#include "distribute.h"
#include "domdec_internal.h"
-static void dd_collect_cg(gmx_domdec_t *dd,
- const t_state *state_local)
+static void dd_collect_cg(gmx_domdec_t* dd, const t_state* state_local)
{
if (state_local->ddp_count == dd->comm->master_cg_ddp_count)
{
}
else
{
- gmx_incons("Attempted to collect a vector for a state for which the charge group distribution is unknown");
+ gmx_incons(
+ "Attempted to collect a vector for a state for which the charge group distribution "
+ "is unknown");
}
- AtomDistribution *ma = dd->ma.get();
+ AtomDistribution* ma = dd->ma.get();
/* Collect the charge group and atom counts on the master */
int localBuffer[2] = { static_cast<int>(atomGroups.size()), nat_home };
- dd_gather(dd, 2*sizeof(int), localBuffer,
- DDMASTER(dd) ? ma->intBuffer.data() : nullptr);
+ dd_gather(dd, 2 * sizeof(int), localBuffer, DDMASTER(dd) ? ma->intBuffer.data() : nullptr);
if (DDMASTER(dd))
{
int groupOffset = 0;
for (int rank = 0; rank < dd->nnodes; rank++)
{
- auto &domainGroups = ma->domainGroups[rank];
- int numGroups = ma->intBuffer[2*rank];
+ auto& domainGroups = ma->domainGroups[rank];
+ int numGroups = ma->intBuffer[2 * rank];
- domainGroups.atomGroups = gmx::constArrayRefFromArray(ma->atomGroups.data() + groupOffset, numGroups);
+ domainGroups.atomGroups =
+ gmx::constArrayRefFromArray(ma->atomGroups.data() + groupOffset, numGroups);
- domainGroups.numAtoms = ma->intBuffer[2*rank + 1];
+ domainGroups.numAtoms = ma->intBuffer[2 * rank + 1];
- groupOffset += numGroups;
+ groupOffset += numGroups;
}
if (debug)
int offset = 0;
for (int rank = 0; rank < dd->nnodes; rank++)
{
- int numGroups = ma->domainGroups[rank].atomGroups.size();
- ma->intBuffer[rank] = numGroups*sizeof(int);
- ma->intBuffer[dd->nnodes + rank] = offset*sizeof(int);
- offset += numGroups;
+ int numGroups = ma->domainGroups[rank].atomGroups.size();
+ ma->intBuffer[rank] = numGroups * sizeof(int);
+ ma->intBuffer[dd->nnodes + rank] = offset * sizeof(int);
+ offset += numGroups;
}
}
/* Collect the charge group indices on the master */
- dd_gatherv(dd,
- atomGroups.size()*sizeof(int), atomGroups.data(),
+ dd_gatherv(dd, atomGroups.size() * sizeof(int), atomGroups.data(),
DDMASTER(dd) ? ma->intBuffer.data() : nullptr,
DDMASTER(dd) ? ma->intBuffer.data() + dd->nnodes : nullptr,
DDMASTER(dd) ? ma->atomGroups.data() : nullptr);
dd->comm->master_cg_ddp_count = state_local->ddp_count;
}
-static void dd_collect_vec_sendrecv(gmx_domdec_t *dd,
+static void dd_collect_vec_sendrecv(gmx_domdec_t* dd,
gmx::ArrayRef<const gmx::RVec> lv,
gmx::ArrayRef<gmx::RVec> v)
{
{
#if GMX_MPI
const int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
- MPI_Send(const_cast<void *>(static_cast<const void *>(lv.data())), numHomeAtoms*sizeof(rvec), MPI_BYTE,
- dd->masterrank, dd->rank, dd->mpi_comm_all);
+ MPI_Send(const_cast<void*>(static_cast<const void*>(lv.data())),
+ numHomeAtoms * sizeof(rvec), MPI_BYTE, dd->masterrank, dd->rank, dd->mpi_comm_all);
#endif
}
else
{
- AtomDistribution &ma = *dd->ma;
+ AtomDistribution& ma = *dd->ma;
- int rank = dd->masterrank;
- int localAtom = 0;
- for (const int &globalAtom : ma.domainGroups[rank].atomGroups)
+ int rank = dd->masterrank;
+ int localAtom = 0;
+ for (const int& globalAtom : ma.domainGroups[rank].atomGroups)
{
copy_rvec(lv[localAtom++], v[globalAtom]);
}
{
if (rank != dd->rank)
{
- const auto &domainGroups = ma.domainGroups[rank];
+ const auto& domainGroups = ma.domainGroups[rank];
- GMX_RELEASE_ASSERT(v.data() != ma.rvecBuffer.data(), "We need different communication and return buffers");
+ GMX_RELEASE_ASSERT(v.data() != ma.rvecBuffer.data(),
+ "We need different communication and return buffers");
/* When we send/recv instead of scatter/gather, we might need
* to increase the communication buffer size here.
}
#if GMX_MPI
- MPI_Recv(ma.rvecBuffer.data(), domainGroups.numAtoms*sizeof(rvec), MPI_BYTE, rank,
+ MPI_Recv(ma.rvecBuffer.data(), domainGroups.numAtoms * sizeof(rvec), MPI_BYTE, rank,
rank, dd->mpi_comm_all, MPI_STATUS_IGNORE);
#endif
int localAtom = 0;
- for (const int &globalAtom : domainGroups.atomGroups)
+ for (const int& globalAtom : domainGroups.atomGroups)
{
copy_rvec(ma.rvecBuffer[localAtom++], v[globalAtom]);
}
}
}
-static void dd_collect_vec_gatherv(gmx_domdec_t *dd,
+static void dd_collect_vec_gatherv(gmx_domdec_t* dd,
gmx::ArrayRef<const gmx::RVec> lv,
gmx::ArrayRef<gmx::RVec> v)
{
- int *recvCounts = nullptr;
- int *displacements = nullptr;
+ int* recvCounts = nullptr;
+ int* displacements = nullptr;
if (DDMASTER(dd))
{
}
const int numHomeAtoms = dd->comm->atomRanges.numHomeAtoms();
- dd_gatherv(dd, numHomeAtoms*sizeof(rvec), lv.data(), recvCounts, displacements,
+ dd_gatherv(dd, numHomeAtoms * sizeof(rvec), lv.data(), recvCounts, displacements,
DDMASTER(dd) ? dd->ma->rvecBuffer.data() : nullptr);
if (DDMASTER(dd))
{
- const AtomDistribution &ma = *dd->ma;
+ const AtomDistribution& ma = *dd->ma;
- int bufferAtom = 0;
+ int bufferAtom = 0;
for (int rank = 0; rank < dd->nnodes; rank++)
{
- const auto &domainGroups = ma.domainGroups[rank];
- for (const int &globalAtom : domainGroups.atomGroups)
+ const auto& domainGroups = ma.domainGroups[rank];
+ for (const int& globalAtom : domainGroups.atomGroups)
{
copy_rvec(ma.rvecBuffer[bufferAtom++], v[globalAtom]);
}
}
}
-void dd_collect_vec(gmx_domdec_t *dd,
- const t_state *state_local,
+void dd_collect_vec(gmx_domdec_t* dd,
+ const t_state* state_local,
gmx::ArrayRef<const gmx::RVec> lv,
gmx::ArrayRef<gmx::RVec> v)
{
}
-void dd_collect_state(gmx_domdec_t *dd,
- const t_state *state_local, t_state *state)
+void dd_collect_state(gmx_domdec_t* dd, const t_state* state_local, t_state* state)
{
int nh = state_local->nhchainlength;
if (DDMASTER(dd))
{
- GMX_RELEASE_ASSERT(state->nhchainlength == nh, "The global and local Nose-Hoover chain lengths should match");
+ GMX_RELEASE_ASSERT(state->nhchainlength == nh,
+ "The global and local Nose-Hoover chain lengths should match");
for (int i = 0; i < efptNR; i++)
{
{
for (int j = 0; j < nh; j++)
{
- state->nosehoover_xi[i*nh+j] = state_local->nosehoover_xi[i*nh+j];
- state->nosehoover_vxi[i*nh+j] = state_local->nosehoover_vxi[i*nh+j];
+ state->nosehoover_xi[i * nh + j] = state_local->nosehoover_xi[i * nh + j];
+ state->nosehoover_vxi[i * nh + j] = state_local->nosehoover_vxi[i * nh + j];
}
state->therm_integral[i] = state_local->therm_integral[i];
}
{
for (int j = 0; j < nh; j++)
{
- state->nhpres_xi[i*nh+j] = state_local->nhpres_xi[i*nh+j];
- state->nhpres_vxi[i*nh+j] = state_local->nhpres_vxi[i*nh+j];
+ state->nhpres_xi[i * nh + j] = state_local->nhpres_xi[i * nh + j];
+ state->nhpres_vxi[i * nh + j] = state_local->nhpres_vxi[i * nh + j];
}
}
- state->baros_integral = state_local->baros_integral;
- state->pull_com_prev_step = state_local->pull_com_prev_step;
+ state->baros_integral = state_local->baros_integral;
+ state->pull_com_prev_step = state_local->pull_com_prev_step;
}
if (state_local->flags & (1 << estX))
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff