--- /dev/null
- if (econqCoord)
+/*
+ * 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) 2013,2014,2015, 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.
+ */
+/* This file is completely threadsafe - keep it that way! */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <assert.h>
+#include <math.h>
+#include <stdlib.h>
+
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc-simd.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/simd/simd.h"
+#include "gromacs/simd/simd_math.h"
+#include "gromacs/simd/vector_operations.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/bitmask.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
+/* MSVC 2010 produces buggy SIMD PBC code, disable SIMD for MSVC <= 2010 */
+#if defined GMX_SIMD_HAVE_REAL && !(defined _MSC_VER && _MSC_VER < 1700) && !defined(__ICL)
+#define LINCS_SIMD
+#endif
+
+
+#if defined(GMX_SIMD_X86_AVX_256) || defined(GMX_SIMD_X86_AVX2_256)
+
+// This was originally work-in-progress for augmenting the SIMD module with
+// masked load/store operations. Instead, that turned into and extended SIMD
+// interface that supports gather/scatter in all platforms, which will be
+// part of a future Gromacs version. However, since the code for bonded
+// interactions and LINCS was already written it would be a pity not to get
+// the performance gains in Gromacs-5.1. For this reason we have added it as
+// a bit of a hack in the two files that use it. It will be replaced with the
+// new generic functionality after version 5.1
+
+# ifdef GMX_DOUBLE
+static gmx_inline void gmx_simdcall
+gmx_hack_simd_transpose4_r(gmx_simd_double_t *row0,
+ gmx_simd_double_t *row1,
+ gmx_simd_double_t *row2,
+ gmx_simd_double_t *row3)
+{
+ __m256d tmp0, tmp1, tmp2, tmp3;
+
+ tmp0 = _mm256_unpacklo_pd(*row0, *row1);
+ tmp2 = _mm256_unpacklo_pd(*row2, *row3);
+ tmp1 = _mm256_unpackhi_pd(*row0, *row1);
+ tmp3 = _mm256_unpackhi_pd(*row2, *row3);
+ *row0 = _mm256_permute2f128_pd(tmp0, tmp2, 0x20);
+ *row1 = _mm256_permute2f128_pd(tmp1, tmp3, 0x20);
+ *row2 = _mm256_permute2f128_pd(tmp0, tmp2, 0x31);
+ *row3 = _mm256_permute2f128_pd(tmp1, tmp3, 0x31);
+}
+
+static gmx_inline void gmx_simdcall
+gmx_hack_simd4_transpose_to_simd_r(const gmx_simd4_double_t *a,
+ gmx_simd_double_t *row0,
+ gmx_simd_double_t *row1,
+ gmx_simd_double_t *row2,
+ gmx_simd_double_t *row3)
+{
+ *row0 = a[0];
+ *row1 = a[1];
+ *row2 = a[2];
+ *row3 = a[3];
+
+ gmx_hack_simd_transpose4_r(row0, row1, row2, row3);
+}
+
+static gmx_inline void gmx_simdcall
+gmx_hack_simd_transpose_to_simd4_r(gmx_simd_double_t row0,
+ gmx_simd_double_t row1,
+ gmx_simd_double_t row2,
+ gmx_simd_double_t row3,
+ gmx_simd4_double_t *a)
+{
+ a[0] = row0;
+ a[1] = row1;
+ a[2] = row2;
+ a[3] = row3;
+
+ gmx_hack_simd_transpose4_r(&a[0], &a[1], &a[2], &a[3]);
+}
+
+
+# ifdef GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG
+# define gmx_hack_simd4_load3_r(mem) _mm256_maskload_pd((mem), _mm_castsi128_ps(_mm256_set_epi32(0, 0, -1, -1, -1, -1, -1, -1)))
+# define gmx_hack_simd4_store3_r(mem, x) _mm256_maskstore_pd((mem), _mm_castsi128_ps(_mm256_set_epi32(0, 0, -1, -1, -1, -1, -1, -1)), (x))
+# else
+# define gmx_hack_simd4_load3_r(mem) _mm256_maskload_pd((mem), _mm256_set_epi32(0, 0, -1, -1, -1, -1, -1, -1))
+# define gmx_hack_simd4_store3_r(mem, x) _mm256_maskstore_pd((mem), _mm256_set_epi32(0, 0, -1, -1, -1, -1, -1, -1), (x))
+# endif
+
+# else /* single instead of double */
+static gmx_inline void gmx_simdcall
+gmx_hack_simd_transpose4_r(gmx_simd_float_t *row0,
+ gmx_simd_float_t *row1,
+ gmx_simd_float_t *row2,
+ gmx_simd_float_t *row3)
+{
+ __m256 tmp0, tmp1, tmp2, tmp3;
+
+ tmp0 = _mm256_unpacklo_ps(*row0, *row1);
+ tmp2 = _mm256_unpacklo_ps(*row2, *row3);
+ tmp1 = _mm256_unpackhi_ps(*row0, *row1);
+ tmp3 = _mm256_unpackhi_ps(*row2, *row3);
+ *row0 = _mm256_shuffle_ps(tmp0, tmp2, 0x44);
+ *row1 = _mm256_shuffle_ps(tmp0, tmp2, 0xEE);
+ *row2 = _mm256_shuffle_ps(tmp1, tmp3, 0x44);
+ *row3 = _mm256_shuffle_ps(tmp1, tmp3, 0xEE);
+}
+
+static gmx_inline void gmx_simdcall
+gmx_hack_simd4_transpose_to_simd_r(const gmx_simd4_float_t *a,
+ gmx_simd_float_t *row0,
+ gmx_simd_float_t *row1,
+ gmx_simd_float_t *row2,
+ gmx_simd_float_t *row3)
+{
+ *row0 = _mm256_insertf128_ps(_mm256_castps128_ps256(a[0]), a[4], 1);
+ *row1 = _mm256_insertf128_ps(_mm256_castps128_ps256(a[1]), a[5], 1);
+ *row2 = _mm256_insertf128_ps(_mm256_castps128_ps256(a[2]), a[6], 1);
+ *row3 = _mm256_insertf128_ps(_mm256_castps128_ps256(a[3]), a[7], 1);
+
+ gmx_hack_simd_transpose4_r(row0, row1, row2, row3);
+}
+
+static gmx_inline void gmx_simdcall
+gmx_hack_simd_transpose_to_simd4_r(gmx_simd_float_t row0,
+ gmx_simd_float_t row1,
+ gmx_simd_float_t row2,
+ gmx_simd_float_t row3,
+ gmx_simd4_float_t *a)
+{
+ gmx_hack_simd_transpose4_r(&row0, &row1, &row2, &row3);
+
+ a[0] = _mm256_extractf128_ps(row0, 0);
+ a[1] = _mm256_extractf128_ps(row1, 0);
+ a[2] = _mm256_extractf128_ps(row2, 0);
+ a[3] = _mm256_extractf128_ps(row3, 0);
+ a[4] = _mm256_extractf128_ps(row0, 1);
+ a[5] = _mm256_extractf128_ps(row1, 1);
+ a[6] = _mm256_extractf128_ps(row2, 1);
+ a[7] = _mm256_extractf128_ps(row3, 1);
+}
+#ifdef GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG
+# define gmx_hack_simd4_load3_r(mem) _mm_maskload_ps((mem), _mm_castsi256_pd(_mm_set_epi32(0, -1, -1, -1)))
+# define gmx_hack_simd4_store3_r(mem, x) _mm_maskstore_ps((mem), _mm_castsi256_pd(_mm_set_epi32(0, -1, -1, -1)), (x))
+#else
+# define gmx_hack_simd4_load3_r(mem) _mm_maskload_ps((mem), _mm_set_epi32(0, -1, -1, -1))
+# define gmx_hack_simd4_store3_r(mem, x) _mm_maskstore_ps((mem), _mm_set_epi32(0, -1, -1, -1), (x))
+#endif
+
+#endif /* double */
+
+#endif /* AVX */
+
+#ifdef GMX_SIMD_HAVE_REAL
+/*! \brief Store differences between indexed rvecs in SIMD registers.
+ *
+ * Returns SIMD register with the difference vectors:
+ * v[pair_index[i*2]] - v[pair_index[i*2 + 1]]
+ *
+ * \param[in] v Array of rvecs
+ * \param[in] pair_index Index pairs for GMX_SIMD_REAL_WIDTH vector pairs
+ * \param[in,out] buf Aligned tmp buffer of size 3*GMX_SIMD_REAL_WIDTH
+ * \param[out] dx SIMD register with x difference
+ * \param[out] dy SIMD register with y difference
+ * \param[out] dz SIMD register with z difference
+ */
+static gmx_inline void gmx_simdcall
+gmx_hack_simd_gather_rvec_dist_pair_index(const rvec *v,
+ const int *pair_index,
+ real gmx_unused *buf,
+ gmx_simd_real_t *dx,
+ gmx_simd_real_t *dy,
+ gmx_simd_real_t *dz)
+{
+#if defined(GMX_SIMD_X86_AVX_256) || defined(GMX_SIMD_X86_AVX2_256)
+ int i;
+ gmx_simd4_real_t d[GMX_SIMD_REAL_WIDTH];
+ gmx_simd_real_t tmp;
+
+ for (i = 0; i < GMX_SIMD_REAL_WIDTH; i++)
+ {
+ d[i] = gmx_simd4_sub_r(gmx_hack_simd4_load3_r(&(v[pair_index[i*2 + 0]][0])),
+ gmx_hack_simd4_load3_r(&(v[pair_index[i*2 + 1]][0])));
+ }
+
+ gmx_hack_simd4_transpose_to_simd_r(d, dx, dy, dz, &tmp);
+#else
+#if GMX_ALIGNMENT
+ GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH) buf_aligned[3*GMX_SIMD_REAL_WIDTH];
+#else
+ real* buf_aligned = buf;
+#endif
+
+ int i, m;
+
+ for (i = 0; i < GMX_SIMD_REAL_WIDTH; i++)
+ {
+ /* Store the distances packed and aligned */
+ for (m = 0; m < DIM; m++)
+ {
+ buf_aligned[m*GMX_SIMD_REAL_WIDTH + i] =
+ v[pair_index[i*2]][m] - v[pair_index[i*2 + 1]][m];
+ }
+ }
+ *dx = gmx_simd_load_r(buf_aligned + 0*GMX_SIMD_REAL_WIDTH);
+ *dy = gmx_simd_load_r(buf_aligned + 1*GMX_SIMD_REAL_WIDTH);
+ *dz = gmx_simd_load_r(buf_aligned + 2*GMX_SIMD_REAL_WIDTH);
+#endif
+}
+
+
+/*! \brief Stores SIMD vector into multiple rvecs.
+ *
+ * \param[in] x SIMD register with x-components of the vectors
+ * \param[in] y SIMD register with y-components of the vectors
+ * \param[in] z SIMD register with z-components of the vectors
+ * \param[in,out] buf Aligned tmp buffer of size 3*GMX_SIMD_REAL_WIDTH
+ * \param[out] v Array of GMX_SIMD_REAL_WIDTH rvecs
+ */
+static gmx_inline void gmx_simdcall
+gmx_simd_store_vec_to_rvec(gmx_simd_real_t x,
+ gmx_simd_real_t y,
+ gmx_simd_real_t z,
+ real gmx_unused *buf,
+ rvec *v)
+{
+#if defined(GMX_SIMD_X86_AVX_256) || defined(GMX_SIMD_X86_AVX2_256)
+ int i;
+ gmx_simd4_real_t s4[GMX_SIMD_REAL_WIDTH];
+ gmx_simd_real_t zero = gmx_simd_setzero_r();
+
+ gmx_hack_simd_transpose_to_simd4_r(x, y, z, zero, s4);
+
+ for (i = 0; i < GMX_SIMD_REAL_WIDTH; i++)
+ {
+ gmx_hack_simd4_store3_r(v[i], s4[i]);
+ }
+#else
+#if GMX_ALIGNMENT
+ GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH) buf_aligned[3*GMX_SIMD_REAL_WIDTH];
+#else
+ real* buf_aligned = buf;
+#endif
+
+ int i, m;
+
+ gmx_simd_store_r(buf_aligned + 0*GMX_SIMD_REAL_WIDTH, x);
+ gmx_simd_store_r(buf_aligned + 1*GMX_SIMD_REAL_WIDTH, y);
+ gmx_simd_store_r(buf_aligned + 2*GMX_SIMD_REAL_WIDTH, z);
+
+ for (i = 0; i < GMX_SIMD_REAL_WIDTH; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ v[i][m] = buf_aligned[m*GMX_SIMD_REAL_WIDTH + i];
+ }
+ }
+#endif
+}
+#endif /* GMX_SIMD_HAVE_REAL */
+
+
+typedef struct {
+ int b0; /* first constraint for this task */
+ int b1; /* b1-1 is the last constraint for this task */
+ int ntriangle; /* the number of constraints in triangles */
+ int *triangle; /* the list of triangle constraints */
+ int *tri_bits; /* the bits tell if the matrix element should be used */
+ int tri_alloc; /* allocation size of triangle and tri_bits */
+ int nind; /* number of indices */
+ int *ind; /* constraint index for updating atom data */
+ int nind_r; /* number of indices */
+ int *ind_r; /* constraint index for updating atom data */
+ int ind_nalloc; /* allocation size of ind and ind_r */
+ tensor vir_r_m_dr; /* temporary variable for virial calculation */
+ real dhdlambda; /* temporary variable for lambda derivative */
+ real *simd_buf; /* Aligned work array for SIMD */
+} lincs_task_t;
+
+typedef struct gmx_lincsdata {
+ int ncg; /* the global number of constraints */
+ int ncg_flex; /* the global number of flexible constraints */
+ int ncg_triangle; /* the global number of constraints in triangles */
+ int nIter; /* the number of iterations */
+ int nOrder; /* the order of the matrix expansion */
+ int max_connect; /* the maximum number of constrains connected to a single atom */
+
+ int nc_real; /* the number of real constraints */
+ int nc; /* the number of constraints including padding for SIMD */
+ int nc_alloc; /* the number we allocated memory for */
+ int ncc; /* the number of constraint connections */
+ int ncc_alloc; /* the number we allocated memory for */
+ real matlam; /* the FE lambda value used for filling blc and blmf */
+ int *con_index; /* mapping from topology to LINCS constraints */
+ real *bllen0; /* the reference distance in topology A */
+ real *ddist; /* the reference distance in top B - the r.d. in top A */
+ int *bla; /* the atom pairs involved in the constraints */
+ real *blc; /* 1/sqrt(invmass1 + invmass2) */
+ real *blc1; /* as blc, but with all masses 1 */
+ int *blnr; /* index into blbnb and blmf */
+ int *blbnb; /* list of constraint connections */
+ int ntriangle; /* the local number of constraints in triangles */
+ int ncc_triangle; /* the number of constraint connections in triangles */
+ gmx_bool bCommIter; /* communicate before each LINCS interation */
+ real *blmf; /* matrix of mass factors for constraint connections */
+ real *blmf1; /* as blmf, but with all masses 1 */
+ real *bllen; /* the reference bond length */
+ int *nlocat; /* the local atom count per constraint, can be NULL */
+
+ int ntask; /* The number of tasks = #threads for LINCS */
+ lincs_task_t *task; /* LINCS thread division */
+ gmx_bitmask_t *atf; /* atom flags for thread parallelization */
+ int atf_nalloc; /* allocation size of atf */
+ gmx_bool bTaskDep; /* are the LINCS tasks interdependent? */
+ /* arrays for temporary storage in the LINCS algorithm */
+ rvec *tmpv;
+ real *tmpncc;
+ real *tmp1;
+ real *tmp2;
+ real *tmp3;
+ real *tmp4;
+ real *mlambda; /* the Lagrange multipliers * -1 */
+ /* storage for the constraint RMS relative deviation output */
+ real rmsd_data[3];
+} t_gmx_lincsdata;
+
+/* Define simd_width for memory allocation used for SIMD code */
+#ifdef LINCS_SIMD
+static const int simd_width = GMX_SIMD_REAL_WIDTH;
+#else
+static const int simd_width = 1;
+#endif
+/* We can't use small memory alignments on many systems, so use min 64 bytes*/
+static const int align_bytes = std::max<int>(64, simd_width*sizeof(real));
+
+real *lincs_rmsd_data(struct gmx_lincsdata *lincsd)
+{
+ return lincsd->rmsd_data;
+}
+
+real lincs_rmsd(struct gmx_lincsdata *lincsd, gmx_bool bSD2)
+{
+ if (lincsd->rmsd_data[0] > 0)
+ {
+ return sqrt(lincsd->rmsd_data[bSD2 ? 2 : 1]/lincsd->rmsd_data[0]);
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+/* Do a set of nrec LINCS matrix multiplications.
+ * This function will return with up to date thread-local
+ * constraint data, without an OpenMP barrier.
+ */
+static void lincs_matrix_expand(const struct gmx_lincsdata *lincsd,
+ const lincs_task_t *li_task,
+ const real *blcc,
+ real *rhs1, real *rhs2, real *sol)
+{
+ int b0, b1, nrec, rec;
+ const int *blnr = lincsd->blnr;
+ const int *blbnb = lincsd->blbnb;
+
+ b0 = li_task->b0;
+ b1 = li_task->b1;
+ nrec = lincsd->nOrder;
+
+ for (rec = 0; rec < nrec; rec++)
+ {
+ int b;
+
+ if (lincsd->bTaskDep)
+ {
+#pragma omp barrier
+ }
+ for (b = b0; b < b1; b++)
+ {
+ real mvb;
+ int n;
+
+ mvb = 0;
+ for (n = blnr[b]; n < blnr[b+1]; n++)
+ {
+ mvb = mvb + blcc[n]*rhs1[blbnb[n]];
+ }
+ rhs2[b] = mvb;
+ sol[b] = sol[b] + mvb;
+ }
+
+ real *swap;
+
+ swap = rhs1;
+ rhs1 = rhs2;
+ rhs2 = swap;
+ } /* nrec*(ncons+2*nrtot) flops */
+
+ if (lincsd->ntriangle > 0)
+ {
+ /* Perform an extra nrec recursions for only the constraints
+ * involved in rigid triangles.
+ * In this way their accuracy should come close to those of the other
+ * constraints, since traingles of constraints can produce eigenvalues
+ * around 0.7, while the effective eigenvalue for bond constraints
+ * is around 0.4 (and 0.7*0.7=0.5).
+ */
+
+ if (lincsd->bTaskDep)
+ {
+ /* We need a barrier here, since other threads might still be
+ * reading the contents of rhs1 and/o rhs2.
+ * We could avoid this barrier by introducing two extra rhs
+ * arrays for the triangle constraints only.
+ */
+#pragma omp barrier
+ }
+
+ /* Constraints involved in a triangle are ensured to be in the same
+ * LINCS task. This means no barriers are required during the extra
+ * iterations for the triangle constraints.
+ */
+ const int *triangle = li_task->triangle;
+ const int *tri_bits = li_task->tri_bits;
+
+ for (rec = 0; rec < nrec; rec++)
+ {
+ int tb;
+
+ for (tb = 0; tb < li_task->ntriangle; tb++)
+ {
+ int b, bits, nr0, nr1, n;
+ real mvb;
+
+ b = triangle[tb];
+ bits = tri_bits[tb];
+ mvb = 0;
+ nr0 = blnr[b];
+ nr1 = blnr[b+1];
+ for (n = nr0; n < nr1; n++)
+ {
+ if (bits & (1 << (n - nr0)))
+ {
+ mvb = mvb + blcc[n]*rhs1[blbnb[n]];
+ }
+ }
+ rhs2[b] = mvb;
+ sol[b] = sol[b] + mvb;
+ }
+
+ real *swap;
+
+ swap = rhs1;
+ rhs1 = rhs2;
+ rhs2 = swap;
+ } /* nrec*(ntriangle + ncc_triangle*2) flops */
+ }
+}
+
+static void lincs_update_atoms_noind(int ncons, const int *bla,
+ real prefac,
+ const real *fac, rvec *r,
+ const real *invmass,
+ rvec *x)
+{
+ int b, i, j;
+ real mvb, im1, im2, tmp0, tmp1, tmp2;
+
+ if (invmass != NULL)
+ {
+ for (b = 0; b < ncons; b++)
+ {
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = prefac*fac[b];
+ im1 = invmass[i];
+ im2 = invmass[j];
+ tmp0 = r[b][0]*mvb;
+ tmp1 = r[b][1]*mvb;
+ tmp2 = r[b][2]*mvb;
+ x[i][0] -= tmp0*im1;
+ x[i][1] -= tmp1*im1;
+ x[i][2] -= tmp2*im1;
+ x[j][0] += tmp0*im2;
+ x[j][1] += tmp1*im2;
+ x[j][2] += tmp2*im2;
+ } /* 16 ncons flops */
+ }
+ else
+ {
+ for (b = 0; b < ncons; b++)
+ {
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = prefac*fac[b];
+ tmp0 = r[b][0]*mvb;
+ tmp1 = r[b][1]*mvb;
+ tmp2 = r[b][2]*mvb;
+ x[i][0] -= tmp0;
+ x[i][1] -= tmp1;
+ x[i][2] -= tmp2;
+ x[j][0] += tmp0;
+ x[j][1] += tmp1;
+ x[j][2] += tmp2;
+ }
+ }
+}
+
+static void lincs_update_atoms_ind(int ncons, const int *ind, const int *bla,
+ real prefac,
+ const real *fac, rvec *r,
+ const real *invmass,
+ rvec *x)
+{
+ int bi, b, i, j;
+ real mvb, im1, im2, tmp0, tmp1, tmp2;
+
+ if (invmass != NULL)
+ {
+ for (bi = 0; bi < ncons; bi++)
+ {
+ b = ind[bi];
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = prefac*fac[b];
+ im1 = invmass[i];
+ im2 = invmass[j];
+ tmp0 = r[b][0]*mvb;
+ tmp1 = r[b][1]*mvb;
+ tmp2 = r[b][2]*mvb;
+ x[i][0] -= tmp0*im1;
+ x[i][1] -= tmp1*im1;
+ x[i][2] -= tmp2*im1;
+ x[j][0] += tmp0*im2;
+ x[j][1] += tmp1*im2;
+ x[j][2] += tmp2*im2;
+ } /* 16 ncons flops */
+ }
+ else
+ {
+ for (bi = 0; bi < ncons; bi++)
+ {
+ b = ind[bi];
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = prefac*fac[b];
+ tmp0 = r[b][0]*mvb;
+ tmp1 = r[b][1]*mvb;
+ tmp2 = r[b][2]*mvb;
+ x[i][0] -= tmp0;
+ x[i][1] -= tmp1;
+ x[i][2] -= tmp2;
+ x[j][0] += tmp0;
+ x[j][1] += tmp1;
+ x[j][2] += tmp2;
+ } /* 16 ncons flops */
+ }
+}
+
+static void lincs_update_atoms(struct gmx_lincsdata *li, int th,
+ real prefac,
+ const real *fac, rvec *r,
+ const real *invmass,
+ rvec *x)
+{
+ if (li->ntask == 1)
+ {
+ /* Single thread, we simply update for all constraints */
+ lincs_update_atoms_noind(li->nc_real,
+ li->bla, prefac, fac, r, invmass, x);
+ }
+ else
+ {
+ /* Update the atom vector components for our thread local
+ * constraints that only access our local atom range.
+ * This can be done without a barrier.
+ */
+ lincs_update_atoms_ind(li->task[th].nind, li->task[th].ind,
+ li->bla, prefac, fac, r, invmass, x);
+
+ if (li->task[li->ntask].nind > 0)
+ {
+ /* Update the constraints that operate on atoms
+ * in multiple thread atom blocks on the master thread.
+ */
+#pragma omp barrier
+#pragma omp master
+ {
+ lincs_update_atoms_ind(li->task[li->ntask].nind,
+ li->task[li->ntask].ind,
+ li->bla, prefac, fac, r, invmass, x);
+ }
+ }
+ }
+}
+
+#ifdef LINCS_SIMD
+/* Calculate the constraint distance vectors r to project on from x.
+ * Determine the right-hand side of the matrix equation using quantity f.
+ * This function only differs from calc_dr_x_xp_simd below in that
+ * no constraint length is subtracted and no PBC is used for f.
+ */
+static void gmx_simdcall
+calc_dr_x_f_simd(int b0,
+ int b1,
+ const int * bla,
+ const rvec * gmx_restrict x,
+ const rvec * gmx_restrict f,
+ const real * gmx_restrict blc,
+ const pbc_simd_t * pbc_simd,
+ real * gmx_restrict vbuf1,
+ real * gmx_restrict vbuf2,
+ rvec * gmx_restrict r,
+ real * gmx_restrict rhs,
+ real * gmx_restrict sol)
+{
+ int bs;
+
+ assert(b0 % GMX_SIMD_REAL_WIDTH == 0);
+
+ for (bs = b0; bs < b1; bs += GMX_SIMD_REAL_WIDTH)
+ {
+ gmx_simd_real_t rx_S, ry_S, rz_S, n2_S, il_S;
+ gmx_simd_real_t fx_S, fy_S, fz_S, ip_S, rhs_S;
+
+ gmx_hack_simd_gather_rvec_dist_pair_index(x, bla + bs*2, vbuf1,
+ &rx_S, &ry_S, &rz_S);
+
+ pbc_correct_dx_simd(&rx_S, &ry_S, &rz_S, pbc_simd);
+
+ n2_S = gmx_simd_norm2_r(rx_S, ry_S, rz_S);
+ il_S = gmx_simd_invsqrt_r(n2_S);
+
+ rx_S = gmx_simd_mul_r(rx_S, il_S);
+ ry_S = gmx_simd_mul_r(ry_S, il_S);
+ rz_S = gmx_simd_mul_r(rz_S, il_S);
+
+ gmx_simd_store_vec_to_rvec(rx_S, ry_S, rz_S, vbuf1, r + bs);
+
+ gmx_hack_simd_gather_rvec_dist_pair_index(f, bla + bs*2, vbuf2,
+ &fx_S, &fy_S, &fz_S);
+
+ ip_S = gmx_simd_iprod_r(rx_S, ry_S, rz_S,
+ fx_S, fy_S, fz_S);
+
+ rhs_S = gmx_simd_mul_r(gmx_simd_load_r(blc + bs), ip_S);
+
+ gmx_simd_store_r(rhs + bs, rhs_S);
+ gmx_simd_store_r(sol + bs, rhs_S);
+ }
+}
+#endif /* LINCS_SIMD */
+
+/* LINCS projection, works on derivatives of the coordinates */
+static void do_lincsp(rvec *x, rvec *f, rvec *fp, t_pbc *pbc,
+ struct gmx_lincsdata *lincsd, int th,
+ real *invmass,
+ int econq, gmx_bool bCalcDHDL,
+ gmx_bool bCalcVir, tensor rmdf)
+{
+ int b0, b1, b;
+ int *bla, *blnr, *blbnb;
+ rvec *r;
+ real *blc, *blmf, *blcc, *rhs1, *rhs2, *sol;
+
+ b0 = lincsd->task[th].b0;
+ b1 = lincsd->task[th].b1;
+
+ bla = lincsd->bla;
+ r = lincsd->tmpv;
+ blnr = lincsd->blnr;
+ blbnb = lincsd->blbnb;
+ if (econq != econqForce)
+ {
+ /* Use mass-weighted parameters */
+ blc = lincsd->blc;
+ blmf = lincsd->blmf;
+ }
+ else
+ {
+ /* Use non mass-weighted parameters */
+ blc = lincsd->blc1;
+ blmf = lincsd->blmf1;
+ }
+ blcc = lincsd->tmpncc;
+ rhs1 = lincsd->tmp1;
+ rhs2 = lincsd->tmp2;
+ sol = lincsd->tmp3;
+
+#ifdef LINCS_SIMD
+
+ /* This SIMD code does the same as the plain-C code after the #else.
+ * The only difference is that we always call pbc code, as with SIMD
+ * the overhead of pbc computation (when not needed) is small.
+ */
+ pbc_simd_t pbc_simd;
+
+ /* Convert the pbc struct for SIMD */
+ set_pbc_simd(pbc, &pbc_simd);
+
+ /* Compute normalized x i-j vectors, store in r.
+ * Compute the inner product of r and xp i-j and store in rhs1.
+ */
+ calc_dr_x_f_simd(b0, b1, bla, x, f, blc,
+ &pbc_simd,
+ lincsd->task[th].simd_buf,
+ lincsd->task[th].simd_buf + GMX_SIMD_REAL_WIDTH*DIM,
+ r, rhs1, sol);
+
+#else /* LINCS_SIMD */
+
+ /* Compute normalized i-j vectors */
+ if (pbc)
+ {
+ for (b = b0; b < b1; b++)
+ {
+ rvec dx;
+
+ pbc_dx_aiuc(pbc, x[bla[2*b]], x[bla[2*b+1]], dx);
+ unitv(dx, r[b]);
+ }
+ }
+ else
+ {
+ for (b = b0; b < b1; b++)
+ {
+ rvec dx;
+
+ rvec_sub(x[bla[2*b]], x[bla[2*b+1]], dx);
+ unitv(dx, r[b]);
+ } /* 16 ncons flops */
+ }
+
+ for (b = b0; b < b1; b++)
+ {
+ int i, j;
+ real mvb;
+
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = blc[b]*(r[b][0]*(f[i][0] - f[j][0]) +
+ r[b][1]*(f[i][1] - f[j][1]) +
+ r[b][2]*(f[i][2] - f[j][2]));
+ rhs1[b] = mvb;
+ sol[b] = mvb;
+ /* 7 flops */
+ }
+
+#endif /* LINCS_SIMD */
+
+ if (lincsd->bTaskDep)
+ {
+ /* We need a barrier, since the matrix construction below
+ * can access entries in r of other threads.
+ */
+#pragma omp barrier
+ }
+
+ /* Construct the (sparse) LINCS matrix */
+ for (b = b0; b < b1; b++)
+ {
+ int n;
+
+ for (n = blnr[b]; n < blnr[b+1]; n++)
+ {
+ blcc[n] = blmf[n]*iprod(r[b], r[blbnb[n]]);
+ } /* 6 nr flops */
+ }
+ /* Together: 23*ncons + 6*nrtot flops */
+
+ lincs_matrix_expand(lincsd, &lincsd->task[th], blcc, rhs1, rhs2, sol);
+ /* nrec*(ncons+2*nrtot) flops */
+
+ if (econq == econqDeriv_FlexCon)
+ {
+ /* We only want to constraint the flexible constraints,
+ * so we mask out the normal ones by setting sol to 0.
+ */
+ for (b = b0; b < b1; b++)
+ {
+ if (!(lincsd->bllen0[b] == 0 && lincsd->ddist[b] == 0))
+ {
+ sol[b] = 0;
+ }
+ }
+ }
+
+ /* We multiply sol by blc, so we can use lincs_update_atoms for OpenMP */
+ for (b = b0; b < b1; b++)
+ {
+ sol[b] *= blc[b];
+ }
+
+ /* When constraining forces, we should not use mass weighting,
+ * so we pass invmass=NULL, which results in the use of 1 for all atoms.
+ */
+ lincs_update_atoms(lincsd, th, 1.0, sol, r,
+ (econq != econqForce) ? invmass : NULL, fp);
+
+ if (bCalcDHDL)
+ {
+ real dhdlambda;
+
+ dhdlambda = 0;
+ for (b = b0; b < b1; b++)
+ {
+ dhdlambda -= sol[b]*lincsd->ddist[b];
+ }
+
+ lincsd->task[th].dhdlambda = dhdlambda;
+ }
+
+ if (bCalcVir)
+ {
+ /* Constraint virial,
+ * determines sum r_bond x delta f,
+ * where delta f is the constraint correction
+ * of the quantity that is being constrained.
+ */
+ for (b = b0; b < b1; b++)
+ {
+ real mvb, tmp1;
+ int i, j;
+
+ mvb = lincsd->bllen[b]*sol[b];
+ for (i = 0; i < DIM; i++)
+ {
+ tmp1 = mvb*r[b][i];
+ for (j = 0; j < DIM; j++)
+ {
+ rmdf[i][j] += tmp1*r[b][j];
+ }
+ }
+ } /* 23 ncons flops */
+ }
+}
+
+#ifdef LINCS_SIMD
+/* Calculate the constraint distance vectors r to project on from x.
+ * Determine the right-hand side of the matrix equation using coordinates xp.
+ */
+static void gmx_simdcall
+calc_dr_x_xp_simd(int b0,
+ int b1,
+ const int * bla,
+ const rvec * gmx_restrict x,
+ const rvec * gmx_restrict xp,
+ const real * gmx_restrict bllen,
+ const real * gmx_restrict blc,
+ const pbc_simd_t * pbc_simd,
+ real * gmx_restrict vbuf1,
+ real * gmx_restrict vbuf2,
+ rvec * gmx_restrict r,
+ real * gmx_restrict rhs,
+ real * gmx_restrict sol)
+{
+ int bs;
+
+ assert(b0 % GMX_SIMD_REAL_WIDTH == 0);
+
+ for (bs = b0; bs < b1; bs += GMX_SIMD_REAL_WIDTH)
+ {
+ gmx_simd_real_t rx_S, ry_S, rz_S, n2_S, il_S;
+ gmx_simd_real_t rxp_S, ryp_S, rzp_S, ip_S, rhs_S;
+
+ gmx_hack_simd_gather_rvec_dist_pair_index(x, bla + bs*2, vbuf1,
+ &rx_S, &ry_S, &rz_S);
+
+ pbc_correct_dx_simd(&rx_S, &ry_S, &rz_S, pbc_simd);
+
+ n2_S = gmx_simd_norm2_r(rx_S, ry_S, rz_S);
+ il_S = gmx_simd_invsqrt_r(n2_S);
+
+ rx_S = gmx_simd_mul_r(rx_S, il_S);
+ ry_S = gmx_simd_mul_r(ry_S, il_S);
+ rz_S = gmx_simd_mul_r(rz_S, il_S);
+
+ gmx_simd_store_vec_to_rvec(rx_S, ry_S, rz_S, vbuf1, r + bs);
+
+ gmx_hack_simd_gather_rvec_dist_pair_index(xp, bla + bs*2, vbuf2,
+ &rxp_S, &ryp_S, &rzp_S);
+
+ pbc_correct_dx_simd(&rxp_S, &ryp_S, &rzp_S, pbc_simd);
+
+ ip_S = gmx_simd_iprod_r(rx_S, ry_S, rz_S,
+ rxp_S, ryp_S, rzp_S);
+
+ rhs_S = gmx_simd_mul_r(gmx_simd_load_r(blc + bs),
+ gmx_simd_sub_r(ip_S, gmx_simd_load_r(bllen + bs)));
+
+ gmx_simd_store_r(rhs + bs, rhs_S);
+ gmx_simd_store_r(sol + bs, rhs_S);
+ }
+}
+#endif /* LINCS_SIMD */
+
+/* Determine the distances and right-hand side for the next iteration */
+static void calc_dist_iter(int b0,
+ int b1,
+ const int * bla,
+ const rvec * gmx_restrict xp,
+ const real * gmx_restrict bllen,
+ const real * gmx_restrict blc,
+ const t_pbc * pbc,
+ real wfac,
+ real * gmx_restrict rhs,
+ real * gmx_restrict sol,
+ gmx_bool * bWarn)
+{
+ int b;
+
+ for (b = b0; b < b1; b++)
+ {
+ real len, len2, dlen2, mvb;
+ rvec dx;
+
+ len = bllen[b];
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, xp[bla[2*b]], xp[bla[2*b+1]], dx);
+ }
+ else
+ {
+ rvec_sub(xp[bla[2*b]], xp[bla[2*b+1]], dx);
+ }
+ len2 = len*len;
+ dlen2 = 2*len2 - norm2(dx);
+ if (dlen2 < wfac*len2)
+ {
+ /* not race free - see detailed comment in caller */
+ *bWarn = TRUE;
+ }
+ if (dlen2 > 0)
+ {
+ mvb = blc[b]*(len - dlen2*gmx_invsqrt(dlen2));
+ }
+ else
+ {
+ mvb = blc[b]*len;
+ }
+ rhs[b] = mvb;
+ sol[b] = mvb;
+ } /* 20*ncons flops */
+}
+
+#ifdef LINCS_SIMD
+/* As the function above, but using SIMD intrinsics */
+static void gmx_simdcall
+calc_dist_iter_simd(int b0,
+ int b1,
+ const int * bla,
+ const rvec * gmx_restrict x,
+ const real * gmx_restrict bllen,
+ const real * gmx_restrict blc,
+ const pbc_simd_t * pbc_simd,
+ real wfac,
+ real * gmx_restrict vbuf,
+ real * gmx_restrict rhs,
+ real * gmx_restrict sol,
+ gmx_bool * bWarn)
+{
+ gmx_simd_real_t min_S = gmx_simd_set1_r(GMX_REAL_MIN);
+ gmx_simd_real_t two_S = gmx_simd_set1_r(2.0);
+ gmx_simd_real_t wfac_S = gmx_simd_set1_r(wfac);
+ gmx_simd_bool_t warn_S;
+
+ int bs;
+
+ assert(b0 % GMX_SIMD_REAL_WIDTH == 0);
+
+ /* Initialize all to FALSE */
+ warn_S = gmx_simd_cmplt_r(two_S, gmx_simd_setzero_r());
+
+ for (bs = b0; bs < b1; bs += GMX_SIMD_REAL_WIDTH)
+ {
+ gmx_simd_real_t rx_S, ry_S, rz_S, n2_S;
+ gmx_simd_real_t len_S, len2_S, dlen2_S, lc_S, blc_S;
+
+ gmx_hack_simd_gather_rvec_dist_pair_index(x, bla + bs*2, vbuf,
+ &rx_S, &ry_S, &rz_S);
+
+ pbc_correct_dx_simd(&rx_S, &ry_S, &rz_S, pbc_simd);
+
+ n2_S = gmx_simd_norm2_r(rx_S, ry_S, rz_S);
+
+ len_S = gmx_simd_load_r(bllen + bs);
+ len2_S = gmx_simd_mul_r(len_S, len_S);
+
+ dlen2_S = gmx_simd_fmsub_r(two_S, len2_S, n2_S);
+
+ warn_S = gmx_simd_or_b(warn_S,
+ gmx_simd_cmplt_r(dlen2_S,
+ gmx_simd_mul_r(wfac_S, len2_S)));
+
+ /* Avoid 1/0 by taking the max with REAL_MIN.
+ * Note: when dlen2 is close to zero (90 degree constraint rotation),
+ * the accuracy of the algorithm is no longer relevant.
+ */
+ dlen2_S = gmx_simd_max_r(dlen2_S, min_S);
+
+ lc_S = gmx_simd_fnmadd_r(dlen2_S, gmx_simd_invsqrt_r(dlen2_S), len_S);
+
+ blc_S = gmx_simd_load_r(blc + bs);
+
+ lc_S = gmx_simd_mul_r(blc_S, lc_S);
+
+ gmx_simd_store_r(rhs + bs, lc_S);
+ gmx_simd_store_r(sol + bs, lc_S);
+ }
+
+ if (gmx_simd_anytrue_b(warn_S))
+ {
+ *bWarn = TRUE;
+ }
+}
+#endif /* LINCS_SIMD */
+
+static void do_lincs(rvec *x, rvec *xp, matrix box, t_pbc *pbc,
+ struct gmx_lincsdata *lincsd, int th,
+ const real *invmass,
+ t_commrec *cr,
+ gmx_bool bCalcDHDL,
+ real wangle, gmx_bool *bWarn,
+ real invdt, rvec * gmx_restrict v,
+ gmx_bool bCalcVir, tensor vir_r_m_dr)
+{
+ int b0, b1, b, i, j, n, iter;
+ int *bla, *blnr, *blbnb;
+ rvec *r;
+ real *blc, *blmf, *bllen, *blcc, *rhs1, *rhs2, *sol, *blc_sol, *mlambda;
+ int *nlocat;
+
+ b0 = lincsd->task[th].b0;
+ b1 = lincsd->task[th].b1;
+
+ bla = lincsd->bla;
+ r = lincsd->tmpv;
+ blnr = lincsd->blnr;
+ blbnb = lincsd->blbnb;
+ blc = lincsd->blc;
+ blmf = lincsd->blmf;
+ bllen = lincsd->bllen;
+ blcc = lincsd->tmpncc;
+ rhs1 = lincsd->tmp1;
+ rhs2 = lincsd->tmp2;
+ sol = lincsd->tmp3;
+ blc_sol = lincsd->tmp4;
+ mlambda = lincsd->mlambda;
+ nlocat = lincsd->nlocat;
+
+#ifdef LINCS_SIMD
+
+ /* This SIMD code does the same as the plain-C code after the #else.
+ * The only difference is that we always call pbc code, as with SIMD
+ * the overhead of pbc computation (when not needed) is small.
+ */
+ pbc_simd_t pbc_simd;
+
+ /* Convert the pbc struct for SIMD */
+ set_pbc_simd(pbc, &pbc_simd);
+
+ /* Compute normalized x i-j vectors, store in r.
+ * Compute the inner product of r and xp i-j and store in rhs1.
+ */
+ calc_dr_x_xp_simd(b0, b1, bla, x, xp, bllen, blc,
+ &pbc_simd,
+ lincsd->task[th].simd_buf,
+ lincsd->task[th].simd_buf + GMX_SIMD_REAL_WIDTH*DIM,
+ r, rhs1, sol);
+
+#else /* LINCS_SIMD */
+
+ if (pbc)
+ {
+ /* Compute normalized i-j vectors */
+ for (b = b0; b < b1; b++)
+ {
+ rvec dx;
+ real mvb;
+
+ pbc_dx_aiuc(pbc, x[bla[2*b]], x[bla[2*b+1]], dx);
+ unitv(dx, r[b]);
+
+ pbc_dx_aiuc(pbc, xp[bla[2*b]], xp[bla[2*b+1]], dx);
+ mvb = blc[b]*(iprod(r[b], dx) - bllen[b]);
+ rhs1[b] = mvb;
+ sol[b] = mvb;
+ }
+ }
+ else
+ {
+ /* Compute normalized i-j vectors */
+ for (b = b0; b < b1; b++)
+ {
+ real tmp0, tmp1, tmp2, rlen, mvb;
+
+ i = bla[2*b];
+ j = bla[2*b+1];
+ tmp0 = x[i][0] - x[j][0];
+ tmp1 = x[i][1] - x[j][1];
+ tmp2 = x[i][2] - x[j][2];
+ rlen = gmx_invsqrt(tmp0*tmp0 + tmp1*tmp1 + tmp2*tmp2);
+ r[b][0] = rlen*tmp0;
+ r[b][1] = rlen*tmp1;
+ r[b][2] = rlen*tmp2;
+ /* 16 ncons flops */
+
+ i = bla[2*b];
+ j = bla[2*b+1];
+ mvb = blc[b]*(r[b][0]*(xp[i][0] - xp[j][0]) +
+ r[b][1]*(xp[i][1] - xp[j][1]) +
+ r[b][2]*(xp[i][2] - xp[j][2]) - bllen[b]);
+ rhs1[b] = mvb;
+ sol[b] = mvb;
+ /* 10 flops */
+ }
+ /* Together: 26*ncons + 6*nrtot flops */
+ }
+
+#endif /* LINCS_SIMD */
+
+ if (lincsd->bTaskDep)
+ {
+ /* We need a barrier, since the matrix construction below
+ * can access entries in r of other threads.
+ */
+#pragma omp barrier
+ }
+
+ /* Construct the (sparse) LINCS matrix */
+ for (b = b0; b < b1; b++)
+ {
+ for (n = blnr[b]; n < blnr[b+1]; n++)
+ {
+ blcc[n] = blmf[n]*iprod(r[b], r[blbnb[n]]);
+ }
+ }
+ /* Together: 26*ncons + 6*nrtot flops */
+
+ lincs_matrix_expand(lincsd, &lincsd->task[th], blcc, rhs1, rhs2, sol);
+ /* nrec*(ncons+2*nrtot) flops */
+
+#ifndef LINCS_SIMD
+ for (b = b0; b < b1; b++)
+ {
+ mlambda[b] = blc[b]*sol[b];
+ }
+#else
+ for (b = b0; b < b1; b += GMX_SIMD_REAL_WIDTH)
+ {
+ gmx_simd_store_r(mlambda + b,
+ gmx_simd_mul_r(gmx_simd_load_r(blc + b),
+ gmx_simd_load_r(sol + b)));
+ }
+#endif
+
+ /* Update the coordinates */
+ lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
+
+ /*
+ ******** Correction for centripetal effects ********
+ */
+
+ real wfac;
+
+ wfac = cos(DEG2RAD*wangle);
+ wfac = wfac*wfac;
+
+ for (iter = 0; iter < lincsd->nIter; iter++)
+ {
+ if ((lincsd->bCommIter && DOMAINDECOMP(cr) && cr->dd->constraints))
+ {
+#pragma omp barrier
+#pragma omp master
+ {
+ /* Communicate the corrected non-local coordinates */
+ if (DOMAINDECOMP(cr))
+ {
+ dd_move_x_constraints(cr->dd, box, xp, NULL, FALSE);
+ }
+ }
+#pragma omp barrier
+ }
+ else if (lincsd->bTaskDep)
+ {
+#pragma omp barrier
+ }
+
+#ifdef LINCS_SIMD
+ calc_dist_iter_simd(b0, b1, bla, xp, bllen, blc, &pbc_simd, wfac,
+ lincsd->task[th].simd_buf, rhs1, sol, bWarn);
+#else
+ calc_dist_iter(b0, b1, bla, xp, bllen, blc, pbc, wfac,
+ rhs1, sol, bWarn);
+ /* 20*ncons flops */
+#endif
+
+ lincs_matrix_expand(lincsd, &lincsd->task[th], blcc, rhs1, rhs2, sol);
+ /* nrec*(ncons+2*nrtot) flops */
+
+#ifndef LINCS_SIMD
+ for (b = b0; b < b1; b++)
+ {
+ real mvb;
+
+ mvb = blc[b]*sol[b];
+ blc_sol[b] = mvb;
+ mlambda[b] += mvb;
+ }
+#else
+ for (b = b0; b < b1; b += GMX_SIMD_REAL_WIDTH)
+ {
+ gmx_simd_real_t mvb;
+
+ mvb = gmx_simd_mul_r(gmx_simd_load_r(blc + b),
+ gmx_simd_load_r(sol + b));
+ gmx_simd_store_r(blc_sol + b, mvb);
+ gmx_simd_store_r(mlambda + b,
+ gmx_simd_add_r(gmx_simd_load_r(mlambda + b), mvb));
+ }
+#endif
+
+ /* Update the coordinates */
+ lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
+ }
+ /* nit*ncons*(37+9*nrec) flops */
+
+ if (v != NULL)
+ {
+ /* Update the velocities */
+ lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
+ /* 16 ncons flops */
+ }
+
+ if (nlocat != NULL && (bCalcDHDL || bCalcVir))
+ {
+ if (lincsd->bTaskDep)
+ {
+ /* In lincs_update_atoms threads might cross-read mlambda */
+#pragma omp barrier
+ }
+
+ /* Only account for local atoms */
+ for (b = b0; b < b1; b++)
+ {
+ mlambda[b] *= 0.5*nlocat[b];
+ }
+ }
+
+ if (bCalcDHDL)
+ {
+ real dhdl;
+
+ dhdl = 0;
+ for (b = b0; b < b1; b++)
+ {
+ /* Note that this this is dhdl*dt^2, the dt^2 factor is corrected
+ * later after the contributions are reduced over the threads.
+ */
+ dhdl -= lincsd->mlambda[b]*lincsd->ddist[b];
+ }
+ lincsd->task[th].dhdlambda = dhdl;
+ }
+
+ if (bCalcVir)
+ {
+ /* Constraint virial */
+ for (b = b0; b < b1; b++)
+ {
+ real tmp0, tmp1;
+
+ tmp0 = -bllen[b]*mlambda[b];
+ for (i = 0; i < DIM; i++)
+ {
+ tmp1 = tmp0*r[b][i];
+ for (j = 0; j < DIM; j++)
+ {
+ vir_r_m_dr[i][j] -= tmp1*r[b][j];
+ }
+ }
+ } /* 22 ncons flops */
+ }
+
+ /* Total:
+ * 26*ncons + 6*nrtot + nrec*(ncons+2*nrtot)
+ * + nit * (20*ncons + nrec*(ncons+2*nrtot) + 17 ncons)
+ *
+ * (26+nrec)*ncons + (6+2*nrec)*nrtot
+ * + nit * ((37+nrec)*ncons + 2*nrec*nrtot)
+ * if nit=1
+ * (63+nrec)*ncons + (6+4*nrec)*nrtot
+ */
+}
+
+/* Sets the elements in the LINCS matrix for task li_task */
+static void set_lincs_matrix_task(struct gmx_lincsdata *li,
+ lincs_task_t *li_task,
+ const real *invmass,
+ int *ncc_triangle)
+{
+ int i;
+
+ /* Construct the coupling coefficient matrix blmf */
+ li_task->ntriangle = 0;
+ *ncc_triangle = 0;
+ for (i = li_task->b0; i < li_task->b1; i++)
+ {
+ int a1, a2, n;
+
+ a1 = li->bla[2*i];
+ a2 = li->bla[2*i+1];
+ for (n = li->blnr[i]; (n < li->blnr[i+1]); n++)
+ {
+ int k, sign, center, end;
+
+ k = li->blbnb[n];
+
+ /* If we are using multiple, independent tasks for LINCS,
+ * the calls to check_assign_connected should have
+ * put all connected constraints in our task.
+ */
+ assert(li->bTaskDep || (k >= li_task->b0 && k < li_task->b1));
+
+ if (a1 == li->bla[2*k] || a2 == li->bla[2*k+1])
+ {
+ sign = -1;
+ }
+ else
+ {
+ sign = 1;
+ }
+ if (a1 == li->bla[2*k] || a1 == li->bla[2*k+1])
+ {
+ center = a1;
+ end = a2;
+ }
+ else
+ {
+ center = a2;
+ end = a1;
+ }
+ li->blmf[n] = sign*invmass[center]*li->blc[i]*li->blc[k];
+ li->blmf1[n] = sign*0.5;
+ if (li->ncg_triangle > 0)
+ {
+ int nk, kk;
+
+ /* Look for constraint triangles */
+ for (nk = li->blnr[k]; (nk < li->blnr[k+1]); nk++)
+ {
+ kk = li->blbnb[nk];
+ if (kk != i && kk != k &&
+ (li->bla[2*kk] == end || li->bla[2*kk+1] == end))
+ {
+ /* If we are using multiple tasks for LINCS,
+ * the calls to check_assign_triangle should have
+ * put all constraints in the triangle in our task.
+ */
+ assert(k >= li_task->b0 && k < li_task->b1);
+ assert(kk >= li_task->b0 && kk < li_task->b1);
+
+ if (li_task->ntriangle == 0 ||
+ li_task->triangle[li_task->ntriangle - 1] < i)
+ {
+ /* Add this constraint to the triangle list */
+ li_task->triangle[li_task->ntriangle] = i;
+ li_task->tri_bits[li_task->ntriangle] = 0;
+ li_task->ntriangle++;
+ if (li->blnr[i+1] - li->blnr[i] > static_cast<int>(sizeof(li_task->tri_bits[0])*8 - 1))
+ {
+ gmx_fatal(FARGS, "A constraint is connected to %d constraints, this is more than the %d allowed for constraints participating in triangles",
+ li->blnr[i+1] - li->blnr[i],
+ sizeof(li_task->tri_bits[0])*8-1);
+ }
+ }
+ li_task->tri_bits[li_task->ntriangle-1] |= (1 << (n - li->blnr[i]));
+ (*ncc_triangle)++;
+ }
+ }
+ }
+ }
+ }
+}
+
+/* Sets the elements in the LINCS matrix */
+void set_lincs_matrix(struct gmx_lincsdata *li, real *invmass, real lambda)
+{
+ int i;
+ const real invsqrt2 = 0.7071067811865475244;
+
+ for (i = 0; (i < li->nc); i++)
+ {
+ int a1, a2;
+
+ a1 = li->bla[2*i];
+ a2 = li->bla[2*i+1];
+ li->blc[i] = gmx_invsqrt(invmass[a1] + invmass[a2]);
+ li->blc1[i] = invsqrt2;
+ }
+
+ /* Construct the coupling coefficient matrix blmf */
+ int th, ntriangle = 0, ncc_triangle = 0;
+#pragma omp parallel for reduction(+: ntriangle, ncc_triangle) num_threads(li->ntask) schedule(static)
+ for (th = 0; th < li->ntask; th++)
+ {
+ set_lincs_matrix_task(li, &li->task[th], invmass, &ncc_triangle);
+ ntriangle = li->task[th].ntriangle;
+ }
+ li->ntriangle = ntriangle;
+ li->ncc_triangle = ncc_triangle;
+
+ if (debug)
+ {
+ fprintf(debug, "Of the %d constraints %d participate in triangles\n",
+ li->nc, li->ntriangle);
+ fprintf(debug, "There are %d couplings of which %d in triangles\n",
+ li->ncc, li->ncc_triangle);
+ }
+
+ /* Set matlam,
+ * so we know with which lambda value the masses have been set.
+ */
+ li->matlam = lambda;
+}
+
+static int count_triangle_constraints(t_ilist *ilist, t_blocka *at2con)
+{
+ int ncon1, ncon_tot;
+ int c0, a00, a01, n1, c1, a10, a11, ac1, n2, c2, a20, a21;
+ int ncon_triangle;
+ gmx_bool bTriangle;
+ t_iatom *ia1, *ia2, *iap;
+
+ ncon1 = ilist[F_CONSTR].nr/3;
+ ncon_tot = ncon1 + ilist[F_CONSTRNC].nr/3;
+
+ ia1 = ilist[F_CONSTR].iatoms;
+ ia2 = ilist[F_CONSTRNC].iatoms;
+
+ ncon_triangle = 0;
+ for (c0 = 0; c0 < ncon_tot; c0++)
+ {
+ bTriangle = FALSE;
+ iap = constr_iatomptr(ncon1, ia1, ia2, c0);
+ a00 = iap[1];
+ a01 = iap[2];
+ for (n1 = at2con->index[a01]; n1 < at2con->index[a01+1]; n1++)
+ {
+ c1 = at2con->a[n1];
+ if (c1 != c0)
+ {
+ iap = constr_iatomptr(ncon1, ia1, ia2, c1);
+ a10 = iap[1];
+ a11 = iap[2];
+ if (a10 == a01)
+ {
+ ac1 = a11;
+ }
+ else
+ {
+ ac1 = a10;
+ }
+ for (n2 = at2con->index[ac1]; n2 < at2con->index[ac1+1]; n2++)
+ {
+ c2 = at2con->a[n2];
+ if (c2 != c0 && c2 != c1)
+ {
+ iap = constr_iatomptr(ncon1, ia1, ia2, c2);
+ a20 = iap[1];
+ a21 = iap[2];
+ if (a20 == a00 || a21 == a00)
+ {
+ bTriangle = TRUE;
+ }
+ }
+ }
+ }
+ }
+ if (bTriangle)
+ {
+ ncon_triangle++;
+ }
+ }
+
+ return ncon_triangle;
+}
+
+static gmx_bool more_than_two_sequential_constraints(const t_ilist *ilist,
+ const t_blocka *at2con)
+{
+ t_iatom *ia1, *ia2, *iap;
+ int ncon1, ncon_tot, c;
+ int a1, a2;
+ gmx_bool bMoreThanTwoSequentialConstraints;
+
+ ncon1 = ilist[F_CONSTR].nr/3;
+ ncon_tot = ncon1 + ilist[F_CONSTRNC].nr/3;
+
+ ia1 = ilist[F_CONSTR].iatoms;
+ ia2 = ilist[F_CONSTRNC].iatoms;
+
+ bMoreThanTwoSequentialConstraints = FALSE;
+ for (c = 0; c < ncon_tot && !bMoreThanTwoSequentialConstraints; c++)
+ {
+ iap = constr_iatomptr(ncon1, ia1, ia2, c);
+ a1 = iap[1];
+ a2 = iap[2];
+ /* Check if this constraint has constraints connected at both atoms */
+ if (at2con->index[a1+1] - at2con->index[a1] > 1 &&
+ at2con->index[a2+1] - at2con->index[a2] > 1)
+ {
+ bMoreThanTwoSequentialConstraints = TRUE;
+ }
+ }
+
+ return bMoreThanTwoSequentialConstraints;
+}
+
+static int int_comp(const void *a, const void *b)
+{
+ return (*(int *)a) - (*(int *)b);
+}
+
+gmx_lincsdata_t init_lincs(FILE *fplog, gmx_mtop_t *mtop,
+ int nflexcon_global, t_blocka *at2con,
+ gmx_bool bPLINCS, int nIter, int nProjOrder)
+{
+ struct gmx_lincsdata *li;
+ int mt, mb;
+ gmx_moltype_t *molt;
+ gmx_bool bMoreThanTwoSeq;
+
+ if (fplog)
+ {
+ fprintf(fplog, "\nInitializing%s LINear Constraint Solver\n",
+ bPLINCS ? " Parallel" : "");
+ }
+
+ snew(li, 1);
+
+ li->ncg =
+ gmx_mtop_ftype_count(mtop, F_CONSTR) +
+ gmx_mtop_ftype_count(mtop, F_CONSTRNC);
+ li->ncg_flex = nflexcon_global;
+
+ li->nIter = nIter;
+ li->nOrder = nProjOrder;
+
+ li->max_connect = 0;
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ int a;
+
+ molt = &mtop->moltype[mt];
+ for (a = 0; a < molt->atoms.nr; a++)
+ {
+ li->max_connect = std::max(li->max_connect,
+ at2con[mt].index[a + 1] - at2con[mt].index[a]);
+ }
+ }
+
+ li->ncg_triangle = 0;
+ bMoreThanTwoSeq = FALSE;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+
+ li->ncg_triangle +=
+ mtop->molblock[mb].nmol*
+ count_triangle_constraints(molt->ilist,
+ &at2con[mtop->molblock[mb].type]);
+
+ if (!bMoreThanTwoSeq &&
+ more_than_two_sequential_constraints(molt->ilist, &at2con[mtop->molblock[mb].type]))
+ {
+ bMoreThanTwoSeq = TRUE;
+ }
+ }
+
+ /* Check if we need to communicate not only before LINCS,
+ * but also before each iteration.
+ * The check for only two sequential constraints is only
+ * useful for the common case of H-bond only constraints.
+ * With more effort we could also make it useful for small
+ * molecules with nr. sequential constraints <= nOrder-1.
+ */
+ li->bCommIter = (bPLINCS && (li->nOrder < 1 || bMoreThanTwoSeq));
+
+ if (debug && bPLINCS)
+ {
+ fprintf(debug, "PLINCS communication before each iteration: %d\n",
+ li->bCommIter);
+ }
+
+ /* LINCS can run on any number of threads.
+ * Currently the number is fixed for the whole simulation,
+ * but it could be set in set_lincs().
+ * The current constraint to task assignment code can create independent
+ * tasks only when not more than two constraints are connected sequentially.
+ */
+ li->ntask = gmx_omp_nthreads_get(emntLINCS);
+ li->bTaskDep = (li->ntask > 1 && bMoreThanTwoSeq);
+ if (debug)
+ {
+ fprintf(debug, "LINCS: using %d threads, tasks are %sdependent\n",
+ li->ntask, li->bTaskDep ? "" : "in");
+ }
+ if (li->ntask == 1)
+ {
+ snew(li->task, 1);
+ }
+ else
+ {
+ /* Allocate an extra elements for "task-overlap" constraints */
+ snew(li->task, li->ntask + 1);
+ }
+ int th;
+#pragma omp parallel for num_threads(li->ntask)
+ for (th = 0; th < li->ntask; th++)
+ {
+ /* Per thread SIMD load buffer for loading 2 simd_width rvecs */
+ snew_aligned(li->task[th].simd_buf, 2*simd_width*DIM,
+ align_bytes);
+ }
+
+ if (bPLINCS || li->ncg_triangle > 0)
+ {
+ please_cite(fplog, "Hess2008a");
+ }
+ else
+ {
+ please_cite(fplog, "Hess97a");
+ }
+
+ if (fplog)
+ {
+ fprintf(fplog, "The number of constraints is %d\n", li->ncg);
+ if (bPLINCS)
+ {
+ fprintf(fplog, "There are inter charge-group constraints,\n"
+ "will communicate selected coordinates each lincs iteration\n");
+ }
+ if (li->ncg_triangle > 0)
+ {
+ fprintf(fplog,
+ "%d constraints are involved in constraint triangles,\n"
+ "will apply an additional matrix expansion of order %d for couplings\n"
+ "between constraints inside triangles\n",
+ li->ncg_triangle, li->nOrder);
+ }
+ }
+
+ return li;
+}
+
+/* Sets up the work division over the threads */
+static void lincs_thread_setup(struct gmx_lincsdata *li, int natoms)
+{
+ lincs_task_t *li_m;
+ int th;
+ gmx_bitmask_t *atf;
+ int a;
+
+ if (natoms > li->atf_nalloc)
+ {
+ li->atf_nalloc = over_alloc_large(natoms);
+ srenew(li->atf, li->atf_nalloc);
+ }
+
+ atf = li->atf;
+ /* Clear the atom flags */
+ for (a = 0; a < natoms; a++)
+ {
+ bitmask_clear(&atf[a]);
+ }
+
+ if (li->ntask > BITMASK_SIZE)
+ {
+ gmx_fatal(FARGS, "More than %d threads is not supported for LINCS.", BITMASK_SIZE);
+ }
+
+ for (th = 0; th < li->ntask; th++)
+ {
+ lincs_task_t *li_task;
+ int b;
+
+ li_task = &li->task[th];
+
+ /* For each atom set a flag for constraints from each */
+ for (b = li_task->b0; b < li_task->b1; b++)
+ {
+ bitmask_set_bit(&atf[li->bla[b*2 ]], th);
+ bitmask_set_bit(&atf[li->bla[b*2 + 1]], th);
+ }
+ }
+
+#pragma omp parallel for num_threads(li->ntask) schedule(static)
+ for (th = 0; th < li->ntask; th++)
+ {
+ lincs_task_t *li_task;
+ gmx_bitmask_t mask;
+ int b;
+
+ li_task = &li->task[th];
+
+ if (li_task->b1 - li_task->b0 > li_task->ind_nalloc)
+ {
+ li_task->ind_nalloc = over_alloc_large(li_task->b1-li_task->b0);
+ srenew(li_task->ind, li_task->ind_nalloc);
+ srenew(li_task->ind_r, li_task->ind_nalloc);
+ }
+
+ bitmask_init_low_bits(&mask, th);
+
+ li_task->nind = 0;
+ li_task->nind_r = 0;
+ for (b = li_task->b0; b < li_task->b1; b++)
+ {
+ /* We let the constraint with the lowest thread index
+ * operate on atoms with constraints from multiple threads.
+ */
+ if (bitmask_is_disjoint(atf[li->bla[b*2]], mask) &&
+ bitmask_is_disjoint(atf[li->bla[b*2+1]], mask))
+ {
+ /* Add the constraint to the local atom update index */
+ li_task->ind[li_task->nind++] = b;
+ }
+ else
+ {
+ /* Add the constraint to the rest block */
+ li_task->ind_r[li_task->nind_r++] = b;
+ }
+ }
+ }
+
+ /* We need to copy all constraints which have not be assigned
+ * to a thread to a separate list which will be handled by one thread.
+ */
+ li_m = &li->task[li->ntask];
+
+ li_m->nind = 0;
+ for (th = 0; th < li->ntask; th++)
+ {
+ lincs_task_t *li_task;
+ int b;
+
+ li_task = &li->task[th];
+
+ if (li_m->nind + li_task->nind_r > li_m->ind_nalloc)
+ {
+ li_m->ind_nalloc = over_alloc_large(li_m->nind+li_task->nind_r);
+ srenew(li_m->ind, li_m->ind_nalloc);
+ }
+
+ for (b = 0; b < li_task->nind_r; b++)
+ {
+ li_m->ind[li_m->nind++] = li_task->ind_r[b];
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "LINCS thread %d: %d constraints\n",
+ th, li_task->nind);
+ }
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "LINCS thread r: %d constraints\n",
+ li_m->nind);
+ }
+}
+
+/* There is no realloc with alignment, so here we make one for reals.
+ * Note that this function does not preserve the contents of the memory.
+ */
+static void resize_real_aligned(real **ptr, int nelem)
+{
+ sfree_aligned(*ptr);
+ snew_aligned(*ptr, nelem, align_bytes);
+}
+
+static void assign_constraint(struct gmx_lincsdata *li,
+ int constraint_index,
+ int a1, int a2,
+ real lenA, real lenB,
+ const t_blocka *at2con)
+{
+ int con;
+
+ con = li->nc;
+
+ /* Make an mapping of local topology constraint index to LINCS index */
+ li->con_index[constraint_index] = con;
+
+ li->bllen0[con] = lenA;
+ li->ddist[con] = lenB - lenA;
+ /* Set the length to the topology A length */
+ li->bllen[con] = lenA;
+ li->bla[2*con] = a1;
+ li->bla[2*con+1] = a2;
+
+ /* Make space in the constraint connection matrix for constraints
+ * connected to both end of the current constraint.
+ */
+ li->ncc +=
+ at2con->index[a1 + 1] - at2con->index[a1] - 1 +
+ at2con->index[a2 + 1] - at2con->index[a2] - 1;
+
+ li->blnr[con + 1] = li->ncc;
+
+ /* Increase the constraint count */
+ li->nc++;
+}
+
+/* Check if constraint with topology index constraint_index is connected
+ * to other constraints, and if so add those connected constraints to our task.
+ */
+static void check_assign_connected(struct gmx_lincsdata *li,
+ const t_iatom *iatom,
+ const t_idef *idef,
+ int bDynamics,
+ int a1, int a2,
+ const t_blocka *at2con)
+{
+ /* Currently this function only supports constraint groups
+ * in which all constraints share at least one atom
+ * (e.g. H-bond constraints).
+ * Check both ends of the current constraint for
+ * connected constraints. We need to assign those
+ * to the same task.
+ */
+ int end;
+
+ for (end = 0; end < 2; end++)
+ {
+ int a, k;
+
+ a = (end == 0 ? a1 : a2);
+
+ for (k = at2con->index[a]; k < at2con->index[a + 1]; k++)
+ {
+ int cc;
+
+ cc = at2con->a[k];
+ /* Check if constraint cc has not yet been assigned */
+ if (li->con_index[cc] == -1)
+ {
+ int type;
+ real lenA, lenB;
+
+ type = iatom[cc*3];
+ lenA = idef->iparams[type].constr.dA;
+ lenB = idef->iparams[type].constr.dB;
+
+ if (bDynamics || lenA != 0 || lenB != 0)
+ {
+ assign_constraint(li, cc, iatom[3*cc + 1], iatom[3*cc + 2], lenA, lenB, at2con);
+ }
+ }
+ }
+ }
+}
+
+/* Check if constraint with topology index constraint_index is involved
+ * in a constraint triangle, and if so add the other two constraints
+ * in the triangle to our task.
+ */
+static void check_assign_triangle(struct gmx_lincsdata *li,
+ const t_iatom *iatom,
+ const t_idef *idef,
+ int bDynamics,
+ int constraint_index,
+ int a1, int a2,
+ const t_blocka *at2con)
+{
+ int nca, cc[32], ca[32], k;
+ int c_triangle[2] = { -1, -1 };
+
+ nca = 0;
+ for (k = at2con->index[a1]; k < at2con->index[a1 + 1]; k++)
+ {
+ int c;
+
+ c = at2con->a[k];
+ if (c != constraint_index)
+ {
+ int aa1, aa2;
+
+ aa1 = iatom[c*3 + 1];
+ aa2 = iatom[c*3 + 2];
+ if (aa1 != a1)
+ {
+ cc[nca] = c;
+ ca[nca] = aa1;
+ nca++;
+ }
+ if (aa2 != a1)
+ {
+ cc[nca] = c;
+ ca[nca] = aa2;
+ nca++;
+ }
+ }
+ }
+
+ for (k = at2con->index[a2]; k < at2con->index[a2 + 1]; k++)
+ {
+ int c;
+
+ c = at2con->a[k];
+ if (c != constraint_index)
+ {
+ int aa1, aa2, i;
+
+ aa1 = iatom[c*3 + 1];
+ aa2 = iatom[c*3 + 2];
+ if (aa1 != a2)
+ {
+ for (i = 0; i < nca; i++)
+ {
+ if (aa1 == ca[i])
+ {
+ c_triangle[0] = cc[i];
+ c_triangle[1] = c;
+ }
+ }
+ }
+ if (aa2 != a2)
+ {
+ for (i = 0; i < nca; i++)
+ {
+ if (aa2 == ca[i])
+ {
+ c_triangle[0] = cc[i];
+ c_triangle[1] = c;
+ }
+ }
+ }
+ }
+ }
+
+ if (c_triangle[0] >= 0)
+ {
+ int end;
+
+ for (end = 0; end < 2; end++)
+ {
+ /* Check if constraint c_triangle[end] has not yet been assigned */
+ if (li->con_index[c_triangle[end]] == -1)
+ {
+ int i, type;
+ real lenA, lenB;
+
+ i = c_triangle[end]*3;
+ type = iatom[i];
+ lenA = idef->iparams[type].constr.dA;
+ lenB = idef->iparams[type].constr.dB;
+
+ if (bDynamics || lenA != 0 || lenB != 0)
+ {
+ assign_constraint(li, c_triangle[end], iatom[i + 1], iatom[i + 2], lenA, lenB, at2con);
+ }
+ }
+ }
+ }
+}
+
+static void set_matrix_indices(struct gmx_lincsdata *li,
+ const lincs_task_t *li_task,
+ const t_blocka *at2con,
+ gmx_bool bSortMatrix)
+{
+ int b;
+
+ for (b = li_task->b0; b < li_task->b1; b++)
+ {
+ int a1, a2, i, k;
+
+ a1 = li->bla[b*2];
+ a2 = li->bla[b*2 + 1];
+
+ i = li->blnr[b];
+ for (k = at2con->index[a1]; k < at2con->index[a1 + 1]; k++)
+ {
+ int concon;
+
+ concon = li->con_index[at2con->a[k]];
+ if (concon != b)
+ {
+ li->blbnb[i++] = concon;
+ }
+ }
+ for (k = at2con->index[a2]; k < at2con->index[a2 + 1]; k++)
+ {
+ int concon;
+
+ concon = li->con_index[at2con->a[k]];
+ if (concon != b)
+ {
+ li->blbnb[i++] = concon;
+ }
+ }
+
+ if (bSortMatrix)
+ {
+ /* Order the blbnb matrix to optimize memory access */
+ qsort(&(li->blbnb[li->blnr[b]]), li->blnr[b + 1] - li->blnr[b],
+ sizeof(li->blbnb[0]), int_comp);
+ }
+ }
+}
+
+void set_lincs(t_idef *idef, t_mdatoms *md,
+ gmx_bool bDynamics, t_commrec *cr,
+ struct gmx_lincsdata *li)
+{
+ int natoms, nflexcon;
+ t_blocka at2con;
+ t_iatom *iatom;
+ int i, ncc_alloc_old, ncon_tot;
+
+ li->nc_real = 0;
+ li->nc = 0;
+ li->ncc = 0;
+ /* Zero the thread index ranges.
+ * Otherwise without local constraints we could return with old ranges.
+ */
+ for (i = 0; i < li->ntask; i++)
+ {
+ li->task[i].b0 = 0;
+ li->task[i].b1 = 0;
+ li->task[i].nind = 0;
+ }
+ if (li->ntask > 1)
+ {
+ li->task[li->ntask].nind = 0;
+ }
+
+ /* This is the local topology, so there are only F_CONSTR constraints */
+ if (idef->il[F_CONSTR].nr == 0)
+ {
+ /* There are no constraints,
+ * we do not need to fill any data structures.
+ */
+ return;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Building the LINCS connectivity\n");
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ if (cr->dd->constraints)
+ {
+ int start;
+
+ dd_get_constraint_range(cr->dd, &start, &natoms);
+ }
+ else
+ {
+ natoms = cr->dd->nat_home;
+ }
+ }
+ else
+ {
+ natoms = md->homenr;
+ }
+ at2con = make_at2con(0, natoms, idef->il, idef->iparams, bDynamics,
+ &nflexcon);
+
+ ncon_tot = idef->il[F_CONSTR].nr/3;
+
+ /* Ensure we have enough padding for aligned loads for each thread */
+ if (ncon_tot + li->ntask*simd_width > li->nc_alloc || li->nc_alloc == 0)
+ {
+ li->nc_alloc = over_alloc_dd(ncon_tot + li->ntask*simd_width);
+ srenew(li->con_index, li->nc_alloc);
+ resize_real_aligned(&li->bllen0, li->nc_alloc);
+ resize_real_aligned(&li->ddist, li->nc_alloc);
+ srenew(li->bla, 2*li->nc_alloc);
+ resize_real_aligned(&li->blc, li->nc_alloc);
+ resize_real_aligned(&li->blc1, li->nc_alloc);
+ srenew(li->blnr, li->nc_alloc + 1);
+ resize_real_aligned(&li->bllen, li->nc_alloc);
+ srenew(li->tmpv, li->nc_alloc);
+ if (DOMAINDECOMP(cr))
+ {
+ srenew(li->nlocat, li->nc_alloc);
+ }
+ resize_real_aligned(&li->tmp1, li->nc_alloc);
+ resize_real_aligned(&li->tmp2, li->nc_alloc);
+ resize_real_aligned(&li->tmp3, li->nc_alloc);
+ resize_real_aligned(&li->tmp4, li->nc_alloc);
+ resize_real_aligned(&li->mlambda, li->nc_alloc);
+ }
+
+ iatom = idef->il[F_CONSTR].iatoms;
+
+ ncc_alloc_old = li->ncc_alloc;
+ li->blnr[0] = li->ncc;
+
+ /* Assign the constraints for li->ntask LINCS tasks.
+ * We target a uniform distribution of constraints over the tasks.
+ * Note that when flexible constraints are present, but are removed here
+ * (e.g. because we are doing EM) we get imbalance, but since that doesn't
+ * happen during normal MD, that's ok.
+ */
+ int ncon_assign, ncon_target, con, th;
+
+ /* Determine the number of constraints we need to assign here */
+ ncon_assign = ncon_tot;
+ if (!bDynamics)
+ {
+ /* With energy minimization, flexible constraints are ignored
+ * (and thus minimized, as they should be).
+ */
+ ncon_assign -= nflexcon;
+ }
+
+ /* Set the target constraint count per task to exactly uniform,
+ * this might be overridden below.
+ */
+ ncon_target = (ncon_assign + li->ntask - 1)/li->ntask;
+
+ /* Mark all constraints as unassigned by setting their index to -1 */
+ for (con = 0; con < ncon_tot; con++)
+ {
+ li->con_index[con] = -1;
+ }
+
+ con = 0;
+ for (th = 0; th < li->ntask; th++)
+ {
+ lincs_task_t *li_task;
+
+ li_task = &li->task[th];
+
+#ifdef LINCS_SIMD
+ /* With indepedent tasks we likely have H-bond constraints or constraint
+ * pairs. The connected constraints will be pulled into the task, so the
+ * constraints per task will often exceed ncon_target.
+ * Triangle constraints can also increase the count, but there are
+ * relatively few of those, so we usually expect to get ncon_target.
+ */
+ if (li->bTaskDep)
+ {
+ /* We round ncon_target to a multiple of GMX_SIMD_WIDTH,
+ * since otherwise a lot of operations can be wasted.
+ * There are several ways to round here, we choose the one
+ * that alternates block sizes, which helps with Intel HT.
+ */
+ ncon_target = ((ncon_assign*(th + 1))/li->ntask - li->nc_real + GMX_SIMD_REAL_WIDTH - 1) & ~(GMX_SIMD_REAL_WIDTH - 1);
+ }
+#endif
+
+ /* Continue filling the arrays where we left off with the previous task,
+ * including padding for SIMD.
+ */
+ li_task->b0 = li->nc;
+
+ while (con < ncon_tot && li->nc - li_task->b0 < ncon_target)
+ {
+ if (li->con_index[con] == -1)
+ {
+ int type, a1, a2;
+ real lenA, lenB;
+
+ type = iatom[3*con];
+ a1 = iatom[3*con + 1];
+ a2 = iatom[3*con + 2];
+ lenA = idef->iparams[type].constr.dA;
+ lenB = idef->iparams[type].constr.dB;
+ /* Skip the flexible constraints when not doing dynamics */
+ if (bDynamics || lenA != 0 || lenB != 0)
+ {
+ assign_constraint(li, con, a1, a2, lenA, lenB, &at2con);
+
+ if (li->ntask > 1 && !li->bTaskDep)
+ {
+ /* We can generate independent tasks. Check if we
+ * need to assign connected constraints to our task.
+ */
+ check_assign_connected(li, iatom, idef, bDynamics,
+ a1, a2, &at2con);
+ }
+ if (li->ntask > 1 && li->ncg_triangle > 0)
+ {
+ /* Ensure constraints in one triangle are assigned
+ * to the same task.
+ */
+ check_assign_triangle(li, iatom, idef, bDynamics,
+ con, a1, a2, &at2con);
+ }
+ }
+ }
+
+ con++;
+ }
+
+ li_task->b1 = li->nc;
+
+ if (simd_width > 1)
+ {
+ /* Copy the last atom pair indices and lengths for constraints
+ * up to a multiple of simd_width, such that we can do all
+ * SIMD operations without having to worry about end effects.
+ */
+ int i, last;
+
+ li->nc = ((li_task->b1 + simd_width - 1)/simd_width)*simd_width;
+ last = li_task->b1 - 1;
+ for (i = li_task->b1; i < li->nc; i++)
+ {
+ li->bla[i*2 ] = li->bla[last*2 ];
+ li->bla[i*2 + 1] = li->bla[last*2 + 1];
+ li->bllen0[i] = li->bllen0[last];
+ li->ddist[i] = li->ddist[last];
+ li->bllen[i] = li->bllen[last];
+ li->blnr[i + 1] = li->blnr[last + 1];
+ }
+ }
+
+ /* Keep track of how many constraints we assigned */
+ li->nc_real += li_task->b1 - li_task->b0;
+
+ if (debug)
+ {
+ fprintf(debug, "LINCS task %d constraints %d - %d\n",
+ th, li_task->b0, li_task->b1);
+ }
+ }
+
+ assert(li->nc_real == ncon_assign);
+
+ gmx_bool bSortMatrix;
+
+ /* Without DD we order the blbnb matrix to optimize memory access.
+ * With DD the overhead of sorting is more than the gain during access.
+ */
+ bSortMatrix = !DOMAINDECOMP(cr);
+
+ if (li->ncc > li->ncc_alloc)
+ {
+ li->ncc_alloc = over_alloc_small(li->ncc);
+ srenew(li->blbnb, li->ncc_alloc);
+ }
+
+#pragma omp parallel for num_threads(li->ntask) schedule(static)
+ for (th = 0; th < li->ntask; th++)
+ {
+ lincs_task_t *li_task;
+
+ li_task = &li->task[th];
+
+ if (li->ncg_triangle > 0 &&
+ li_task->b1 - li_task->b0 > li_task->tri_alloc)
+ {
+ /* This is allocating too much, but it is difficult to improve */
+ li_task->tri_alloc = over_alloc_dd(li_task->b1 - li_task->b0);
+ srenew(li_task->triangle, li_task->tri_alloc);
+ srenew(li_task->tri_bits, li_task->tri_alloc);
+ }
+
+ set_matrix_indices(li, li_task, &at2con, bSortMatrix);
+ }
+
+ done_blocka(&at2con);
+
+ if (cr->dd == NULL)
+ {
+ /* Since the matrix is static, we should free some memory */
+ li->ncc_alloc = li->ncc;
+ srenew(li->blbnb, li->ncc_alloc);
+ }
+
+ if (li->ncc_alloc > ncc_alloc_old)
+ {
+ srenew(li->blmf, li->ncc_alloc);
+ srenew(li->blmf1, li->ncc_alloc);
+ srenew(li->tmpncc, li->ncc_alloc);
+ }
+
+ if (DOMAINDECOMP(cr) && dd_constraints_nlocalatoms(cr->dd) != NULL)
+ {
+ int *nlocat_dd;
+
+ nlocat_dd = dd_constraints_nlocalatoms(cr->dd);
+
+ /* Convert nlocat from local topology to LINCS constraint indexing */
+ for (con = 0; con < ncon_tot; con++)
+ {
+ li->nlocat[li->con_index[con]] = nlocat_dd[con];
+ }
+ }
+ else
+ {
+ li->nlocat = NULL;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Number of constraints is %d, padded %d, couplings %d\n",
+ li->nc_real, li->nc, li->ncc);
+ }
+
+ if (li->ntask > 1)
+ {
+ lincs_thread_setup(li, md->nr);
+ }
+
+ set_lincs_matrix(li, md->invmass, md->lambda);
+}
+
+static void lincs_warning(FILE *fplog,
+ gmx_domdec_t *dd, rvec *x, rvec *xprime, t_pbc *pbc,
+ int ncons, int *bla, real *bllen, real wangle,
+ int maxwarn, int *warncount)
+{
+ int b, i, j;
+ rvec v0, v1;
+ real wfac, d0, d1, cosine;
+ char buf[STRLEN];
+
+ wfac = cos(DEG2RAD*wangle);
+
+ sprintf(buf, "bonds that rotated more than %g degrees:\n"
+ " atom 1 atom 2 angle previous, current, constraint length\n",
+ wangle);
+ fprintf(stderr, "%s", buf);
+ if (fplog)
+ {
+ fprintf(fplog, "%s", buf);
+ }
+
+ for (b = 0; b < ncons; b++)
+ {
+ i = bla[2*b];
+ j = bla[2*b+1];
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, x[i], x[j], v0);
+ pbc_dx_aiuc(pbc, xprime[i], xprime[j], v1);
+ }
+ else
+ {
+ rvec_sub(x[i], x[j], v0);
+ rvec_sub(xprime[i], xprime[j], v1);
+ }
+ d0 = norm(v0);
+ d1 = norm(v1);
+ cosine = iprod(v0, v1)/(d0*d1);
+ if (cosine < wfac)
+ {
+ sprintf(buf, " %6d %6d %5.1f %8.4f %8.4f %8.4f\n",
+ ddglatnr(dd, i), ddglatnr(dd, j),
+ RAD2DEG*acos(cosine), d0, d1, bllen[b]);
+ fprintf(stderr, "%s", buf);
+ if (fplog)
+ {
+ fprintf(fplog, "%s", buf);
+ }
+ if (!gmx_isfinite(d1))
+ {
+ gmx_fatal(FARGS, "Bond length not finite.");
+ }
+
+ (*warncount)++;
+ }
+ }
+ if (*warncount > maxwarn)
+ {
+ too_many_constraint_warnings(econtLINCS, *warncount);
+ }
+}
+
+static void cconerr(const struct gmx_lincsdata *lincsd,
+ rvec *x, t_pbc *pbc,
+ real *ncons_loc, real *ssd, real *max, int *imax)
+{
+ const int *bla, *nlocat;
+ const real *bllen;
+ real ma, ssd2;
+ int count, im, task;
+
+ bla = lincsd->bla;
+ bllen = lincsd->bllen;
+ nlocat = lincsd->nlocat;
+
+ ma = 0;
+ ssd2 = 0;
+ im = 0;
+ count = 0;
+ for (task = 0; task < lincsd->ntask; task++)
+ {
+ int b;
+
+ for (b = lincsd->task[task].b0; b < lincsd->task[task].b1; b++)
+ {
+ real len, d, r2;
+ rvec dx;
+
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, x[bla[2*b]], x[bla[2*b+1]], dx);
+ }
+ else
+ {
+ rvec_sub(x[bla[2*b]], x[bla[2*b+1]], dx);
+ }
+ r2 = norm2(dx);
+ len = r2*gmx_invsqrt(r2);
+ d = fabs(len/bllen[b]-1);
+ if (d > ma && (nlocat == NULL || nlocat[b]))
+ {
+ ma = d;
+ im = b;
+ }
+ if (nlocat == NULL)
+ {
+ ssd2 += d*d;
+ count++;
+ }
+ else
+ {
+ ssd2 += nlocat[b]*d*d;
+ count += nlocat[b];
+ }
+ }
+ }
+
+ *ncons_loc = (nlocat ? 0.5 : 1)*count;
+ *ssd = (nlocat ? 0.5 : 1)*ssd2;
+ *max = ma;
+ *imax = im;
+}
+
+gmx_bool constrain_lincs(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
+ t_inputrec *ir,
+ gmx_int64_t step,
+ struct gmx_lincsdata *lincsd, t_mdatoms *md,
+ t_commrec *cr,
+ rvec *x, rvec *xprime, rvec *min_proj,
+ matrix box, t_pbc *pbc,
+ real lambda, real *dvdlambda,
+ real invdt, rvec *v,
+ gmx_bool bCalcVir, tensor vir_r_m_dr,
+ int econq,
+ t_nrnb *nrnb,
+ int maxwarn, int *warncount)
+{
+ gmx_bool bCalcDHDL;
+ char buf[STRLEN], buf2[22], buf3[STRLEN];
+ int i, p_imax;
+ real ncons_loc, p_ssd, p_max = 0;
+ rvec dx;
+ gmx_bool bOK, bWarn;
+
+ bOK = TRUE;
+
+ /* This boolean should be set by a flag passed to this routine.
+ * We can also easily check if any constraint length is changed,
+ * if not dH/dlambda=0 and we can also set the boolean to FALSE.
+ */
+ bCalcDHDL = (ir->efep != efepNO && dvdlambda != NULL);
+
+ if (lincsd->nc == 0 && cr->dd == NULL)
+ {
+ if (bLog || bEner)
+ {
+ lincsd->rmsd_data[0] = 0;
+ if (ir->eI == eiSD2 && v == NULL)
+ {
+ i = 2;
+ }
+ else
+ {
+ i = 1;
+ }
+ lincsd->rmsd_data[i] = 0;
+ }
+
+ return bOK;
+ }
+
+ if (econq == econqCoord)
+ {
+ /* We can't use bCalcDHDL here, since NULL can be passed for dvdlambda
+ * also with efep!=fepNO.
+ */
+ if (ir->efep != efepNO)
+ {
+ if (md->nMassPerturbed && lincsd->matlam != md->lambda)
+ {
+ set_lincs_matrix(lincsd, md->invmass, md->lambda);
+ }
+
+ for (i = 0; i < lincsd->nc; i++)
+ {
+ lincsd->bllen[i] = lincsd->bllen0[i] + lambda*lincsd->ddist[i];
+ }
+ }
+
+ if (lincsd->ncg_flex)
+ {
+ /* Set the flexible constraint lengths to the old lengths */
+ if (pbc != NULL)
+ {
+ for (i = 0; i < lincsd->nc; i++)
+ {
+ if (lincsd->bllen[i] == 0)
+ {
+ pbc_dx_aiuc(pbc, x[lincsd->bla[2*i]], x[lincsd->bla[2*i+1]], dx);
+ lincsd->bllen[i] = norm(dx);
+ }
+ }
+ }
+ else
+ {
+ for (i = 0; i < lincsd->nc; i++)
+ {
+ if (lincsd->bllen[i] == 0)
+ {
+ lincsd->bllen[i] =
+ sqrt(distance2(x[lincsd->bla[2*i]],
+ x[lincsd->bla[2*i+1]]));
+ }
+ }
+ }
+ }
+
+ if (bLog && fplog)
+ {
+ cconerr(lincsd, xprime, pbc,
+ &ncons_loc, &p_ssd, &p_max, &p_imax);
+ }
+
+ /* This bWarn var can be updated by multiple threads
+ * at the same time. But as we only need to detect
+ * if a warning occured or not, this is not an issue.
+ */
+ bWarn = FALSE;
+
+ /* The OpenMP parallel region of constrain_lincs for coords */
+#pragma omp parallel num_threads(lincsd->ntask)
+ {
+ int th = gmx_omp_get_thread_num();
+
+ clear_mat(lincsd->task[th].vir_r_m_dr);
+
+ do_lincs(x, xprime, box, pbc, lincsd, th,
+ md->invmass, cr,
+ bCalcDHDL,
+ ir->LincsWarnAngle, &bWarn,
+ invdt, v, bCalcVir,
+ th == 0 ? vir_r_m_dr : lincsd->task[th].vir_r_m_dr);
+ }
+
+ if (bLog && fplog && lincsd->nc > 0)
+ {
+ fprintf(fplog, " Rel. Constraint Deviation: RMS MAX between atoms\n");
+ fprintf(fplog, " Before LINCS %.6f %.6f %6d %6d\n",
+ sqrt(p_ssd/ncons_loc), p_max,
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax]),
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax+1]));
+ }
+ if (bLog || bEner)
+ {
+ cconerr(lincsd, xprime, pbc,
+ &ncons_loc, &p_ssd, &p_max, &p_imax);
+ /* Check if we are doing the second part of SD */
+ if (ir->eI == eiSD2 && v == NULL)
+ {
+ i = 2;
+ }
+ else
+ {
+ i = 1;
+ }
+ lincsd->rmsd_data[0] = ncons_loc;
+ lincsd->rmsd_data[i] = p_ssd;
+ }
+ else
+ {
+ lincsd->rmsd_data[0] = 0;
+ lincsd->rmsd_data[1] = 0;
+ lincsd->rmsd_data[2] = 0;
+ }
+ if (bLog && fplog && lincsd->nc > 0)
+ {
+ fprintf(fplog,
+ " After LINCS %.6f %.6f %6d %6d\n\n",
+ sqrt(p_ssd/ncons_loc), p_max,
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax]),
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax+1]));
+ }
+
+ if (bWarn)
+ {
+ if (maxwarn >= 0)
+ {
+ cconerr(lincsd, xprime, pbc,
+ &ncons_loc, &p_ssd, &p_max, &p_imax);
+ if (MULTISIM(cr))
+ {
+ sprintf(buf3, " in simulation %d", cr->ms->sim);
+ }
+ else
+ {
+ buf3[0] = 0;
+ }
+ sprintf(buf, "\nStep %s, time %g (ps) LINCS WARNING%s\n"
+ "relative constraint deviation after LINCS:\n"
+ "rms %.6f, max %.6f (between atoms %d and %d)\n",
+ gmx_step_str(step, buf2), ir->init_t+step*ir->delta_t,
+ buf3,
+ sqrt(p_ssd/ncons_loc), p_max,
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax]),
+ ddglatnr(cr->dd, lincsd->bla[2*p_imax+1]));
+ if (fplog)
+ {
+ fprintf(fplog, "%s", buf);
+ }
+ fprintf(stderr, "%s", buf);
+ lincs_warning(fplog, cr->dd, x, xprime, pbc,
+ lincsd->nc, lincsd->bla, lincsd->bllen,
+ ir->LincsWarnAngle, maxwarn, warncount);
+ }
+ bOK = (p_max < 0.5);
+ }
+
+ if (lincsd->ncg_flex)
+ {
+ for (i = 0; (i < lincsd->nc); i++)
+ {
+ if (lincsd->bllen0[i] == 0 && lincsd->ddist[i] == 0)
+ {
+ lincsd->bllen[i] = 0;
+ }
+ }
+ }
+ }
+ else
+ {
+ /* The OpenMP parallel region of constrain_lincs for derivatives */
+#pragma omp parallel num_threads(lincsd->ntask)
+ {
+ int th = gmx_omp_get_thread_num();
+
+ do_lincsp(x, xprime, min_proj, pbc, lincsd, th,
+ md->invmass, econq, bCalcDHDL,
+ bCalcVir, th == 0 ? vir_r_m_dr : lincsd->task[th].vir_r_m_dr);
+ }
+ }
+
+ if (bCalcDHDL)
+ {
+ /* Reduce the dH/dlambda contributions over the threads */
+ real dhdlambda;
+ int th;
+
+ dhdlambda = 0;
+ for (th = 0; th < lincsd->ntask; th++)
+ {
+ dhdlambda += lincsd->task[th].dhdlambda;
+ }
++ if (econq == econqCoord)
+ {
+ /* dhdlambda contains dH/dlambda*dt^2, correct for this */
+ /* TODO This should probably use invdt, so that sd integrator scaling works properly */
+ dhdlambda /= ir->delta_t*ir->delta_t;
+ }
+ *dvdlambda += dhdlambda;
+ }
+
+ if (bCalcVir && lincsd->ntask > 1)
+ {
+ for (i = 1; i < lincsd->ntask; i++)
+ {
+ m_add(vir_r_m_dr, lincsd->task[i].vir_r_m_dr, vir_r_m_dr);
+ }
+ }
+
+ /* count assuming nit=1 */
+ inc_nrnb(nrnb, eNR_LINCS, lincsd->nc_real);
+ inc_nrnb(nrnb, eNR_LINCSMAT, (2+lincsd->nOrder)*lincsd->ncc);
+ if (lincsd->ntriangle > 0)
+ {
+ inc_nrnb(nrnb, eNR_LINCSMAT, lincsd->nOrder*lincsd->ncc_triangle);
+ }
+ if (v)
+ {
+ inc_nrnb(nrnb, eNR_CONSTR_V, lincsd->nc_real*2);
+ }
+ if (bCalcVir)
+ {
+ inc_nrnb(nrnb, eNR_CONSTR_VIR, lincsd->nc_real);
+ }
+
+ return bOK;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff