gmx_ddbox_t ddbox = {0};
int npme_major, npme_minor;
t_nrnb *nrnb;
- gmx_mtop_t *mtop = nullptr;
t_forcerec *fr = nullptr;
t_fcdata *fcd = nullptr;
real ewaldcoeff_q = 0;
std::unique_ptr<gmx::MDModules> mdModules(new gmx::MDModules);
t_inputrec inputrecInstance;
t_inputrec *inputrec = &inputrecInstance;
- snew(mtop, 1);
+ gmx_mtop_t mtop;
if (mdrunOptions.continuationOptions.appendFiles)
{
globalState = std::unique_ptr<t_state>(new t_state);
/* Read (nearly) all data required for the simulation */
- read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, globalState.get(), mtop);
+ read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, globalState.get(), &mtop);
if (inputrec->cutoff_scheme != ecutsVERLET)
{
gpuIdsToUse,
useGpuForNonbonded,
useGpuForPme,
- inputrec, mtop,
+ inputrec, &mtop,
mdlog,
doMembed);
if (PAR(cr))
{
/* now broadcast everything to the non-master nodes/threads: */
- init_parallel(cr, inputrec, mtop);
+ init_parallel(cr, inputrec, &mtop);
}
// Now each rank knows the inputrec that SIMMASTER read and used,
snew(fcd, 1);
/* This needs to be called before read_checkpoint to extend the state */
- init_disres(fplog, mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
+ init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
- init_orires(fplog, mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
+ init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
if (inputrecDeform(inputrec))
{
/* Update rlist and nstlist. */
if (inputrec->cutoff_scheme == ecutsVERLET)
{
- prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, mtop, box,
+ prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes), *hwinfo->cpuInfo);
}
const rvec *xOnMaster = (SIMMASTER(cr) ? as_rvec_array(globalState->x.data()) : nullptr);
cr->dd = init_domain_decomposition(fplog, cr, domdecOptions, mdrunOptions,
- mtop, inputrec,
+ &mtop, inputrec,
box, xOnMaster,
&ddbox, &npme_major, &npme_minor);
// Note that local state still does not exist yet.
/* Check and update the number of OpenMP threads requested */
checkAndUpdateRequestedNumOpenmpThreads(&hw_opt, *hwinfo, cr, ms, physicalNodeComm.size_,
- pmeRunMode, *mtop);
+ pmeRunMode, mtop);
gmx_omp_nthreads_init(mdlog, cr,
hwinfo->nthreads_hw_avail,
/* Note that membed cannot work in parallel because mtop is
* changed here. Fix this if we ever want to make it run with
* multiple ranks. */
- membed = init_membed(fplog, nfile, fnm, mtop, inputrec, globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
+ membed = init_membed(fplog, nfile, fnm, &mtop, inputrec, globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
}
std::unique_ptr<MDAtoms> mdAtoms;
fr = mk_forcerec();
fr->forceProviders = mdModules->initForceProviders();
init_forcerec(fplog, mdlog, fr, fcd,
- inputrec, mtop, cr, box,
+ inputrec, &mtop, cr, box,
opt2fn("-table", nfile, fnm),
opt2fn("-tablep", nfile, fnm),
opt2fns("-tableb", nfile, fnm),
appendText("Large parts of the QM/MM support is deprecated, and may be removed in a future "
"version. Please get in touch with the developers if you find the support useful, "
"as help is needed if the functionality is to continue to be available.");
- init_QMMMrec(cr, mtop, inputrec, fr);
+ init_QMMMrec(cr, &mtop, inputrec, fr);
}
/* Initialize the mdAtoms structure.
* as this can not be done now with domain decomposition.
*/
const bool useGpuForPme = (pmeRunMode == PmeRunMode::GPU) || (pmeRunMode == PmeRunMode::Mixed);
- mdAtoms = makeMDAtoms(fplog, *mtop, *inputrec, useGpuForPme && thisRankHasDuty(cr, DUTY_PME));
+ mdAtoms = makeMDAtoms(fplog, mtop, *inputrec, useGpuForPme && thisRankHasDuty(cr, DUTY_PME));
if (globalState)
{
// The pinning of coordinates in the global state object works, because we only use
}
/* Initialize the virtual site communication */
- vsite = initVsite(*mtop, cr);
+ vsite = initVsite(mtop, cr);
calc_shifts(box, fr->shift_vec);
if (fr->ePBC != epbcNONE)
{
rvec *xGlobal = as_rvec_array(globalState->x.data());
- do_pbc_first_mtop(fplog, inputrec->ePBC, box, mtop, xGlobal);
+ do_pbc_first_mtop(fplog, inputrec->ePBC, box, &mtop, xGlobal);
}
if (vsite)
{
* for the initial distribution in the domain decomposition
* and for the initial shell prediction.
*/
- constructVsitesGlobal(*mtop, globalState->x);
+ constructVsitesGlobal(mtop, globalState->x);
}
}
try
{
pmedata = gmx_pme_init(cr, npme_major, npme_minor, inputrec,
- mtop ? mtop->natoms : 0, nChargePerturbed, nTypePerturbed,
+ mtop.natoms, nChargePerturbed, nTypePerturbed,
mdrunOptions.reproducible,
ewaldcoeff_q, ewaldcoeff_lj,
nthreads_pme,
/* Initialize pull code */
inputrec->pull_work =
init_pull(fplog, inputrec->pull, inputrec,
- mtop, cr, inputrec->fepvals->init_lambda);
+ &mtop, cr, inputrec->fepvals->init_lambda);
if (EI_DYNAMICS(inputrec->eI) && MASTER(cr))
{
init_pull_output_files(inputrec->pull_work,
if (inputrec->bRot)
{
/* Initialize enforced rotation code */
- init_rot(fplog, inputrec, nfile, fnm, cr, globalState.get(), mtop, oenv, mdrunOptions);
+ init_rot(fplog, inputrec, nfile, fnm, cr, globalState.get(), &mtop, oenv, mdrunOptions);
}
/* Let init_constraints know whether we have essential dynamics constraints.
*/
bool doEdsam = (opt2fn_null("-ei", nfile, fnm) != nullptr || observablesHistory.edsamHistory);
- constr = init_constraints(fplog, mtop, inputrec, doEdsam, cr);
+ constr = init_constraints(fplog, &mtop, inputrec, doEdsam, cr);
if (DOMAINDECOMP(cr))
{
/* This call is not included in init_domain_decomposition mainly
* because fr->cginfo_mb is set later.
*/
- dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
+ dd_init_bondeds(fplog, cr->dd, &mtop, vsite, inputrec,
domdecOptions.checkBondedInteractions,
fr->cginfo_mb);
}
mdrunOptions,
vsite, constr,
mdModules->outputProvider(),
- inputrec, mtop,
+ inputrec, &mtop,
fcd,
globalState.get(),
&observablesHistory,
free_gpu_resources(fr, physicalNodeComm);
free_gpu(nonbondedDeviceInfo);
free_gpu(pmeDeviceInfo);
- done_forcerec(fr, mtop->nmolblock, mtop->groups.grps[egcENER].nr);
- done_mtop(mtop);
+ done_forcerec(fr, mtop.molblock.size(), mtop.groups.grps[egcENER].nr);
sfree(fcd);
if (doMembed)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff