/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* But old code can not read a new entry that is present in the file
* (but can read a new format when new entries are not present).
*/
-static const int cpt_version = 15;
+static const int cpt_version = 16;
const char *est_names[estNR] =
int *natoms, int *ngtc, int *nnhpres, int *nhchainlength,
int *nlambda, int *flags_state,
int *flags_eks, int *flags_enh, int *flags_dfh,
- int *nED,
+ int *nED, int *eSwapCoords,
FILE *list)
{
bool_t res = 0;
{
*nED = 0;
}
+ if (*file_version >= 16)
+ {
+ do_cpt_int_err(xd, "swap", eSwapCoords, list);
+ }
}
static int do_cpt_footer(XDR *xd, int file_version)
}
+static int do_cpt_swapstate(XDR *xd, gmx_bool bRead, swapstate_t *swapstate, FILE *list)
+{
+ int ii, ic, j;
+ int ret = 0;
+ int swap_cpt_version = 1;
+
+
+ if (eswapNO == swapstate->eSwapCoords)
+ {
+ return ret;
+ }
+
+ swapstate->bFromCpt = bRead;
+
+ do_cpt_int_err(xd, "swap checkpoint version", &swap_cpt_version, list);
+ do_cpt_int_err(xd, "swap coupling steps", &swapstate->nAverage, list);
+
+ /* When reading, init_swapcoords has not been called yet,
+ * so we have to allocate memory first. */
+
+ for (ic = 0; ic < eCompNR; ic++)
+ {
+ for (ii = 0; ii < eIonNR; ii++)
+ {
+ if (bRead)
+ {
+ do_cpt_int_err(xd, "swap requested atoms", &swapstate->nat_req[ic][ii], list);
+ }
+ else
+ {
+ do_cpt_int_err(xd, "swap requested atoms p", swapstate->nat_req_p[ic][ii], list);
+ }
+
+ if (bRead)
+ {
+ do_cpt_int_err(xd, "swap influx netto", &swapstate->inflow_netto[ic][ii], list);
+ }
+ else
+ {
+ do_cpt_int_err(xd, "swap influx netto p", swapstate->inflow_netto_p[ic][ii], list);
+ }
+
+ if (bRead && (NULL == swapstate->nat_past[ic][ii]) )
+ {
+ snew(swapstate->nat_past[ic][ii], swapstate->nAverage);
+ }
+
+ for (j = 0; j < swapstate->nAverage; j++)
+ {
+ if (bRead)
+ {
+ do_cpt_int_err(xd, "swap past atom counts", &swapstate->nat_past[ic][ii][j], list);
+ }
+ else
+ {
+ do_cpt_int_err(xd, "swap past atom counts p", &swapstate->nat_past_p[ic][ii][j], list);
+ }
+ }
+ }
+ }
+
+ /* Ion flux per channel */
+ for (ic = 0; ic < eChanNR; ic++)
+ {
+ for (ii = 0; ii < eIonNR; ii++)
+ {
+ if (bRead)
+ {
+ do_cpt_int_err(xd, "channel flux", &swapstate->fluxfromAtoB[ic][ii], list);
+ }
+ else
+ {
+ do_cpt_int_err(xd, "channel flux p", swapstate->fluxfromAtoB_p[ic][ii], list);
+ }
+ }
+ }
+
+ /* Ion flux leakage */
+ if (bRead)
+ {
+ snew(swapstate->fluxleak, 1);
+ }
+ do_cpt_int_err(xd, "flux leakage", swapstate->fluxleak, list);
+
+ /* Ion history */
+ do_cpt_int_err(xd, "number of ions", &swapstate->nions, list);
+
+ if (bRead)
+ {
+ snew(swapstate->channel_label, swapstate->nions);
+ snew(swapstate->comp_from, swapstate->nions);
+ }
+
+ do_cpt_u_chars(xd, "channel history", swapstate->nions, swapstate->channel_label, list);
+ do_cpt_u_chars(xd, "domain history", swapstate->nions, swapstate->comp_from, list);
+
+ /* Save the last known whole positions to checkpoint
+ * file to be able to also make multimeric channels whole in PBC */
+ do_cpt_int_err(xd, "Ch0 atoms", &swapstate->nat[eChan0], list);
+ do_cpt_int_err(xd, "Ch1 atoms", &swapstate->nat[eChan1], list);
+ if (bRead)
+ {
+ snew(swapstate->xc_old_whole[eChan0], swapstate->nat[eChan0]);
+ snew(swapstate->xc_old_whole[eChan1], swapstate->nat[eChan1]);
+ do_cpt_n_rvecs_err(xd, "Ch0 whole x", swapstate->nat[eChan0], swapstate->xc_old_whole[eChan0], list);
+ do_cpt_n_rvecs_err(xd, "Ch1 whole x", swapstate->nat[eChan1], swapstate->xc_old_whole[eChan1], list);
+ }
+ else
+ {
+ do_cpt_n_rvecs_err(xd, "Ch0 whole x", swapstate->nat[eChan0], *swapstate->xc_old_whole_p[eChan0], list);
+ do_cpt_n_rvecs_err(xd, "Ch1 whole x", swapstate->nat[eChan1], *swapstate->xc_old_whole_p[eChan1], list);
+ }
+
+ return ret;
+}
+
+
static int do_cpt_enerhist(XDR *xd, gmx_bool bRead,
int fflags, energyhistory_t *enerhist,
FILE *list)
DOMAINDECOMP(cr) ? cr->dd->nc : NULL, &npmenodes,
&state->natoms, &state->ngtc, &state->nnhpres,
&state->nhchainlength, &(state->dfhist.nlambda), &state->flags, &flags_eks, &flags_enh, &flags_dfh,
- &state->edsamstate.nED,
+ &state->edsamstate.nED, &state->swapstate.eSwapCoords,
NULL);
sfree(version);
(do_cpt_enerhist(gmx_fio_getxdr(fp), FALSE, flags_enh, &state->enerhist, NULL) < 0) ||
(do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, &state->dfhist, NULL) < 0) ||
(do_cpt_EDstate(gmx_fio_getxdr(fp), FALSE, &state->edsamstate, NULL) < 0) ||
+ (do_cpt_swapstate(gmx_fio_getxdr(fp), FALSE, &state->swapstate, NULL) < 0) ||
(do_cpt_files(gmx_fio_getxdr(fp), FALSE, &outputfiles, &noutputfiles, NULL,
file_version) < 0))
{
&nppnodes_f, dd_nc_f, &npmenodes_f,
&natoms, &ngtc, &nnhpres, &nhchainlength, &nlambda,
&fflags, &flags_eks, &flags_enh, &flags_dfh,
- &state->edsamstate.nED, NULL);
+ &state->edsamstate.nED, &state->swapstate.eSwapCoords, NULL);
if (bAppendOutputFiles &&
file_version >= 13 && double_prec != GMX_CPT_BUILD_DP)
cp_error();
}
+ ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, &state->swapstate, NULL);
+ if (ret)
+ {
+ cp_error();
+ }
+
ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, &state->edsamstate, NULL);
if (ret)
{
&eIntegrator, simulation_part, step, t, &nppnodes, dd_nc, &npme,
&state->natoms, &state->ngtc, &state->nnhpres, &state->nhchainlength,
&(state->dfhist.nlambda), &state->flags, &flags_eks, &flags_enh, &flags_dfh,
- &state->edsamstate.nED, NULL);
+ &state->edsamstate.nED, &state->swapstate.eSwapCoords, NULL);
ret =
do_cpt_state(gmx_fio_getxdr(fp), TRUE, state->flags, state, bReadRNG, NULL);
if (ret)
cp_error();
}
+ ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, &state->swapstate, NULL);
+ if (ret)
+ {
+ cp_error();
+ }
+
ret = do_cpt_files(gmx_fio_getxdr(fp), TRUE,
outputfiles != NULL ? outputfiles : &files_loc,
outputfiles != NULL ? nfiles : &nfiles_loc,
&eIntegrator, &simulation_part, &step, &t, &nppnodes, dd_nc, &npme,
&state.natoms, &state.ngtc, &state.nnhpres, &state.nhchainlength,
&(state.dfhist.nlambda), &state.flags,
- &flags_eks, &flags_enh, &flags_dfh, &state.edsamstate.nED, out);
+ &flags_eks, &flags_enh, &flags_dfh, &state.edsamstate.nED,
+ &state.swapstate.eSwapCoords, out);
ret = do_cpt_state(gmx_fio_getxdr(fp), TRUE, state.flags, &state, TRUE, out);
if (ret)
{
ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, &state.edsamstate, out);
}
+ if (ret == 0)
+ {
+ ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, &state.swapstate, out);
+ }
+
if (ret == 0)
{
do_cpt_files(gmx_fio_getxdr(fp), TRUE, &outputfiles, &nfiles, out, file_version);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff