namespace gmx
{
-MDAtoms::MDAtoms()
- : mdatoms_(nullptr)
-{
-}
+MDAtoms::MDAtoms() : mdatoms_(nullptr) {}
MDAtoms::~MDAtoms()
{
mdatoms_->chargeA = chargeA_.data();
}
-std::unique_ptr<MDAtoms>
-makeMDAtoms(FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir,
- const bool rankHasPmeGpuTask)
+std::unique_ptr<MDAtoms> makeMDAtoms(FILE* fp, const gmx_mtop_t& mtop, const t_inputrec& ir, const bool rankHasPmeGpuTask)
{
- auto mdAtoms = std::make_unique<MDAtoms>();
+ auto mdAtoms = std::make_unique<MDAtoms>();
// GPU transfers may want to use a suitable pinning mode.
if (rankHasPmeGpuTask)
{
changePinningPolicy(&mdAtoms->chargeA_, pme_get_pinning_policy());
}
- t_mdatoms *md;
+ t_mdatoms* md;
snew(md, 1);
mdAtoms->mdatoms_.reset(md);
}
/* Determine the total system mass and perturbed atom counts */
- double totalMassA = 0.0;
- double totalMassB = 0.0;
+ double totalMassA = 0.0;
+ double totalMassB = 0.0;
- md->haveVsites = FALSE;
- gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(&mtop);
- const t_atom *atom;
- int nmol;
+ md->haveVsites = FALSE;
+ gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(&mtop);
+ const t_atom* atom;
+ int nmol;
while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
{
- totalMassA += nmol*atom->m;
- totalMassB += nmol*atom->mB;
+ totalMassA += nmol * atom->m;
+ totalMassB += nmol * atom->mB;
if (atom->ptype == eptVSite)
{
if (ir.efep != efepNO && fp)
{
- fprintf(fp,
- "There are %d atoms and %d charges for free energy perturbation\n",
+ fprintf(fp, "There are %d atoms and %d charges for free energy perturbation\n",
md->nPerturbed, md->nChargePerturbed);
}
return mdAtoms;
}
-} // namespace gmx
+} // namespace gmx
-void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir,
- int nindex, const int *index,
- int homenr,
- gmx::MDAtoms *mdAtoms)
+void atoms2md(const gmx_mtop_t* mtop, const t_inputrec* ir, int nindex, const int* index, int homenr, gmx::MDAtoms* mdAtoms)
{
- gmx_bool bLJPME;
- const t_grpopts *opts;
- int nthreads gmx_unused;
+ gmx_bool bLJPME;
+ const t_grpopts* opts;
+ int nthreads gmx_unused;
bLJPME = EVDW_PME(ir->vdwtype);
opts = &ir->opts;
- const SimulationGroups &groups = mtop->groups;
+ const SimulationGroups& groups = mtop->groups;
- auto md = mdAtoms->mdatoms();
+ auto md = mdAtoms->mdatoms();
/* nindex>=0 indicates DD where we use an index */
if (nindex >= 0)
{
* The padding needs to be with zeros, which we set later below.
*/
gmx::AlignedAllocationPolicy::free(md->invmass);
- md->invmass = new(gmx::AlignedAllocationPolicy::malloc((md->nalloc + GMX_REAL_MAX_SIMD_WIDTH)*sizeof(*md->invmass)))real;
+ md->invmass = new (gmx::AlignedAllocationPolicy::malloc(
+ (md->nalloc + GMX_REAL_MAX_SIMD_WIDTH) * sizeof(*md->invmass))) real;
srenew(md->invMassPerDim, md->nalloc);
// TODO eventually we will have vectors and just resize
// everything, but for now the semantics of md->nalloc being
{
srenew(md->cACC, md->nalloc);
}
- if (opts->nFreeze &&
- (opts->ngfrz > 1 ||
- opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
+ if (opts->nFreeze
+ && (opts->ngfrz > 1 || opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
{
srenew(md->cFREEZE, md->nalloc);
}
}
}
- int molb = 0;
+ int molb = 0;
nthreads = gmx_omp_nthreads_get(emntDefault);
#pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
{
try
{
- int g, ag;
- real mA, mB, fac;
- real c6, c12;
+ int g, ag;
+ real mA, mB, fac;
+ real c6, c12;
if (index == nullptr)
{
{
ag = index[i];
}
- const t_atom &atom = mtopGetAtomParameters(mtop, ag, &molb);
+ const t_atom& atom = mtopGetAtomParameters(mtop, ag, &molb);
if (md->cFREEZE)
{
*/
if (ir->bd_fric > 0)
{
- mA = 0.5*ir->bd_fric*ir->delta_t;
- mB = 0.5*ir->bd_fric*ir->delta_t;
+ mA = 0.5 * ir->bd_fric * ir->delta_t;
+ mB = 0.5 * ir->bd_fric * ir->delta_t;
}
else
{
/* The friction coefficient is mass/tau_t */
- fac = ir->delta_t/opts->tau_t[md->cTC ?
- groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag] : 0];
- mA = 0.5*atom.m*fac;
- mB = 0.5*atom.mB*fac;
+ fac = ir->delta_t
+ / opts->tau_t[md->cTC ? groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag] : 0];
+ mA = 0.5 * atom.m * fac;
+ mB = 0.5 * atom.mB * fac;
}
}
else
}
if (md->nMassPerturbed)
{
- md->massA[i] = mA;
- md->massB[i] = mB;
+ md->massA[i] = mA;
+ md->massB[i] = mB;
}
- md->massT[i] = mA;
+ md->massT[i] = mA;
if (mA == 0.0)
{
else if (md->cFREEZE)
{
g = md->cFREEZE[i];
- GMX_ASSERT(opts->nFreeze != nullptr, "Must have freeze groups to initialize masses");
+ GMX_ASSERT(opts->nFreeze != nullptr,
+ "Must have freeze groups to initialize masses");
if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
{
/* Set the mass of completely frozen particles to ALMOST_ZERO
* iso 0 to avoid div by zero in lincs or shake.
*/
- md->invmass[i] = ALMOST_ZERO;
+ md->invmass[i] = ALMOST_ZERO;
}
else
{
* If such particles are constrained, the frozen dimensions
* should not be updated with the constrained coordinates.
*/
- md->invmass[i] = 1.0/mA;
+ md->invmass[i] = 1.0 / mA;
}
for (int d = 0; d < DIM; d++)
{
- md->invMassPerDim[i][d] = (opts->nFreeze[g][d] ? 0 : 1.0/mA);
+ md->invMassPerDim[i][d] = (opts->nFreeze[g][d] ? 0 : 1.0 / mA);
}
}
else
{
- md->invmass[i] = 1.0/mA;
+ md->invmass[i] = 1.0 / mA;
for (int d = 0; d < DIM; d++)
{
- md->invMassPerDim[i][d] = 1.0/mA;
+ md->invMassPerDim[i][d] = 1.0 / mA;
}
}
- md->chargeA[i] = atom.q;
- md->typeA[i] = atom.type;
+ md->chargeA[i] = atom.q;
+ md->typeA[i] = atom.type;
if (bLJPME)
{
- c6 = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c6;
- c12 = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c12;
- md->sqrt_c6A[i] = sqrt(c6);
+ c6 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c6;
+ c12 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c12;
+ md->sqrt_c6A[i] = sqrt(c6);
if (c6 == 0.0 || c12 == 0)
{
md->sigmaA[i] = 1.0;
}
else
{
- md->sigmaA[i] = gmx::sixthroot(c12/c6);
+ md->sigmaA[i] = gmx::sixthroot(c12 / c6);
}
- md->sigma3A[i] = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
+ md->sigma3A[i] = 1 / (md->sigmaA[i] * md->sigmaA[i] * md->sigmaA[i]);
}
if (md->nPerturbed)
{
md->typeB[i] = atom.typeB;
if (bLJPME)
{
- c6 = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c6;
- c12 = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c12;
- md->sqrt_c6B[i] = sqrt(c6);
+ c6 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c6;
+ c12 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c12;
+ md->sqrt_c6B[i] = sqrt(c6);
if (c6 == 0.0 || c12 == 0)
{
md->sigmaB[i] = 1.0;
}
else
{
- md->sigmaB[i] = gmx::sixthroot(c12/c6);
+ md->sigmaB[i] = gmx::sixthroot(c12 / c6);
}
- md->sigma3B[i] = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
+ md->sigma3B[i] = 1 / (md->sigmaB[i] * md->sigmaB[i] * md->sigmaB[i]);
}
}
- md->ptype[i] = atom.ptype;
+ md->ptype[i] = atom.ptype;
if (md->cTC)
{
- md->cTC[i] = groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag];
+ md->cTC[i] = groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag];
}
- md->cENER[i] = getGroupType(groups, SimulationAtomGroupType::EnergyOutput, ag);
+ md->cENER[i] = getGroupType(groups, SimulationAtomGroupType::EnergyOutput, ag);
if (md->cACC)
{
- md->cACC[i] = groups.groupNumbers[SimulationAtomGroupType::Acceleration][ag];
+ md->cACC[i] = groups.groupNumbers[SimulationAtomGroupType::Acceleration][ag];
}
if (md->cVCM)
{
- md->cVCM[i] = groups.groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][ag];
+ md->cVCM[i] = groups.groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][ag];
}
if (md->cORF)
{
- md->cORF[i] = getGroupType(groups, SimulationAtomGroupType::OrientationRestraintsFit, ag);
+ md->cORF[i] = getGroupType(groups, SimulationAtomGroupType::OrientationRestraintsFit, ag);
}
if (md->cU1)
{
- md->cU1[i] = groups.groupNumbers[SimulationAtomGroupType::User1][ag];
+ md->cU1[i] = groups.groupNumbers[SimulationAtomGroupType::User1][ag];
}
if (md->cU2)
{
- md->cU2[i] = groups.groupNumbers[SimulationAtomGroupType::User2][ag];
+ md->cU2[i] = groups.groupNumbers[SimulationAtomGroupType::User2][ag];
}
if (ir->bQMMM)
{
- if (groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].empty() ||
- groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][ag] < groups.groups[SimulationAtomGroupType::QuantumMechanics].size()-1)
+ if (groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].empty()
+ || groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][ag]
+ < groups.groups[SimulationAtomGroupType::QuantumMechanics].size() - 1)
{
- md->bQM[i] = TRUE;
+ md->bQM[i] = TRUE;
}
else
{
- md->bQM[i] = FALSE;
+ md->bQM[i] = FALSE;
}
}
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
if (md->nr > 0)
md->lambda = 0;
}
-void update_mdatoms(t_mdatoms *md, real lambda)
+void update_mdatoms(t_mdatoms* md, real lambda)
{
if (md->nMassPerturbed && lambda != md->lambda)
{
{
if (md->bPerturbed[i])
{
- md->massT[i] = L1*md->massA[i] + lambda*md->massB[i];
+ md->massT[i] = L1 * md->massA[i] + lambda * md->massB[i];
/* Atoms with invmass 0 or ALMOST_ZERO are massless or frozen
* and their invmass does not depend on lambda.
*/
- if (md->invmass[i] > 1.1*ALMOST_ZERO)
+ if (md->invmass[i] > 1.1 * ALMOST_ZERO)
{
- md->invmass[i] = 1.0/md->massT[i];
+ md->invmass[i] = 1.0 / md->massT[i];
for (int d = 0; d < DIM; d++)
{
- if (md->invMassPerDim[i][d] > 1.1*ALMOST_ZERO)
+ if (md->invMassPerDim[i][d] > 1.1 * ALMOST_ZERO)
{
md->invMassPerDim[i][d] = md->invmass[i];
}
}
/* Update the system mass for the change in lambda */
- md->tmass = L1*md->tmassA + lambda*md->tmassB;
+ md->tmass = L1 * md->tmassA + lambda * md->tmassB;
}
md->lambda = lambda;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff