void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b)
{
if (inputrecPreserveShape(ir))
{
do_box_rel(ir, box_rel, b, FALSE);
}
}
void set_box_rel(t_inputrec *ir, t_state *state)
{
/* Make sure the box obeys the restrictions before we fix the ratios */
correct_box(NULL, 0, state->box, NULL);
clear_mat(state->box_rel);
if (inputrecPreserveShape(ir))
{
do_box_rel(ir, state->box_rel, state->box, TRUE);
}
}
void set_state_entries(t_state *state, const t_inputrec *ir)
{
/* The entries in the state in the tpx file might not correspond
* with what is needed, so we correct this here.
*/
state->flags = 0;
if (ir->efep != efepNO || ir->bExpanded)
{
state->flags |= (1<<estLAMBDA);
state->flags |= (1<<estFEPSTATE);
}
state->flags |= (1<<estX);
if (state->lambda == NULL)
{
snew(state->lambda, efptNR);
}
if (state->x == NULL)
{
/* We need to allocate one element extra, since we might use
* (unaligned) 4-wide SIMD loads to access rvec entries.
*/
snew(state->x, state->nalloc + 1);
}
if (EI_DYNAMICS(ir->eI))
{
state->flags |= (1<<estV);
if (state->v == NULL)
{
snew(state->v, state->nalloc + 1);
}
}
if (ir->eI == eiCG)
{
state->flags |= (1<<estCGP);
if (state->cg_p == NULL)
{
/* cg_p is not stored in the tpx file, so we need to allocate it */
snew(state->cg_p, state->nalloc + 1);
}
}
state->nnhpres = 0;
if (ir->ePBC != epbcNONE)
{
state->flags |= (1<<estBOX);
if (inputrecPreserveShape(ir))
{
state->flags |= (1<<estBOX_REL);
}
if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
{
state->flags |= (1<<estBOXV);
}
if (ir->epc != epcNO)
{
if (inputrecNptTrotter(ir) || (inputrecNphTrotter(ir)))
{
state->nnhpres = 1;
state->flags |= (1<<estNHPRES_XI);
state->flags |= (1<<estNHPRES_VXI);
state->flags |= (1<<estSVIR_PREV);
state->flags |= (1<<estFVIR_PREV);
state->flags |= (1<<estVETA);
state->flags |= (1<<estVOL0);
}
else
{
state->flags |= (1<<estPRES_PREV);
}
}
}
if (ir->etc == etcNOSEHOOVER)
{
state->flags |= (1<<estNH_XI);
state->flags |= (1<<estNH_VXI);
}
if (ir->etc == etcVRESCALE)
{
state->flags |= (1<<estTC_INT);
}
init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
init_ekinstate(&state->ekinstate, ir);
snew(state->enerhist, 1);
init_energyhistory(state->enerhist);
init_df_history(&state->dfhist, ir->fepvals->n_lambda);
state->swapstate.eSwapCoords = ir->eSwapCoords;
}
void set_state_entries(t_state *state, const t_inputrec *ir)
{
/* The entries in the state in the tpx file might not correspond
* with what is needed, so we correct this here.
*/
state->flags = 0;
if (ir->efep != efepNO || ir->bExpanded)
{
state->flags |= (1<<estLAMBDA);
state->flags |= (1<<estFEPSTATE);
}
state->flags |= (1<<estX);
state->lambda.resize(efptNR);
GMX_RELEASE_ASSERT(state->x.size() >= static_cast<unsigned int>(state->natoms), "We should start a run with an initialized state->x");
if (EI_DYNAMICS(ir->eI))
{
state->flags |= (1<<estV);
state->v.resize(state->natoms + 1);
}
if (ir->eI == eiCG)
{
state->flags |= (1<<estCGP);
/* cg_p is not stored in the tpx file, so we need to allocate it */
state->cg_p.resize(state->natoms + 1);
}
state->nnhpres = 0;
if (ir->ePBC != epbcNONE)
{
state->flags |= (1<<estBOX);
if (inputrecPreserveShape(ir))
{
state->flags |= (1<<estBOX_REL);
}
if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
{
state->flags |= (1<<estBOXV);
state->flags |= (1<<estPRES_PREV);
}
if (inputrecNptTrotter(ir) || (inputrecNphTrotter(ir)))
{
state->nnhpres = 1;
state->flags |= (1<<estNHPRES_XI);
state->flags |= (1<<estNHPRES_VXI);
state->flags |= (1<<estSVIR_PREV);
state->flags |= (1<<estFVIR_PREV);
state->flags |= (1<<estVETA);
state->flags |= (1<<estVOL0);
}
}
if (ir->etc == etcNOSEHOOVER)
{
state->flags |= (1<<estNH_XI);
state->flags |= (1<<estNH_VXI);
}
if (ir->etc == etcVRESCALE)
{
state->flags |= (1<<estTC_INT);
}
init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
init_ekinstate(&state->ekinstate, ir);
if (ir->bExpanded)
{
snew(state->dfhist, 1);
init_df_history(state->dfhist, ir->fepvals->n_lambda);
}
if (ir->eSwapCoords != eswapNO)
{
if (state->swapstate == NULL)
{
snew(state->swapstate, 1);
}
state->swapstate->eSwapCoords = ir->eSwapCoords;
}
}
