* 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 <config.h>
-#endif
+/*! \internal \file
+ *
+ * \brief This file defines functions necessary for mdrun and tools to
+ * compute energies and forces for bonded interactions.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_listed-forces
+ */
+#include "gmxpre.h"
+
+#include "bonded.h"
+
+#include "config.h"
-#include <math.h>
#include <assert.h>
-#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 <cmath>
+
+#include <algorithm>
+
+#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,
};
-
+/* 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;
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)
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;
}
}
-/* 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)
#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))
* 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[],
return vtot;
}
+//! \cond
real cubic_bonds(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[], rvec fshift[],
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;
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);
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 */
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); )
{
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);
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 */
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;
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);
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;
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);
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
}
}
+/*! \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,
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);
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 */
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! */
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;
{
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;
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.
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
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;
}
-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;
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;
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 */
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 */
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<int>(xphi1/dx);
+ iphi2 = static_cast<int>(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);
e = 0;
df1 = 0;
df2 = 0;
- ddf1 = 0;
- ddf2 = 0;
- ddf12 = 0;
for (i = 3; i >= 0; i--)
{
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;
}
-
+//! \cond
/***********************************************************
*
* G R O M O S 9 6 F U N C T I O N S
/* 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;
/* 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);
{
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;
VFtab = table->data;
rt = r*tabscale;
- n0 = rt;
+ n0 = static_cast<int>(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",
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;
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) &&
(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<<fr->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<<b))
- {
- fr->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<<fr->red_ashift);
- fprintf(debug, "Reduction density %.2f density/#thread %.2f\n",
- ctot*(1<<fr->red_ashift)/(double)fr->natoms_force,
- ctot*(1<<fr->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)
{
if (f_t->red_mask && (1U<<b))
{
a0 = b*blocksize;
- a1 = min((b+1)*blocksize, n);
+ a1 = std::min((b+1)*blocksize, n);
for (a = a0; a < a1; a++)
{
clear_rvec(f_t->f[a]);
}
}
+/*! \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)
/* 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++)
}
}
+/*! \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,
}
}
-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,
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;
{
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);
}
/* 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;
#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;
{
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)
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);
{
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)
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)
{
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;
}
}
}
}
-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;
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;
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff