/*
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*
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*
- * Gromacs is a library for molecular simulation and trajectory analysis,
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
-#include "vec.h"
-#include "smalloc.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
-#include "partdec.h"
-#include "network.h"
-#include "physics.h"
-#include "genborn.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/genborn.h"
#include "genborn_allvsall.h"
-#if 0 && defined (GMX_X86_SSE2)
+#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
#include <gmx_sse2_double.h>
aadata->fz_align[i] = 0.0;
}
- setup_gb_exclusions_and_indices(aadata, top->idef.il, mdatoms->start, mdatoms->start+mdatoms->homenr, mdatoms->nr,
+ setup_gb_exclusions_and_indices(aadata, top->idef.il, 0, mdatoms->homenr, mdatoms->nr,
bInclude12, bInclude13, bInclude14);
}
__m128d still_p4_SSE, still_p5inv_SSE, still_pip5_SSE;
natoms = mdatoms->nr;
- ni0 = (mdatoms->start/SIMD_WIDTH)*SIMD_WIDTH;
- ni1 = mdatoms->start+mdatoms->homenr;
+ ni0 = 0;
+ ni1 = mdatoms->homenr;
n = 0;
work[i-natoms] += work[i];
}
- /* Parallel summations */
- if (PARTDECOMP(cr))
- {
- gmx_sum(natoms, work, cr);
- }
+ /* Parallel summations would go here if ever implemented with DD */
factor = 0.5 * ONE_4PI_EPS0;
/* Calculate the radii - should we do all atoms, or just our local ones? */
__m128d doffset_SSE, tmpSSE;
natoms = mdatoms->nr;
- ni0 = (mdatoms->start/SIMD_WIDTH)*SIMD_WIDTH;
- ni1 = mdatoms->start+mdatoms->homenr;
+ ni0 = 0;
+ ni1 = mdatoms->homenr;
n = 0;
work[i] += work[natoms+i];
}
- /* Parallel summations */
-
- if (PARTDECOMP(cr))
- {
- gmx_sum(natoms, work, cr);
- }
+ /* Parallel summations would go here if ever implemented in DD */
if (gb_algorithm == egbHCT)
{
__m128d t1, t2, tmpSSE;
natoms = mdatoms->nr;
- ni0 = (mdatoms->start/SIMD_WIDTH)*SIMD_WIDTH;
- ni1 = mdatoms->start+mdatoms->homenr;
+ ni0 = 0;
+ ni1 = mdatoms->homenr;
aadata = (gmx_allvsallgb2_data_t *)paadata;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff