*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020, 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.
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/pbcutil/ishift.h"
-#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/pbc_simd.h"
#include "gromacs/simd/simd.h"
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms* md,
/*! \brief Spreads and accumulates the bonded forces to the two atoms and adds the virial contribution when needed
*
- * When \p g==nullptr, \p shiftIndex is used as the periodic shift.
- * When \p g!=nullptr, the graph is used to compute the periodic shift.
+ * \p shiftIndex is used as the periodic shift.
*/
template<BondedKernelFlavor flavor>
-inline void spreadBondForces(const real bondForce,
- const rvec dx,
- const int ai,
- const int aj,
- rvec4* f,
- int shiftIndex,
- const t_graph* g,
- rvec* fshift)
+inline void spreadBondForces(const real bondForce,
+ const rvec dx,
+ const int ai,
+ const int aj,
+ rvec4* f,
+ int shiftIndex,
+ rvec* fshift)
{
- if (computeVirial(flavor) && g)
- {
- ivec dt;
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
- shiftIndex = IVEC2IS(dt);
- }
-
for (int m = 0; m < DIM; m++) /* 15 */
{
const real fij = bondForce * dx[m];
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
*dvdlambda += (cbB - cbA) * omtemp * omtemp
- (2 - 2 * omtemp) * omtemp * cb * ((b0B - b0A) * be - (beB - beA) * (dr - b0)); /* 15 */
- spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, g, fshift); /* 15 */
- } /* 83 TOTAL */
+ spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, fshift); /* 15 */
+ } /* 83 TOTAL */
return vtot;
}
rvec4 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,
vtot += vbond; /* 21 */
- spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, g, fshift); /* 15 */
- } /* 54 TOTAL */
+ spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, fshift); /* 15 */
+ } /* 54 TOTAL */
return vtot;
}
rvec4 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,
vtot += vbond; /* 35 */
- spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, g, fshift); /* 15 */
- } /* 58 TOTAL */
+ spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, fshift); /* 15 */
+ } /* 58 TOTAL */
return vtot;
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
vtot += vbond; /* 1*/
fbond *= gmx::invsqrt(dr2); /* 6 */
- spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, g, fshift); /* 15 */
- } /* 59 TOTAL */
+ spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, fshift); /* 15 */
+ } /* 59 TOTAL */
return vtot;
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
vtot += vbond; /* 1*/
fbond *= gmx::invsqrt(dr2); /* 6 */
- spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, g, fshift); /* 15 */
- } /* 59 TOTAL */
+ spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, fshift); /* 15 */
+ } /* 59 TOTAL */
return vtot;
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms* md,
vtot += vbond; /* 1*/
fbond *= gmx::invsqrt(dr2); /* 6 */
- spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, g, fshift); /* 15 */
- } /* 59 TOTAL */
+ spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, fshift); /* 15 */
+ } /* 59 TOTAL */
return vtot;
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms* md,
fbond *= gmx::invsqrt(dr2); /* 6 */
vtot += vbond; /* 1*/
- spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, g, fshift); /* 15 */
- } /* 72 TOTAL */
+ spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, fshift); /* 15 */
+ } /* 72 TOTAL */
return vtot;
}
rvec4 f[],
rvec gmx_unused fshift[],
const t_pbc gmx_unused* pbc,
- const t_graph gmx_unused* g,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
const t_mdatoms gmx_unused* md,
* three spatial dimensions in the molecular frame.
*/
int i, m, aO, aH1, aH2, aD, aS, type, type0, ki;
- ivec dt;
rvec dOH1, dOH2, dHH, dOD, dDS, nW, kk, dx, kdx, proj;
real vtot, fij, r_HH, r_OD, r_nW, tx, ty, tz, qS;
kdx[ZZ] = kk[ZZ] * dx[ZZ];
vtot += iprod(dx, kdx);
- if (computeVirial(flavor) && g)
- {
- ivec_sub(SHIFT_IVEC(g, aS), SHIFT_IVEC(g, aD), dt);
- ki = IVEC2IS(dt);
- }
-
for (m = 0; (m < DIM); m++)
{
/* This is a tensor operation but written out for speed */
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph gmx_unused* g,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
const t_mdatoms* md,
return V;
}
-// Avoid gcc 386 -O3 code generation bug in this function (see Redmine
+// Avoid gcc 386 -O3 code generation bug in this function (see Issue
// #3205 for more information)
#if defined(__GNUC__) && defined(__i386__) && defined(__OPTIMIZE__)
# pragma GCC push_options
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
int i, ai, aj, ak, t1, t2, type;
rvec r_ij, r_kj;
real cos_theta, cos_theta2, theta, dVdt, va, vtot;
- ivec jt, dt_ij, dt_kj;
vtot = 0.0;
for (i = 0; i < nbonds;)
}
if (computeVirial(flavor))
{
- if (g != nullptr)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
-
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- }
rvec_inc(fshift[t1], f_i);
rvec_inc(fshift[CENTRAL], f_j);
rvec_inc(fshift[t2], f_k);
rvec4 f[],
rvec gmx_unused fshift[],
const t_pbc* pbc,
- const t_graph gmx_unused* g,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
const t_mdatoms gmx_unused* md,
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
int i, m, ai, aj, ak, t1, t2, type;
rvec f_i, f_j, f_k;
real L1, kA, kB, aA, aB, dr, dr2, va, vtot, a, b, klin;
- ivec jt, dt_ij, dt_kj;
rvec r_ij, r_kj, r_ik, dx;
L1 = 1 - lambda;
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
-
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- }
rvec_inc(fshift[t1], f_i);
rvec_inc(fshift[CENTRAL], f_j);
rvec_inc(fshift[t2], f_k);
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
real cos_theta, cos_theta2, theta;
real dVdt, va, vtot, dr, dr2, vbond, fbond, fik;
real kthA, th0A, kUBA, r13A, kthB, th0B, kUBB, r13B;
- ivec jt, dt_ij, dt_kj, dt_ik;
vtot = 0.0;
for (i = 0; (i < nbonds);)
}
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
-
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- }
rvec_inc(fshift[t1], f_i);
rvec_inc(fshift[CENTRAL], f_j);
rvec_inc(fshift[t2], f_k);
vtot += vbond; /* 1*/
fbond *= gmx::invsqrt(dr2); /* 6 */
- if (computeVirial(flavor) && g)
- {
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, ak), dt_ik);
- ki = IVEC2IS(dt_ik);
- }
for (m = 0; (m < DIM); m++) /* 15 */
{
fik = fbond * r_ik[m];
rvec4 f[],
rvec gmx_unused fshift[],
const t_pbc* pbc,
- const t_graph gmx_unused* g,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
const t_mdatoms gmx_unused* md,
rvec4 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,
int i, j, ai, aj, ak, t1, t2, type;
rvec r_ij, r_kj;
real cos_theta, cos_theta2, theta, dt, dVdt, va, dtp, c, vtot;
- ivec jt, dt_ij, dt_kj;
vtot = 0.0;
for (i = 0; (i < nbonds);)
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
-
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- }
rvec_inc(fshift[t1], f_i);
rvec_inc(fshift[CENTRAL], f_j);
rvec_inc(fshift[t2], f_k);
} // namespace
template<BondedKernelFlavor flavor>
-void do_dih_fup(int i,
- int j,
- int k,
- int l,
- real ddphi,
- rvec r_ij,
- rvec r_kj,
- rvec r_kl,
- rvec m,
- rvec n,
- rvec4 f[],
- rvec fshift[],
- const t_pbc* pbc,
- const t_graph* g,
- const rvec x[],
- int t1,
- int t2,
- int t3)
+void do_dih_fup(int i,
+ int j,
+ int k,
+ int l,
+ real ddphi,
+ rvec r_ij,
+ rvec r_kj,
+ rvec r_kl,
+ rvec m,
+ rvec n,
+ rvec4 f[],
+ rvec fshift[],
+ const t_pbc* pbc,
+ const rvec x[],
+ int t1,
+ int t2,
+ int t3)
{
/* 143 FLOPS */
rvec f_i, f_j, f_k, f_l;
rvec uvec, vvec, svec, dx_jl;
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 */
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, j), jt);
- ivec_sub(SHIFT_IVEC(g, i), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, k), jt, dt_kj);
- ivec_sub(SHIFT_IVEC(g, l), jt, dt_lj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- t3 = IVEC2IS(dt_lj);
- }
- else if (pbc)
+ if (pbc)
{
t3 = pbc_rvec_sub(pbc, x[l], x[j], dx_jl);
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
} while (i < nbonds && forceatoms[i + 1] == ai && forceatoms[i + 2] == aj
&& forceatoms[i + 3] == ak && forceatoms[i + 4] == al);
- do_dih_fup<flavor>(ai, aj, ak, al, ddphi_tot, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, g, x,
- t1, t2, t3); /* 112 */
- } /* 223 TOTAL */
+ do_dih_fup<flavor>(ai, aj, ak, al, ddphi_tot, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1,
+ t2, t3); /* 112 */
+ } /* 223 TOTAL */
return vtot;
}
rvec4 f[],
rvec gmx_unused fshift[],
const t_pbc* pbc,
- const t_graph gmx_unused* g,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
const t_mdatoms gmx_unused* md,
rvec4 f[],
rvec gmx_unused fshift[],
const t_pbc* pbc,
- const t_graph gmx_unused* g,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
const t_mdatoms gmx_unused* md,
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
dvdl_term += 0.5 * (kB - kA) * dp2 - kk * dphi0 * dp;
- do_dih_fup<flavor>(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, g, x, t1,
+ do_dih_fup<flavor>(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1,
t2, t3); /* 112 */
/* 218 TOTAL */
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
gmx_bool bZAxis)
rvec r_ij, r_kl, f_i, f_k = { 0, 0, 0 };
real st, sth, nrij2, nrkl2, c, cij, ckl;
- ivec dt;
t2 = 0; /* avoid warning with gcc-3.3. It is never used uninitialized */
vtot = 0.0;
if (computeVirial(flavor))
{
- if (g)
- {
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
- t1 = IVEC2IS(dt);
- }
rvec_inc(fshift[t1], f_i);
rvec_dec(fshift[CENTRAL], f_i);
if (!bZAxis)
{
- if (g)
- {
- ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, al), dt);
- t2 = IVEC2IS(dt);
- }
rvec_inc(fshift[t2], f_k);
rvec_dec(fshift[CENTRAL], f_k);
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
t_fcdata gmx_unused* fcd,
int gmx_unused* global_atom_index)
{
- return low_angres<flavor>(nbonds, forceatoms, forceparams, x, f, fshift, pbc, g, lambda,
- dvdlambda, FALSE);
+ return low_angres<flavor>(nbonds, forceatoms, forceparams, x, f, fshift, pbc, lambda, dvdlambda, FALSE);
}
template<BondedKernelFlavor flavor>
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
t_fcdata gmx_unused* fcd,
int gmx_unused* global_atom_index)
{
- return low_angres<flavor>(nbonds, forceatoms, forceparams, x, f, fshift, pbc, g, lambda,
- dvdlambda, TRUE);
+ return low_angres<flavor>(nbonds, forceatoms, forceparams, x, f, fshift, pbc, lambda, dvdlambda, TRUE);
}
template<BondedKernelFlavor flavor>
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
{
*dvdlambda += kfac * ddp * ((dphiB - dphiA) - (phi0B - phi0A));
}
- do_dih_fup<flavor>(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, g, x,
- t1, t2, t3); /* 112 */
+ do_dih_fup<flavor>(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1,
+ t2, t3); /* 112 */
}
}
return vtot;
rvec4 gmx_unused f[],
rvec gmx_unused fshift[],
const t_pbc gmx_unused* pbc,
- const t_graph gmx_unused* g,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
const t_mdatoms gmx_unused* md,
rvec4 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,
int i, d, ai, aj, ak, type, m;
int t1, t2;
real v, vtot;
- ivec jt, dt_ij, dt_kj;
rvec f_i, f_j, f_k;
double prefactor, ratio_ante, ratio_post;
rvec delta_ante, delta_post, vec_temp;
real restrangles(int nbonds,
const t_iatom forceatoms[],const t_iparams forceparams[],
const rvec x[],rvec4 f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
+ const t_pbc *pbc,
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 t1, t2;
rvec r_ij,r_kj;
real v, vtot;
- ivec jt,dt_ij,dt_kj;
rvec f_i, f_j, f_k;
real prefactor, ratio_ante, ratio_post;
rvec delta_ante, delta_post, vec_temp;
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- }
-
rvec_inc(fshift[t1], f_i);
rvec_inc(fshift[CENTRAL], f_j);
rvec_inc(fshift[t2], f_k);
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real gmx_unused lambda,
real gmx_unused* dvlambda,
const t_mdatoms gmx_unused* md,
int i, d, type, ai, aj, ak, al;
rvec f_i, f_j, f_k, f_l;
rvec dx_jl;
- ivec jt, dt_ij, dt_kj, dt_lj;
int t1, t2, t3;
real v, vtot;
rvec delta_ante, delta_crnt, delta_post, vec_temp;
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- ivec_sub(SHIFT_IVEC(g, al), jt, dt_lj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- t3 = IVEC2IS(dt_lj);
- }
- else if (pbc)
+ if (pbc)
{
t3 = pbc_rvec_sub(pbc, x[al], x[aj], dx_jl);
}
rvec4 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,
real v, vtot;
rvec vec_temp;
rvec f_i, f_j, f_k, f_l;
- ivec jt, dt_ij, dt_kj, dt_lj;
rvec dx_jl;
rvec delta_ante, delta_crnt, delta_post;
rvec f_phi_ai, f_phi_aj, f_phi_ak, f_phi_al;
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- ivec_sub(SHIFT_IVEC(g, al), jt, dt_lj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- t3 = IVEC2IS(dt_lj);
- }
- else if (pbc)
+ if (pbc)
{
t3 = pbc_rvec_sub(pbc, x[al], x[aj], dx_jl);
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
ddphi = -ddphi * sin_phi; /* 11 */
- do_dih_fup<flavor>(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, g, x, t1,
- t2, t3); /* 112 */
+ do_dih_fup<flavor>(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1, t2,
+ t3); /* 112 */
vtot += v;
}
*dvdlambda += dvdl_term;
} // namespace
-real cmap_dihs(int nbonds,
- const t_iatom forceatoms[],
- const t_iparams forceparams[],
- const gmx_cmap_t* cmap_grid,
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const struct t_pbc* pbc,
- const struct t_graph* g,
+real cmap_dihs(int nbonds,
+ const t_iatom forceatoms[],
+ const t_iparams forceparams[],
+ const gmx_cmap_t* cmap_grid,
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const struct t_pbc* pbc,
real gmx_unused lambda,
real gmx_unused* dvdlambda,
const t_mdatoms gmx_unused* md,
rvec a1, b1, a2, b2;
rvec f1, g1, h1, f2, g2, h2;
rvec dtf1, dtg1, dth1, dtf2, dtg2, dth2;
- ivec jt1, dt1_ij, dt1_kj, dt1_lj;
- ivec jt2, dt2_ij, dt2_kj, dt2_lj;
int loop_index[4][4] = { { 0, 4, 8, 12 }, { 1, 5, 9, 13 }, { 2, 6, 10, 14 }, { 3, 7, 11, 15 } };
/* Shift forces */
if (fshift != nullptr)
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, a1j), jt1);
- ivec_sub(SHIFT_IVEC(g, a1i), jt1, dt1_ij);
- ivec_sub(SHIFT_IVEC(g, a1k), jt1, dt1_kj);
- ivec_sub(SHIFT_IVEC(g, a1l), jt1, dt1_lj);
- t11 = IVEC2IS(dt1_ij);
- t21 = IVEC2IS(dt1_kj);
- t31 = IVEC2IS(dt1_lj);
-
- copy_ivec(SHIFT_IVEC(g, a2j), jt2);
- ivec_sub(SHIFT_IVEC(g, a2i), jt2, dt2_ij);
- ivec_sub(SHIFT_IVEC(g, a2k), jt2, dt2_kj);
- ivec_sub(SHIFT_IVEC(g, a2l), jt2, dt2_lj);
- t12 = IVEC2IS(dt2_ij);
- t22 = IVEC2IS(dt2_kj);
- t32 = IVEC2IS(dt2_lj);
- }
- else if (pbc)
+ if (pbc)
{
t31 = pbc_rvec_sub(pbc, x[a1l], x[a1j], h1);
t32 = pbc_rvec_sub(pbc, x[a2l], x[a2j], h2);
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
vtot += 0.5 * vbond; /* 1*/
- spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, g, fshift); /* 15 */
- } /* 44 TOTAL */
+ spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, fshift); /* 15 */
+ } /* 44 TOTAL */
return vtot;
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
real cos_theta, dVdt, va, vtot;
real rij_1, rij_2, rkj_1, rkj_2, rijrkj_1;
rvec f_i, f_j, f_k;
- ivec jt, dt_ij, dt_kj;
vtot = 0.0;
for (i = 0; (i < nbonds);)
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
-
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- }
rvec_inc(fshift[t1], f_i);
rvec_inc(fshift[CENTRAL], f_j);
rvec_inc(fshift[t2], f_k); /* 9 */
rvec4 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,
rvec r_ij, r_kj;
real vtot, vrr, s1, s2, r1, r2, r1e, r2e, krr;
rvec f_i, f_j, f_k;
- ivec jt, dt_ij, dt_kj;
vtot = 0.0;
for (i = 0; (i < nbonds);)
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
-
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- }
rvec_inc(fshift[t1], f_i);
rvec_inc(fshift[CENTRAL], f_j);
rvec_inc(fshift[t2], f_k); /* 9 */
rvec4 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,
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;
- ivec jt, dt_ij, dt_kj;
vtot = 0.0;
for (i = 0; (i < nbonds);)
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
-
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- }
rvec_inc(fshift[t1], f_i);
rvec_inc(fshift[CENTRAL], f_j);
rvec_inc(fshift[t2], f_k); /* 9 */
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
vtot += vbond; /* 1*/
fbond *= gmx::invsqrt(dr2); /* 6 */
- spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, g, fshift); /* 15 */
- } /* 62 TOTAL */
+ spreadBondForces<flavor>(fbond, dx, ai, aj, f, ki, fshift); /* 15 */
+ } /* 62 TOTAL */
return vtot;
}
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
int i, ai, aj, ak, t1, t2, type, table;
rvec r_ij, r_kj;
real cos_theta, cos_theta2, theta, dVdt, va, vtot;
- ivec jt, dt_ij, dt_kj;
vtot = 0.0;
for (i = 0; (i < nbonds);)
if (computeVirial(flavor))
{
- if (g)
- {
- copy_ivec(SHIFT_IVEC(g, aj), jt);
-
- ivec_sub(SHIFT_IVEC(g, ai), jt, dt_ij);
- ivec_sub(SHIFT_IVEC(g, ak), jt, dt_kj);
- t1 = IVEC2IS(dt_ij);
- t2 = IVEC2IS(dt_kj);
- }
rvec_inc(fshift[t1], f_i);
rvec_inc(fshift[CENTRAL], f_j);
rvec_inc(fshift[t2], f_k);
rvec4 f[],
rvec fshift[],
const t_pbc* pbc,
- const t_graph* g,
real lambda,
real* dvdlambda,
const t_mdatoms gmx_unused* md,
forceparams[type].tab.kB, phi + M_PI, lambda, &vpd, &ddphi);
vtot += vpd;
- do_dih_fup<flavor>(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, g, x, t1,
+ do_dih_fup<flavor>(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n, f, fshift, pbc, x, t1,
t2, t3); /* 112 */
} /* 227 TOTAL */
} // namespace
-real calculateSimpleBond(const int ftype,
- const int numForceatoms,
- const t_iatom forceatoms[],
- const t_iparams forceparams[],
- const rvec x[],
- rvec4 f[],
- rvec fshift[],
- const struct t_pbc* pbc,
- const struct t_graph gmx_unused* g,
- const real lambda,
- real* dvdlambda,
- const t_mdatoms* md,
- t_fcdata* fcd,
+real calculateSimpleBond(const int ftype,
+ const int numForceatoms,
+ const t_iatom forceatoms[],
+ const t_iparams forceparams[],
+ const rvec x[],
+ rvec4 f[],
+ rvec fshift[],
+ const struct t_pbc* pbc,
+ const real lambda,
+ real* dvdlambda,
+ const t_mdatoms* md,
+ t_fcdata* fcd,
int gmx_unused* global_atom_index,
const BondedKernelFlavor bondedKernelFlavor)
{
const BondedInteractions& bonded = c_bondedInteractionFunctionsPerFlavor[bondedKernelFlavor][ftype];
- real v = bonded.function(numForceatoms, forceatoms, forceparams, x, f, fshift, pbc, g, lambda,
+ real v = bonded.function(numForceatoms, forceatoms, forceparams, x, f, fshift, pbc, lambda,
dvdlambda, md, fcd, global_atom_index);
return v;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff