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37 #include "nbnxn_kernel_common.h"
39 #include "gromacs/pbcutil/ishift.h"
40 #include "gromacs/utility/gmxassert.h"
43 clear_f_all(const nbnxn_atomdata_t *nbat, real *f)
47 for (i = 0; i < nbat->natoms*nbat->fstride; i++)
54 clear_f_flagged(const nbnxn_atomdata_t *nbat, int output_index, real *f)
56 GMX_ASSERT(nbat->fstride == DIM, "For performance we use compile time constant DIM instead of nbat->fstride");
58 const nbnxn_buffer_flags_t &flags = nbat->buffer_flags;
59 gmx_bitmask_t our_flag;
60 bitmask_init_bit(&our_flag, output_index);
62 for (int b = 0; b < flags.nflag; b++)
64 if (!bitmask_is_disjoint(flags.flag[b], our_flag))
66 int a0 = b*NBNXN_BUFFERFLAG_SIZE;
67 int a1 = a0 + NBNXN_BUFFERFLAG_SIZE;
68 for (int i = a0*DIM; i < a1*DIM; i++)
77 clear_f(const nbnxn_atomdata_t *nbat, int output_index, real *f)
79 if (nbat->bUseBufferFlags)
81 clear_f_flagged(nbat, output_index, f);
90 clear_fshift(real *fshift)
94 for (i = 0; i < SHIFTS*DIM; i++)
101 reduce_energies_over_lists(const nbnxn_atomdata_t *nbat,
109 for (nb = 0; nb < nlist; nb++)
111 for (i = 0; i < nbat->nenergrp; i++)
113 /* Reduce the diagonal terms */
114 ind = i*nbat->nenergrp + i;
115 Vvdw[ind] += nbat->out[nb].Vvdw[ind];
116 Vc[ind] += nbat->out[nb].Vc[ind];
118 /* Reduce the off-diagonal terms */
119 for (j = i+1; j < nbat->nenergrp; j++)
121 /* The output should contain only one off-diagonal part */
122 ind = i*nbat->nenergrp + j;
123 indr = j*nbat->nenergrp + i;
124 Vvdw[ind] += nbat->out[nb].Vvdw[ind] + nbat->out[nb].Vvdw[indr];
125 Vc[ind] += nbat->out[nb].Vc[ind] + nbat->out[nb].Vc[indr];