*/
#include "gmxpre.h"
+#include "bonded.h"
+
#include "config.h"
#include <assert.h>
-#include <math.h>
+#include <cmath>
+
+#include <algorithm>
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/utilities.h"
#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/bondf.h"
#include "gromacs/legacyheaders/ns.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/orires.h"
#include "gromacs/legacyheaders/force.h"
#include "gromacs/legacyheaders/nonbonded.h"
-#include "restcbt.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+#include "restcbt.h"
+
/* Find a better place for this? */
const int cmap_coeff_matrix[] = {
1, 0, -3, 2, 0, 0, 0, 0, -3, 0, 9, -6, 2, 0, -6, 4,
};
-
+/* TODO This function should go and live in nonbonded.c where it is
+ really needed. Here, it only supports giving a fatal error message
+ with FENE_bonds */
int glatnr(int *global_atom_index, int i)
{
int atnr;
return atnr;
}
+/* TODO This kind of code appears in many places. Consolidate it */
static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
{
if (pbc)
const real half = 0.5;
const real one = 1.0;
real bm, kb;
- real dr, dr2, bm2, omdr2obm2, fbond, vbond, fij, vtot;
+ real dr2, bm2, omdr2obm2, fbond, vbond, fij, vtot;
rvec dx;
int i, m, ki, type, ai, aj;
ivec dt;
kk[YY] = sqr(qS)*ONE_4PI_EPS0/forceparams[type0].wpol.al_y;
kk[ZZ] = sqr(qS)*ONE_4PI_EPS0/forceparams[type0].wpol.al_z;
r_HH = 1.0/forceparams[type0].wpol.rHH;
- r_OD = 1.0/forceparams[type0].wpol.rOD;
if (debug)
{
fprintf(debug, "WPOL: qS = %10.5f aS = %5d\n", qS, aS);
rvec fshift[], real afac)
{
rvec r12;
- real r12sq, r12_1, r12n, r12bar, v0, v1, fscal, ebar, fff;
+ real r12sq, r12_1, r12bar, v0, v1, fscal, ebar, fff;
int m, t;
t = pbc_rvec_sub(pbc, xi, xj, r12); /* 3 */
int gmx_unused *global_atom_index)
{
/* Interaction between two pairs of particles with opposite charge */
- int i, type, a1, da1, a2, da2;
- real q1, q2, qq, a, al1, al2, afac;
- real V = 0;
+ int i, type, a1, da1, a2, da2;
+ real q1, q2, qq, a, al1, al2, afac;
+ real V = 0;
+ const real minusOneOnSix = -1.0/6.0;
for (i = 0; (i < nbonds); )
{
al1 = forceparams[type].thole.alpha1;
al2 = forceparams[type].thole.alpha2;
qq = q1*q2;
- afac = a*pow(al1*al2, -1.0/6.0);
+ afac = a*pow(al1*al2, minusOneOnSix);
V += do_1_thole(x[a1], x[a2], f[a1], f[a2], pbc, qq, fshift, afac);
V += do_1_thole(x[da1], x[a2], f[da1], f[a2], pbc, -qq, fshift, afac);
V += do_1_thole(x[a1], x[da2], f[a1], f[da2], pbc, -qq, fshift, afac);
rvec m, rvec n, rvec f[])
{
rvec f_i, f_j, f_k, f_l;
- rvec uvec, vvec, svec, dx_jl;
+ rvec uvec, vvec, svec;
real iprm, iprn, nrkj, nrkj2, nrkj_1, nrkj_2;
real a, b, p, q, toler;
- ivec jt, dt_ij, dt_kj, dt_lj;
iprm = iprod(m, m); /* 5 */
iprn = iprod(n, n); /* 5 */
const int nfa1 = 5;
int i, iu, s;
int type, ai[GMX_SIMD_REAL_WIDTH], aj[GMX_SIMD_REAL_WIDTH], ak[GMX_SIMD_REAL_WIDTH], al[GMX_SIMD_REAL_WIDTH];
- int t1[GMX_SIMD_REAL_WIDTH], t2[GMX_SIMD_REAL_WIDTH], t3[GMX_SIMD_REAL_WIDTH];
- real ddphi;
real dr_array[3*DIM*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *dr;
real buf_array[7*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *buf;
- real *cp, *phi0, *mult, *phi, *p, *q, *sf_i, *msf_l;
+ real *cp, *phi0, *mult, *p, *q;
gmx_simd_real_t phi0_S, phi_S;
gmx_simd_real_t mx_S, my_S, mz_S;
gmx_simd_real_t nx_S, ny_S, nz_S;
mult = buf + 2*GMX_SIMD_REAL_WIDTH;
p = buf + 3*GMX_SIMD_REAL_WIDTH;
q = buf + 4*GMX_SIMD_REAL_WIDTH;
- sf_i = buf + 5*GMX_SIMD_REAL_WIDTH;
- msf_l = buf + 6*GMX_SIMD_REAL_WIDTH;
set_pbc_simd(pbc, &pbc_simd);
dvdl_term += 0.5*(kB - kA)*dp2 - kk*dphi0*dp;
- do_dih_fup(ai, aj, ak, al, (real)(-ddphi), r_ij, r_kj, r_kl, m, n,
+ do_dih_fup(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n,
f, fshift, pbc, g, x, t1, t2, t3); /* 112 */
/* 218 TOTAL */
#ifdef DEBUG
int i, ai, m, d, type, npbcdim = 0, fbdim;
const t_iparams *pr;
real vtot, kk, v;
- real ref = 0, dr, dr2, rpot, rfb, rfb2, fact, invdr;
- rvec com_sc, rdist, pos, dx, dpdl, fm;
+ real dr, dr2, rfb, rfb2, fact, invdr;
+ rvec com_sc, rdist, dx, dpdl, fm;
gmx_bool bInvert;
npbcdim = ePBC2npbcdim(ePBC);
real lambda, real *dvdlambda,
int refcoord_scaling, int ePBC, rvec comA, rvec comB)
{
- int i, ai, m, d, type, ki, npbcdim = 0;
+ int i, ai, m, d, type, npbcdim = 0;
const t_iparams *pr;
real L1;
real vtot, kk, fm;
- real posA, posB, ref = 0;
- rvec comA_sc, comB_sc, rdist, dpdl, pos, dx;
+ rvec comA_sc, comB_sc, rdist, dpdl, dx;
gmx_bool bForceValid = TRUE;
if ((f == NULL) || (vir_diag == NULL)) /* should both be null together! */
real vtot = 0;
int ai, aj, ak, al, i, k, type, t1, t2, t3;
real phi0A, phi0B, dphiA, dphiB, kfacA, kfacB, phi0, dphi, kfac;
- real phi, ddphi, ddp, ddp2, dp, sign, d2r, fc, L1;
+ real phi, ddphi, ddp, ddp2, dp, sign, d2r, L1;
rvec r_ij, r_kj, r_kl, m, n;
L1 = 1.0-lambda;
{
int i, d, ai, aj, ak, type, m;
int t1, t2;
- rvec r_ij, r_kj;
real v, vtot;
ivec jt, dt_ij, dt_kj;
rvec f_i, f_j, f_k;
t1 = pbc_rvec_sub(pbc, x[ai], x[aj], vec_temp);
pbc_rvec_sub(pbc, x[aj], x[ai], delta_ante);
t2 = pbc_rvec_sub(pbc, x[ak], x[aj], delta_crnt);
- t3 = pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
+ pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
pbc_rvec_sub(pbc, x[al], x[ak], delta_post);
/* This function computes factors needed for restricted angle potential.
pbc_rvec_sub(pbc, x[aj], x[ai], delta_ante);
t2 = pbc_rvec_sub(pbc, x[ak], x[aj], vec_temp);
pbc_rvec_sub(pbc, x[ak], x[aj], delta_crnt);
- t3 = pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
+ pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
pbc_rvec_sub(pbc, x[al], x[ak], delta_post);
/* \brief Compute factors for CBT potential
int t11, t21, t31, t12, t22, t32;
int iphi1, ip1m1, ip1p1, ip1p2;
int iphi2, ip2m1, ip2p1, ip2p2;
- int l1, l2, l3, l4;
- int pos1, pos2, pos3, pos4, tmp;
+ int l1, l2, l3;
+ int pos1, pos2, pos3, pos4;
real ty[4], ty1[4], ty2[4], ty12[4], tc[16], tx[16];
- real phi1, psi1, cos_phi1, sin_phi1, sign1, xphi1;
- real phi2, psi2, cos_phi2, sin_phi2, sign2, xphi2;
- real dx, xx, tt, tu, e, df1, df2, ddf1, ddf2, ddf12, vtot;
+ real phi1, cos_phi1, sin_phi1, sign1, xphi1;
+ real phi2, cos_phi2, sin_phi2, sign2, xphi2;
+ real dx, xx, tt, tu, e, df1, df2, vtot;
real ra21, rb21, rg21, rg1, rgr1, ra2r1, rb2r1, rabr1;
real ra22, rb22, rg22, rg2, rgr2, ra2r2, rb2r2, rabr2;
real fg1, hg1, fga1, hgb1, gaa1, gbb1;
b1[1] = r1_kl[2]*r1_kj[0]-r1_kl[0]*r1_kj[2];
b1[2] = r1_kl[0]*r1_kj[1]-r1_kl[1]*r1_kj[0]; /* 9 */
- tmp = pbc_rvec_sub(pbc, x[a1l], x[a1k], h1);
+ pbc_rvec_sub(pbc, x[a1l], x[a1k], h1);
ra21 = iprod(a1, a1); /* 5 */
rb21 = iprod(b1, b1); /* 5 */
b2[1] = r2_kl[2]*r2_kj[0]-r2_kl[0]*r2_kj[2];
b2[2] = r2_kl[0]*r2_kj[1]-r2_kl[1]*r2_kj[0]; /* 9 */
- tmp = pbc_rvec_sub(pbc, x[a2l], x[a2k], h2);
+ pbc_rvec_sub(pbc, x[a2l], x[a2k], h2);
ra22 = iprod(a2, a2); /* 5 */
rb22 = iprod(b2, b2); /* 5 */
dx = 2*M_PI / cmap_grid->grid_spacing;
/* Where on the grid are we */
- iphi1 = (int)(xphi1/dx);
- iphi2 = (int)(xphi2/dx);
+ iphi1 = static_cast<int>(xphi1/dx);
+ iphi2 = static_cast<int>(xphi2/dx);
iphi1 = cmap_setup_grid_index(iphi1, cmap_grid->grid_spacing, &ip1m1, &ip1p1, &ip1p2);
iphi2 = cmap_setup_grid_index(iphi2, cmap_grid->grid_spacing, &ip2m1, &ip2p1, &ip2p2);
e = 0;
df1 = 0;
df2 = 0;
- ddf1 = 0;
- ddf2 = 0;
- ddf12 = 0;
for (i = 3; i >= 0; i--)
{
e = tt * e + ((tc[i*4+3]*tu+tc[i*4+2])*tu + tc[i*4+1])*tu+tc[i*4];
df1 = tu * df1 + (3.0*tc[l1]*tt+2.0*tc[l2])*tt+tc[l3];
df2 = tt * df2 + (3.0*tc[i*4+3]*tu+2.0*tc[i*4+2])*tu+tc[i*4+1];
- ddf1 = tu * ddf1 + 2.0*3.0*tc[l1]*tt+2.0*tc[l2];
- ddf2 = tt * ddf2 + 2.0*3.0*tc[4*i+3]*tu+2.0*tc[4*i+2];
}
- ddf12 = tc[5] + 2.0*tc[9]*tt + 3.0*tc[13]*tt*tt + 2.0*tu*(tc[6]+2.0*tc[10]*tt+3.0*tc[14]*tt*tt) +
- 3.0*tu*tu*(tc[7]+2.0*tc[11]*tt+3.0*tc[15]*tt*tt);
-
fac = RAD2DEG/dx;
df1 = df1 * fac;
df2 = df2 * fac;
- ddf1 = ddf1 * fac * fac;
- ddf2 = ddf2 * fac * fac;
- ddf12 = ddf12 * fac * fac;
/* CMAP energy */
vtot += e;
/* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
* pp. 842-847
*/
- int i, ai, aj, ak, type, m, t1, t2, t3;
+ int i, ai, aj, ak, type, m, t1, t2;
rvec r_ij, r_kj, r_ik;
real vtot, vrt, s1, s2, s3, r1, r2, r3, r1e, r2e, r3e, krt, k1, k2, k3;
rvec f_i, f_j, f_k;
/* Compute distance vectors ... */
t1 = pbc_rvec_sub(pbc, x[ai], x[aj], r_ij);
t2 = pbc_rvec_sub(pbc, x[ak], x[aj], r_kj);
- t3 = pbc_rvec_sub(pbc, x[ai], x[ak], r_ik);
+ pbc_rvec_sub(pbc, x[ai], x[ak], r_ik);
/* ... and their lengths */
r1 = norm(r_ij);
{
real k, tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps2, Fp, VV, FF;
int n0, nnn;
- real v, f, dvdlambda;
+ real dvdlambda;
k = (1.0 - lambda)*kA + lambda*kB;
VFtab = table->data;
rt = r*tabscale;
- n0 = rt;
+ n0 = static_cast<int>(rt);
if (n0 >= table->n)
{
gmx_fatal(FARGS, "A tabulated %s interaction table number %d is out of the table range: r %f, between table indices %d and %d, table length %d",
if (cos_theta2 < 1)
{
int m;
- real snt, st, sth;
+ real st, sth;
real cik, cii, ckk;
real nrkj2, nrij2;
rvec f_i, f_j, f_k;
return vtot;
}
-/* Return if this is a potential calculated in bondfree.c,
- * i.e. an interaction that actually calculates a potential and
- * works on multiple atoms (not e.g. a connection or a position restraint).
- */
-static gmx_inline gmx_bool ftype_is_bonded_potential(int ftype)
+/* TODO This function could go away when idef is not a big bucket of
+ everything. */
+gmx_bool ftype_is_bonded_potential(int ftype)
{
return
(interaction_function[ftype].flags & IF_BOND) &&
(ftype < F_GB12 || ftype > F_GB14);
}
-static void divide_bondeds_over_threads(t_idef *idef, int nthreads)
-{
- int ftype;
- int nat1;
- int t;
- int il_nr_thread;
-
- idef->nthreads = nthreads;
-
- if (F_NRE*(nthreads+1) > idef->il_thread_division_nalloc)
- {
- idef->il_thread_division_nalloc = F_NRE*(nthreads+1);
- snew(idef->il_thread_division, idef->il_thread_division_nalloc);
- }
-
- for (ftype = 0; ftype < F_NRE; ftype++)
- {
- if (ftype_is_bonded_potential(ftype))
- {
- nat1 = interaction_function[ftype].nratoms + 1;
-
- for (t = 0; t <= nthreads; t++)
- {
- /* Divide the interactions equally over the threads.
- * When the different types of bonded interactions
- * are distributed roughly equally over the threads,
- * this should lead to well localized output into
- * the force buffer on each thread.
- * If this is not the case, a more advanced scheme
- * (not implemented yet) will do better.
- */
- il_nr_thread = (((idef->il[ftype].nr/nat1)*t)/nthreads)*nat1;
-
- /* Ensure that distance restraint pairs with the same label
- * end up on the same thread.
- * This is slighlty tricky code, since the next for iteration
- * may have an initial il_nr_thread lower than the final value
- * in the previous iteration, but this will anyhow be increased
- * to the approriate value again by this while loop.
- */
- while (ftype == F_DISRES &&
- il_nr_thread > 0 &&
- il_nr_thread < idef->il[ftype].nr &&
- idef->iparams[idef->il[ftype].iatoms[il_nr_thread]].disres.label ==
- idef->iparams[idef->il[ftype].iatoms[il_nr_thread-nat1]].disres.label)
- {
- il_nr_thread += nat1;
- }
-
- idef->il_thread_division[ftype*(nthreads+1)+t] = il_nr_thread;
- }
- }
- }
-}
-
-static unsigned
-calc_bonded_reduction_mask(const t_idef *idef,
- int shift,
- int t, int nt)
-{
- unsigned mask;
- int ftype, nb, nat1, nb0, nb1, i, a;
-
- mask = 0;
-
- for (ftype = 0; ftype < F_NRE; ftype++)
- {
- if (ftype_is_bonded_potential(ftype))
- {
- nb = idef->il[ftype].nr;
- if (nb > 0)
- {
- nat1 = interaction_function[ftype].nratoms + 1;
-
- /* Divide this interaction equally over the threads.
- * This is not stored: should match division in calc_bonds.
- */
- nb0 = idef->il_thread_division[ftype*(nt+1)+t];
- nb1 = idef->il_thread_division[ftype*(nt+1)+t+1];
-
- for (i = nb0; i < nb1; i += nat1)
- {
- for (a = 1; a < nat1; a++)
- {
- mask |= (1U << (idef->il[ftype].iatoms[i+a]>>shift));
- }
- }
- }
- }
- }
-
- return mask;
-}
-
-void setup_bonded_threading(t_forcerec *fr, t_idef *idef)
-{
-#define MAX_BLOCK_BITS 32
- int t;
- int ctot, c, b;
-
- assert(fr->nthreads >= 1);
-
- /* Divide the bonded interaction over the threads */
- divide_bondeds_over_threads(idef, fr->nthreads);
-
- if (fr->nthreads == 1)
- {
- fr->red_nblock = 0;
-
- return;
- }
-
- /* We divide the force array in a maximum of 32 blocks.
- * Minimum force block reduction size is 2^6=64.
- */
- fr->red_ashift = 6;
- while (fr->natoms_force > (int)(MAX_BLOCK_BITS*(1U<<fr->red_ashift)))
- {
- fr->red_ashift++;
- }
- if (debug)
- {
- fprintf(debug, "bonded force buffer block atom shift %d bits\n",
- fr->red_ashift);
- }
-
- /* Determine to which blocks each thread's bonded force calculation
- * contributes. Store this is a mask for each thread.
- */
-#pragma omp parallel for num_threads(fr->nthreads) schedule(static)
- for (t = 1; t < fr->nthreads; t++)
- {
- fr->f_t[t].red_mask =
- calc_bonded_reduction_mask(idef, fr->red_ashift, t, fr->nthreads);
- }
-
- /* Determine the maximum number of blocks we need to reduce over */
- fr->red_nblock = 0;
- ctot = 0;
- for (t = 0; t < fr->nthreads; t++)
- {
- c = 0;
- for (b = 0; b < MAX_BLOCK_BITS; b++)
- {
- if (fr->f_t[t].red_mask & (1U<<b))
- {
- fr->red_nblock = max(fr->red_nblock, b+1);
- c++;
- }
- }
- if (debug)
- {
- fprintf(debug, "thread %d flags %x count %d\n",
- t, fr->f_t[t].red_mask, c);
- }
- ctot += c;
- }
- if (debug)
- {
- fprintf(debug, "Number of blocks to reduce: %d of size %d\n",
- fr->red_nblock, 1<<fr->red_ashift);
- fprintf(debug, "Reduction density %.2f density/#thread %.2f\n",
- ctot*(1<<fr->red_ashift)/(double)fr->natoms_force,
- ctot*(1<<fr->red_ashift)/(double)(fr->natoms_force*fr->nthreads));
- }
-}
-
static void zero_thread_forces(f_thread_t *f_t, int n,
int nblock, int blocksize)
{
if (f_t->red_mask && (1U<<b))
{
a0 = b*blocksize;
- a1 = min((b+1)*blocksize, n);
+ a1 = std::min((b+1)*blocksize, n);
for (a = a0; a < a1; a++)
{
clear_rvec(f_t->f[a]);
/* Reduce force buffers for threads that contribute */
a0 = b *block_size;
a1 = (b+1)*block_size;
- a1 = min(a1, n);
+ a1 = std::min(a1, n);
for (a = a0; a < a1; a++)
{
for (fb = 0; fb < nfb; fb++)
static real calc_one_bond(int thread,
int ftype, const t_idef *idef,
- rvec x[], rvec f[], rvec fshift[],
+ const rvec x[], rvec f[], rvec fshift[],
t_forcerec *fr,
const t_pbc *pbc, const t_graph *g,
gmx_grppairener_t *grpp,
{
v = cmap_dihs(nbn, iatoms+nb0,
idef->iparams, &idef->cmap_grid,
- (const rvec*)x, f, fshift,
+ x, f, fshift,
pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
md, fcd, global_atom_index);
}
/* No energies, shift forces, dvdl */
angles_noener_simd(nbn, idef->il[ftype].iatoms+nb0,
idef->iparams,
- (const rvec*)x, f,
+ x, f,
pbc, g, lambda[efptFTYPE], md, fcd,
global_atom_index);
v = 0;
#endif
(nbn, idef->il[ftype].iatoms+nb0,
idef->iparams,
- (const rvec*)x, f,
+ x, f,
pbc, g, lambda[efptFTYPE], md, fcd,
global_atom_index);
v = 0;
{
v = interaction_function[ftype].ifunc(nbn, iatoms+nb0,
idef->iparams,
- (const rvec*)x, f, fshift,
+ x, f, fshift,
pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
md, fcd, global_atom_index);
}
}
else
{
- v = do_nonbonded_listed(ftype, nbn, iatoms+nb0, idef->iparams, (const rvec*)x, f, fshift,
+ v = do_nonbonded_listed(ftype, nbn, iatoms+nb0, idef->iparams, x, f, fshift,
pbc, g, lambda, dvdl, md, fr, grpp, global_atom_index);
}
void calc_bonds(const gmx_multisim_t *ms,
const t_idef *idef,
- rvec x[], history_t *hist,
+ const rvec x[], history_t *hist,
rvec f[], t_forcerec *fr,
const t_pbc *pbc, const t_graph *g,
gmx_enerdata_t *enerd, t_nrnb *nrnb,
real *lambda,
const t_mdatoms *md,
t_fcdata *fcd, int *global_atom_index,
- t_atomtypes gmx_unused *atype, gmx_genborn_t gmx_unused *born,
int force_flags)
{
gmx_bool bCalcEnerVir;
int i;
- real v, dvdl[efptNR], dvdl_dum[efptNR]; /* The dummy array is to have a place to store the dhdl at other values
+ real dvdl[efptNR]; /* The dummy array is to have a place to store the dhdl at other values
of lambda, which will be thrown away in the end*/
const t_pbc *pbc_null;
- char buf[22];
int thread;
assert(fr->nthreads == idef->nthreads);
enerd->term[F_ORIRESDEV] =
calc_orires_dev(ms, idef->il[F_ORIRES].nr,
idef->il[F_ORIRES].iatoms,
- idef->iparams, md, (const rvec*)x,
+ idef->iparams, md, x,
pbc_null, fcd, hist);
}
if (idef->il[F_DISRES].nr)
{
calc_disres_R_6(idef->il[F_DISRES].nr,
idef->il[F_DISRES].iatoms,
- idef->iparams, (const rvec*)x, pbc_null,
+ idef->iparams, x, pbc_null,
fcd, hist);
#ifdef GMX_MPI
if (fcd->disres.nsystems > 1)
}
void calc_bonds_lambda(const t_idef *idef,
- rvec x[],
+ const rvec x[],
t_forcerec *fr,
const t_pbc *pbc, const t_graph *g,
gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
t_fcdata *fcd,
int *global_atom_index)
{
- int i, ftype, nr_nonperturbed, nr;
+ int ftype, nr_nonperturbed, nr;
real v;
real dvdl_dum[efptNR];
rvec *f, *fshift;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/bonded-threading.h"
+
+#include <assert.h>
+
+#include <algorithm>
+
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
+static void divide_bondeds_over_threads(t_idef *idef, int nthreads)
+{
+ int ftype;
+ int nat1;
+ int t;
+ int il_nr_thread;
+
+ idef->nthreads = nthreads;
+
+ if (F_NRE*(nthreads+1) > idef->il_thread_division_nalloc)
+ {
+ idef->il_thread_division_nalloc = F_NRE*(nthreads+1);
+ snew(idef->il_thread_division, idef->il_thread_division_nalloc);
+ }
+
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (ftype_is_bonded_potential(ftype))
+ {
+ nat1 = interaction_function[ftype].nratoms + 1;
+
+ for (t = 0; t <= nthreads; t++)
+ {
+ /* Divide the interactions equally over the threads.
+ * When the different types of bonded interactions
+ * are distributed roughly equally over the threads,
+ * this should lead to well localized output into
+ * the force buffer on each thread.
+ * If this is not the case, a more advanced scheme
+ * (not implemented yet) will do better.
+ */
+ il_nr_thread = (((idef->il[ftype].nr/nat1)*t)/nthreads)*nat1;
+
+ /* Ensure that distance restraint pairs with the same label
+ * end up on the same thread.
+ * This is slighlty tricky code, since the next for iteration
+ * may have an initial il_nr_thread lower than the final value
+ * in the previous iteration, but this will anyhow be increased
+ * to the approriate value again by this while loop.
+ */
+ while (ftype == F_DISRES &&
+ il_nr_thread > 0 &&
+ il_nr_thread < idef->il[ftype].nr &&
+ idef->iparams[idef->il[ftype].iatoms[il_nr_thread]].disres.label ==
+ idef->iparams[idef->il[ftype].iatoms[il_nr_thread-nat1]].disres.label)
+ {
+ il_nr_thread += nat1;
+ }
+
+ idef->il_thread_division[ftype*(nthreads+1)+t] = il_nr_thread;
+ }
+ }
+ }
+}
+
+static unsigned
+calc_bonded_reduction_mask(const t_idef *idef,
+ int shift,
+ int t, int nt)
+{
+ unsigned mask;
+ int ftype, nb, nat1, nb0, nb1, i, a;
+
+ mask = 0;
+
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (ftype_is_bonded_potential(ftype))
+ {
+ nb = idef->il[ftype].nr;
+ if (nb > 0)
+ {
+ nat1 = interaction_function[ftype].nratoms + 1;
+
+ /* Divide this interaction equally over the threads.
+ * This is not stored: should match division in calc_bonds.
+ */
+ nb0 = idef->il_thread_division[ftype*(nt+1)+t];
+ nb1 = idef->il_thread_division[ftype*(nt+1)+t+1];
+
+ for (i = nb0; i < nb1; i += nat1)
+ {
+ for (a = 1; a < nat1; a++)
+ {
+ mask |= (1U << (idef->il[ftype].iatoms[i+a]>>shift));
+ }
+ }
+ }
+ }
+ }
+
+ return mask;
+}
+
+void setup_bonded_threading(t_forcerec *fr, t_idef *idef)
+{
+#define MAX_BLOCK_BITS 32
+ int t;
+ int ctot, c, b;
+
+ assert(fr->nthreads >= 1);
+
+ /* Divide the bonded interaction over the threads */
+ divide_bondeds_over_threads(idef, fr->nthreads);
+
+ if (fr->nthreads == 1)
+ {
+ fr->red_nblock = 0;
+
+ return;
+ }
+
+ /* We divide the force array in a maximum of 32 blocks.
+ * Minimum force block reduction size is 2^6=64.
+ */
+ fr->red_ashift = 6;
+ while (fr->natoms_force > (int)(MAX_BLOCK_BITS*(1U<<fr->red_ashift)))
+ {
+ fr->red_ashift++;
+ }
+ if (debug)
+ {
+ fprintf(debug, "bonded force buffer block atom shift %d bits\n",
+ fr->red_ashift);
+ }
+
+ /* Determine to which blocks each thread's bonded force calculation
+ * contributes. Store this is a mask for each thread.
+ */
+#pragma omp parallel for num_threads(fr->nthreads) schedule(static)
+ for (t = 1; t < fr->nthreads; t++)
+ {
+ fr->f_t[t].red_mask =
+ calc_bonded_reduction_mask(idef, fr->red_ashift, t, fr->nthreads);
+ }
+
+ /* Determine the maximum number of blocks we need to reduce over */
+ fr->red_nblock = 0;
+ ctot = 0;
+ for (t = 0; t < fr->nthreads; t++)
+ {
+ c = 0;
+ for (b = 0; b < MAX_BLOCK_BITS; b++)
+ {
+ if (fr->f_t[t].red_mask & (1U<<b))
+ {
+ fr->red_nblock = std::max(fr->red_nblock, b+1);
+ c++;
+ }
+ }
+ if (debug)
+ {
+ fprintf(debug, "thread %d flags %x count %d\n",
+ t, fr->f_t[t].red_mask, c);
+ }
+ ctot += c;
+ }
+ if (debug)
+ {
+ fprintf(debug, "Number of blocks to reduce: %d of size %d\n",
+ fr->red_nblock, 1<<fr->red_ashift);
+ fprintf(debug, "Reduction density %.2f density/#thread %.2f\n",
+ ctot*(1<<fr->red_ashift)/(double)fr->natoms_force,
+ ctot*(1<<fr->red_ashift)/(double)(fr->natoms_force*fr->nthreads));
+ }
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff