength * nnhpres, 0);
+ state->nhpres_vxi.resize(state->nhchainlength * nnhpres, 0);
}
/* Checkpoint code relies on this function having no effect if
state->natoms is > 0 and passed as natoms. */
-void state_change_natoms(t_state *state, int natoms)
+void state_change_natoms(t_state* state, int natoms)
{
state->natoms = natoms;
}
}
-void init_dfhist_state(t_state *state, int dfhistNumLambda)
+void init_dfhist_state(t_state* state, int dfhistNumLambda)
{
if (dfhistNumLambda > 0)
{
}
}
-void comp_state(const t_state *st1, const t_state *st2,
- gmx_bool bRMSD, real ftol, real abstol)
+void comp_state(const t_state* st1, const t_state* st2, gmx_bool bRMSD, real ftol, real abstol)
{
int i, j, nc;
cmp_rvecs(stdout, "box_rel", DIM, st1->box_rel, st2->box_rel, FALSE, ftol, abstol);
fprintf(stdout, "comparing boxv\n");
cmp_rvecs(stdout, "boxv", DIM, st1->boxv, st2->boxv, FALSE, ftol, abstol);
- if (st1->flags & (1<<estSVIR_PREV))
+ if (st1->flags & (1 << estSVIR_PREV))
{
fprintf(stdout, "comparing shake vir_prev\n");
cmp_rvecs(stdout, "svir_prev", DIM, st1->svir_prev, st2->svir_prev, FALSE, ftol, abstol);
}
- if (st1->flags & (1<<estFVIR_PREV))
+ if (st1->flags & (1 << estFVIR_PREV))
{
fprintf(stdout, "comparing force vir_prev\n");
cmp_rvecs(stdout, "fvir_prev", DIM, st1->fvir_prev, st2->fvir_prev, FALSE, ftol, abstol);
}
- if (st1->flags & (1<<estPRES_PREV))
+ if (st1->flags & (1 << estPRES_PREV))
{
fprintf(stdout, "comparing prev_pres\n");
cmp_rvecs(stdout, "pres_prev", DIM, st1->pres_prev, st2->pres_prev, FALSE, ftol, abstol);
{
for (i = 0; i < st1->ngtc; i++)
{
- nc = i*st1->nhchainlength;
+ nc = i * st1->nhchainlength;
for (j = 0; j < nc; j++)
{
- cmp_real(stdout, "nosehoover_xi",
- i, st1->nosehoover_xi[nc+j], st2->nosehoover_xi[nc+j], ftol, abstol);
+ cmp_real(stdout, "nosehoover_xi", i, st1->nosehoover_xi[nc + j],
+ st2->nosehoover_xi[nc + j], ftol, abstol);
}
}
}
{
for (i = 0; i < st1->nnhpres; i++)
{
- nc = i*st1->nhchainlength;
+ nc = i * st1->nhchainlength;
for (j = 0; j < nc; j++)
{
- cmp_real(stdout, "nosehoover_xi",
- i, st1->nhpres_xi[nc+j], st2->nhpres_xi[nc+j], ftol, abstol);
+ cmp_real(stdout, "nosehoover_xi", i, st1->nhpres_xi[nc + j], st2->nhpres_xi[nc + j],
+ ftol, abstol);
}
}
}
cmp_int(stdout, "natoms", -1, st1->natoms, st2->natoms);
if (st1->natoms == st2->natoms)
{
- if ((st1->flags & (1<<estX)) && (st2->flags & (1<<estX)))
+ if ((st1->flags & (1 << estX)) && (st2->flags & (1 << estX)))
{
fprintf(stdout, "comparing x\n");
- cmp_rvecs(stdout, "x", st1->natoms, st1->x.rvec_array(), st2->x.rvec_array(), bRMSD, ftol, abstol);
+ cmp_rvecs(stdout, "x", st1->natoms, st1->x.rvec_array(), st2->x.rvec_array(), bRMSD,
+ ftol, abstol);
}
- if ((st1->flags & (1<<estV)) && (st2->flags & (1<<estV)))
+ if ((st1->flags & (1 << estV)) && (st2->flags & (1 << estV)))
{
fprintf(stdout, "comparing v\n");
- cmp_rvecs(stdout, "v", st1->natoms, st1->v.rvec_array(), st2->v.rvec_array(), bRMSD, ftol, abstol);
+ cmp_rvecs(stdout, "v", st1->natoms, st1->v.rvec_array(), st2->v.rvec_array(), bRMSD,
+ ftol, abstol);
}
}
}
-rvec *makeRvecArray(gmx::ArrayRef<const gmx::RVec> v,
- gmx::index n)
+rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
{
GMX_ASSERT(v.ssize() >= n, "We can't copy more elements than the vector size");
- rvec *dest;
+ rvec* dest;
snew(dest, n);
- const rvec *vPtr = as_rvec_array(v.data());
+ const rvec* vPtr = as_rvec_array(v.data());
for (gmx::index i = 0; i < n; i++)
{
copy_rvec(vPtr[i], dest[i]);
return dest;
}
-t_state::t_state() : natoms(0),
- ngtc(0),
- nnhpres(0),
- nhchainlength(0),
- flags(0),
- fep_state(0),
- lambda(),
-
- baros_integral(0),
- veta(0),
- vol0(0),
-
- ekinstate(),
- hist(),
- dfhist(nullptr),
- awhHistory(nullptr),
- ddp_count(0),
- ddp_count_cg_gl(0)
+t_state::t_state() :
+ natoms(0),
+ ngtc(0),
+ nnhpres(0),
+ nhchainlength(0),
+ flags(0),
+ fep_state(0),
+ lambda(),
+
+ baros_integral(0),
+ veta(0),
+ vol0(0),
+
+ ekinstate(),
+ hist(),
+ dfhist(nullptr),
+ awhHistory(nullptr),
+ ddp_count(0),
+ ddp_count_cg_gl(0)
{
// It would be nicer to initialize these with {} or {{0}} in the
// above initialization list, but uncrustify doesn't understand
// that.
// TODO Fix this if we switch to clang-format some time.
- lambda = {{ 0 }};
+ lambda = { { 0 } };
clear_mat(box);
clear_mat(box_rel);
clear_mat(boxv);
clear_mat(fvir_prev);
}
-void set_box_rel(const t_inputrec *ir, t_state *state)
+void set_box_rel(const t_inputrec* ir, t_state* state)
{
/* Make sure the box obeys the restrictions before we fix the ratios */
correct_box(nullptr, 0, state->box, nullptr);
}
}
-void preserve_box_shape(const t_inputrec *ir, matrix box_rel, matrix box)
+void preserve_box_shape(const t_inputrec* ir, matrix box_rel, matrix box)
{
if (inputrecPreserveShape(ir))
{
}
}
-void initialize_lambdas(FILE *fplog,
- const t_inputrec &ir,
+void initialize_lambdas(FILE* fplog,
+ const t_inputrec& ir,
bool isMaster,
- int *fep_state,
+ int* fep_state,
gmx::ArrayRef<real> lambda,
- double *lam0)
+ double* lam0)
{
/* TODO: Clean up initialization of fep_state and lambda in
t_state. This function works, but could probably use a logic
return;
}
- const t_lambda *fep = ir.fepvals;
+ const t_lambda* fep = ir.fepvals;
if (isMaster)
{
*fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
if (fplog != nullptr)
{
fprintf(fplog, "Initial vector of lambda components:[ ");
- for (const auto &l : lambda)
+ for (const auto& l : lambda)
{
fprintf(fplog, "%10.4f ", l);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff