X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=blobdiff_plain;f=src%2Fgromacs%2Flisted-forces%2Fbonded.cpp;fp=src%2Fgromacs%2Fgmxlib%2Fbondfree.c;h=dfb846d9e700d1492bd6314d68537a9e21fb8860;hb=19d3c2e5d0c401eb59010960d11a18b6ba2c54c6;hp=0eb8d55791b983c0b5909786b7dffdb1c5ef462a;hpb=a349e4beffcbe43be945226384d2a590b27263f0;p=alexxy%2Fgromacs.git diff --git a/src/gromacs/gmxlib/bondfree.c b/src/gromacs/listed-forces/bonded.cpp similarity index 92% rename from src/gromacs/gmxlib/bondfree.c rename to src/gromacs/listed-forces/bonded.cpp index 0eb8d55791..dfb846d9e7 100644 --- a/src/gromacs/gmxlib/bondfree.c +++ b/src/gromacs/listed-forces/bonded.cpp @@ -34,36 +34,50 @@ * To help us fund GROMACS development, we humbly ask that you cite * the research papers on the package. Check out http://www.gromacs.org. */ -#ifdef HAVE_CONFIG_H -#include -#endif +/*! \internal \file + * + * \brief This file defines functions necessary for mdrun and tools to + * compute energies and forces for bonded interactions. + * + * \author Mark Abraham + * + * \ingroup module_listed-forces + */ +#include "gmxpre.h" + +#include "bonded.h" + +#include "config.h" -#include #include -#include "physics.h" -#include "vec.h" -#include "gromacs/math/utilities.h" -#include "txtdump.h" -#include "bondf.h" -#include "gromacs/utility/smalloc.h" -#include "pbc.h" -#include "ns.h" -#include "macros.h" -#include "names.h" -#include "gmx_fatal.h" -#include "mshift.h" -#include "main.h" -#include "disre.h" -#include "orires.h" -#include "force.h" -#include "nonbonded.h" -#include "restcbt.h" +#include + +#include + +#include "gromacs/legacyheaders/disre.h" +#include "gromacs/legacyheaders/force.h" +#include "gromacs/legacyheaders/macros.h" +#include "gromacs/legacyheaders/names.h" +#include "gromacs/legacyheaders/nonbonded.h" +#include "gromacs/legacyheaders/ns.h" +#include "gromacs/legacyheaders/orires.h" +#include "gromacs/legacyheaders/txtdump.h" +#include "gromacs/math/units.h" +#include "gromacs/math/utilities.h" +#include "gromacs/math/vec.h" +#include "gromacs/pbcutil/ishift.h" +#include "gromacs/pbcutil/mshift.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/utility/fatalerror.h" +#include "gromacs/utility/smalloc.h" -/* Find a better place for this? */ +#include "restcbt.h" + +/*! \brief Mysterious CMAP coefficient matrix */ const int cmap_coeff_matrix[] = { 1, 0, -3, 2, 0, 0, 0, 0, -3, 0, 9, -6, 2, 0, -6, 4, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, -9, 6, -2, 0, 6, -4, @@ -84,7 +98,9 @@ const int cmap_coeff_matrix[] = { }; - +/* 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; @@ -101,6 +117,9 @@ int glatnr(int *global_atom_index, int i) return atnr; } +/*! \brief Compute dx = xi - xj, modulo PBC if non-NULL + * + * \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) @@ -129,7 +148,7 @@ typedef struct { gmx_simd_real_t bxx; } pbc_simd_t; -/* Set the SIMD pbc data from a normal t_pbc struct */ +/*! \brief Set the SIMD pbc data from a normal t_pbc struct */ static void set_pbc_simd(const t_pbc *pbc, pbc_simd_t *pbc_simd) { rvec inv_bdiag; @@ -169,7 +188,7 @@ static void set_pbc_simd(const t_pbc *pbc, pbc_simd_t *pbc_simd) } } -/* Correct distance vector *dx,*dy,*dz for PBC using SIMD */ +/*! \brief Correct distance vector *dx,*dy,*dz for PBC using SIMD */ static gmx_inline void pbc_dx_simd(gmx_simd_real_t *dx, gmx_simd_real_t *dy, gmx_simd_real_t *dz, const pbc_simd_t *pbc) @@ -191,10 +210,9 @@ pbc_dx_simd(gmx_simd_real_t *dx, gmx_simd_real_t *dy, gmx_simd_real_t *dz, #endif /* GMX_SIMD_HAVE_REAL */ -/* - * Morse potential bond by Frank Everdij +/*! \brief Morse potential bond * - * Three parameters needed: + * By Frank Everdij. Three parameters needed: * * b0 = equilibrium distance in nm * be = beta in nm^-1 (actually, it's nu_e*Sqrt(2*pi*pi*mu/D_e)) @@ -203,7 +221,6 @@ pbc_dx_simd(gmx_simd_real_t *dx, gmx_simd_real_t *dy, gmx_simd_real_t *dz, * Note: the potential is referenced to be +cb at infinite separation * and zero at the equilibrium distance! */ - real morse_bonds(int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec f[], rvec fshift[], @@ -278,6 +295,7 @@ real morse_bonds(int nbonds, return vtot; } +//! \cond real cubic_bonds(int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec f[], rvec fshift[], @@ -351,7 +369,7 @@ real FENE_bonds(int nbonds, 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; @@ -751,7 +769,6 @@ real water_pol(int nbonds, 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); @@ -875,7 +892,7 @@ static real do_1_thole(const rvec xi, const rvec xj, rvec fi, rvec fj, 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 */ @@ -914,9 +931,10 @@ real thole_pol(int nbonds, 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); ) { @@ -931,7 +949,7 @@ real thole_pol(int 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); @@ -1716,10 +1734,9 @@ do_dih_fup_noshiftf(int i, int j, int k, int l, real ddphi, 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 */ @@ -1989,10 +2006,9 @@ pdihs_noener_simd(int nbonds, 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]; - 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; @@ -2013,8 +2029,6 @@ pdihs_noener_simd(int nbonds, 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); @@ -2119,10 +2133,9 @@ rbdihs_noener_simd(int nbonds, 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; + real *parm, *p, *q; gmx_simd_real_t phi_S; gmx_simd_real_t ddphi_S, cosfac_S; @@ -2145,8 +2158,6 @@ rbdihs_noener_simd(int nbonds, 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); @@ -2310,7 +2321,7 @@ real idihs(int nbonds, 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 @@ -2400,6 +2411,44 @@ static void posres_dx(const rvec x, const rvec pos0A, const rvec pos0B, } } +/*! \brief Computes forces and potential for flat-bottom cylindrical restraints. + * Returns the flat-bottom potential. */ +static real do_fbposres_cylinder(int fbdim, rvec fm, rvec dx, real rfb, real kk, gmx_bool bInvert) +{ + int d; + real dr, dr2, invdr, v, rfb2; + + dr2 = 0.0; + rfb2 = sqr(rfb); + v = 0.0; + + for (d = 0; d < DIM; d++) + { + if (d != fbdim) + { + dr2 += sqr(dx[d]); + } + } + + if (dr2 > 0.0 && + ( (dr2 > rfb2 && bInvert == FALSE ) || (dr2 < rfb2 && bInvert == TRUE ) ) + ) + { + dr = sqrt(dr2); + invdr = 1./dr; + v = 0.5*kk*sqr(dr - rfb); + for (d = 0; d < DIM; d++) + { + if (d != fbdim) + { + fm[d] = -kk*(dr-rfb)*dx[d]*invdr; /* Force pointing to the center */ + } + } + } + + return v; +} + /*! \brief Adds forces of flat-bottomed positions restraints to f[] * and fixes vir_diag. Returns the flat-bottomed potential. */ real fbposres(int nbonds, @@ -2412,8 +2461,8 @@ real fbposres(int nbonds, 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; + rvec com_sc, rdist, dx, dpdl, fm; gmx_bool bInvert; npbcdim = ePBC2npbcdim(ePBC); @@ -2474,19 +2523,22 @@ real fbposres(int nbonds, svmul(fact, dx, fm); } break; + case efbposresCYLINDERX: + /* cylindrical flat-bottom posres in y-z plane. fm[XX] = 0. */ + fbdim = XX; + v = do_fbposres_cylinder(fbdim, fm, dx, rfb, kk, bInvert); + break; + case efbposresCYLINDERY: + /* cylindrical flat-bottom posres in x-z plane. fm[YY] = 0. */ + fbdim = YY; + v = do_fbposres_cylinder(fbdim, fm, dx, rfb, kk, bInvert); + break; case efbposresCYLINDER: - /* cylidrical flat-bottom posres in x-y plane. fm[ZZ] = 0. */ - dr2 = sqr(dx[XX])+sqr(dx[YY]); - if (dr2 > 0.0 && - ( (dr2 > rfb2 && bInvert == FALSE ) || (dr2 < rfb2 && bInvert == TRUE ) ) - ) - { - dr = sqrt(dr2); - invdr = 1./dr; - v = 0.5*kk*sqr(dr - rfb); - fm[XX] = -kk*(dr-rfb)*dx[XX]*invdr; /* Force pointing to the center */ - fm[YY] = -kk*(dr-rfb)*dx[YY]*invdr; - } + /* equivalent to efbposresCYLINDERZ for backwards compatibility */ + case efbposresCYLINDERZ: + /* cylindrical flat-bottom posres in x-y plane. fm[ZZ] = 0. */ + fbdim = ZZ; + v = do_fbposres_cylinder(fbdim, fm, dx, rfb, kk, bInvert); break; case efbposresX: /* fbdim=XX */ case efbposresY: /* fbdim=YY */ @@ -2528,12 +2580,11 @@ real posres(int nbonds, 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! */ @@ -2726,7 +2777,7 @@ real dihres(int nbonds, 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; @@ -2833,7 +2884,6 @@ real restrangles(int nbonds, { 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; @@ -2961,7 +3011,7 @@ real restrdihs(int nbonds, 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. @@ -3072,7 +3122,7 @@ real cbtdihs(int nbonds, 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 @@ -3247,7 +3297,11 @@ real rbdihs(int nbonds, return vtot; } -int cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2) +//! \endcond + +/*! \brief Mysterious undocumented function */ +static int +cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2) { int im1, ip1, ip2; @@ -3286,14 +3340,16 @@ int cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *i } -real cmap_dihs(int nbonds, - const t_iatom forceatoms[], const t_iparams forceparams[], - const gmx_cmap_t *cmap_grid, - const rvec x[], rvec f[], rvec fshift[], - const t_pbc *pbc, const t_graph *g, - real gmx_unused lambda, real gmx_unused *dvdlambda, - const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd, - int gmx_unused *global_atom_index) +/*! \brief Compute CMAP dihedral energies and forces */ +static real +cmap_dihs(int nbonds, + const t_iatom forceatoms[], const t_iparams forceparams[], + const gmx_cmap_t *cmap_grid, + const rvec x[], rvec f[], rvec fshift[], + const t_pbc *pbc, const t_graph *g, + real gmx_unused lambda, real gmx_unused *dvdlambda, + const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd, + int gmx_unused *global_atom_index) { int i, j, k, n, idx; int ai, aj, ak, al, am; @@ -3302,13 +3358,13 @@ real cmap_dihs(int nbonds, 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; @@ -3370,7 +3426,7 @@ real cmap_dihs(int nbonds, 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 */ @@ -3431,7 +3487,7 @@ real cmap_dihs(int nbonds, 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 */ @@ -3496,8 +3552,8 @@ real cmap_dihs(int nbonds, 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(xphi1/dx); + iphi2 = static_cast(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); @@ -3562,9 +3618,6 @@ real cmap_dihs(int nbonds, e = 0; df1 = 0; df2 = 0; - ddf1 = 0; - ddf2 = 0; - ddf12 = 0; for (i = 3; i >= 0; i--) { @@ -3575,19 +3628,11 @@ real cmap_dihs(int nbonds, 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; @@ -3694,7 +3739,7 @@ real cmap_dihs(int nbonds, } - +//! \cond /*********************************************************** * * G R O M O S 9 6 F U N C T I O N S @@ -3953,7 +3998,7 @@ real cross_bond_angle(int nbonds, /* 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; @@ -3974,7 +4019,7 @@ real cross_bond_angle(int nbonds, /* 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); @@ -4032,7 +4077,7 @@ static real bonded_tab(const char *type, int table_nr, { 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; @@ -4040,7 +4085,7 @@ static real bonded_tab(const char *type, int table_nr, VFtab = table->data; rt = r*tabscale; - n0 = rt; + n0 = static_cast(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", @@ -4167,7 +4212,7 @@ real tab_angles(int nbonds, 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; @@ -4261,11 +4306,10 @@ real tab_dihs(int nbonds, 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) +//! \endcond + +gmx_bool +ftype_is_bonded_potential(int ftype) { return (interaction_function[ftype].flags & IF_BOND) && @@ -4273,173 +4317,7 @@ static gmx_inline gmx_bool ftype_is_bonded_potential(int ftype) (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<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<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<red_ashift); - fprintf(debug, "Reduction density %.2f density/#thread %.2f\n", - ctot*(1<red_ashift)/(double)fr->natoms_force, - ctot*(1<red_ashift)/(double)(fr->natoms_force*fr->nthreads)); - } -} - +/*! \brief Zero thread-local force-output buffers */ static void zero_thread_forces(f_thread_t *f_t, int n, int nblock, int blocksize) { @@ -4458,7 +4336,7 @@ static void zero_thread_forces(f_thread_t *f_t, int n, if (f_t->red_mask && (1U<f[a]); @@ -4487,15 +4365,16 @@ static void zero_thread_forces(f_thread_t *f_t, int n, } } +/*! \brief The max thread number is arbitrary, we used a fixed number + * to avoid memory management. Using more than 16 threads is probably + * never useful performance wise. */ +#define MAX_BONDED_THREADS 256 + +/*! \brief Reduce thread-local force buffers */ static void reduce_thread_force_buffer(int n, rvec *f, int nthreads, f_thread_t *f_t, int nblock, int block_size) { - /* The max thread number is arbitrary, - * we used a fixed number to avoid memory management. - * Using more than 16 threads is probably never useful performance wise. - */ -#define MAX_BONDED_THREADS 256 int b; if (nthreads > MAX_BONDED_THREADS) @@ -4528,7 +4407,7 @@ static void reduce_thread_force_buffer(int n, rvec *f, /* 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++) @@ -4540,6 +4419,7 @@ static void reduce_thread_force_buffer(int n, rvec *f, } } +/*! \brief Reduce thread-local forces */ static void reduce_thread_forces(int n, rvec *f, rvec *fshift, real *ener, gmx_grppairener_t *grpp, real *dvdl, int nthreads, f_thread_t *f_t, @@ -4597,9 +4477,11 @@ static void reduce_thread_forces(int n, rvec *f, rvec *fshift, } } -static real calc_one_bond(FILE *fplog, int thread, +/*! \brief Calculate one element of the list of bonded interactions + for this thread */ +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, @@ -4607,7 +4489,7 @@ static real calc_one_bond(FILE *fplog, int thread, real *lambda, real *dvdl, const t_mdatoms *md, t_fcdata *fcd, gmx_bool bCalcEnerVir, - int *global_atom_index, gmx_bool bPrintSepPot) + int *global_atom_index) { int nat1, nbonds, efptFTYPE; real v = 0; @@ -4636,7 +4518,7 @@ static real calc_one_bond(FILE *fplog, int thread, { 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); } @@ -4647,7 +4529,7 @@ static real calc_one_bond(FILE *fplog, int thread, /* 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; @@ -4664,7 +4546,7 @@ static real calc_one_bond(FILE *fplog, int thread, #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; @@ -4686,31 +4568,15 @@ static real calc_one_bond(FILE *fplog, int thread, { 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); } - if (bPrintSepPot) - { - fprintf(fplog, " %-23s #%4d V %12.5e dVdl %12.5e\n", - interaction_function[ftype].longname, - nbonds, v, lambda[efptFTYPE]); - } } 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); - - if (bPrintSepPot) - { - fprintf(fplog, " %-5s + %-15s #%4d dVdl %12.5e\n", - interaction_function[ftype].longname, - interaction_function[F_LJ14].longname, nbonds, dvdl[efptVDW]); - fprintf(fplog, " %-5s + %-15s #%4d dVdl %12.5e\n", - interaction_function[ftype].longname, - interaction_function[F_COUL14].longname, nbonds, dvdl[efptCOUL]); - } } if (thread == 0) @@ -4721,25 +4587,22 @@ static real calc_one_bond(FILE *fplog, int thread, return v; } -void calc_bonds(FILE *fplog, const gmx_multisim_t *ms, +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, + const struct t_pbc *pbc, const struct 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 bPrintSepPot, gmx_int64_t step) + 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); @@ -4758,11 +4621,6 @@ void calc_bonds(FILE *fplog, const gmx_multisim_t *ms, { pbc_null = NULL; } - if (bPrintSepPot) - { - fprintf(fplog, "Step %s: bonded V and dVdl for this rank\n", - gmx_step_str(step, buf)); - } #ifdef DEBUG if (g && debug) @@ -4777,14 +4635,14 @@ void calc_bonds(FILE *fplog, const gmx_multisim_t *ms, 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) @@ -4828,11 +4686,11 @@ void calc_bonds(FILE *fplog, const gmx_multisim_t *ms, { if (idef->il[ftype].nr > 0 && ftype_is_bonded_potential(ftype)) { - v = calc_one_bond(fplog, thread, ftype, idef, x, + v = calc_one_bond(thread, ftype, idef, x, ft, fshift, fr, pbc_null, g, grpp, nrnb, lambda, dvdlt, md, fcd, bCalcEnerVir, - global_atom_index, bPrintSepPot); + global_atom_index); epot[ftype] += v; } } @@ -4862,18 +4720,17 @@ void calc_bonds(FILE *fplog, const gmx_multisim_t *ms, } } -void calc_bonds_lambda(FILE *fplog, - const t_idef *idef, - rvec x[], +void calc_bonds_lambda(const t_idef *idef, + const rvec x[], t_forcerec *fr, - const t_pbc *pbc, const t_graph *g, + const struct t_pbc *pbc, const struct t_graph *g, gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb, real *lambda, const t_mdatoms *md, 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; @@ -4914,11 +4771,11 @@ void calc_bonds_lambda(FILE *fplog, if (nr - nr_nonperturbed > 0) { - v = calc_one_bond(fplog, 0, ftype, &idef_fe, + v = calc_one_bond(0, ftype, &idef_fe, x, f, fshift, fr, pbc_null, g, grpp, nrnb, lambda, dvdl_dum, md, fcd, TRUE, - global_atom_index, FALSE); + global_atom_index); epot[ftype] += v; } }