/* initialize the collection*/
void mde_delta_h_coll_init(t_mde_delta_h_coll *dhc, const t_inputrec *ir)
{
int i;
double lambda;
int ndhmax=ir->nstenergy/ir->nstcalcenergy;
dhc->temperature=ir->opts.ref_t[0]; /* only store system temperature */
dhc->start_time=0.;
dhc->delta_time=ir->delta_t*ir->fepvals->nstdhdl;
dhc->start_time_set=FALSE;
/* for continuous change of lambda values */
dhc->start_lambda=ir->fepvals->init_lambda;
dhc->delta_lambda=ir->fepvals->delta_lambda*ir->fepvals->nstdhdl;
/* total number of raw data points in the sample */
dhc->ndh = 0;
/* include one more for the specification of the state, by lambda or fep_state, store as double for now*/
if (ir->expandedvals->elamstats > elamstatsNO) {
dhc->ndh +=1;
}
/* whether to print energies */
if (ir->fepvals->bPrintEnergy) {
dhc->ndh += 1;
}
/* add the dhdl's */
for (i=0;i<efptNR;i++)
{
if (ir->fepvals->separate_dvdl[i])
{
dhc->ndh+=1;
}
}
/* add the lambdas */
dhc->ndh += ir->fepvals->n_lambda;
if (ir->epc > epcNO) {
dhc->ndh += 1; /* include pressure-volume work */
}
snew(dhc->dh, dhc->ndh);
for(i=0;i<dhc->ndh;i++)
{
mde_delta_h_init(dhc->dh+i, ir->fepvals->dh_hist_size,
ir->fepvals->dh_hist_spacing, ndhmax);
}
}
/* initialize the collection*/
void mde_delta_h_coll_init(t_mde_delta_h_coll *dhc, const t_inputrec *ir)
{
int i, j, n;
double lambda;
double *lambda_vec;
int ndhmax = ir->nstenergy/ir->nstcalcenergy;
t_lambda *fep = ir->fepvals;
dhc->temperature = ir->opts.ref_t[0]; /* only store system temperature */
dhc->start_time = 0.;
dhc->delta_time = ir->delta_t*ir->fepvals->nstdhdl;
dhc->start_time_set = FALSE;
/* this is the compatibility lambda value. If it is >=0, it is valid,
and there is either an old-style lambda or a slow growth simulation. */
dhc->start_lambda = ir->fepvals->init_lambda;
/* for continuous change of lambda values */
dhc->delta_lambda = ir->fepvals->delta_lambda*ir->fepvals->nstdhdl;
if (dhc->start_lambda < 0)
{
/* create the native lambda vectors */
dhc->lambda_index = fep->init_fep_state;
dhc->n_lambda_vec = 0;
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
dhc->n_lambda_vec++;
}
}
snew(dhc->native_lambda_vec, dhc->n_lambda_vec);
snew(dhc->native_lambda_components, dhc->n_lambda_vec);
j = 0;
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
dhc->native_lambda_components[j] = i;
if (fep->init_fep_state >= 0 &&
fep->init_fep_state < fep->n_lambda)
{
dhc->native_lambda_vec[j] =
fep->all_lambda[i][fep->init_fep_state];
}
else
{
dhc->native_lambda_vec[j] = -1;
}
j++;
}
}
}
else
{
/* don't allocate the meta-data subblocks for lambda vectors */
dhc->native_lambda_vec = NULL;
dhc->n_lambda_vec = 0;
dhc->native_lambda_components = 0;
dhc->lambda_index = -1;
}
/* allocate metadata subblocks */
snew(dhc->subblock_d, 5 + dhc->n_lambda_vec);
snew(dhc->subblock_i, 1 + dhc->n_lambda_vec);
/* now decide which data to write out */
dhc->nlambda = 0;
dhc->ndhdl = 0;
dhc->dh_expanded = NULL;
dhc->dh_energy = NULL;
dhc->dh_pv = NULL;
/* total number of raw data point collections in the sample */
dhc->ndh = 0;
{
gmx_bool bExpanded = FALSE;
gmx_bool bEnergy = FALSE;
gmx_bool bPV = FALSE;
int n_lambda_components = 0;
/* first count the number of states */
/* add the dhdl's */
if (fep->dhdl_derivatives == edhdlderivativesYES)
{
for (i = 0; i < efptNR; i++)
{
if (ir->fepvals->separate_dvdl[i])
{
dhc->ndh += 1;
dhc->ndhdl += 1;
}
}
}
/* add the lambdas */
dhc->nlambda = ir->fepvals->lambda_stop_n - ir->fepvals->lambda_start_n;
dhc->ndh += dhc->nlambda;
/* another compatibility check */
if (dhc->start_lambda < 0)
{
/* include one more for the specification of the state, by lambda or
fep_state*/
if (ir->expandedvals->elmcmove > elmcmoveNO)
{
dhc->ndh += 1;
bExpanded = TRUE;
}
/* whether to print energies */
if (ir->fepvals->bPrintEnergy)
{
dhc->ndh += 1;
bEnergy = TRUE;
}
if (ir->epc > epcNO)
{
dhc->ndh += 1; /* include pressure-volume work */
bPV = TRUE;
}
}
/* allocate them */
snew(dhc->dh, dhc->ndh);
/* now initialize them */
/* the order, for now, must match that of the dhdl.xvg file because of
how g_energy -odh is implemented */
n = 0;
if (bExpanded)
{
dhc->dh_expanded = dhc->dh+n;
mde_delta_h_init(dhc->dh+n, ir->fepvals->dh_hist_size,
ir->fepvals->dh_hist_spacing, ndhmax,
dhbtEXPANDED, 0, 0, NULL);
n++;
}
if (bEnergy)
{
dhc->dh_energy = dhc->dh+n;
mde_delta_h_init(dhc->dh+n, ir->fepvals->dh_hist_size,
ir->fepvals->dh_hist_spacing, ndhmax,
dhbtEN, 0, 0, NULL);
n++;
}
/* add the dhdl's */
n_lambda_components = 0;
if (fep->dhdl_derivatives == edhdlderivativesYES)
{
dhc->dh_dhdl = dhc->dh + n;
for (i = 0; i < efptNR; i++)
{
if (ir->fepvals->separate_dvdl[i])
{
/* we give it init_lambda for compatibility */
mde_delta_h_init(dhc->dh+n, ir->fepvals->dh_hist_size,
ir->fepvals->dh_hist_spacing, ndhmax,
dhbtDHDL, n_lambda_components, 1,
&(fep->init_lambda));
n++;
n_lambda_components++;
}
}
}
else
{
for (i = 0; i < efptNR; i++)
{
if (ir->fepvals->separate_dvdl[i])
{
n_lambda_components++; /* count the components */
}
}
}
/* add the lambdas */
dhc->dh_du = dhc->dh + n;
snew(lambda_vec, n_lambda_components);
for (i = ir->fepvals->lambda_start_n; i < ir->fepvals->lambda_stop_n; i++)
{
int k = 0;
for (j = 0; j < efptNR; j++)
{
if (ir->fepvals->separate_dvdl[j])
{
lambda_vec[k++] = fep->all_lambda[j][i];
}
}
mde_delta_h_init(dhc->dh+n, ir->fepvals->dh_hist_size,
ir->fepvals->dh_hist_spacing, ndhmax,
dhbtDH, 0, n_lambda_components, lambda_vec);
n++;
}
sfree(lambda_vec);
if (bPV)
{
dhc->dh_pv = dhc->dh+n;
mde_delta_h_init(dhc->dh+n, ir->fepvals->dh_hist_size,
ir->fepvals->dh_hist_spacing, ndhmax,
dhbtPV, 0, 0, NULL);
n++;
}
}
}