/*! \brief Checks if the Verlet buffer and constraint accuracy is sufficient for decoupled dynamic modes.
*
- * When decoupled modes are present and the accuray in insufficient,
+ * When decoupled modes are present and the accuracy in insufficient,
* this routine issues a warning if the accuracy is insufficient.
*/
static void checkDecoupledModeAccuracy(const gmx_mtop_t* mtop, const t_inputrec* ir, warninp* wi)
{ efEDR, "-e", nullptr, ffOPTRD },
/* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
{ efGRO, "-imd", "imdgroup", ffOPTWR },
- { efTRN, "-ref", "rotref", ffOPTRW | ffALLOW_MISSING } };
+ { efTRN, "-ref", "rotref", ffOPTRW | ffALLOW_MISSING },
+ /* This group is needed by the QMMM MDModule: */
+ { efQMI, "-qmi", nullptr, ffOPTRD } };
#define NFILE asize(fnm)
/* Command line options */
// to eventual notifications during pre-processing their data
mdModules.subscribeToPreProcessingNotifications();
+ // Notify MDModules of existing logger
+ mdModules.notifiers().preProcessingNotifier_.notify(logger);
+
+ // Notify MDModules of existing warninp
+ mdModules.notifiers().preProcessingNotifier_.notify(wi);
+
+ // Notify QMMM MDModule of external QM input file command-line option
+ {
+ gmx::QMInputFileName qmInputFileName = { ftp2bSet(efQMI, NFILE, fnm), ftp2fn(efQMI, NFILE, fnm) };
+ mdModules.notifiers().preProcessingNotifier_.notify(qmInputFileName);
+ }
if (bVerbose)
{
}
do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm), &sys, bVerbose, mdModules.notifiers(), ir, wi);
+ // Notify topology to MdModules for pre-processing after all indexes were built
+ mdModules.notifiers().preProcessingNotifier_.notify(&sys);
+
if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0)
{
if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
{
/* Calculate the optimal grid dimensions */
matrix scaledBox;
- EwaldBoxZScaler boxScaler(*ir);
+ EwaldBoxZScaler boxScaler(inputrecPbcXY2Walls(ir), ir->wall_ewald_zfac);
boxScaler.scaleBox(state.box, scaledBox);
if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
}
}
+ // Hand over box and coordiantes to MdModules before they evaluate their final parameters
+ {
+ gmx::CoordinatesAndBoxPreprocessed coordinatesAndBoxPreprocessed;
+ coordinatesAndBoxPreprocessed.coordinates_ = state.x.arrayRefWithPadding();
+ copy_mat(state.box, coordinatesAndBoxPreprocessed.box_);
+ coordinatesAndBoxPreprocessed.pbc_ = ir->pbcType;
+ mdModules.notifiers().preProcessingNotifier_.notify(coordinatesAndBoxPreprocessed);
+ }
+
// Add the md modules internal parameters that are not mdp options
// e.g., atom indices