using gmx::RVec;
-static void init_ilist(t_ilist *ilist)
+static void init_ilist(t_ilist* ilist)
{
for (int i = 0; i < F_NRE; i++)
{
}
/*! \brief List of atom indices belonging to a task */
-struct AtomIndex {
+struct AtomIndex
+{
//! List of atom indices
std::vector<int> atom;
};
struct InterdependentTask
{
//! The interaction lists, only vsite entries are used
- t_ilist ilist[F_NRE];
+ t_ilist ilist[F_NRE];
//! Thread/task-local force buffer
- std::vector<RVec> force;
+ std::vector<RVec> force;
//! The atom indices of the vsites of our task
- std::vector<int> vsite;
+ std::vector<int> vsite;
//! Flags if elements in force are spread to or not
- std::vector<bool> use;
+ std::vector<bool> use;
//! The number of entries set to true in use
- int nuse;
+ int nuse;
//! Array of atoms indices, size nthreads, covering all nuse set elements in use
std::vector<AtomIndex> atomIndex;
//! List of tasks (force blocks) this task spread forces to
- std::vector<int> spreadTask;
+ std::vector<int> spreadTask;
//! List of tasks that write to this tasks force block range
- std::vector<int> reduceTask;
+ std::vector<int> reduceTask;
InterdependentTask()
{
struct VsiteThread
{
//! Start of atom range of this task
- int rangeStart;
+ int rangeStart;
//! End of atom range of this task
- int rangeEnd;
+ int rangeEnd;
//! The interaction lists, only vsite entries are used
- t_ilist ilist[F_NRE];
+ t_ilist ilist[F_NRE];
//! Local fshift accumulation buffer
- rvec fshift[SHIFTS];
+ rvec fshift[SHIFTS];
//! Local virial dx*df accumulation buffer
- matrix dxdf;
+ matrix dxdf;
//! Tells if interdependent task idTask should be used (in addition to the rest of this task), this bool has the same value on all threads
- bool useInterdependentTask;
+ bool useInterdependentTask;
//! Data for vsites that involve constructing atoms in the atom range of other threads/tasks
InterdependentTask idTask;
/*! \brief Constructor */
VsiteThread()
{
- rangeStart = -1;
- rangeEnd = -1;
+ rangeStart = -1;
+ rangeEnd = -1;
init_ilist(ilist);
clear_rvecs(SHIFTS, fshift);
clear_mat(dxdf);
*
* \param[in] ilist The interaction list
*/
-template <typename T>
-static int vsiteIlistNrCount(const T *ilist)
+template<typename T>
+static int vsiteIlistNrCount(const T* ilist)
{
int nr = 0;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
return nr;
}
-static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
+static int pbc_rvec_sub(const t_pbc* pbc, const rvec xi, const rvec xj, rvec dx)
{
if (pbc)
{
/* Vsite construction routines */
-static void constr_vsite2(const rvec xi, const rvec xj, rvec x, real a, const t_pbc *pbc)
+static void constr_vsite2(const rvec xi, const rvec xj, rvec x, real a, const t_pbc* pbc)
{
real b = 1 - a;
/* 1 flop */
{
rvec dx;
pbc_dx_aiuc(pbc, xj, xi, dx);
- x[XX] = xi[XX] + a*dx[XX];
- x[YY] = xi[YY] + a*dx[YY];
- x[ZZ] = xi[ZZ] + a*dx[ZZ];
+ x[XX] = xi[XX] + a * dx[XX];
+ x[YY] = xi[YY] + a * dx[YY];
+ x[ZZ] = xi[ZZ] + a * dx[ZZ];
}
else
{
- x[XX] = b*xi[XX] + a*xj[XX];
- x[YY] = b*xi[YY] + a*xj[YY];
- x[ZZ] = b*xi[ZZ] + a*xj[ZZ];
+ x[XX] = b * xi[XX] + a * xj[XX];
+ x[YY] = b * xi[YY] + a * xj[YY];
+ x[ZZ] = b * xi[ZZ] + a * xj[ZZ];
/* 9 Flops */
}
/* TOTAL: 10 flops */
}
-static void constr_vsite2FD(const rvec xi, const rvec xj, rvec x, real a,
- const t_pbc *pbc)
+static void constr_vsite2FD(const rvec xi, const rvec xj, rvec x, real a, const t_pbc* pbc)
{
rvec xij;
pbc_rvec_sub(pbc, xj, xi, xij);
/* 3 flops */
- const real b = a*inverseNorm(xij);
+ const real b = a * inverseNorm(xij);
/* 6 + 10 flops */
- x[XX] = xi[XX] + b*xij[XX];
- x[YY] = xi[YY] + b*xij[YY];
- x[ZZ] = xi[ZZ] + b*xij[ZZ];
+ x[XX] = xi[XX] + b * xij[XX];
+ x[YY] = xi[YY] + b * xij[YY];
+ x[ZZ] = xi[ZZ] + b * xij[ZZ];
/* 6 Flops */
/* TOTAL: 25 flops */
}
-static void constr_vsite3(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b,
- const t_pbc *pbc)
+static void constr_vsite3(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, const t_pbc* pbc)
{
real c = 1 - a - b;
/* 2 flops */
pbc_dx_aiuc(pbc, xj, xi, dxj);
pbc_dx_aiuc(pbc, xk, xi, dxk);
- x[XX] = xi[XX] + a*dxj[XX] + b*dxk[XX];
- x[YY] = xi[YY] + a*dxj[YY] + b*dxk[YY];
- x[ZZ] = xi[ZZ] + a*dxj[ZZ] + b*dxk[ZZ];
+ x[XX] = xi[XX] + a * dxj[XX] + b * dxk[XX];
+ x[YY] = xi[YY] + a * dxj[YY] + b * dxk[YY];
+ x[ZZ] = xi[ZZ] + a * dxj[ZZ] + b * dxk[ZZ];
}
else
{
- x[XX] = c*xi[XX] + a*xj[XX] + b*xk[XX];
- x[YY] = c*xi[YY] + a*xj[YY] + b*xk[YY];
- x[ZZ] = c*xi[ZZ] + a*xj[ZZ] + b*xk[ZZ];
+ x[XX] = c * xi[XX] + a * xj[XX] + b * xk[XX];
+ x[YY] = c * xi[YY] + a * xj[YY] + b * xk[YY];
+ x[ZZ] = c * xi[ZZ] + a * xj[ZZ] + b * xk[ZZ];
/* 15 Flops */
}
/* TOTAL: 17 flops */
}
-static void constr_vsite3FD(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b,
- const t_pbc *pbc)
+static void constr_vsite3FD(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, const t_pbc* pbc)
{
rvec xij, xjk, temp;
real c;
/* 6 flops */
/* temp goes from i to a point on the line jk */
- temp[XX] = xij[XX] + a*xjk[XX];
- temp[YY] = xij[YY] + a*xjk[YY];
- temp[ZZ] = xij[ZZ] + a*xjk[ZZ];
+ temp[XX] = xij[XX] + a * xjk[XX];
+ temp[YY] = xij[YY] + a * xjk[YY];
+ temp[ZZ] = xij[ZZ] + a * xjk[ZZ];
/* 6 flops */
- c = b*inverseNorm(temp);
+ c = b * inverseNorm(temp);
/* 6 + 10 flops */
- x[XX] = xi[XX] + c*temp[XX];
- x[YY] = xi[YY] + c*temp[YY];
- x[ZZ] = xi[ZZ] + c*temp[ZZ];
+ x[XX] = xi[XX] + c * temp[XX];
+ x[YY] = xi[YY] + c * temp[YY];
+ x[ZZ] = xi[ZZ] + c * temp[ZZ];
/* 6 Flops */
/* TOTAL: 34 flops */
}
-static void constr_vsite3FAD(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, const t_pbc *pbc)
+static void constr_vsite3FAD(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, const t_pbc* pbc)
{
rvec xij, xjk, xp;
real a1, b1, c1, invdij;
invdij = inverseNorm(xij);
c1 = invdij * invdij * iprod(xij, xjk);
- xp[XX] = xjk[XX] - c1*xij[XX];
- xp[YY] = xjk[YY] - c1*xij[YY];
- xp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
- a1 = a*invdij;
- b1 = b*inverseNorm(xp);
+ xp[XX] = xjk[XX] - c1 * xij[XX];
+ xp[YY] = xjk[YY] - c1 * xij[YY];
+ xp[ZZ] = xjk[ZZ] - c1 * xij[ZZ];
+ a1 = a * invdij;
+ b1 = b * inverseNorm(xp);
/* 45 */
- x[XX] = xi[XX] + a1*xij[XX] + b1*xp[XX];
- x[YY] = xi[YY] + a1*xij[YY] + b1*xp[YY];
- x[ZZ] = xi[ZZ] + a1*xij[ZZ] + b1*xp[ZZ];
+ x[XX] = xi[XX] + a1 * xij[XX] + b1 * xp[XX];
+ x[YY] = xi[YY] + a1 * xij[YY] + b1 * xp[YY];
+ x[ZZ] = xi[ZZ] + a1 * xij[ZZ] + b1 * xp[ZZ];
/* 12 Flops */
/* TOTAL: 63 flops */
}
-static void constr_vsite3OUT(const rvec xi, const rvec xj, const rvec xk, rvec x,
- real a, real b, real c, const t_pbc *pbc)
+static void
+constr_vsite3OUT(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, real c, const t_pbc* pbc)
{
rvec xij, xik, temp;
cprod(xij, xik, temp);
/* 15 Flops */
- x[XX] = xi[XX] + a*xij[XX] + b*xik[XX] + c*temp[XX];
- x[YY] = xi[YY] + a*xij[YY] + b*xik[YY] + c*temp[YY];
- x[ZZ] = xi[ZZ] + a*xij[ZZ] + b*xik[ZZ] + c*temp[ZZ];
+ x[XX] = xi[XX] + a * xij[XX] + b * xik[XX] + c * temp[XX];
+ x[YY] = xi[YY] + a * xij[YY] + b * xik[YY] + c * temp[YY];
+ x[ZZ] = xi[ZZ] + a * xij[ZZ] + b * xik[ZZ] + c * temp[ZZ];
/* 18 Flops */
/* TOTAL: 33 flops */
}
-static void constr_vsite4FD(const rvec xi, const rvec xj, const rvec xk, const rvec xl, rvec x,
- real a, real b, real c, const t_pbc *pbc)
+static void constr_vsite4FD(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ const rvec xl,
+ rvec x,
+ real a,
+ real b,
+ real c,
+ const t_pbc* pbc)
{
rvec xij, xjk, xjl, temp;
real d;
/* 9 flops */
/* temp goes from i to a point on the plane jkl */
- temp[XX] = xij[XX] + a*xjk[XX] + b*xjl[XX];
- temp[YY] = xij[YY] + a*xjk[YY] + b*xjl[YY];
- temp[ZZ] = xij[ZZ] + a*xjk[ZZ] + b*xjl[ZZ];
+ temp[XX] = xij[XX] + a * xjk[XX] + b * xjl[XX];
+ temp[YY] = xij[YY] + a * xjk[YY] + b * xjl[YY];
+ temp[ZZ] = xij[ZZ] + a * xjk[ZZ] + b * xjl[ZZ];
/* 12 flops */
- d = c*inverseNorm(temp);
+ d = c * inverseNorm(temp);
/* 6 + 10 flops */
- x[XX] = xi[XX] + d*temp[XX];
- x[YY] = xi[YY] + d*temp[YY];
- x[ZZ] = xi[ZZ] + d*temp[ZZ];
+ x[XX] = xi[XX] + d * temp[XX];
+ x[YY] = xi[YY] + d * temp[YY];
+ x[ZZ] = xi[ZZ] + d * temp[ZZ];
/* 6 Flops */
/* TOTAL: 43 flops */
}
-static void constr_vsite4FDN(const rvec xi, const rvec xj, const rvec xk, const rvec xl, rvec x,
- real a, real b, real c, const t_pbc *pbc)
+static void constr_vsite4FDN(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ const rvec xl,
+ rvec x,
+ real a,
+ real b,
+ real c,
+ const t_pbc* pbc)
{
rvec xij, xik, xil, ra, rb, rja, rjb, rm;
real d;
pbc_rvec_sub(pbc, xl, xi, xil);
/* 9 flops */
- ra[XX] = a*xik[XX];
- ra[YY] = a*xik[YY];
- ra[ZZ] = a*xik[ZZ];
+ ra[XX] = a * xik[XX];
+ ra[YY] = a * xik[YY];
+ ra[ZZ] = a * xik[ZZ];
- rb[XX] = b*xil[XX];
- rb[YY] = b*xil[YY];
- rb[ZZ] = b*xil[ZZ];
+ rb[XX] = b * xil[XX];
+ rb[YY] = b * xil[YY];
+ rb[ZZ] = b * xil[ZZ];
/* 6 flops */
cprod(rja, rjb, rm);
/* 9 flops */
- d = c*inverseNorm(rm);
+ d = c * inverseNorm(rm);
/* 5+5+1 flops */
- x[XX] = xi[XX] + d*rm[XX];
- x[YY] = xi[YY] + d*rm[YY];
- x[ZZ] = xi[ZZ] + d*rm[ZZ];
+ x[XX] = xi[XX] + d * rm[XX];
+ x[YY] = xi[YY] + d * rm[YY];
+ x[ZZ] = xi[ZZ] + d * rm[ZZ];
/* 6 Flops */
/* TOTAL: 47 flops */
}
-static int constr_vsiten(const t_iatom *ia, const t_iparams ip[],
- rvec *x, const t_pbc *pbc)
+static int constr_vsiten(const t_iatom* ia, const t_iparams ip[], rvec* x, const t_pbc* pbc)
{
rvec x1, dx;
dvec dsum;
int n3, av, ai;
real a;
- n3 = 3*ip[ia[0]].vsiten.n;
+ n3 = 3 * ip[ia[0]].vsiten.n;
av = ia[1];
ai = ia[2];
copy_rvec(x[ai], x1);
clear_dvec(dsum);
for (int i = 3; i < n3; i += 3)
{
- ai = ia[i+2];
+ ai = ia[i + 2];
a = ip[ia[i]].vsiten.a;
if (pbc)
{
{
rvec_sub(x[ai], x1, dx);
}
- dsum[XX] += a*dx[XX];
- dsum[YY] += a*dx[YY];
- dsum[ZZ] += a*dx[ZZ];
+ dsum[XX] += a * dx[XX];
+ dsum[YY] += a * dx[YY];
+ dsum[ZZ] += a * dx[ZZ];
/* 9 Flops */
}
/*! \brief PBC modes for vsite construction and spreading */
enum class PbcMode
{
- all, // Apply normal, simple PBC for all vsites
- none // No PBC treatment needed
+ all, // Apply normal, simple PBC for all vsites
+ none // No PBC treatment needed
};
/*! \brief Returns the PBC mode based on the system PBC and vsite properties
*
* \param[in] pbcPtr A pointer to a PBC struct or nullptr when no PBC treatment is required
*/
-static PbcMode getPbcMode(const t_pbc *pbcPtr)
+static PbcMode getPbcMode(const t_pbc* pbcPtr)
{
if (pbcPtr == nullptr)
{
}
}
-static void construct_vsites_thread(rvec x[],
- real dt, rvec *v,
- const t_iparams ip[], const t_ilist ilist[],
- const t_pbc *pbc_null)
+static void construct_vsites_thread(rvec x[],
+ real dt,
+ rvec* v,
+ const t_iparams ip[],
+ const t_ilist ilist[],
+ const t_pbc* pbc_null)
{
- real inv_dt;
+ real inv_dt;
if (v != nullptr)
{
- inv_dt = 1.0/dt;
+ inv_dt = 1.0 / dt;
}
else
{
inv_dt = 1.0;
}
- const PbcMode pbcMode = getPbcMode(pbc_null);
+ const PbcMode pbcMode = getPbcMode(pbc_null);
/* We need another pbc pointer, as with charge groups we switch per vsite */
- const t_pbc *pbc_null2 = pbc_null;
+ const t_pbc* pbc_null2 = pbc_null;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
continue;
}
- { // TODO remove me
- int nra = interaction_function[ftype].nratoms;
- int inc = 1 + nra;
- int nr = ilist[ftype].nr;
+ { // TODO remove me
+ int nra = interaction_function[ftype].nratoms;
+ int inc = 1 + nra;
+ int nr = ilist[ftype].nr;
- const t_iatom *ia = ilist[ftype].iatoms;
+ const t_iatom* ia = ilist[ftype].iatoms;
- for (int i = 0; i < nr; )
+ for (int i = 0; i < nr;)
{
- int tp = ia[0];
+ int tp = ia[0];
/* The vsite and constructing atoms */
- int avsite = ia[1];
- int ai = ia[2];
+ int avsite = ia[1];
+ int ai = ia[2];
/* Constants for constructing vsites */
- real a1 = ip[tp].vsite.a;
+ real a1 = ip[tp].vsite.a;
/* Copy the old position */
rvec xv;
copy_rvec(x[avsite], xv);
al = ia[5];
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- constr_vsite4FD(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1,
- pbc_null2);
+ constr_vsite4FD(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1, pbc_null2);
break;
case F_VSITE4FDN:
aj = ia[3];
al = ia[5];
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- constr_vsite4FDN(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1,
- pbc_null2);
- break;
- case F_VSITEN:
- inc = constr_vsiten(ia, ip, x, pbc_null2);
+ constr_vsite4FDN(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1, pbc_null2);
break;
+ case F_VSITEN: inc = constr_vsiten(ia, ip, x, pbc_null2); break;
default:
- gmx_fatal(FARGS, "No such vsite type %d in %s, line %d",
- ftype, __FILE__, __LINE__);
+ gmx_fatal(FARGS, "No such vsite type %d in %s, line %d", ftype, __FILE__, __LINE__);
}
if (pbcMode == PbcMode::all)
}
/* Increment loop variables */
- i += inc;
+ i += inc;
ia += inc;
}
}
}
}
-void construct_vsites(const gmx_vsite_t *vsite,
- rvec x[],
- real dt, rvec *v,
- const t_iparams ip[], const t_ilist ilist[],
- int ePBC, gmx_bool bMolPBC,
- const t_commrec *cr,
- const matrix box)
+void construct_vsites(const gmx_vsite_t* vsite,
+ rvec x[],
+ real dt,
+ rvec* v,
+ const t_iparams ip[],
+ const t_ilist ilist[],
+ int ePBC,
+ gmx_bool bMolPBC,
+ const t_commrec* cr,
+ const matrix box)
{
const bool useDomdec = (vsite != nullptr && vsite->useDomdec);
- GMX_ASSERT(!useDomdec || (cr != nullptr && DOMAINDECOMP(cr)), "When vsites are set up with domain decomposition, we need a valid commrec");
+ GMX_ASSERT(!useDomdec || (cr != nullptr && DOMAINDECOMP(cr)),
+ "When vsites are set up with domain decomposition, we need a valid commrec");
// TODO: Remove this assertion when we remove charge groups
- GMX_ASSERT(vsite != nullptr || ePBC == epbcNONE, "Without a vsite struct we can not do PBC (in case we have charge groups)");
+ GMX_ASSERT(vsite != nullptr || ePBC == epbcNONE,
+ "Without a vsite struct we can not do PBC (in case we have charge groups)");
- t_pbc pbc, *pbc_null;
+ t_pbc pbc, *pbc_null;
/* We only need to do pbc when we have inter-cg vsites.
* Note that with domain decomposition we do not need to apply PBC here
* when we have at least 3 domains along each dimension. Currently we
* do not optimize this case.
*/
- if (ePBC != epbcNONE && (useDomdec || bMolPBC) &&
- !(vsite != nullptr && vsite->numInterUpdategroupVsites == 0))
+ if (ePBC != epbcNONE && (useDomdec || bMolPBC)
+ && !(vsite != nullptr && vsite->numInterUpdategroupVsites == 0))
{
/* This is wasting some CPU time as we now do this multiple times
* per MD step.
*/
ivec null_ivec;
clear_ivec(null_ivec);
- pbc_null = set_pbc_dd(&pbc, ePBC,
- useDomdec ? cr->dd->nc : null_ivec,
- FALSE, box);
+ pbc_null = set_pbc_dd(&pbc, ePBC, useDomdec ? cr->dd->nc : null_ivec, FALSE, box);
}
else
{
if (vsite == nullptr || vsite->nthreads == 1)
{
- construct_vsites_thread(x, dt, v,
- ip, ilist,
- pbc_null);
+ construct_vsites_thread(x, dt, v, ip, ilist, pbc_null);
}
else
{
try
{
const int th = gmx_omp_get_thread_num();
- const VsiteThread &tData = *vsite->tData[th];
- GMX_ASSERT(tData.rangeStart >= 0, "The thread data should be initialized before calling construct_vsites");
+ const VsiteThread& tData = *vsite->tData[th];
+ GMX_ASSERT(tData.rangeStart >= 0,
+ "The thread data should be initialized before calling construct_vsites");
- construct_vsites_thread(x, dt, v,
- ip, tData.ilist,
- pbc_null);
+ construct_vsites_thread(x, dt, v, ip, tData.ilist, pbc_null);
if (tData.useInterdependentTask)
{
/* Here we don't need a barrier (unlike the spreading),
* since both tasks only construct vsites from particles,
* or local vsites, not from non-local vsites.
*/
- construct_vsites_thread(x, dt, v,
- ip, tData.idTask.ilist,
- pbc_null);
+ construct_vsites_thread(x, dt, v, ip, tData.idTask.ilist, pbc_null);
}
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/* Now we can construct the vsites that might depend on other vsites */
- construct_vsites_thread(x, dt, v,
- ip, vsite->tData[vsite->nthreads]->ilist,
- pbc_null);
+ construct_vsites_thread(x, dt, v, ip, vsite->tData[vsite->nthreads]->ilist, pbc_null);
}
}
-static void spread_vsite2(const t_iatom ia[], real a,
- const rvec x[],
- rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g)
+static void spread_vsite2(const t_iatom ia[],
+ real a,
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ const t_graph* g)
{
rvec fi, fj, dx;
t_iatom av, ai, aj;
aj = ia[3];
svmul(1 - a, f[av], fi);
- svmul( a, f[av], fj);
+ svmul(a, f[av], fj);
/* 7 flop */
rvec_inc(f[ai], fi);
/* TOTAL: 13 flops */
}
-void constructVsitesGlobal(const gmx_mtop_t &mtop,
- gmx::ArrayRef<gmx::RVec> x)
+void constructVsitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
{
GMX_ASSERT(x.ssize() >= mtop.natoms, "x should contain the whole system");
- GMX_ASSERT(!mtop.moleculeBlockIndices.empty(), "molblock indices are needed in constructVsitesGlobal");
+ GMX_ASSERT(!mtop.moleculeBlockIndices.empty(),
+ "molblock indices are needed in constructVsitesGlobal");
for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
{
- const gmx_molblock_t &molb = mtop.molblock[mb];
- const gmx_moltype_t &molt = mtop.moltype[molb.type];
+ const gmx_molblock_t& molb = mtop.molblock[mb];
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
if (vsiteIlistNrCount(molt.ilist.data()) > 0)
{
int atomOffset = mtop.moleculeBlockIndices[mb].globalAtomStart;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
ilist[ftype].nr = molt.ilist[ftype].size();
- ilist[ftype].iatoms = const_cast<t_iatom *>(molt.ilist[ftype].iatoms.data());
+ ilist[ftype].iatoms = const_cast<t_iatom*>(molt.ilist[ftype].iatoms.data());
}
- construct_vsites(nullptr, as_rvec_array(x.data()) + atomOffset,
- 0.0, nullptr,
- mtop.ffparams.iparams.data(), ilist,
- epbcNONE, TRUE, nullptr, nullptr);
+ construct_vsites(nullptr, as_rvec_array(x.data()) + atomOffset, 0.0, nullptr,
+ mtop.ffparams.iparams.data(), ilist, epbcNONE, TRUE, nullptr, nullptr);
atomOffset += molt.atoms.nr;
}
}
}
}
-static void spread_vsite2FD(const t_iatom ia[], real a,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+static void spread_vsite2FD(const t_iatom ia[],
+ real a,
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ gmx_bool VirCorr,
+ matrix dxdf,
+ const t_pbc* pbc,
+ const t_graph* g)
{
const int av = ia[1];
const int ai = ia[2];
/* 6 flops */
const real invDistance = inverseNorm(xij);
- const real b = a*invDistance;
+ const real b = a * invDistance;
/* 4 + ?10? flops */
- const real fproj = iprod(xij, fv)*invDistance*invDistance;
+ const real fproj = iprod(xij, fv) * invDistance * invDistance;
- rvec fj;
- fj[XX] = b*(fv[XX] - fproj*xij[XX]);
- fj[YY] = b*(fv[YY] - fproj*xij[YY]);
- fj[ZZ] = b*(fv[ZZ] - fproj*xij[ZZ]);
+ rvec fj;
+ fj[XX] = b * (fv[XX] - fproj * xij[XX]);
+ fj[YY] = b * (fv[YY] - fproj * xij[YY]);
+ fj[ZZ] = b * (fv[ZZ] - fproj * xij[ZZ]);
/* 9 */
/* b is already calculated in constr_vsite2FD
fshift[CENTRAL][XX] += fv[XX] - fj[XX];
fshift[CENTRAL][YY] += fv[YY] - fj[YY];
fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ];
- fshift[ sji][XX] += fj[XX];
- fshift[ sji][YY] += fj[YY];
- fshift[ sji][ZZ] += fj[ZZ];
+ fshift[sji][XX] += fj[XX];
+ fshift[sji][YY] += fj[YY];
+ fshift[sji][ZZ] += fj[ZZ];
}
}
for (int j = 0; j < DIM; j++)
{
/* As xix is a linear combination of j and k, use that here */
- dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xij[i] * fj[j];
}
}
}
/* TOTAL: 38 flops */
}
-static void spread_vsite3(const t_iatom ia[], real a, real b,
- const rvec x[],
- rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g)
+static void spread_vsite3(const t_iatom ia[],
+ real a,
+ real b,
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ const t_graph* g)
{
- rvec fi, fj, fk, dx;
- int av, ai, aj, ak;
- ivec di;
- int siv, sij, sik;
+ rvec fi, fj, fk, dx;
+ int av, ai, aj, ak;
+ ivec di;
+ int siv, sij, sik;
av = ia[1];
ai = ia[2];
ak = ia[4];
svmul(1 - a - b, f[av], fi);
- svmul( a, f[av], fj);
- svmul( b, f[av], fk);
+ svmul(a, f[av], fj);
+ svmul(b, f[av], fk);
/* 11 flops */
rvec_inc(f[ai], fi);
/* TOTAL: 20 flops */
}
-static void spread_vsite3FD(const t_iatom ia[], real a, real b,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+static void spread_vsite3FD(const t_iatom ia[],
+ real a,
+ real b,
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ gmx_bool VirCorr,
+ matrix dxdf,
+ const t_pbc* pbc,
+ const t_graph* g)
{
real fproj, a1;
rvec xvi, xij, xjk, xix, fv, temp;
/* 6 flops */
/* xix goes from i to point x on the line jk */
- xix[XX] = xij[XX]+a*xjk[XX];
- xix[YY] = xij[YY]+a*xjk[YY];
- xix[ZZ] = xij[ZZ]+a*xjk[ZZ];
+ xix[XX] = xij[XX] + a * xjk[XX];
+ xix[YY] = xij[YY] + a * xjk[YY];
+ xix[ZZ] = xij[ZZ] + a * xjk[ZZ];
/* 6 flops */
const real invDistance = inverseNorm(xix);
- const real c = b*invDistance;
+ const real c = b * invDistance;
/* 4 + ?10? flops */
- fproj = iprod(xix, fv)*invDistance*invDistance; /* = (xix . f)/(xix . xix) */
+ fproj = iprod(xix, fv) * invDistance * invDistance; /* = (xix . f)/(xix . xix) */
- temp[XX] = c*(fv[XX]-fproj*xix[XX]);
- temp[YY] = c*(fv[YY]-fproj*xix[YY]);
- temp[ZZ] = c*(fv[ZZ]-fproj*xix[ZZ]);
+ temp[XX] = c * (fv[XX] - fproj * xix[XX]);
+ temp[YY] = c * (fv[YY] - fproj * xix[YY]);
+ temp[ZZ] = c * (fv[ZZ] - fproj * xix[ZZ]);
/* 16 */
/* c is already calculated in constr_vsite3FD
storing c somewhere will save 26 flops! */
- a1 = 1 - a;
+ a1 = 1 - a;
f[ai][XX] += fv[XX] - temp[XX];
f[ai][YY] += fv[YY] - temp[YY];
f[ai][ZZ] += fv[ZZ] - temp[ZZ];
- f[aj][XX] += a1*temp[XX];
- f[aj][YY] += a1*temp[YY];
- f[aj][ZZ] += a1*temp[ZZ];
- f[ak][XX] += a*temp[XX];
- f[ak][YY] += a*temp[YY];
- f[ak][ZZ] += a*temp[ZZ];
+ f[aj][XX] += a1 * temp[XX];
+ f[aj][YY] += a1 * temp[YY];
+ f[aj][ZZ] += a1 * temp[ZZ];
+ f[ak][XX] += a * temp[XX];
+ f[ak][YY] += a * temp[YY];
+ f[ak][ZZ] += a * temp[ZZ];
/* 19 Flops */
if (g)
if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL))
{
rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - (1 + a)*temp[XX];
- fshift[CENTRAL][YY] += fv[YY] - (1 + a)*temp[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - (1 + a)*temp[ZZ];
- fshift[ sji][XX] += temp[XX];
- fshift[ sji][YY] += temp[YY];
- fshift[ sji][ZZ] += temp[ZZ];
- fshift[ skj][XX] += a*temp[XX];
- fshift[ skj][YY] += a*temp[YY];
- fshift[ skj][ZZ] += a*temp[ZZ];
+ fshift[CENTRAL][XX] += fv[XX] - (1 + a) * temp[XX];
+ fshift[CENTRAL][YY] += fv[YY] - (1 + a) * temp[YY];
+ fshift[CENTRAL][ZZ] += fv[ZZ] - (1 + a) * temp[ZZ];
+ fshift[sji][XX] += temp[XX];
+ fshift[sji][YY] += temp[YY];
+ fshift[sji][ZZ] += temp[ZZ];
+ fshift[skj][XX] += a * temp[XX];
+ fshift[skj][YY] += a * temp[YY];
+ fshift[skj][ZZ] += a * temp[ZZ];
}
if (VirCorr)
for (int j = 0; j < DIM; j++)
{
/* As xix is a linear combination of j and k, use that here */
- dxdf[i][j] += -xiv[i]*fv[j] + xix[i]*temp[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xix[i] * temp[j];
}
}
}
/* TOTAL: 61 flops */
}
-static void spread_vsite3FAD(const t_iatom ia[], real a, real b,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+static void spread_vsite3FAD(const t_iatom ia[],
+ real a,
+ real b,
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ gmx_bool VirCorr,
+ matrix dxdf,
+ const t_pbc* pbc,
+ const t_graph* g)
{
rvec xvi, xij, xjk, xperp, Fpij, Fppp, fv, f1, f2, f3;
real a1, b1, c1, c2, invdij, invdij2, invdp, fproj;
invdij = inverseNorm(xij);
invdij2 = invdij * invdij;
c1 = iprod(xij, xjk) * invdij2;
- xperp[XX] = xjk[XX] - c1*xij[XX];
- xperp[YY] = xjk[YY] - c1*xij[YY];
- xperp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
+ xperp[XX] = xjk[XX] - c1 * xij[XX];
+ xperp[YY] = xjk[YY] - c1 * xij[YY];
+ xperp[ZZ] = xjk[ZZ] - c1 * xij[ZZ];
/* xperp in plane ijk, perp. to ij */
invdp = inverseNorm(xperp);
- a1 = a*invdij;
- b1 = b*invdp;
+ a1 = a * invdij;
+ b1 = b * invdp;
/* 45 flops */
/* a1, b1 and c1 are already calculated in constr_vsite3FAD
storing them somewhere will save 45 flops! */
- fproj = iprod(xij, fv)*invdij2;
- svmul(fproj, xij, Fpij); /* proj. f on xij */
- svmul(iprod(xperp, fv)*invdp*invdp, xperp, Fppp); /* proj. f on xperp */
- svmul(b1*fproj, xperp, f3);
+ fproj = iprod(xij, fv) * invdij2;
+ svmul(fproj, xij, Fpij); /* proj. f on xij */
+ svmul(iprod(xperp, fv) * invdp * invdp, xperp, Fppp); /* proj. f on xperp */
+ svmul(b1 * fproj, xperp, f3);
/* 23 flops */
rvec_sub(fv, Fpij, f1); /* f1 = f - Fpij */
}
/* 12 flops */
- c2 = 1 + c1;
- f[ai][XX] += fv[XX] - f1[XX] + c1*f2[XX] + f3[XX];
- f[ai][YY] += fv[YY] - f1[YY] + c1*f2[YY] + f3[YY];
- f[ai][ZZ] += fv[ZZ] - f1[ZZ] + c1*f2[ZZ] + f3[ZZ];
- f[aj][XX] += f1[XX] - c2*f2[XX] - f3[XX];
- f[aj][YY] += f1[YY] - c2*f2[YY] - f3[YY];
- f[aj][ZZ] += f1[ZZ] - c2*f2[ZZ] - f3[ZZ];
- f[ak][XX] += f2[XX];
- f[ak][YY] += f2[YY];
- f[ak][ZZ] += f2[ZZ];
+ c2 = 1 + c1;
+ f[ai][XX] += fv[XX] - f1[XX] + c1 * f2[XX] + f3[XX];
+ f[ai][YY] += fv[YY] - f1[YY] + c1 * f2[YY] + f3[YY];
+ f[ai][ZZ] += fv[ZZ] - f1[ZZ] + c1 * f2[ZZ] + f3[ZZ];
+ f[aj][XX] += f1[XX] - c2 * f2[XX] - f3[XX];
+ f[aj][YY] += f1[YY] - c2 * f2[YY] - f3[YY];
+ f[aj][ZZ] += f1[ZZ] - c2 * f2[ZZ] - f3[ZZ];
+ f[ak][XX] += f2[XX];
+ f[ak][YY] += f2[YY];
+ f[ak][ZZ] += f2[ZZ];
/* 30 Flops */
if (g)
if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL))
{
rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - f1[XX] - (1-c1)*f2[XX] + f3[XX];
- fshift[CENTRAL][YY] += fv[YY] - f1[YY] - (1-c1)*f2[YY] + f3[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - f1[ZZ] - (1-c1)*f2[ZZ] + f3[ZZ];
- fshift[ sji][XX] += f1[XX] - c1 *f2[XX] - f3[XX];
- fshift[ sji][YY] += f1[YY] - c1 *f2[YY] - f3[YY];
- fshift[ sji][ZZ] += f1[ZZ] - c1 *f2[ZZ] - f3[ZZ];
- fshift[ skj][XX] += f2[XX];
- fshift[ skj][YY] += f2[YY];
- fshift[ skj][ZZ] += f2[ZZ];
+ fshift[CENTRAL][XX] += fv[XX] - f1[XX] - (1 - c1) * f2[XX] + f3[XX];
+ fshift[CENTRAL][YY] += fv[YY] - f1[YY] - (1 - c1) * f2[YY] + f3[YY];
+ fshift[CENTRAL][ZZ] += fv[ZZ] - f1[ZZ] - (1 - c1) * f2[ZZ] + f3[ZZ];
+ fshift[sji][XX] += f1[XX] - c1 * f2[XX] - f3[XX];
+ fshift[sji][YY] += f1[YY] - c1 * f2[YY] - f3[YY];
+ fshift[sji][ZZ] += f1[ZZ] - c1 * f2[ZZ] - f3[ZZ];
+ fshift[skj][XX] += f2[XX];
+ fshift[skj][YY] += f2[YY];
+ fshift[skj][ZZ] += f2[ZZ];
}
if (VirCorr)
for (j = 0; j < DIM; j++)
{
/* Note that xik=xij+xjk, so we have to add xij*f2 */
- dxdf[i][j] +=
- -xiv[i]*fv[j]
- + xij[i]*(f1[j] + (1 - c2)*f2[j] - f3[j])
- + xjk[i]*f2[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xij[i] * (f1[j] + (1 - c2) * f2[j] - f3[j])
+ + xjk[i] * f2[j];
}
}
}
/* TOTAL: 113 flops */
}
-static void spread_vsite3OUT(const t_iatom ia[], real a, real b, real c,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+static void spread_vsite3OUT(const t_iatom ia[],
+ real a,
+ real b,
+ real c,
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ gmx_bool VirCorr,
+ matrix dxdf,
+ const t_pbc* pbc,
+ const t_graph* g)
{
- rvec xvi, xij, xik, fv, fj, fk;
- real cfx, cfy, cfz;
- int av, ai, aj, ak;
- ivec di;
- int svi, sji, ski;
+ rvec xvi, xij, xik, fv, fj, fk;
+ real cfx, cfy, cfz;
+ int av, ai, aj, ak;
+ ivec di;
+ int svi, sji, ski;
av = ia[1];
ai = ia[2];
copy_rvec(f[av], fv);
- cfx = c*fv[XX];
- cfy = c*fv[YY];
- cfz = c*fv[ZZ];
+ cfx = c * fv[XX];
+ cfy = c * fv[YY];
+ cfz = c * fv[ZZ];
/* 3 Flops */
- fj[XX] = a*fv[XX] - xik[ZZ]*cfy + xik[YY]*cfz;
- fj[YY] = xik[ZZ]*cfx + a*fv[YY] - xik[XX]*cfz;
- fj[ZZ] = -xik[YY]*cfx + xik[XX]*cfy + a*fv[ZZ];
+ fj[XX] = a * fv[XX] - xik[ZZ] * cfy + xik[YY] * cfz;
+ fj[YY] = xik[ZZ] * cfx + a * fv[YY] - xik[XX] * cfz;
+ fj[ZZ] = -xik[YY] * cfx + xik[XX] * cfy + a * fv[ZZ];
- fk[XX] = b*fv[XX] + xij[ZZ]*cfy - xij[YY]*cfz;
- fk[YY] = -xij[ZZ]*cfx + b*fv[YY] + xij[XX]*cfz;
- fk[ZZ] = xij[YY]*cfx - xij[XX]*cfy + b*fv[ZZ];
+ fk[XX] = b * fv[XX] + xij[ZZ] * cfy - xij[YY] * cfz;
+ fk[YY] = -xij[ZZ] * cfx + b * fv[YY] + xij[XX] * cfz;
+ fk[ZZ] = xij[YY] * cfx - xij[XX] * cfy + b * fv[ZZ];
/* 30 Flops */
f[ai][XX] += fv[XX] - fj[XX] - fk[XX];
{
for (int j = 0; j < DIM; j++)
{
- dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j] + xik[i]*fk[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xij[i] * fj[j] + xik[i] * fk[j];
}
}
}
/* TOTAL: 54 flops */
}
-static void spread_vsite4FD(const t_iatom ia[], real a, real b, real c,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+static void spread_vsite4FD(const t_iatom ia[],
+ real a,
+ real b,
+ real c,
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ gmx_bool VirCorr,
+ matrix dxdf,
+ const t_pbc* pbc,
+ const t_graph* g)
{
- real fproj, a1;
- rvec xvi, xij, xjk, xjl, xix, fv, temp;
- int av, ai, aj, ak, al;
- ivec di;
- int svi, sji, skj, slj, m;
+ real fproj, a1;
+ rvec xvi, xij, xjk, xjl, xix, fv, temp;
+ int av, ai, aj, ak, al;
+ ivec di;
+ int svi, sji, skj, slj, m;
av = ia[1];
ai = ia[2];
/* xix goes from i to point x on the plane jkl */
for (m = 0; m < DIM; m++)
{
- xix[m] = xij[m] + a*xjk[m] + b*xjl[m];
+ xix[m] = xij[m] + a * xjk[m] + b * xjl[m];
}
/* 12 flops */
const real invDistance = inverseNorm(xix);
- const real d = c*invDistance;
+ const real d = c * invDistance;
/* 4 + ?10? flops */
copy_rvec(f[av], fv);
- fproj = iprod(xix, fv)*invDistance*invDistance; /* = (xix . f)/(xix . xix) */
+ fproj = iprod(xix, fv) * invDistance * invDistance; /* = (xix . f)/(xix . xix) */
for (m = 0; m < DIM; m++)
{
- temp[m] = d*(fv[m] - fproj*xix[m]);
+ temp[m] = d * (fv[m] - fproj * xix[m]);
}
/* 16 */
for (m = 0; m < DIM; m++)
{
f[ai][m] += fv[m] - temp[m];
- f[aj][m] += a1*temp[m];
- f[ak][m] += a*temp[m];
- f[al][m] += b*temp[m];
+ f[aj][m] += a1 * temp[m];
+ f[ak][m] += a * temp[m];
+ f[al][m] += b * temp[m];
}
/* 26 Flops */
svi = CENTRAL;
}
- if (fshift &&
- (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL || slj != CENTRAL))
+ if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL || slj != CENTRAL))
{
rvec_dec(fshift[svi], fv);
for (m = 0; m < DIM; m++)
{
- fshift[CENTRAL][m] += fv[m] - (1 + a + b)*temp[m];
- fshift[ sji][m] += temp[m];
- fshift[ skj][m] += a*temp[m];
- fshift[ slj][m] += b*temp[m];
+ fshift[CENTRAL][m] += fv[m] - (1 + a + b) * temp[m];
+ fshift[sji][m] += temp[m];
+ fshift[skj][m] += a * temp[m];
+ fshift[slj][m] += b * temp[m];
}
}
{
for (j = 0; j < DIM; j++)
{
- dxdf[i][j] += -xiv[i]*fv[j] + xix[i]*temp[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xix[i] * temp[j];
}
}
}
}
-static void spread_vsite4FDN(const t_iatom ia[], real a, real b, real c,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+static void spread_vsite4FDN(const t_iatom ia[],
+ real a,
+ real b,
+ real c,
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ gmx_bool VirCorr,
+ matrix dxdf,
+ const t_pbc* pbc,
+ const t_graph* g)
{
rvec xvi, xij, xik, xil, ra, rb, rja, rjb, rab, rm, rt;
rvec fv, fj, fk, fl;
sil = pbc_rvec_sub(pbc, x[al], x[ai], xil);
/* 9 flops */
- ra[XX] = a*xik[XX];
- ra[YY] = a*xik[YY];
- ra[ZZ] = a*xik[ZZ];
+ ra[XX] = a * xik[XX];
+ ra[YY] = a * xik[YY];
+ ra[ZZ] = a * xik[ZZ];
- rb[XX] = b*xil[XX];
- rb[YY] = b*xil[YY];
- rb[ZZ] = b*xil[ZZ];
+ rb[XX] = b * xil[XX];
+ rb[YY] = b * xil[YY];
+ rb[ZZ] = b * xil[ZZ];
/* 6 flops */
/* 9 flops */
invrm = inverseNorm(rm);
- denom = invrm*invrm;
+ denom = invrm * invrm;
/* 5+5+2 flops */
- cfx = c*invrm*fv[XX];
- cfy = c*invrm*fv[YY];
- cfz = c*invrm*fv[ZZ];
+ cfx = c * invrm * fv[XX];
+ cfy = c * invrm * fv[YY];
+ cfz = c * invrm * fv[ZZ];
/* 6 Flops */
cprod(rm, rab, rt);
rt[ZZ] *= denom;
/* 3flops */
- fj[XX] = ( -rm[XX]*rt[XX]) * cfx + ( rab[ZZ]-rm[YY]*rt[XX]) * cfy + (-rab[YY]-rm[ZZ]*rt[XX]) * cfz;
- fj[YY] = (-rab[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + ( rab[XX]-rm[ZZ]*rt[YY]) * cfz;
- fj[ZZ] = ( rab[YY]-rm[XX]*rt[ZZ]) * cfx + (-rab[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
+ fj[XX] = (-rm[XX] * rt[XX]) * cfx + (rab[ZZ] - rm[YY] * rt[XX]) * cfy
+ + (-rab[YY] - rm[ZZ] * rt[XX]) * cfz;
+ fj[YY] = (-rab[ZZ] - rm[XX] * rt[YY]) * cfx + (-rm[YY] * rt[YY]) * cfy
+ + (rab[XX] - rm[ZZ] * rt[YY]) * cfz;
+ fj[ZZ] = (rab[YY] - rm[XX] * rt[ZZ]) * cfx + (-rab[XX] - rm[YY] * rt[ZZ]) * cfy
+ + (-rm[ZZ] * rt[ZZ]) * cfz;
/* 30 flops */
cprod(rjb, rm, rt);
/* 9 flops */
- rt[XX] *= denom*a;
- rt[YY] *= denom*a;
- rt[ZZ] *= denom*a;
+ rt[XX] *= denom * a;
+ rt[YY] *= denom * a;
+ rt[ZZ] *= denom * a;
/* 3flops */
- fk[XX] = ( -rm[XX]*rt[XX]) * cfx + (-a*rjb[ZZ]-rm[YY]*rt[XX]) * cfy + ( a*rjb[YY]-rm[ZZ]*rt[XX]) * cfz;
- fk[YY] = ( a*rjb[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + (-a*rjb[XX]-rm[ZZ]*rt[YY]) * cfz;
- fk[ZZ] = (-a*rjb[YY]-rm[XX]*rt[ZZ]) * cfx + ( a*rjb[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
+ fk[XX] = (-rm[XX] * rt[XX]) * cfx + (-a * rjb[ZZ] - rm[YY] * rt[XX]) * cfy
+ + (a * rjb[YY] - rm[ZZ] * rt[XX]) * cfz;
+ fk[YY] = (a * rjb[ZZ] - rm[XX] * rt[YY]) * cfx + (-rm[YY] * rt[YY]) * cfy
+ + (-a * rjb[XX] - rm[ZZ] * rt[YY]) * cfz;
+ fk[ZZ] = (-a * rjb[YY] - rm[XX] * rt[ZZ]) * cfx + (a * rjb[XX] - rm[YY] * rt[ZZ]) * cfy
+ + (-rm[ZZ] * rt[ZZ]) * cfz;
/* 36 flops */
cprod(rm, rja, rt);
/* 9 flops */
- rt[XX] *= denom*b;
- rt[YY] *= denom*b;
- rt[ZZ] *= denom*b;
+ rt[XX] *= denom * b;
+ rt[YY] *= denom * b;
+ rt[ZZ] *= denom * b;
/* 3flops */
- fl[XX] = ( -rm[XX]*rt[XX]) * cfx + ( b*rja[ZZ]-rm[YY]*rt[XX]) * cfy + (-b*rja[YY]-rm[ZZ]*rt[XX]) * cfz;
- fl[YY] = (-b*rja[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + ( b*rja[XX]-rm[ZZ]*rt[YY]) * cfz;
- fl[ZZ] = ( b*rja[YY]-rm[XX]*rt[ZZ]) * cfx + (-b*rja[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
+ fl[XX] = (-rm[XX] * rt[XX]) * cfx + (b * rja[ZZ] - rm[YY] * rt[XX]) * cfy
+ + (-b * rja[YY] - rm[ZZ] * rt[XX]) * cfz;
+ fl[YY] = (-b * rja[ZZ] - rm[XX] * rt[YY]) * cfx + (-rm[YY] * rt[YY]) * cfy
+ + (b * rja[XX] - rm[ZZ] * rt[YY]) * cfz;
+ fl[ZZ] = (b * rja[YY] - rm[XX] * rt[ZZ]) * cfx + (-b * rja[XX] - rm[YY] * rt[ZZ]) * cfy
+ + (-rm[ZZ] * rt[ZZ]) * cfz;
/* 36 flops */
f[ai][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
{
for (j = 0; j < DIM; j++)
{
- dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j] + xik[i]*fk[j] + xil[i]*fl[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xij[i] * fj[j] + xik[i] * fk[j] + xil[i] * fl[j];
}
}
}
}
-static int spread_vsiten(const t_iatom ia[], const t_iparams ip[],
- const rvec x[],
- rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g)
+static int spread_vsiten(const t_iatom ia[],
+ const t_iparams ip[],
+ const rvec x[],
+ rvec f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ const t_graph* g)
{
rvec xv, dx, fi;
int n3, av, i, ai;
ivec di;
int siv;
- n3 = 3*ip[ia[0]].vsiten.n;
+ n3 = 3 * ip[ia[0]].vsiten.n;
av = ia[1];
copy_rvec(x[av], xv);
for (i = 0; i < n3; i += 3)
{
- ai = ia[i+2];
+ ai = ia[i + 2];
if (g)
{
ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, av), di);
}
-static int vsite_count(const t_ilist *ilist, int ftype)
+static int vsite_count(const t_ilist* ilist, int ftype)
{
if (ftype == F_VSITEN)
{
- return ilist[ftype].nr/3;
+ return ilist[ftype].nr / 3;
}
else
{
- return ilist[ftype].nr/(1 + interaction_function[ftype].nratoms);
+ return ilist[ftype].nr / (1 + interaction_function[ftype].nratoms);
}
}
-static void spread_vsite_f_thread(const rvec x[],
- rvec f[], rvec *fshift,
- gmx_bool VirCorr, matrix dxdf,
- t_iparams ip[], const t_ilist ilist[],
- const t_graph *g, const t_pbc *pbc_null)
+static void spread_vsite_f_thread(const rvec x[],
+ rvec f[],
+ rvec* fshift,
+ gmx_bool VirCorr,
+ matrix dxdf,
+ t_iparams ip[],
+ const t_ilist ilist[],
+ const t_graph* g,
+ const t_pbc* pbc_null)
{
- const PbcMode pbcMode = getPbcMode(pbc_null);
+ const PbcMode pbcMode = getPbcMode(pbc_null);
/* We need another pbc pointer, as with charge groups we switch per vsite */
- const t_pbc *pbc_null2 = pbc_null;
+ const t_pbc* pbc_null2 = pbc_null;
gmx::ArrayRef<const int> vsite_pbc;
/* this loop goes backwards to be able to build *
continue;
}
- { // TODO remove me
- int nra = interaction_function[ftype].nratoms;
- int inc = 1 + nra;
- int nr = ilist[ftype].nr;
+ { // TODO remove me
+ int nra = interaction_function[ftype].nratoms;
+ int inc = 1 + nra;
+ int nr = ilist[ftype].nr;
- const t_iatom *ia = ilist[ftype].iatoms;
+ const t_iatom* ia = ilist[ftype].iatoms;
if (pbcMode == PbcMode::all)
{
pbc_null2 = pbc_null;
}
- for (int i = 0; i < nr; )
+ for (int i = 0; i < nr;)
{
int tp = ia[0];
/* Construct the vsite depending on type */
switch (ftype)
{
- case F_VSITE2:
- spread_vsite2(ia, a1, x, f, fshift, pbc_null2, g);
- break;
+ case F_VSITE2: spread_vsite2(ia, a1, x, f, fshift, pbc_null2, g); break;
case F_VSITE2FD:
spread_vsite2FD(ia, a1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
break;
c1 = ip[tp].vsite.c;
spread_vsite4FDN(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
break;
- case F_VSITEN:
- inc = spread_vsiten(ia, ip, x, f, fshift, pbc_null2, g);
- break;
+ case F_VSITEN: inc = spread_vsiten(ia, ip, x, f, fshift, pbc_null2, g); break;
default:
- gmx_fatal(FARGS, "No such vsite type %d in %s, line %d",
- ftype, __FILE__, __LINE__);
+ gmx_fatal(FARGS, "No such vsite type %d in %s, line %d", ftype, __FILE__, __LINE__);
}
clear_rvec(f[ia[1]]);
/* Increment loop variables */
- i += inc;
+ i += inc;
ia += inc;
}
}
}
/*! \brief Clears the task force buffer elements that are written by task idTask */
-static void clearTaskForceBufferUsedElements(InterdependentTask *idTask)
+static void clearTaskForceBufferUsedElements(InterdependentTask* idTask)
{
int ntask = idTask->spreadTask.size();
for (int ti = 0; ti < ntask; ti++)
{
- const AtomIndex *atomList = &idTask->atomIndex[idTask->spreadTask[ti]];
+ const AtomIndex* atomList = &idTask->atomIndex[idTask->spreadTask[ti]];
int natom = atomList->atom.size();
- RVec *force = idTask->force.data();
+ RVec* force = idTask->force.data();
for (int i = 0; i < natom; i++)
{
clear_rvec(force[atomList->atom[i]]);
}
}
-void spread_vsite_f(const gmx_vsite_t *vsite,
- const rvec * gmx_restrict x,
- rvec * gmx_restrict f, rvec * gmx_restrict fshift,
- gmx_bool VirCorr, matrix vir,
- t_nrnb *nrnb, const t_idef *idef,
- int ePBC, gmx_bool bMolPBC, const t_graph *g, const matrix box,
- const t_commrec *cr, gmx_wallcycle *wcycle)
+void spread_vsite_f(const gmx_vsite_t* vsite,
+ const rvec* gmx_restrict x,
+ rvec* gmx_restrict f,
+ rvec* gmx_restrict fshift,
+ gmx_bool VirCorr,
+ matrix vir,
+ t_nrnb* nrnb,
+ const t_idef* idef,
+ int ePBC,
+ gmx_bool bMolPBC,
+ const t_graph* g,
+ const matrix box,
+ const t_commrec* cr,
+ gmx_wallcycle* wcycle)
{
wallcycle_start(wcycle, ewcVSITESPREAD);
const bool useDomdec = vsite->useDomdec;
- GMX_ASSERT(!useDomdec || (cr != nullptr && DOMAINDECOMP(cr)), "When vsites are set up with domain decomposition, we need a valid commrec");
+ GMX_ASSERT(!useDomdec || (cr != nullptr && DOMAINDECOMP(cr)),
+ "When vsites are set up with domain decomposition, we need a valid commrec");
t_pbc pbc, *pbc_null;
{
clear_mat(dxdf);
}
- spread_vsite_f_thread(x, f, fshift,
- VirCorr, dxdf,
- idef->iparams, idef->il,
- g, pbc_null);
+ spread_vsite_f_thread(x, f, fshift, VirCorr, dxdf, idef->iparams, idef->il, g, pbc_null);
if (VirCorr)
{
{
for (int j = 0; j < DIM; j++)
{
- vir[i][j] += -0.5*dxdf[i][j];
+ vir[i][j] += -0.5 * dxdf[i][j];
}
}
}
{
clear_mat(vsite->tData[vsite->nthreads]->dxdf);
}
- spread_vsite_f_thread(x, f, fshift,
- VirCorr, vsite->tData[vsite->nthreads]->dxdf,
- idef->iparams,
- vsite->tData[vsite->nthreads]->ilist,
- g, pbc_null);
+ spread_vsite_f_thread(x, f, fshift, VirCorr, vsite->tData[vsite->nthreads]->dxdf,
+ idef->iparams, vsite->tData[vsite->nthreads]->ilist, g, pbc_null);
#pragma omp parallel num_threads(vsite->nthreads)
{
try
{
int thread = gmx_omp_get_thread_num();
- VsiteThread &tData = *vsite->tData[thread];
+ VsiteThread& tData = *vsite->tData[thread];
- rvec *fshift_t;
+ rvec* fshift_t;
if (thread == 0 || fshift == nullptr)
{
fshift_t = fshift;
* This is done using a thread-local force buffer force.
* First we need to copy the input vsite forces to force.
*/
- InterdependentTask *idTask = &tData.idTask;
+ InterdependentTask* idTask = &tData.idTask;
/* Clear the buffer elements set by our task during
* the last call to spread_vsite_f.
int nvsite = idTask->vsite.size();
for (int i = 0; i < nvsite; i++)
{
- copy_rvec(f[idTask->vsite[i]],
- idTask->force[idTask->vsite[i]]);
+ copy_rvec(f[idTask->vsite[i]], idTask->force[idTask->vsite[i]]);
}
- spread_vsite_f_thread(x, as_rvec_array(idTask->force.data()), fshift_t,
- VirCorr, tData.dxdf,
- idef->iparams,
- tData.idTask.ilist,
- g, pbc_null);
+ spread_vsite_f_thread(x, as_rvec_array(idTask->force.data()), fshift_t, VirCorr,
+ tData.dxdf, idef->iparams, tData.idTask.ilist, g, pbc_null);
/* We need a barrier before reducing forces below
* that have been produced by a different thread above.
int ntask = idTask->reduceTask.size();
for (int ti = 0; ti < ntask; ti++)
{
- const InterdependentTask *idt_foreign = &vsite->tData[idTask->reduceTask[ti]]->idTask;
- const AtomIndex *atomList = &idt_foreign->atomIndex[thread];
- const RVec *f_foreign = idt_foreign->force.data();
+ const InterdependentTask* idt_foreign =
+ &vsite->tData[idTask->reduceTask[ti]]->idTask;
+ const AtomIndex* atomList = &idt_foreign->atomIndex[thread];
+ const RVec* f_foreign = idt_foreign->force.data();
int natom = atomList->atom.size();
for (int i = 0; i < natom; i++)
}
/* Spread the vsites that spread locally only */
- spread_vsite_f_thread(x, f, fshift_t,
- VirCorr, tData.dxdf,
- idef->iparams,
- tData.ilist,
- g, pbc_null);
+ spread_vsite_f_thread(x, f, fshift_t, VirCorr, tData.dxdf, idef->iparams,
+ tData.ilist, g, pbc_null);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
if (fshift != nullptr)
for (int th = 0; th < vsite->nthreads + 1; th++)
{
/* MSVC doesn't like matrix references, so we use a pointer */
- const matrix *dxdf = &vsite->tData[th]->dxdf;
+ const matrix* dxdf = &vsite->tData[th]->dxdf;
for (int i = 0; i < DIM; i++)
{
for (int j = 0; j < DIM; j++)
{
- vir[i][j] += -0.5*(*dxdf)[i][j];
+ vir[i][j] += -0.5 * (*dxdf)[i][j];
}
}
}
dd_move_f_vsites(cr->dd, f, fshift);
}
- inc_nrnb(nrnb, eNR_VSITE2, vsite_count(idef->il, F_VSITE2));
+ inc_nrnb(nrnb, eNR_VSITE2, vsite_count(idef->il, F_VSITE2));
inc_nrnb(nrnb, eNR_VSITE2FD, vsite_count(idef->il, F_VSITE2FD));
- inc_nrnb(nrnb, eNR_VSITE3, vsite_count(idef->il, F_VSITE3));
+ inc_nrnb(nrnb, eNR_VSITE3, vsite_count(idef->il, F_VSITE3));
inc_nrnb(nrnb, eNR_VSITE3FD, vsite_count(idef->il, F_VSITE3FD));
inc_nrnb(nrnb, eNR_VSITE3FAD, vsite_count(idef->il, F_VSITE3FAD));
inc_nrnb(nrnb, eNR_VSITE3OUT, vsite_count(idef->il, F_VSITE3OUT));
inc_nrnb(nrnb, eNR_VSITE4FD, vsite_count(idef->il, F_VSITE4FD));
inc_nrnb(nrnb, eNR_VSITE4FDN, vsite_count(idef->il, F_VSITE4FDN));
- inc_nrnb(nrnb, eNR_VSITEN, vsite_count(idef->il, F_VSITEN));
+ inc_nrnb(nrnb, eNR_VSITEN, vsite_count(idef->il, F_VSITEN));
wallcycle_stop(wcycle, ewcVSITESPREAD);
}
*
* \param[in] grouping The paritioning of the atom range into atom groups
*/
-static std::vector<int> makeAtomToGroupMapping(const gmx::RangePartitioning &grouping)
+static std::vector<int> makeAtomToGroupMapping(const gmx::RangePartitioning& grouping)
{
std::vector<int> atomToGroup(grouping.fullRange().end(), 0);
for (int group = 0; group < grouping.numBlocks(); group++)
{
auto block = grouping.block(group);
- std::fill(atomToGroup.begin() + block.begin(),
- atomToGroup.begin() + block.end(),
- group);
+ std::fill(atomToGroup.begin() + block.begin(), atomToGroup.begin() + block.end(), group);
}
return atomToGroup;
}
-int countNonlinearVsites(const gmx_mtop_t &mtop)
+int countNonlinearVsites(const gmx_mtop_t& mtop)
{
int numNonlinearVsites = 0;
- for (const gmx_molblock_t &molb : mtop.molblock)
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- const gmx_moltype_t &molt = mtop.moltype[molb.type];
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
- for (const auto &ilist : extractILists(molt.ilist, IF_VSITE))
+ for (const auto& ilist : extractILists(molt.ilist, IF_VSITE))
{
- if (ilist.functionType != F_VSITE2 &&
- ilist.functionType != F_VSITE3 &&
- ilist.functionType != F_VSITEN)
+ if (ilist.functionType != F_VSITE2 && ilist.functionType != F_VSITE3
+ && ilist.functionType != F_VSITEN)
{
- numNonlinearVsites += molb.nmol*ilist.iatoms.size()/(1 + NRAL(ilist.functionType));
+ numNonlinearVsites += molb.nmol * ilist.iatoms.size() / (1 + NRAL(ilist.functionType));
}
}
}
return numNonlinearVsites;
}
-int countInterUpdategroupVsites(const gmx_mtop_t &mtop,
- gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingPerMoleculetype)
+int countInterUpdategroupVsites(const gmx_mtop_t& mtop,
+ gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingPerMoleculetype)
{
int n_intercg_vsite = 0;
- for (const gmx_molblock_t &molb : mtop.molblock)
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- const gmx_moltype_t &molt = mtop.moltype[molb.type];
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
- std::vector<int> atomToGroup;
+ std::vector<int> atomToGroup;
if (!updateGroupingPerMoleculetype.empty())
{
atomToGroup = makeAtomToGroupMapping(updateGroupingPerMoleculetype[molb.type]);
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
const int nral = NRAL(ftype);
- const InteractionList &il = molt.ilist[ftype];
+ const InteractionList& il = molt.ilist[ftype];
for (int i = 0; i < il.size(); i += 1 + nral)
{
bool isInterGroup = atomToGroup.empty();
return n_intercg_vsite;
}
-std::unique_ptr<gmx_vsite_t>
-initVsite(const gmx_mtop_t &mtop,
- const t_commrec *cr)
+std::unique_ptr<gmx_vsite_t> initVsite(const gmx_mtop_t& mtop, const t_commrec* cr)
{
GMX_RELEASE_ASSERT(cr != nullptr, "We need a valid commrec");
{
if (interaction_function[ftype].flags & IF_VSITE)
{
- GMX_ASSERT(ftype >= c_ftypeVsiteStart && ftype < c_ftypeVsiteEnd, "c_ftypeVsiteStart and/or c_ftypeVsiteEnd do not have correct values");
+ GMX_ASSERT(ftype >= c_ftypeVsiteStart && ftype < c_ftypeVsiteEnd,
+ "c_ftypeVsiteStart and/or c_ftypeVsiteEnd do not have correct values");
nvsite += gmx_mtop_ftype_count(&mtop, ftype);
}
else
{
- GMX_ASSERT(ftype < c_ftypeVsiteStart || ftype >= c_ftypeVsiteEnd, "c_ftypeVsiteStart and/or c_ftypeVsiteEnd do not have correct values");
+ GMX_ASSERT(ftype < c_ftypeVsiteStart || ftype >= c_ftypeVsiteEnd,
+ "c_ftypeVsiteStart and/or c_ftypeVsiteEnd do not have correct values");
}
}
}
vsite->numInterUpdategroupVsites = countInterUpdategroupVsites(mtop, updateGroupingPerMoleculetype);
- vsite->useDomdec = (DOMAINDECOMP(cr) && cr->dd->nnodes > 1);
+ vsite->useDomdec = (DOMAINDECOMP(cr) && cr->dd->nnodes > 1);
- vsite->nthreads = gmx_omp_nthreads_get(emntVSITE);
+ vsite->nthreads = gmx_omp_nthreads_get(emntVSITE);
if (vsite->nthreads > 1)
{
{
vsite->tData[thread] = std::make_unique<VsiteThread>();
- InterdependentTask &idTask = vsite->tData[thread]->idTask;
+ InterdependentTask& idTask = vsite->tData[thread]->idTask;
idTask.nuse = 0;
idTask.atomIndex.resize(vsite->nthreads);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
if (vsite->nthreads > 1)
{
return vsite;
}
-gmx_vsite_t::gmx_vsite_t()
-{
-}
+gmx_vsite_t::gmx_vsite_t() {}
-gmx_vsite_t::~gmx_vsite_t()
-{
-}
+gmx_vsite_t::~gmx_vsite_t() {}
-static inline void flagAtom(InterdependentTask *idTask, int atom,
- int thread, int nthread, int natperthread)
+static inline void flagAtom(InterdependentTask* idTask, int atom, int thread, int nthread, int natperthread)
{
if (!idTask->use[atom])
{
idTask->use[atom] = true;
- thread = atom/natperthread;
+ thread = atom / natperthread;
/* Assign all non-local atom force writes to thread 0 */
if (thread >= nthread)
{
- thread = 0;
+ thread = 0;
}
idTask->atomIndex[thread].atom.push_back(atom);
}
* taskIndex[] is set for all vsites in our range, either to our local tasks
* or to the single last task as taskIndex[]=2*nthreads.
*/
-static void assignVsitesToThread(VsiteThread *tData,
- int thread,
- int nthread,
- int natperthread,
- gmx::ArrayRef<int> taskIndex,
- const t_ilist *ilist,
- const t_iparams *ip,
- const unsigned short *ptype)
+static void assignVsitesToThread(VsiteThread* tData,
+ int thread,
+ int nthread,
+ int natperthread,
+ gmx::ArrayRef<int> taskIndex,
+ const t_ilist* ilist,
+ const t_iparams* ip,
+ const unsigned short* ptype)
{
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
int nral1 = 1 + NRAL(ftype);
int inc = nral1;
- t_iatom *iat = ilist[ftype].iatoms;
- for (int i = 0; i < ilist[ftype].nr; )
+ t_iatom* iat = ilist[ftype].iatoms;
+ for (int i = 0; i < ilist[ftype].nr;)
{
if (ftype == F_VSITEN)
{
/* The 3 below is from 1+NRAL(ftype)=3 */
- inc = ip[iat[i]].vsiten.n*3;
+ inc = ip[iat[i]].vsiten.n * 3;
}
- if (iat[1 + i] < tData->rangeStart ||
- iat[1 + i] >= tData->rangeEnd)
+ if (iat[1 + i] < tData->rangeStart || iat[1 + i] >= tData->rangeEnd)
{
/* This vsite belongs to a different thread */
i += inc;
for (int j = i + 2; j < i + nral1; j++)
{
/* Do a range check to avoid a harmless race on taskIndex */
- if (iat[j] < tData->rangeStart ||
- iat[j] >= tData->rangeEnd ||
- taskIndex[iat[j]] != thread)
+ if (iat[j] < tData->rangeStart || iat[j] >= tData->rangeEnd || taskIndex[iat[j]] != thread)
{
- if (!tData->useInterdependentTask ||
- ptype[iat[j]] == eptVSite)
+ if (!tData->useInterdependentTask || ptype[iat[j]] == eptVSite)
{
/* At least one constructing atom is a vsite
* that is not assigned to the same thread.
* Put this vsite into a separate task.
*/
- task = 2*nthread;
+ task = 2 * nthread;
break;
}
for (int j = i + 2; j < i + inc; j += 3)
{
/* Do a range check to avoid a harmless race on taskIndex */
- if (iat[j] < tData->rangeStart ||
- iat[j] >= tData->rangeEnd ||
- taskIndex[iat[j]] != thread)
+ if (iat[j] < tData->rangeStart || iat[j] >= tData->rangeEnd || taskIndex[iat[j]] != thread)
{
- GMX_ASSERT(ptype[iat[j]] != eptVSite, "A vsite to be assigned in assignVsitesToThread has a vsite as a constructing atom that does not belong to our task, such vsites should be assigned to the single 'master' task");
+ GMX_ASSERT(ptype[iat[j]] != eptVSite,
+ "A vsite to be assigned in assignVsitesToThread has a vsite as "
+ "a constructing atom that does not belong to our task, such "
+ "vsites should be assigned to the single 'master' task");
task = nthread + thread;
}
}
/* Update this vsite's thread index entry */
- taskIndex[iat[1+i]] = task;
+ taskIndex[iat[1 + i]] = task;
if (task == thread || task == nthread + thread)
{
/* Copy this vsite to the thread data struct of thread */
- t_ilist *il_task;
+ t_ilist* il_task;
if (task == thread)
{
il_task = &tData->ilist[ftype];
{
for (int j = i + 2; j < i + nral1; j++)
{
- flagAtom(&tData->idTask, iat[j],
- thread, nthread, natperthread);
+ flagAtom(&tData->idTask, iat[j], thread, nthread, natperthread);
}
}
else
{
for (int j = i + 2; j < i + inc; j += 3)
{
- flagAtom(&tData->idTask, iat[j],
- thread, nthread, natperthread);
+ flagAtom(&tData->idTask, iat[j], thread, nthread, natperthread);
}
}
}
}
/*! \brief Assign all vsites with taskIndex[]==task to task tData */
-static void assignVsitesToSingleTask(VsiteThread *tData,
- int task,
- gmx::ArrayRef<const int> taskIndex,
- const t_ilist *ilist,
- const t_iparams *ip)
+static void assignVsitesToSingleTask(VsiteThread* tData,
+ int task,
+ gmx::ArrayRef<const int> taskIndex,
+ const t_ilist* ilist,
+ const t_iparams* ip)
{
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
int nral1 = 1 + NRAL(ftype);
int inc = nral1;
- t_iatom *iat = ilist[ftype].iatoms;
- t_ilist *il_task = &tData->ilist[ftype];
+ t_iatom* iat = ilist[ftype].iatoms;
+ t_ilist* il_task = &tData->ilist[ftype];
- for (int i = 0; i < ilist[ftype].nr; )
+ for (int i = 0; i < ilist[ftype].nr;)
{
if (ftype == F_VSITEN)
{
/* The 3 below is from 1+NRAL(ftype)=3 */
- inc = ip[iat[i]].vsiten.n*3;
+ inc = ip[iat[i]].vsiten.n * 3;
}
/* Check if the vsite is assigned to our task */
if (taskIndex[iat[1 + i]] == task)
}
}
-void split_vsites_over_threads(const t_ilist *ilist,
- const t_iparams *ip,
- const t_mdatoms *mdatoms,
- gmx_vsite_t *vsite)
+void split_vsites_over_threads(const t_ilist* ilist, const t_iparams* ip, const t_mdatoms* mdatoms, gmx_vsite_t* vsite)
{
- int vsite_atom_range, natperthread;
+ int vsite_atom_range, natperthread;
if (vsite->nthreads == 1)
{
vsite_atom_range = -1;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- { // TODO remove me
+ { // TODO remove me
if (ftype != F_VSITEN)
{
int nral1 = 1 + NRAL(ftype);
- const t_iatom *iat = ilist[ftype].iatoms;
+ const t_iatom* iat = ilist[ftype].iatoms;
for (int i = 0; i < ilist[ftype].nr; i += nral1)
{
for (int j = i + 1; j < i + nral1; j++)
}
else
{
- int vs_ind_end;
+ int vs_ind_end;
- const t_iatom *iat = ilist[ftype].iatoms;
+ const t_iatom* iat = ilist[ftype].iatoms;
- int i = 0;
+ int i = 0;
while (i < ilist[ftype].nr)
{
/* The 3 below is from 1+NRAL(ftype)=3 */
- vs_ind_end = i + ip[iat[i]].vsiten.n*3;
+ vs_ind_end = i + ip[iat[i]].vsiten.n * 3;
- vsite_atom_range = std::max(vsite_atom_range, iat[i+1]);
+ vsite_atom_range = std::max(vsite_atom_range, iat[i + 1]);
while (i < vs_ind_end)
{
- vsite_atom_range = std::max(vsite_atom_range, iat[i+2]);
- i += 3;
+ vsite_atom_range = std::max(vsite_atom_range, iat[i + 2]);
+ i += 3;
}
}
}
}
}
vsite_atom_range++;
- natperthread = (vsite_atom_range + vsite->nthreads - 1)/vsite->nthreads;
+ natperthread = (vsite_atom_range + vsite->nthreads - 1) / vsite->nthreads;
}
else
{
* threads also covers the non-local range.
*/
vsite_atom_range = mdatoms->nr;
- natperthread = (mdatoms->homenr + vsite->nthreads - 1)/vsite->nthreads;
+ natperthread = (mdatoms->homenr + vsite->nthreads - 1) / vsite->nthreads;
}
if (debug)
{
- fprintf(debug, "virtual site thread dist: natoms %d, range %d, natperthread %d\n", mdatoms->nr, vsite_atom_range, natperthread);
+ fprintf(debug, "virtual site thread dist: natoms %d, range %d, natperthread %d\n",
+ mdatoms->nr, vsite_atom_range, natperthread);
}
/* To simplify the vsite assignment, we make an index which tells us
*/
gmx::ArrayRef<int> taskIndex = vsite->taskIndex;
{
- int thread = 0;
+ int thread = 0;
for (int i = 0; i < mdatoms->nr; i++)
{
if (mdatoms->ptype[i] == eptVSite)
/* assign non-vsite particles to task thread */
taskIndex[i] = thread;
}
- if (i == (thread + 1)*natperthread && thread < vsite->nthreads)
+ if (i == (thread + 1) * natperthread && thread < vsite->nthreads)
{
thread++;
}
try
{
int thread = gmx_omp_get_thread_num();
- VsiteThread &tData = *vsite->tData[thread];
+ VsiteThread& tData = *vsite->tData[thread];
/* Clear the buffer use flags that were set before */
if (tData.useInterdependentTask)
{
- InterdependentTask &idTask = tData.idTask;
+ InterdependentTask& idTask = tData.idTask;
/* To avoid an extra OpenMP barrier in spread_vsite_f,
* we clear the force buffer at the next step,
idTask.vsite.resize(0);
for (int t = 0; t < vsite->nthreads; t++)
{
- AtomIndex &atomIndex = idTask.atomIndex[t];
+ AtomIndex& atomIndex = idTask.atomIndex[t];
int natom = atomIndex.atom.size();
for (int i = 0; i < natom; i++)
{
if (tData.useInterdependentTask)
{
size_t natoms_use_in_vsites = vsite_atom_range;
- InterdependentTask &idTask = tData.idTask;
+ InterdependentTask& idTask = tData.idTask;
/* To avoid resizing and re-clearing every nstlist steps,
* we never down size the force buffer.
*/
- if (natoms_use_in_vsites > idTask.force.size() ||
- natoms_use_in_vsites > idTask.use.size())
+ if (natoms_use_in_vsites > idTask.force.size() || natoms_use_in_vsites > idTask.use.size())
{
idTask.force.resize(natoms_use_in_vsites, { 0, 0, 0 });
idTask.use.resize(natoms_use_in_vsites, false);
}
/* Assign all vsites that can execute independently on threads */
- tData.rangeStart = thread *natperthread;
+ tData.rangeStart = thread * natperthread;
if (thread < vsite->nthreads - 1)
{
- tData.rangeEnd = (thread + 1)*natperthread;
+ tData.rangeEnd = (thread + 1) * natperthread;
}
else
{
/* The last thread should cover up to the end of the range */
- tData.rangeEnd = mdatoms->nr;
+ tData.rangeEnd = mdatoms->nr;
}
- assignVsitesToThread(&tData,
- thread, vsite->nthreads,
- natperthread,
- taskIndex,
- ilist, ip, mdatoms->ptype);
+ assignVsitesToThread(&tData, thread, vsite->nthreads, natperthread, taskIndex, ilist,
+ ip, mdatoms->ptype);
if (tData.useInterdependentTask)
{
* scaling at high thread counts we therefore construct
* an index to only loop over the actually affected tasks.
*/
- InterdependentTask &idTask = tData.idTask;
+ InterdependentTask& idTask = tData.idTask;
/* Ensure assignVsitesToThread finished on other threads */
#pragma omp barrier
}
}
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/* Assign all remaining vsites, that will have taskIndex[]=2*vsite->nthreads,
* to a single task that will not run in parallel with other tasks.
*/
- assignVsitesToSingleTask(vsite->tData[vsite->nthreads].get(),
- 2*vsite->nthreads,
- taskIndex,
+ assignVsitesToSingleTask(vsite->tData[vsite->nthreads].get(), 2 * vsite->nthreads, taskIndex,
ilist, ip);
if (debug && vsite->nthreads > 1)
{
if (ilist[ftype].nr > 0)
{
- fprintf(debug, "%-20s thread dist:",
- interaction_function[ftype].longname);
+ fprintf(debug, "%-20s thread dist:", interaction_function[ftype].longname);
for (int th = 0; th < vsite->nthreads + 1; th++)
{
- fprintf(debug, " %4d %4d ",
- vsite->tData[th]->ilist[ftype].nr,
+ fprintf(debug, " %4d %4d ", vsite->tData[th]->ilist[ftype].nr,
vsite->tData[th]->idTask.ilist[ftype].nr);
}
fprintf(debug, "\n");
int nrThreaded = 0;
for (int th = 0; th < vsite->nthreads + 1; th++)
{
- nrThreaded +=
- vsiteIlistNrCount(vsite->tData[th]->ilist) +
- vsiteIlistNrCount(vsite->tData[th]->idTask.ilist);
+ nrThreaded += vsiteIlistNrCount(vsite->tData[th]->ilist)
+ + vsiteIlistNrCount(vsite->tData[th]->idTask.ilist);
}
- GMX_ASSERT(nrThreaded == nrOrig, "The number of virtual sites assigned to all thread task has to match the total number of virtual sites");
+ GMX_ASSERT(nrThreaded == nrOrig,
+ "The number of virtual sites assigned to all thread task has to match the total "
+ "number of virtual sites");
#endif
}
-void set_vsite_top(gmx_vsite_t *vsite,
- const gmx_localtop_t *top,
- const t_mdatoms *md)
+void set_vsite_top(gmx_vsite_t* vsite, const gmx_localtop_t* top, const t_mdatoms* md)
{
if (vsite->nthreads > 1)
{
- split_vsites_over_threads(top->idef.il, top->idef.iparams,
- md, vsite);
+ split_vsites_over_threads(top->idef.il, top->idef.iparams, md, vsite);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff