#include "gromacs/math/utilities.h"
#include "txtdump.h"
#include "bondf.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
#include "pbc.h"
#include "ns.h"
#include "macros.h"
* a shell connected to a dummy with spring constant that differ in the
* three spatial dimensions in the molecular frame.
*/
- int i, m, aO, aH1, aH2, aD, aS, type, type0;
+ int i, m, aO, aH1, aH2, aD, aS, type, type0, ki;
+ ivec dt;
rvec dOH1, dOH2, dHH, dOD, dDS, nW, kk, dx, kdx, proj;
#ifdef DEBUG
rvec df;
aS = forceatoms[i+5];
/* Compute vectors describing the water frame */
- rvec_sub(x[aH1], x[aO], dOH1);
- rvec_sub(x[aH2], x[aO], dOH2);
- rvec_sub(x[aH2], x[aH1], dHH);
- rvec_sub(x[aD], x[aO], dOD);
- rvec_sub(x[aS], x[aD], dDS);
+ pbc_rvec_sub(pbc, x[aH1], x[aO], dOH1);
+ pbc_rvec_sub(pbc, x[aH2], x[aO], dOH2);
+ pbc_rvec_sub(pbc, x[aH2], x[aH1], dHH);
+ pbc_rvec_sub(pbc, x[aD], x[aO], dOD);
+ ki = pbc_rvec_sub(pbc, x[aS], x[aD], dDS);
cprod(dOH1, dOH2, nW);
/* Compute inverse length of normal vector
kdx[YY] = kk[YY]*dx[YY];
kdx[ZZ] = kk[ZZ]*dx[ZZ];
vtot += iprod(dx, kdx);
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, aS), SHIFT_IVEC(g, aD), dt);
+ ki = IVEC2IS(dt);
+ }
+
for (m = 0; (m < DIM); m++)
{
/* This is a tensor operation but written out for speed */
#ifdef DEBUG
df[m] = fij;
#endif
- f[aS][m] += fij;
- f[aD][m] -= fij;
+ f[aS][m] += fij;
+ f[aD][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
}
#ifdef DEBUG
if (debug)
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;
}
}
+/* This is mostly a copy of pdihs_noener_simd above, but with using
+ * the RB potential instead of a harmonic potential.
+ * This function can replace rbdihs() when no energy and virial are needed.
+ */
+static void
+rbdihs_noener_simd(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const t_pbc *pbc, const t_graph gmx_unused *g,
+ real gmx_unused lambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ const int nfa1 = 5;
+ int i, iu, s, j;
+ int type, ai[GMX_SIMD_REAL_WIDTH], aj[GMX_SIMD_REAL_WIDTH], ak[GMX_SIMD_REAL_WIDTH], al[GMX_SIMD_REAL_WIDTH];
+ real ddphi;
+ real dr_array[3*DIM*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *dr;
+ real buf_array[(NR_RBDIHS + 4)*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *buf;
+ real *parm, *phi, *p, *q, *sf_i, *msf_l;
+
+ gmx_simd_real_t phi_S;
+ gmx_simd_real_t ddphi_S, cosfac_S;
+ gmx_simd_real_t mx_S, my_S, mz_S;
+ gmx_simd_real_t nx_S, ny_S, nz_S;
+ gmx_simd_real_t nrkj_m2_S, nrkj_n2_S;
+ gmx_simd_real_t parm_S, c_S;
+ gmx_simd_real_t sin_S, cos_S;
+ gmx_simd_real_t sf_i_S, msf_l_S;
+ pbc_simd_t pbc_simd;
+
+ gmx_simd_real_t pi_S = gmx_simd_set1_r(M_PI);
+ gmx_simd_real_t one_S = gmx_simd_set1_r(1.0);
+
+ /* Ensure SIMD register alignment */
+ dr = gmx_simd_align_r(dr_array);
+ buf = gmx_simd_align_r(buf_array);
+
+ /* Extract aligned pointer for parameters and variables */
+ parm = buf;
+ p = buf + (NR_RBDIHS + 0)*GMX_SIMD_REAL_WIDTH;
+ q = buf + (NR_RBDIHS + 1)*GMX_SIMD_REAL_WIDTH;
+ sf_i = buf + (NR_RBDIHS + 2)*GMX_SIMD_REAL_WIDTH;
+ msf_l = buf + (NR_RBDIHS + 3)*GMX_SIMD_REAL_WIDTH;
+
+ set_pbc_simd(pbc, &pbc_simd);
+
+ /* nbonds is the number of dihedrals times nfa1, here we step GMX_SIMD_REAL_WIDTH dihs */
+ for (i = 0; (i < nbonds); i += GMX_SIMD_REAL_WIDTH*nfa1)
+ {
+ /* Collect atoms quadruplets for GMX_SIMD_REAL_WIDTH dihedrals.
+ * iu indexes into forceatoms, we should not let iu go beyond nbonds.
+ */
+ iu = i;
+ for (s = 0; s < GMX_SIMD_REAL_WIDTH; s++)
+ {
+ type = forceatoms[iu];
+ ai[s] = forceatoms[iu+1];
+ aj[s] = forceatoms[iu+2];
+ ak[s] = forceatoms[iu+3];
+ al[s] = forceatoms[iu+4];
+
+ /* We don't need the first parameter, since that's a constant
+ * which only affects the energies, not the forces.
+ */
+ for (j = 1; j < NR_RBDIHS; j++)
+ {
+ parm[j*GMX_SIMD_REAL_WIDTH + s] =
+ forceparams[type].rbdihs.rbcA[j];
+ }
+
+ /* At the end fill the arrays with identical entries */
+ if (iu + nfa1 < nbonds)
+ {
+ iu += nfa1;
+ }
+ }
+
+ /* Caclulate GMX_SIMD_REAL_WIDTH dihedral angles at once */
+ dih_angle_simd(x, ai, aj, ak, al, &pbc_simd,
+ dr,
+ &phi_S,
+ &mx_S, &my_S, &mz_S,
+ &nx_S, &ny_S, &nz_S,
+ &nrkj_m2_S,
+ &nrkj_n2_S,
+ p, q);
+
+ /* Change to polymer convention */
+ phi_S = gmx_simd_sub_r(phi_S, pi_S);
+
+ gmx_simd_sincos_r(phi_S, &sin_S, &cos_S);
+
+ ddphi_S = gmx_simd_setzero_r();
+ c_S = one_S;
+ cosfac_S = one_S;
+ for (j = 1; j < NR_RBDIHS; j++)
+ {
+ parm_S = gmx_simd_load_r(parm + j*GMX_SIMD_REAL_WIDTH);
+ ddphi_S = gmx_simd_fmadd_r(gmx_simd_mul_r(c_S, parm_S), cosfac_S, ddphi_S);
+ cosfac_S = gmx_simd_mul_r(cosfac_S, cos_S);
+ c_S = gmx_simd_add_r(c_S, one_S);
+ }
+
+ /* Note that here we do not use the minus sign which is present
+ * in the normal RB code. This is corrected for through (m)sf below.
+ */
+ ddphi_S = gmx_simd_mul_r(ddphi_S, sin_S);
+
+ sf_i_S = gmx_simd_mul_r(ddphi_S, nrkj_m2_S);
+ msf_l_S = gmx_simd_mul_r(ddphi_S, nrkj_n2_S);
+
+ /* After this m?_S will contain f[i] */
+ mx_S = gmx_simd_mul_r(sf_i_S, mx_S);
+ my_S = gmx_simd_mul_r(sf_i_S, my_S);
+ mz_S = gmx_simd_mul_r(sf_i_S, mz_S);
+
+ /* After this m?_S will contain -f[l] */
+ nx_S = gmx_simd_mul_r(msf_l_S, nx_S);
+ ny_S = gmx_simd_mul_r(msf_l_S, ny_S);
+ nz_S = gmx_simd_mul_r(msf_l_S, nz_S);
+
+ gmx_simd_store_r(dr + 0*GMX_SIMD_REAL_WIDTH, mx_S);
+ gmx_simd_store_r(dr + 1*GMX_SIMD_REAL_WIDTH, my_S);
+ gmx_simd_store_r(dr + 2*GMX_SIMD_REAL_WIDTH, mz_S);
+ gmx_simd_store_r(dr + 3*GMX_SIMD_REAL_WIDTH, nx_S);
+ gmx_simd_store_r(dr + 4*GMX_SIMD_REAL_WIDTH, ny_S);
+ gmx_simd_store_r(dr + 5*GMX_SIMD_REAL_WIDTH, nz_S);
+
+ iu = i;
+ s = 0;
+ do
+ {
+ do_dih_fup_noshiftf_precalc(ai[s], aj[s], ak[s], al[s],
+ p[s], q[s],
+ dr[ XX *GMX_SIMD_REAL_WIDTH+s],
+ dr[ YY *GMX_SIMD_REAL_WIDTH+s],
+ dr[ ZZ *GMX_SIMD_REAL_WIDTH+s],
+ dr[(DIM+XX)*GMX_SIMD_REAL_WIDTH+s],
+ dr[(DIM+YY)*GMX_SIMD_REAL_WIDTH+s],
+ dr[(DIM+ZZ)*GMX_SIMD_REAL_WIDTH+s],
+ f);
+ s++;
+ iu += nfa1;
+ }
+ while (s < GMX_SIMD_REAL_WIDTH && iu < nbonds);
+ }
+}
+
#endif /* GMX_SIMD_HAVE_REAL */
/* Box relative coordinates are stored for dimensions with pbc */
posA *= pbc->box[m][m];
posB *= pbc->box[m][m];
+ assert(npbcdim <= DIM);
for (d = m+1; d < npbcdim; d++)
{
posA += pos0A[d]*pbc->box[d][m];
clear_rvec(com_sc);
for (m = 0; m < npbcdim; m++)
{
+ assert(npbcdim <= DIM);
for (d = m; d < npbcdim; d++)
{
com_sc[m] += com[d]*pbc->box[d][m];
clear_rvec(comB_sc);
for (m = 0; m < npbcdim; m++)
{
+ assert(npbcdim <= DIM);
for (d = m; d < npbcdim; d++)
{
comA_sc[m] += comA[d]*pbc->box[d][m];
vtot += 0.5*kk*dx[m]*dx[m];
*dvdlambda +=
0.5*(pr->posres.fcB[m] - pr->posres.fcA[m])*dx[m]*dx[m]
- -fm*dpdl[m];
+ + fm*dpdl[m];
/* Here we correct for the pbc_dx which included rdist */
if (bForceValid)
global_atom_index);
v = 0;
}
+#ifdef GMX_SIMD_HAVE_REAL
+ else if (ftype == F_RBDIHS &&
+ !bCalcEnerVir && fr->efep == efepNO)
+ {
+ /* No energies, shift forces, dvdl */
+ rbdihs_noener_simd(nbn, idef->il[ftype].iatoms+nb0,
+ idef->iparams,
+ (const rvec*)x, f,
+ pbc, g, lambda[efptFTYPE], md, fcd,
+ global_atom_index);
+ v = 0;
+ }
+#endif
else
{
v = interaction_function[ftype].ifunc(nbn, iatoms+nb0,
}
if (bPrintSepPot)
{
- fprintf(fplog, "Step %s: bonded V and dVdl for this node\n",
+ fprintf(fplog, "Step %s: bonded V and dVdl for this rank\n",
gmx_step_str(step, buf));
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff