-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
- *
- * If you want to redistribute modifications, 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 www.gromacs.org.
- *
+ *
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+ * Lesser General Public License for more details.
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+ * 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 papers on the package - you can find them in the top README file.
- *
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- *
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <math.h>
+#include <assert.h>
#include "physics.h"
#include "vec.h"
-#include "maths.h"
+#include "gromacs/math/utilities.h"
#include "txtdump.h"
#include "bondf.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
#include "pbc.h"
#include "ns.h"
#include "macros.h"
#include "orires.h"
#include "force.h"
#include "nonbonded.h"
-#include "mdrun.h"
+#include "restcbt.h"
+
+#include "gromacs/simd/simd.h"
+#include "gromacs/simd/simd_math.h"
+#include "gromacs/simd/vector_operations.h"
/* Find a better place for this? */
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,
-0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, -6, 0, 0, -6, 4 ,
-0, 0, 3, -2, 0, 0, 0, 0, 0, 0, -9, 6, 0, 0, 6, -4,
-0, 0, 0, 0, 1, 0, -3, 2, -2, 0, 6, -4, 1, 0, -3, 2 ,
-0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 3, -2, 1, 0, -3, 2 ,
-0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 2, 0, 0, 3, -2,
-0, 0, 0, 0, 0, 0, 3, -2, 0, 0, -6, 4, 0, 0, 3, -2,
-0, 1, -2, 1, 0, 0, 0, 0, 0, -3, 6, -3, 0, 2, -4, 2 ,
-0, 0, 0, 0, 0, 0, 0, 0, 0, 3, -6, 3, 0, -2, 4, -2,
-0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 3, 0, 0, 2, -2,
-0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 3, -3, 0, 0, -2, 2 ,
-0, 0, 0, 0, 0, 1, -2, 1, 0, -2, 4, -2, 0, 1, -2, 1,
-0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 2, -1, 0, 1, -2, 1,
-0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, -1, 1,
-0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 2, -2, 0, 0, -1, 1
+ 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,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, -6, 0, 0, -6, 4,
+ 0, 0, 3, -2, 0, 0, 0, 0, 0, 0, -9, 6, 0, 0, 6, -4,
+ 0, 0, 0, 0, 1, 0, -3, 2, -2, 0, 6, -4, 1, 0, -3, 2,
+ 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 3, -2, 1, 0, -3, 2,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 2, 0, 0, 3, -2,
+ 0, 0, 0, 0, 0, 0, 3, -2, 0, 0, -6, 4, 0, 0, 3, -2,
+ 0, 1, -2, 1, 0, 0, 0, 0, 0, -3, 6, -3, 0, 2, -4, 2,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, -6, 3, 0, -2, 4, -2,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 3, 0, 0, 2, -2,
+ 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 3, -3, 0, 0, -2, 2,
+ 0, 0, 0, 0, 0, 1, -2, 1, 0, -2, 4, -2, 0, 1, -2, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 2, -1, 0, 1, -2, 1,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, -1, 1,
+ 0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 2, -2, 0, 0, -1, 1
};
-int glatnr(int *global_atom_index,int i)
+int glatnr(int *global_atom_index, int i)
{
int atnr;
- if (global_atom_index == NULL) {
+ if (global_atom_index == NULL)
+ {
atnr = i + 1;
- } else {
+ }
+ else
+ {
atnr = global_atom_index[i] + 1;
}
return atnr;
}
-static int pbc_rvec_sub(const t_pbc *pbc,const rvec xi,const rvec xj,rvec dx)
+static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
+{
+ if (pbc)
+ {
+ return pbc_dx_aiuc(pbc, xi, xj, dx);
+ }
+ else
+ {
+ rvec_sub(xi, xj, dx);
+ return CENTRAL;
+ }
+}
+
+#ifdef GMX_SIMD_HAVE_REAL
+
+/* SIMD PBC data structure, containing 1/boxdiag and the box vectors */
+typedef struct {
+ gmx_simd_real_t inv_bzz;
+ gmx_simd_real_t inv_byy;
+ gmx_simd_real_t inv_bxx;
+ gmx_simd_real_t bzx;
+ gmx_simd_real_t bzy;
+ gmx_simd_real_t bzz;
+ gmx_simd_real_t byx;
+ gmx_simd_real_t byy;
+ gmx_simd_real_t bxx;
+} pbc_simd_t;
+
+/* 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;
+ int d;
+
+ /* Setting inv_bdiag to 0 effectively turns off PBC */
+ clear_rvec(inv_bdiag);
+ if (pbc != NULL)
+ {
+ for (d = 0; d < pbc->ndim_ePBC; d++)
+ {
+ inv_bdiag[d] = 1.0/pbc->box[d][d];
+ }
+ }
+
+ pbc_simd->inv_bzz = gmx_simd_set1_r(inv_bdiag[ZZ]);
+ pbc_simd->inv_byy = gmx_simd_set1_r(inv_bdiag[YY]);
+ pbc_simd->inv_bxx = gmx_simd_set1_r(inv_bdiag[XX]);
+
+ if (pbc != NULL)
+ {
+ pbc_simd->bzx = gmx_simd_set1_r(pbc->box[ZZ][XX]);
+ pbc_simd->bzy = gmx_simd_set1_r(pbc->box[ZZ][YY]);
+ pbc_simd->bzz = gmx_simd_set1_r(pbc->box[ZZ][ZZ]);
+ pbc_simd->byx = gmx_simd_set1_r(pbc->box[YY][XX]);
+ pbc_simd->byy = gmx_simd_set1_r(pbc->box[YY][YY]);
+ pbc_simd->bxx = gmx_simd_set1_r(pbc->box[XX][XX]);
+ }
+ else
+ {
+ pbc_simd->bzx = gmx_simd_setzero_r();
+ pbc_simd->bzy = gmx_simd_setzero_r();
+ pbc_simd->bzz = gmx_simd_setzero_r();
+ pbc_simd->byx = gmx_simd_setzero_r();
+ pbc_simd->byy = gmx_simd_setzero_r();
+ pbc_simd->bxx = gmx_simd_setzero_r();
+ }
+}
+
+/* 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)
{
- if (pbc) {
- return pbc_dx_aiuc(pbc,xi,xj,dx);
- }
- else {
- rvec_sub(xi,xj,dx);
- return CENTRAL;
- }
+ gmx_simd_real_t sh;
+
+ sh = gmx_simd_round_r(gmx_simd_mul_r(*dz, pbc->inv_bzz));
+ *dx = gmx_simd_fnmadd_r(sh, pbc->bzx, *dx);
+ *dy = gmx_simd_fnmadd_r(sh, pbc->bzy, *dy);
+ *dz = gmx_simd_fnmadd_r(sh, pbc->bzz, *dz);
+
+ sh = gmx_simd_round_r(gmx_simd_mul_r(*dy, pbc->inv_byy));
+ *dx = gmx_simd_fnmadd_r(sh, pbc->byx, *dx);
+ *dy = gmx_simd_fnmadd_r(sh, pbc->byy, *dy);
+
+ sh = gmx_simd_round_r(gmx_simd_mul_r(*dx, pbc->inv_bxx));
+ *dx = gmx_simd_fnmadd_r(sh, pbc->bxx, *dx);
}
+#endif /* GMX_SIMD_HAVE_REAL */
+
/*
* Morse potential bond by Frank Everdij
*
*/
real morse_bonds(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdl,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- const real one=1.0;
- const real two=2.0;
- real dr,dr2,temp,omtemp,cbomtemp,fbond,vbond,fij,b0,be,cb,vtot;
- rvec dx;
- int i,m,ki,type,ai,aj;
- ivec dt;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
-
- b0 = forceparams[type].morse.b0;
- be = forceparams[type].morse.beta;
- cb = forceparams[type].morse.cb;
-
- ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx); /* 3 */
- dr2 = iprod(dx,dx); /* 5 */
- dr = dr2*gmx_invsqrt(dr2); /* 10 */
- temp = exp(-be*(dr-b0)); /* 12 */
-
- if (temp == one)
- continue;
-
- omtemp = one-temp; /* 1 */
- cbomtemp = cb*omtemp; /* 1 */
- vbond = cbomtemp*omtemp; /* 1 */
- fbond = -two*be*temp*cbomtemp*gmx_invsqrt(dr2); /* 9 */
- vtot += vbond; /* 1 */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
- ki = IVEC2IS(dt);
- }
-
- for (m=0; (m<DIM); m++) { /* 15 */
- fij=fbond*dx[m];
- f[ai][m]+=fij;
- f[aj][m]-=fij;
- fshift[ki][m]+=fij;
- fshift[CENTRAL][m]-=fij;
- }
- } /* 58 TOTAL */
- return vtot;
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ const real one = 1.0;
+ const real two = 2.0;
+ real dr, dr2, temp, omtemp, cbomtemp, fbond, vbond, fij, vtot;
+ real b0, be, cb, b0A, beA, cbA, b0B, beB, cbB, L1;
+ rvec dx;
+ int i, m, ki, type, ai, aj;
+ ivec dt;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+
+ b0A = forceparams[type].morse.b0A;
+ beA = forceparams[type].morse.betaA;
+ cbA = forceparams[type].morse.cbA;
+
+ b0B = forceparams[type].morse.b0B;
+ beB = forceparams[type].morse.betaB;
+ cbB = forceparams[type].morse.cbB;
+
+ L1 = one-lambda; /* 1 */
+ b0 = L1*b0A + lambda*b0B; /* 3 */
+ be = L1*beA + lambda*beB; /* 3 */
+ cb = L1*cbA + lambda*cbB; /* 3 */
+
+ ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
+ dr2 = iprod(dx, dx); /* 5 */
+ dr = dr2*gmx_invsqrt(dr2); /* 10 */
+ temp = exp(-be*(dr-b0)); /* 12 */
+
+ if (temp == one)
+ {
+ /* bonds are constrainted. This may _not_ include bond constraints if they are lambda dependent */
+ *dvdlambda += cbB-cbA;
+ continue;
+ }
+
+ omtemp = one-temp; /* 1 */
+ cbomtemp = cb*omtemp; /* 1 */
+ vbond = cbomtemp*omtemp; /* 1 */
+ fbond = -two*be*temp*cbomtemp*gmx_invsqrt(dr2); /* 9 */
+ vtot += vbond; /* 1 */
+
+ *dvdlambda += (cbB - cbA) * omtemp * omtemp - (2-2*omtemp)*omtemp * cb * ((b0B-b0A)*be - (beB-beA)*(dr-b0)); /* 15 */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ ki = IVEC2IS(dt);
+ }
+
+ for (m = 0; (m < DIM); m++) /* 15 */
+ {
+ fij = fbond*dx[m];
+ f[ai][m] += fij;
+ f[aj][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
+ }
+ } /* 83 TOTAL */
+ return vtot;
}
real cubic_bonds(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdl,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- const real three = 3.0;
- const real two = 2.0;
- real kb,b0,kcub;
- real dr,dr2,dist,kdist,kdist2,fbond,vbond,fij,vtot;
- rvec dx;
- int i,m,ki,type,ai,aj;
- ivec dt;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
-
- b0 = forceparams[type].cubic.b0;
- kb = forceparams[type].cubic.kb;
- kcub = forceparams[type].cubic.kcub;
-
- ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx); /* 3 */
- dr2 = iprod(dx,dx); /* 5 */
-
- if (dr2 == 0.0)
- continue;
-
- dr = dr2*gmx_invsqrt(dr2); /* 10 */
- dist = dr-b0;
- kdist = kb*dist;
- kdist2 = kdist*dist;
-
- vbond = kdist2 + kcub*kdist2*dist;
- fbond = -(two*kdist + three*kdist2*kcub)/dr;
-
- vtot += vbond; /* 21 */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
- ki=IVEC2IS(dt);
- }
- for (m=0; (m<DIM); m++) { /* 15 */
- fij=fbond*dx[m];
- f[ai][m]+=fij;
- f[aj][m]-=fij;
- fshift[ki][m]+=fij;
- fshift[CENTRAL][m]-=fij;
- }
- } /* 54 TOTAL */
- return vtot;
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ 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)
+{
+ const real three = 3.0;
+ const real two = 2.0;
+ real kb, b0, kcub;
+ real dr, dr2, dist, kdist, kdist2, fbond, vbond, fij, vtot;
+ rvec dx;
+ int i, m, ki, type, ai, aj;
+ ivec dt;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+
+ b0 = forceparams[type].cubic.b0;
+ kb = forceparams[type].cubic.kb;
+ kcub = forceparams[type].cubic.kcub;
+
+ ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
+ dr2 = iprod(dx, dx); /* 5 */
+
+ if (dr2 == 0.0)
+ {
+ continue;
+ }
+
+ dr = dr2*gmx_invsqrt(dr2); /* 10 */
+ dist = dr-b0;
+ kdist = kb*dist;
+ kdist2 = kdist*dist;
+
+ vbond = kdist2 + kcub*kdist2*dist;
+ fbond = -(two*kdist + three*kdist2*kcub)/dr;
+
+ vtot += vbond; /* 21 */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ ki = IVEC2IS(dt);
+ }
+ for (m = 0; (m < DIM); m++) /* 15 */
+ {
+ fij = fbond*dx[m];
+ f[ai][m] += fij;
+ f[aj][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
+ }
+ } /* 54 TOTAL */
+ return vtot;
}
real FENE_bonds(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdl,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- const real half=0.5;
- const real one=1.0;
- real bm,kb;
- real dr,dr2,bm2,omdr2obm2,fbond,vbond,fij,vtot;
- rvec dx;
- int i,m,ki,type,ai,aj;
- ivec dt;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
-
- bm = forceparams[type].fene.bm;
- kb = forceparams[type].fene.kb;
-
- ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx); /* 3 */
- dr2 = iprod(dx,dx); /* 5 */
-
- if (dr2 == 0.0)
- continue;
-
- bm2 = bm*bm;
-
- if (dr2 >= bm2)
- gmx_fatal(FARGS,
- "r^2 (%f) >= bm^2 (%f) in FENE bond between atoms %d and %d",
- dr2,bm2,
- glatnr(global_atom_index,ai),
- glatnr(global_atom_index,aj));
-
- omdr2obm2 = one - dr2/bm2;
-
- vbond = -half*kb*bm2*log(omdr2obm2);
- fbond = -kb/omdr2obm2;
-
- vtot += vbond; /* 35 */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
- ki=IVEC2IS(dt);
- }
- for (m=0; (m<DIM); m++) { /* 15 */
- fij=fbond*dx[m];
- f[ai][m]+=fij;
- f[aj][m]-=fij;
- fshift[ki][m]+=fij;
- fshift[CENTRAL][m]-=fij;
- }
- } /* 58 TOTAL */
- return vtot;
-}
-
-real harmonic(real kA,real kB,real xA,real xB,real x,real lambda,
- real *V,real *F)
-{
- const real half=0.5;
- real L1,kk,x0,dx,dx2;
- real v,f,dvdl;
-
- L1 = 1.0-lambda;
- kk = L1*kA+lambda*kB;
- x0 = L1*xA+lambda*xB;
-
- dx = x-x0;
- dx2 = dx*dx;
-
- f = -kk*dx;
- v = half*kk*dx2;
- dvdl = half*(kB-kA)*dx2 + (xA-xB)*kk*dx;
-
- *F = f;
- *V = v;
-
- return dvdl;
-
- /* That was 19 flops */
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ 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 *global_atom_index)
+{
+ const real half = 0.5;
+ const real one = 1.0;
+ real bm, kb;
+ real dr, dr2, bm2, omdr2obm2, fbond, vbond, fij, vtot;
+ rvec dx;
+ int i, m, ki, type, ai, aj;
+ ivec dt;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+
+ bm = forceparams[type].fene.bm;
+ kb = forceparams[type].fene.kb;
+
+ ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
+ dr2 = iprod(dx, dx); /* 5 */
+
+ if (dr2 == 0.0)
+ {
+ continue;
+ }
+
+ bm2 = bm*bm;
+
+ if (dr2 >= bm2)
+ {
+ gmx_fatal(FARGS,
+ "r^2 (%f) >= bm^2 (%f) in FENE bond between atoms %d and %d",
+ dr2, bm2,
+ glatnr(global_atom_index, ai),
+ glatnr(global_atom_index, aj));
+ }
+
+ omdr2obm2 = one - dr2/bm2;
+
+ vbond = -half*kb*bm2*log(omdr2obm2);
+ fbond = -kb/omdr2obm2;
+
+ vtot += vbond; /* 35 */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ ki = IVEC2IS(dt);
+ }
+ for (m = 0; (m < DIM); m++) /* 15 */
+ {
+ fij = fbond*dx[m];
+ f[ai][m] += fij;
+ f[aj][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
+ }
+ } /* 58 TOTAL */
+ return vtot;
+}
+
+real harmonic(real kA, real kB, real xA, real xB, real x, real lambda,
+ real *V, real *F)
+{
+ const real half = 0.5;
+ real L1, kk, x0, dx, dx2;
+ real v, f, dvdlambda;
+
+ L1 = 1.0-lambda;
+ kk = L1*kA+lambda*kB;
+ x0 = L1*xA+lambda*xB;
+
+ dx = x-x0;
+ dx2 = dx*dx;
+
+ f = -kk*dx;
+ v = half*kk*dx2;
+ dvdlambda = half*(kB-kA)*dx2 + (xA-xB)*kk*dx;
+
+ *F = f;
+ *V = v;
+
+ return dvdlambda;
+
+ /* That was 19 flops */
}
real bonds(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,m,ki,ai,aj,type;
- real dr,dr2,fbond,vbond,fij,vtot;
- rvec dx;
- ivec dt;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
-
- ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx); /* 3 */
- dr2 = iprod(dx,dx); /* 5 */
- dr = dr2*gmx_invsqrt(dr2); /* 10 */
-
- *dvdlambda += harmonic(forceparams[type].harmonic.krA,
- forceparams[type].harmonic.krB,
- forceparams[type].harmonic.rA,
- forceparams[type].harmonic.rB,
- dr,lambda,&vbond,&fbond); /* 19 */
-
- if (dr2 == 0.0)
- continue;
-
-
- vtot += vbond;/* 1*/
- fbond *= gmx_invsqrt(dr2); /* 6 */
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ int i, m, ki, ai, aj, type;
+ real dr, dr2, fbond, vbond, fij, vtot;
+ rvec dx;
+ ivec dt;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+
+ ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
+ dr2 = iprod(dx, dx); /* 5 */
+ dr = dr2*gmx_invsqrt(dr2); /* 10 */
+
+ *dvdlambda += harmonic(forceparams[type].harmonic.krA,
+ forceparams[type].harmonic.krB,
+ forceparams[type].harmonic.rA,
+ forceparams[type].harmonic.rB,
+ dr, lambda, &vbond, &fbond); /* 19 */
+
+ if (dr2 == 0.0)
+ {
+ continue;
+ }
+
+
+ vtot += vbond; /* 1*/
+ fbond *= gmx_invsqrt(dr2); /* 6 */
#ifdef DEBUG
- if (debug)
- fprintf(debug,"BONDS: dr = %10g vbond = %10g fbond = %10g\n",
- dr,vbond,fbond);
+ if (debug)
+ {
+ fprintf(debug, "BONDS: dr = %10g vbond = %10g fbond = %10g\n",
+ dr, vbond, fbond);
+ }
#endif
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
- ki=IVEC2IS(dt);
- }
- for (m=0; (m<DIM); m++) { /* 15 */
- fij=fbond*dx[m];
- f[ai][m]+=fij;
- f[aj][m]-=fij;
- fshift[ki][m]+=fij;
- fshift[CENTRAL][m]-=fij;
- }
- } /* 59 TOTAL */
- return vtot;
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ ki = IVEC2IS(dt);
+ }
+ for (m = 0; (m < DIM); m++) /* 15 */
+ {
+ fij = fbond*dx[m];
+ f[ai][m] += fij;
+ f[aj][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
+ }
+ } /* 59 TOTAL */
+ return vtot;
}
real restraint_bonds(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,m,ki,ai,aj,type;
- real dr,dr2,fbond,vbond,fij,vtot;
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ int i, m, ki, ai, aj, type;
+ real dr, dr2, fbond, vbond, fij, vtot;
real L1;
- real low,dlow,up1,dup1,up2,dup2,k,dk;
- real drh,drh2;
+ real low, dlow, up1, dup1, up2, dup2, k, dk;
+ real drh, drh2;
rvec dx;
ivec dt;
L1 = 1.0 - lambda;
vtot = 0.0;
- for(i=0; (i<nbonds); )
+ for (i = 0; (i < nbonds); )
{
type = forceatoms[i++];
ai = forceatoms[i++];
aj = forceatoms[i++];
-
- ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx); /* 3 */
- dr2 = iprod(dx,dx); /* 5 */
- dr = dr2*gmx_invsqrt(dr2); /* 10 */
+
+ ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
+ dr2 = iprod(dx, dx); /* 5 */
+ dr = dr2*gmx_invsqrt(dr2); /* 10 */
low = L1*forceparams[type].restraint.lowA + lambda*forceparams[type].restraint.lowB;
dlow = -forceparams[type].restraint.lowA + forceparams[type].restraint.lowB;
if (dr < low)
{
- drh = dr - low;
- drh2 = drh*drh;
- vbond = 0.5*k*drh2;
- fbond = -k*drh;
+ drh = dr - low;
+ drh2 = drh*drh;
+ vbond = 0.5*k*drh2;
+ fbond = -k*drh;
*dvdlambda += 0.5*dk*drh2 - k*dlow*drh;
} /* 11 */
else if (dr <= up1)
}
else if (dr <= up2)
{
- drh = dr - up1;
- drh2 = drh*drh;
- vbond = 0.5*k*drh2;
- fbond = -k*drh;
+ drh = dr - up1;
+ drh2 = drh*drh;
+ vbond = 0.5*k*drh2;
+ fbond = -k*drh;
*dvdlambda += 0.5*dk*drh2 - k*dup1*drh;
} /* 11 */
else
{
- drh = dr - up2;
- vbond = k*(up2 - up1)*(0.5*(up2 - up1) + drh);
- fbond = -k*(up2 - up1);
+ drh = dr - up2;
+ vbond = k*(up2 - up1)*(0.5*(up2 - up1) + drh);
+ fbond = -k*(up2 - up1);
*dvdlambda += dk*(up2 - up1)*(0.5*(up2 - up1) + drh)
+ k*(dup2 - dup1)*(up2 - up1 + drh)
- k*(up2 - up1)*dup2;
}
-
+
if (dr2 == 0.0)
+ {
continue;
-
- vtot += vbond;/* 1*/
- fbond *= gmx_invsqrt(dr2); /* 6 */
+ }
+
+ vtot += vbond; /* 1*/
+ fbond *= gmx_invsqrt(dr2); /* 6 */
#ifdef DEBUG
if (debug)
- fprintf(debug,"BONDS: dr = %10g vbond = %10g fbond = %10g\n",
- dr,vbond,fbond);
+ {
+ fprintf(debug, "BONDS: dr = %10g vbond = %10g fbond = %10g\n",
+ dr, vbond, fbond);
+ }
#endif
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
- ki=IVEC2IS(dt);
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ ki = IVEC2IS(dt);
}
- for (m=0; (m<DIM); m++) { /* 15 */
- fij=fbond*dx[m];
- f[ai][m]+=fij;
- f[aj][m]-=fij;
- fshift[ki][m]+=fij;
- fshift[CENTRAL][m]-=fij;
+ for (m = 0; (m < DIM); m++) /* 15 */
+ {
+ fij = fbond*dx[m];
+ f[ai][m] += fij;
+ f[aj][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
}
- } /* 59 TOTAL */
+ } /* 59 TOTAL */
return vtot;
}
real polarize(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,m,ki,ai,aj,type;
- real dr,dr2,fbond,vbond,fij,vtot,ksh;
- rvec dx;
- ivec dt;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ksh = sqr(md->chargeA[aj])*ONE_4PI_EPS0/forceparams[type].polarize.alpha;
- if (debug)
- fprintf(debug,"POL: local ai = %d aj = %d ksh = %.3f\n",ai,aj,ksh);
-
- ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx); /* 3 */
- dr2 = iprod(dx,dx); /* 5 */
- dr = dr2*gmx_invsqrt(dr2); /* 10 */
-
- *dvdlambda += harmonic(ksh,ksh,0,0,dr,lambda,&vbond,&fbond); /* 19 */
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const t_pbc *pbc, const t_graph *g,
+ real lambda, real *dvdlambda,
+ const t_mdatoms *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ int i, m, ki, ai, aj, type;
+ real dr, dr2, fbond, vbond, fij, vtot, ksh;
+ rvec dx;
+ ivec dt;
- if (dr2 == 0.0)
- continue;
-
- vtot += vbond;/* 1*/
- fbond *= gmx_invsqrt(dr2); /* 6 */
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ksh = sqr(md->chargeA[aj])*ONE_4PI_EPS0/forceparams[type].polarize.alpha;
+ if (debug)
+ {
+ fprintf(debug, "POL: local ai = %d aj = %d ksh = %.3f\n", ai, aj, ksh);
+ }
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
- ki=IVEC2IS(dt);
- }
- for (m=0; (m<DIM); m++) { /* 15 */
- fij=fbond*dx[m];
- f[ai][m]+=fij;
- f[aj][m]-=fij;
- fshift[ki][m]+=fij;
- fshift[CENTRAL][m]-=fij;
- }
- } /* 59 TOTAL */
- return vtot;
-}
+ ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
+ dr2 = iprod(dx, dx); /* 5 */
+ dr = dr2*gmx_invsqrt(dr2); /* 10 */
-real water_pol(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- /* This routine implements anisotropic polarizibility for water, through
- * a shell connected to a dummy with spring constant that differ in the
- * three spatial dimensions in the molecular frame.
- */
- int i,m,aO,aH1,aH2,aD,aS,type,type0;
- rvec dOH1,dOH2,dHH,dOD,dDS,nW,kk,dx,kdx,proj;
-#ifdef DEBUG
- rvec df;
-#endif
- real vtot,fij,r_HH,r_OD,r_nW,tx,ty,tz,qS;
-
- vtot = 0.0;
- if (nbonds > 0) {
- type0 = forceatoms[0];
- aS = forceatoms[5];
- qS = md->chargeA[aS];
- kk[XX] = sqr(qS)*ONE_4PI_EPS0/forceparams[type0].wpol.al_x;
- 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);
- fprintf(debug,"WPOL: kk = %10.3f %10.3f %10.3f\n",
- kk[XX],kk[YY],kk[ZZ]);
- fprintf(debug,"WPOL: rOH = %10.3f rHH = %10.3f rOD = %10.3f\n",
- forceparams[type0].wpol.rOH,
- forceparams[type0].wpol.rHH,
- forceparams[type0].wpol.rOD);
- }
- for(i=0; (i<nbonds); i+=6) {
- type = forceatoms[i];
- if (type != type0)
- gmx_fatal(FARGS,"Sorry, type = %d, type0 = %d, file = %s, line = %d",
- type,type0,__FILE__,__LINE__);
- aO = forceatoms[i+1];
- aH1 = forceatoms[i+2];
- aH2 = forceatoms[i+3];
- aD = forceatoms[i+4];
- aS = forceatoms[i+5];
-
- /* Compute vectors describing the water frame */
- rvec_sub(x[aH1],x[aO], dOH1);
- rvec_sub(x[aH2],x[aO], dOH2);
- rvec_sub(x[aH2],x[aH1],dHH);
- rvec_sub(x[aD], x[aO], dOD);
- rvec_sub(x[aS], x[aD], dDS);
- cprod(dOH1,dOH2,nW);
-
- /* Compute inverse length of normal vector
- * (this one could be precomputed, but I'm too lazy now)
- */
- r_nW = gmx_invsqrt(iprod(nW,nW));
- /* This is for precision, but does not make a big difference,
- * it can go later.
- */
- r_OD = gmx_invsqrt(iprod(dOD,dOD));
-
- /* Normalize the vectors in the water frame */
- svmul(r_nW,nW,nW);
- svmul(r_HH,dHH,dHH);
- svmul(r_OD,dOD,dOD);
-
- /* Compute displacement of shell along components of the vector */
- dx[ZZ] = iprod(dDS,dOD);
- /* Compute projection on the XY plane: dDS - dx[ZZ]*dOD */
- for(m=0; (m<DIM); m++)
- proj[m] = dDS[m]-dx[ZZ]*dOD[m];
-
- /*dx[XX] = iprod(dDS,nW);
- dx[YY] = iprod(dDS,dHH);*/
- dx[XX] = iprod(proj,nW);
- for(m=0; (m<DIM); m++)
- proj[m] -= dx[XX]*nW[m];
- dx[YY] = iprod(proj,dHH);
- /*#define DEBUG*/
-#ifdef DEBUG
- if (debug) {
- fprintf(debug,"WPOL: dx2=%10g dy2=%10g dz2=%10g sum=%10g dDS^2=%10g\n",
- sqr(dx[XX]),sqr(dx[YY]),sqr(dx[ZZ]),iprod(dx,dx),iprod(dDS,dDS));
- fprintf(debug,"WPOL: dHH=(%10g,%10g,%10g)\n",dHH[XX],dHH[YY],dHH[ZZ]);
- fprintf(debug,"WPOL: dOD=(%10g,%10g,%10g), 1/r_OD = %10g\n",
- dOD[XX],dOD[YY],dOD[ZZ],1/r_OD);
- fprintf(debug,"WPOL: nW =(%10g,%10g,%10g), 1/r_nW = %10g\n",
- nW[XX],nW[YY],nW[ZZ],1/r_nW);
- fprintf(debug,"WPOL: dx =%10g, dy =%10g, dz =%10g\n",
- dx[XX],dx[YY],dx[ZZ]);
- fprintf(debug,"WPOL: dDSx=%10g, dDSy=%10g, dDSz=%10g\n",
- dDS[XX],dDS[YY],dDS[ZZ]);
- }
-#endif
- /* Now compute the forces and energy */
- kdx[XX] = kk[XX]*dx[XX];
- kdx[YY] = kk[YY]*dx[YY];
- kdx[ZZ] = kk[ZZ]*dx[ZZ];
- vtot += iprod(dx,kdx);
- for(m=0; (m<DIM); m++) {
- /* This is a tensor operation but written out for speed */
- tx = nW[m]*kdx[XX];
- ty = dHH[m]*kdx[YY];
- tz = dOD[m]*kdx[ZZ];
- fij = -tx-ty-tz;
-#ifdef DEBUG
- df[m] = fij;
-#endif
- f[aS][m] += fij;
- f[aD][m] -= fij;
- }
-#ifdef DEBUG
- if (debug) {
- fprintf(debug,"WPOL: vwpol=%g\n",0.5*iprod(dx,kdx));
- fprintf(debug,"WPOL: df = (%10g, %10g, %10g)\n",df[XX],df[YY],df[ZZ]);
- }
-#endif
- }
- }
- return 0.5*vtot;
-}
-
-static real do_1_thole(const rvec xi,const rvec xj,rvec fi,rvec fj,
- const t_pbc *pbc,real qq,
- rvec fshift[],real afac)
-{
- rvec r12;
- real r12sq,r12_1,r12n,r12bar,v0,v1,fscal,ebar,fff;
- int m,t;
-
- t = pbc_rvec_sub(pbc,xi,xj,r12); /* 3 */
-
- r12sq = iprod(r12,r12); /* 5 */
- r12_1 = gmx_invsqrt(r12sq); /* 5 */
- r12bar = afac/r12_1; /* 5 */
- v0 = qq*ONE_4PI_EPS0*r12_1; /* 2 */
- ebar = exp(-r12bar); /* 5 */
- v1 = (1-(1+0.5*r12bar)*ebar); /* 4 */
- fscal = ((v0*r12_1)*v1 - v0*0.5*afac*ebar*(r12bar+1))*r12_1; /* 9 */
- if (debug)
- fprintf(debug,"THOLE: v0 = %.3f v1 = %.3f r12= % .3f r12bar = %.3f fscal = %.3f ebar = %.3f\n",v0,v1,1/r12_1,r12bar,fscal,ebar);
-
- for(m=0; (m<DIM); m++) {
- fff = fscal*r12[m];
- fi[m] += fff;
- fj[m] -= fff;
- fshift[t][m] += fff;
- fshift[CENTRAL][m] -= fff;
- } /* 15 */
-
- return v0*v1; /* 1 */
- /* 54 */
-}
+ *dvdlambda += harmonic(ksh, ksh, 0, 0, dr, lambda, &vbond, &fbond); /* 19 */
-real thole_pol(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *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;
-
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- a1 = forceatoms[i++];
- da1 = forceatoms[i++];
- a2 = forceatoms[i++];
- da2 = forceatoms[i++];
- q1 = md->chargeA[da1];
- q2 = md->chargeA[da2];
- a = forceparams[type].thole.a;
- al1 = forceparams[type].thole.alpha1;
- al2 = forceparams[type].thole.alpha2;
- qq = q1*q2;
- afac = a*pow(al1*al2,-1.0/6.0);
- 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);
- V += do_1_thole(x[da1],x[da2],f[da1],f[da2],pbc, qq,fshift,afac);
- }
- /* 290 flops */
- return V;
-}
-
-real bond_angle(const rvec xi,const rvec xj,const rvec xk,const t_pbc *pbc,
- rvec r_ij,rvec r_kj,real *costh,
- int *t1,int *t2)
-/* Return value is the angle between the bonds i-j and j-k */
-{
- /* 41 FLOPS */
- real th;
-
- *t1 = pbc_rvec_sub(pbc,xi,xj,r_ij); /* 3 */
- *t2 = pbc_rvec_sub(pbc,xk,xj,r_kj); /* 3 */
+ if (dr2 == 0.0)
+ {
+ continue;
+ }
- *costh=cos_angle(r_ij,r_kj); /* 25 */
- th=acos(*costh); /* 10 */
- /* 41 TOTAL */
- return th;
-}
+ vtot += vbond; /* 1*/
+ fbond *= gmx_invsqrt(dr2); /* 6 */
-real angles(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- 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); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
-
- theta = bond_angle(x[ai],x[aj],x[ak],pbc,
- r_ij,r_kj,&cos_theta,&t1,&t2); /* 41 */
-
- *dvdlambda += harmonic(forceparams[type].harmonic.krA,
- forceparams[type].harmonic.krB,
- forceparams[type].harmonic.rA*DEG2RAD,
- forceparams[type].harmonic.rB*DEG2RAD,
- theta,lambda,&va,&dVdt); /* 21 */
- vtot += va;
-
- cos_theta2 = sqr(cos_theta);
- if (cos_theta2 < 1) {
- int m;
- real st,sth;
- real cik,cii,ckk;
- real nrkj2,nrij2;
- rvec f_i,f_j,f_k;
-
- st = dVdt*gmx_invsqrt(1 - cos_theta2); /* 12 */
- sth = st*cos_theta; /* 1 */
-#ifdef DEBUG
- if (debug)
- fprintf(debug,"ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
- theta*RAD2DEG,va,dVdt);
-#endif
- nrkj2=iprod(r_kj,r_kj); /* 5 */
- nrij2=iprod(r_ij,r_ij);
-
- cik=st*gmx_invsqrt(nrkj2*nrij2); /* 12 */
- cii=sth/nrij2; /* 10 */
- ckk=sth/nrkj2; /* 10 */
-
- for (m=0; (m<DIM); m++) { /* 39 */
- f_i[m]=-(cik*r_kj[m]-cii*r_ij[m]);
- f_k[m]=-(cik*r_ij[m]-ckk*r_kj[m]);
- f_j[m]=-f_i[m]-f_k[m];
- f[ai][m]+=f_i[m];
- f[aj][m]+=f_j[m];
- f[ak][m]+=f_k[m];
- }
- 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);
- } /* 161 TOTAL */
- }
- return vtot;
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ ki = IVEC2IS(dt);
+ }
+ for (m = 0; (m < DIM); m++) /* 15 */
+ {
+ fij = fbond*dx[m];
+ f[ai][m] += fij;
+ f[aj][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
+ }
+ } /* 59 TOTAL */
+ return vtot;
}
-real urey_bradley(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,m,ai,aj,ak,t1,t2,type,ki;
- rvec r_ij,r_kj,r_ik;
- real cos_theta,cos_theta2,theta;
- real dVdt,va,vtot,kth,th0,kUB,r13,dr,dr2,vbond,fbond,fik;
- ivec jt,dt_ij,dt_kj,dt_ik;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
- th0 = forceparams[type].u_b.theta*DEG2RAD;
- kth = forceparams[type].u_b.ktheta;
- r13 = forceparams[type].u_b.r13;
- kUB = forceparams[type].u_b.kUB;
-
- theta = bond_angle(x[ai],x[aj],x[ak],pbc,
- r_ij,r_kj,&cos_theta,&t1,&t2); /* 41 */
-
- *dvdlambda += harmonic(kth,kth,th0,th0,theta,lambda,&va,&dVdt); /* 21 */
- vtot += va;
-
- ki = pbc_rvec_sub(pbc,x[ai],x[ak],r_ik); /* 3 */
- dr2 = iprod(r_ik,r_ik); /* 5 */
- dr = dr2*gmx_invsqrt(dr2); /* 10 */
-
- *dvdlambda += harmonic(kUB,kUB,r13,r13,dr,lambda,&vbond,&fbond); /* 19 */
-
- cos_theta2 = sqr(cos_theta); /* 1 */
- if (cos_theta2 < 1) {
- real st,sth;
- real cik,cii,ckk;
- real nrkj2,nrij2;
- rvec f_i,f_j,f_k;
-
- st = dVdt*gmx_invsqrt(1 - cos_theta2); /* 12 */
- sth = st*cos_theta; /* 1 */
-#ifdef DEBUG
- if (debug)
- fprintf(debug,"ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
- theta*RAD2DEG,va,dVdt);
-#endif
- nrkj2=iprod(r_kj,r_kj); /* 5 */
- nrij2=iprod(r_ij,r_ij);
-
- cik=st*gmx_invsqrt(nrkj2*nrij2); /* 12 */
- cii=sth/nrij2; /* 10 */
- ckk=sth/nrkj2; /* 10 */
-
- for (m=0; (m<DIM); m++) { /* 39 */
- f_i[m]=-(cik*r_kj[m]-cii*r_ij[m]);
- f_k[m]=-(cik*r_ij[m]-ckk*r_kj[m]);
- f_j[m]=-f_i[m]-f_k[m];
- f[ai][m]+=f_i[m];
- f[aj][m]+=f_j[m];
- f[ak][m]+=f_k[m];
- }
- 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);
- } /* 161 TOTAL */
- /* Time for the bond calculations */
- if (dr2 == 0.0)
- continue;
-
- vtot += vbond; /* 1*/
- fbond *= gmx_invsqrt(dr2); /* 6 */
-
- if (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];
- f[ai][m]+=fik;
- f[ak][m]-=fik;
- fshift[ki][m]+=fik;
- fshift[CENTRAL][m]-=fik;
- }
- }
- return vtot;
-}
+real anharm_polarize(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const t_pbc *pbc, const t_graph *g,
+ real lambda, real *dvdlambda,
+ const t_mdatoms *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ int i, m, ki, ai, aj, type;
+ real dr, dr2, fbond, vbond, fij, vtot, ksh, khyp, drcut, ddr, ddr3;
+ rvec dx;
+ ivec dt;
-real quartic_angles(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- 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); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
-
- theta = bond_angle(x[ai],x[aj],x[ak],pbc,
- r_ij,r_kj,&cos_theta,&t1,&t2); /* 41 */
-
- dt = theta - forceparams[type].qangle.theta*DEG2RAD; /* 2 */
-
- dVdt = 0;
- va = forceparams[type].qangle.c[0];
- dtp = 1.0;
- for(j=1; j<=4; j++) {
- c = forceparams[type].qangle.c[j];
- dVdt -= j*c*dtp;
- dtp *= dt;
- va += c*dtp;
- }
- /* 20 */
-
- vtot += va;
-
- cos_theta2 = sqr(cos_theta); /* 1 */
- if (cos_theta2 < 1) {
- int m;
- real st,sth;
- real cik,cii,ckk;
- real nrkj2,nrij2;
- rvec f_i,f_j,f_k;
-
- st = dVdt*gmx_invsqrt(1 - cos_theta2); /* 12 */
- sth = st*cos_theta; /* 1 */
-#ifdef DEBUG
- if (debug)
- fprintf(debug,"ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
- theta*RAD2DEG,va,dVdt);
-#endif
- nrkj2=iprod(r_kj,r_kj); /* 5 */
- nrij2=iprod(r_ij,r_ij);
-
- cik=st*gmx_invsqrt(nrkj2*nrij2); /* 12 */
- cii=sth/nrij2; /* 10 */
- ckk=sth/nrkj2; /* 10 */
-
- for (m=0; (m<DIM); m++) { /* 39 */
- f_i[m]=-(cik*r_kj[m]-cii*r_ij[m]);
- f_k[m]=-(cik*r_ij[m]-ckk*r_kj[m]);
- f_j[m]=-f_i[m]-f_k[m];
- f[ai][m]+=f_i[m];
- f[aj][m]+=f_j[m];
- f[ak][m]+=f_k[m];
- }
- 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);
- } /* 153 TOTAL */
- }
- return vtot;
-}
-
-real dih_angle(const rvec xi,const rvec xj,const rvec xk,const rvec xl,
- const t_pbc *pbc,
- rvec r_ij,rvec r_kj,rvec r_kl,rvec m,rvec n,
- real *sign,int *t1,int *t2,int *t3)
-{
- real ipr,phi;
-
- *t1 = pbc_rvec_sub(pbc,xi,xj,r_ij); /* 3 */
- *t2 = pbc_rvec_sub(pbc,xk,xj,r_kj); /* 3 */
- *t3 = pbc_rvec_sub(pbc,xk,xl,r_kl); /* 3 */
-
- cprod(r_ij,r_kj,m); /* 9 */
- cprod(r_kj,r_kl,n); /* 9 */
- phi=gmx_angle(m,n); /* 49 (assuming 25 for atan2) */
- ipr=iprod(r_ij,n); /* 5 */
- (*sign)=(ipr<0.0)?-1.0:1.0;
- phi=(*sign)*phi; /* 1 */
- /* 82 TOTAL */
- return phi;
-}
-
-
-
-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,rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- 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;
- real a,p,q,toler;
- ivec jt,dt_ij,dt_kj,dt_lj;
-
- iprm = iprod(m,m); /* 5 */
- iprn = iprod(n,n); /* 5 */
- nrkj2 = iprod(r_kj,r_kj); /* 5 */
- toler = nrkj2*GMX_REAL_EPS;
- if ((iprm > toler) && (iprn > toler)) {
- nrkj = nrkj2*gmx_invsqrt(nrkj2); /* 10 */
- a = -ddphi*nrkj/iprm; /* 11 */
- svmul(a,m,f_i); /* 3 */
- a = ddphi*nrkj/iprn; /* 11 */
- svmul(a,n,f_l); /* 3 */
- p = iprod(r_ij,r_kj); /* 5 */
- p /= nrkj2; /* 10 */
- q = iprod(r_kl,r_kj); /* 5 */
- q /= nrkj2; /* 10 */
- svmul(p,f_i,uvec); /* 3 */
- svmul(q,f_l,vvec); /* 3 */
- rvec_sub(uvec,vvec,svec); /* 3 */
- rvec_sub(f_i,svec,f_j); /* 3 */
- rvec_add(f_l,svec,f_k); /* 3 */
- rvec_inc(f[i],f_i); /* 3 */
- rvec_dec(f[j],f_j); /* 3 */
- rvec_dec(f[k],f_k); /* 3 */
- rvec_inc(f[l],f_l); /* 3 */
-
- 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) {
- t3 = pbc_rvec_sub(pbc,x[l],x[j],dx_jl);
- } else {
- t3 = CENTRAL;
- }
-
- rvec_inc(fshift[t1],f_i);
- rvec_dec(fshift[CENTRAL],f_j);
- rvec_dec(fshift[t2],f_k);
- rvec_inc(fshift[t3],f_l);
- }
- /* 112 TOTAL */
-}
-
-
-real dopdihs(real cpA,real cpB,real phiA,real phiB,int mult,
- real phi,real lambda,real *V,real *F)
-{
- real v,dvdl,mdphi,v1,sdphi,ddphi;
- real L1 = 1.0 - lambda;
- real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD;
- real dph0 = (phiB - phiA)*DEG2RAD;
- real cp = L1*cpA + lambda*cpB;
-
- mdphi = mult*phi - ph0;
- sdphi = sin(mdphi);
- ddphi = -cp*mult*sdphi;
- v1 = 1.0 + cos(mdphi);
- v = cp*v1;
-
- dvdl = (cpB - cpA)*v1 + cp*dph0*sdphi;
-
- *V = v;
- *F = ddphi;
-
- return dvdl;
-
- /* That was 40 flops */
-}
-
-static real dopdihs_min(real cpA,real cpB,real phiA,real phiB,int mult,
- real phi,real lambda,real *V,real *F)
- /* similar to dopdihs, except for a minus sign *
- * and a different treatment of mult/phi0 */
-{
- real v,dvdl,mdphi,v1,sdphi,ddphi;
- real L1 = 1.0 - lambda;
- real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD;
- real dph0 = (phiB - phiA)*DEG2RAD;
- real cp = L1*cpA + lambda*cpB;
-
- mdphi = mult*(phi-ph0);
- sdphi = sin(mdphi);
- ddphi = cp*mult*sdphi;
- v1 = 1.0-cos(mdphi);
- v = cp*v1;
-
- dvdl = (cpB-cpA)*v1 + cp*dph0*sdphi;
-
- *V = v;
- *F = ddphi;
-
- return dvdl;
-
- /* That was 40 flops */
-}
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ksh = sqr(md->chargeA[aj])*ONE_4PI_EPS0/forceparams[type].anharm_polarize.alpha; /* 7*/
+ khyp = forceparams[type].anharm_polarize.khyp;
+ drcut = forceparams[type].anharm_polarize.drcut;
+ if (debug)
+ {
+ fprintf(debug, "POL: local ai = %d aj = %d ksh = %.3f\n", ai, aj, ksh);
+ }
-real pdihs(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,type,ai,aj,ak,al;
- int t1,t2,t3;
- rvec r_ij,r_kj,r_kl,m,n;
- real phi,sign,ddphi,vpd,vtot;
-
- vtot = 0.0;
-
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
- al = forceatoms[i++];
-
- phi=dih_angle(x[ai],x[aj],x[ak],x[al],pbc,r_ij,r_kj,r_kl,m,n,
- &sign,&t1,&t2,&t3); /* 84 */
-
- *dvdlambda += dopdihs(forceparams[type].pdihs.cpA,
- forceparams[type].pdihs.cpB,
- forceparams[type].pdihs.phiA,
- forceparams[type].pdihs.phiB,
- forceparams[type].pdihs.mult,
- phi,lambda,&vpd,&ddphi);
-
- vtot += vpd;
- 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 */
+ ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
+ dr2 = iprod(dx, dx); /* 5 */
+ dr = dr2*gmx_invsqrt(dr2); /* 10 */
-#ifdef DEBUG
- fprintf(debug,"pdih: (%d,%d,%d,%d) phi=%g\n",
- ai,aj,ak,al,phi);
-#endif
- } /* 223 TOTAL */
+ *dvdlambda += harmonic(ksh, ksh, 0, 0, dr, lambda, &vbond, &fbond); /* 19 */
- return vtot;
-}
+ if (dr2 == 0.0)
+ {
+ continue;
+ }
+ if (dr > drcut)
+ {
+ ddr = dr-drcut;
+ ddr3 = ddr*ddr*ddr;
+ vbond += khyp*ddr*ddr3;
+ fbond -= 4*khyp*ddr3;
+ }
+ fbond *= gmx_invsqrt(dr2); /* 6 */
+ vtot += vbond; /* 1*/
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ ki = IVEC2IS(dt);
+ }
+ for (m = 0; (m < DIM); m++) /* 15 */
+ {
+ fij = fbond*dx[m];
+ f[ai][m] += fij;
+ f[aj][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
+ }
+ } /* 72 TOTAL */
+ return vtot;
+}
-real idihs(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,type,ai,aj,ak,al;
- int t1,t2,t3;
- real phi,phi0,dphi0,ddphi,sign,vtot;
- rvec r_ij,r_kj,r_kl,m,n;
- real L1,kk,dp,dp2,kA,kB,pA,pB,dvdl;
-
- L1 = 1.0-lambda;
- dvdl = 0;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
- al = forceatoms[i++];
-
- phi=dih_angle(x[ai],x[aj],x[ak],x[al],pbc,r_ij,r_kj,r_kl,m,n,
- &sign,&t1,&t2,&t3); /* 84 */
-
- /* phi can jump if phi0 is close to Pi/-Pi, which will cause huge
- * force changes if we just apply a normal harmonic.
- * Instead, we first calculate phi-phi0 and take it modulo (-Pi,Pi).
- * This means we will never have the periodicity problem, unless
- * the dihedral is Pi away from phiO, which is very unlikely due to
- * the potential.
+real water_pol(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ /* This routine implements anisotropic polarizibility for water, through
+ * a shell connected to a dummy with spring constant that differ in the
+ * three spatial dimensions in the molecular frame.
*/
- kA = forceparams[type].harmonic.krA;
- kB = forceparams[type].harmonic.krB;
- pA = forceparams[type].harmonic.rA;
- pB = forceparams[type].harmonic.rB;
-
- kk = L1*kA + lambda*kB;
- phi0 = (L1*pA + lambda*pB)*DEG2RAD;
- dphi0 = (pB - pA)*DEG2RAD;
-
- /* dp = (phi-phi0), modulo (-pi,pi) */
- dp = phi-phi0;
- /* dp cannot be outside (-2*pi,2*pi) */
- if (dp >= M_PI)
- dp -= 2*M_PI;
- else if(dp < -M_PI)
- dp += 2*M_PI;
-
- dp2 = dp*dp;
-
- vtot += 0.5*kk*dp2;
- ddphi = -kk*dp;
-
- dvdl += 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,
- f,fshift,pbc,g,x,t1,t2,t3); /* 112 */
- /* 217 TOTAL */
+ int i, m, aO, aH1, aH2, aD, aS, type, type0, ki;
+ ivec dt;
+ rvec dOH1, dOH2, dHH, dOD, dDS, nW, kk, dx, kdx, proj;
#ifdef DEBUG
- if (debug)
- fprintf(debug,"idih: (%d,%d,%d,%d) phi=%g\n",
- ai,aj,ak,al,phi);
+ rvec df;
#endif
- }
-
- *dvdlambda += dvdl;
- return vtot;
-}
-
-
-real posres(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec vir_diag,
- t_pbc *pbc,
- real lambda,real *dvdlambda,
- int refcoord_scaling,int ePBC,rvec comA,rvec comB)
-{
- int i,ai,m,d,type,ki,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;
-
- npbcdim = ePBC2npbcdim(ePBC);
+ real vtot, fij, r_HH, r_OD, r_nW, tx, ty, tz, qS;
- if (refcoord_scaling == erscCOM)
+ vtot = 0.0;
+ if (nbonds > 0)
{
- clear_rvec(comA_sc);
- clear_rvec(comB_sc);
- for(m=0; m<npbcdim; m++)
+ type0 = forceatoms[0];
+ aS = forceatoms[5];
+ qS = md->chargeA[aS];
+ kk[XX] = sqr(qS)*ONE_4PI_EPS0/forceparams[type0].wpol.al_x;
+ 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);
+ fprintf(debug, "WPOL: kk = %10.3f %10.3f %10.3f\n",
+ kk[XX], kk[YY], kk[ZZ]);
+ fprintf(debug, "WPOL: rOH = %10.3f rHH = %10.3f rOD = %10.3f\n",
+ forceparams[type0].wpol.rOH,
+ forceparams[type0].wpol.rHH,
+ forceparams[type0].wpol.rOD);
+ }
+ for (i = 0; (i < nbonds); i += 6)
{
- for(d=m; d<npbcdim; d++)
+ type = forceatoms[i];
+ if (type != type0)
{
- comA_sc[m] += comA[d]*pbc->box[d][m];
- comB_sc[m] += comB[d]*pbc->box[d][m];
+ gmx_fatal(FARGS, "Sorry, type = %d, type0 = %d, file = %s, line = %d",
+ type, type0, __FILE__, __LINE__);
+ }
+ aO = forceatoms[i+1];
+ aH1 = forceatoms[i+2];
+ aH2 = forceatoms[i+3];
+ aD = forceatoms[i+4];
+ aS = forceatoms[i+5];
+
+ /* Compute vectors describing the water frame */
+ pbc_rvec_sub(pbc, x[aH1], x[aO], dOH1);
+ pbc_rvec_sub(pbc, x[aH2], x[aO], dOH2);
+ pbc_rvec_sub(pbc, x[aH2], x[aH1], dHH);
+ pbc_rvec_sub(pbc, x[aD], x[aO], dOD);
+ ki = pbc_rvec_sub(pbc, x[aS], x[aD], dDS);
+ cprod(dOH1, dOH2, nW);
+
+ /* Compute inverse length of normal vector
+ * (this one could be precomputed, but I'm too lazy now)
+ */
+ r_nW = gmx_invsqrt(iprod(nW, nW));
+ /* This is for precision, but does not make a big difference,
+ * it can go later.
+ */
+ r_OD = gmx_invsqrt(iprod(dOD, dOD));
+
+ /* Normalize the vectors in the water frame */
+ svmul(r_nW, nW, nW);
+ svmul(r_HH, dHH, dHH);
+ svmul(r_OD, dOD, dOD);
+
+ /* Compute displacement of shell along components of the vector */
+ dx[ZZ] = iprod(dDS, dOD);
+ /* Compute projection on the XY plane: dDS - dx[ZZ]*dOD */
+ for (m = 0; (m < DIM); m++)
+ {
+ proj[m] = dDS[m]-dx[ZZ]*dOD[m];
+ }
+
+ /*dx[XX] = iprod(dDS,nW);
+ dx[YY] = iprod(dDS,dHH);*/
+ dx[XX] = iprod(proj, nW);
+ for (m = 0; (m < DIM); m++)
+ {
+ proj[m] -= dx[XX]*nW[m];
+ }
+ dx[YY] = iprod(proj, dHH);
+ /*#define DEBUG*/
+#ifdef DEBUG
+ if (debug)
+ {
+ fprintf(debug, "WPOL: dx2=%10g dy2=%10g dz2=%10g sum=%10g dDS^2=%10g\n",
+ sqr(dx[XX]), sqr(dx[YY]), sqr(dx[ZZ]), iprod(dx, dx), iprod(dDS, dDS));
+ fprintf(debug, "WPOL: dHH=(%10g,%10g,%10g)\n", dHH[XX], dHH[YY], dHH[ZZ]);
+ fprintf(debug, "WPOL: dOD=(%10g,%10g,%10g), 1/r_OD = %10g\n",
+ dOD[XX], dOD[YY], dOD[ZZ], 1/r_OD);
+ fprintf(debug, "WPOL: nW =(%10g,%10g,%10g), 1/r_nW = %10g\n",
+ nW[XX], nW[YY], nW[ZZ], 1/r_nW);
+ fprintf(debug, "WPOL: dx =%10g, dy =%10g, dz =%10g\n",
+ dx[XX], dx[YY], dx[ZZ]);
+ fprintf(debug, "WPOL: dDSx=%10g, dDSy=%10g, dDSz=%10g\n",
+ dDS[XX], dDS[YY], dDS[ZZ]);
+ }
+#endif
+ /* Now compute the forces and energy */
+ kdx[XX] = kk[XX]*dx[XX];
+ kdx[YY] = kk[YY]*dx[YY];
+ kdx[ZZ] = kk[ZZ]*dx[ZZ];
+ vtot += iprod(dx, kdx);
+
+ if (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 */
+ tx = nW[m]*kdx[XX];
+ ty = dHH[m]*kdx[YY];
+ tz = dOD[m]*kdx[ZZ];
+ fij = -tx-ty-tz;
+#ifdef DEBUG
+ df[m] = fij;
+#endif
+ f[aS][m] += fij;
+ f[aD][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
+ }
+#ifdef DEBUG
+ if (debug)
+ {
+ fprintf(debug, "WPOL: vwpol=%g\n", 0.5*iprod(dx, kdx));
+ fprintf(debug, "WPOL: df = (%10g, %10g, %10g)\n", df[XX], df[YY], df[ZZ]);
}
+#endif
}
}
+ return 0.5*vtot;
+}
- L1 = 1.0 - lambda;
+static real do_1_thole(const rvec xi, const rvec xj, rvec fi, rvec fj,
+ const t_pbc *pbc, real qq,
+ rvec fshift[], real afac)
+{
+ rvec r12;
+ real r12sq, r12_1, r12n, r12bar, v0, v1, fscal, ebar, fff;
+ int m, t;
+
+ t = pbc_rvec_sub(pbc, xi, xj, r12); /* 3 */
+
+ r12sq = iprod(r12, r12); /* 5 */
+ r12_1 = gmx_invsqrt(r12sq); /* 5 */
+ r12bar = afac/r12_1; /* 5 */
+ v0 = qq*ONE_4PI_EPS0*r12_1; /* 2 */
+ ebar = exp(-r12bar); /* 5 */
+ v1 = (1-(1+0.5*r12bar)*ebar); /* 4 */
+ fscal = ((v0*r12_1)*v1 - v0*0.5*afac*ebar*(r12bar+1))*r12_1; /* 9 */
+ if (debug)
+ {
+ fprintf(debug, "THOLE: v0 = %.3f v1 = %.3f r12= % .3f r12bar = %.3f fscal = %.3f ebar = %.3f\n", v0, v1, 1/r12_1, r12bar, fscal, ebar);
+ }
+
+ for (m = 0; (m < DIM); m++)
+ {
+ fff = fscal*r12[m];
+ fi[m] += fff;
+ fj[m] -= fff;
+ fshift[t][m] += fff;
+ fshift[CENTRAL][m] -= fff;
+ } /* 15 */
+
+ return v0*v1; /* 1 */
+ /* 54 */
+}
+
+real thole_pol(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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, t_fcdata gmx_unused *fcd,
+ 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;
+
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ a1 = forceatoms[i++];
+ da1 = forceatoms[i++];
+ a2 = forceatoms[i++];
+ da2 = forceatoms[i++];
+ q1 = md->chargeA[da1];
+ q2 = md->chargeA[da2];
+ a = forceparams[type].thole.a;
+ al1 = forceparams[type].thole.alpha1;
+ al2 = forceparams[type].thole.alpha2;
+ qq = q1*q2;
+ afac = a*pow(al1*al2, -1.0/6.0);
+ 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);
+ V += do_1_thole(x[da1], x[da2], f[da1], f[da2], pbc, qq, fshift, afac);
+ }
+ /* 290 flops */
+ return V;
+}
+
+real bond_angle(const rvec xi, const rvec xj, const rvec xk, const t_pbc *pbc,
+ rvec r_ij, rvec r_kj, real *costh,
+ int *t1, int *t2)
+/* Return value is the angle between the bonds i-j and j-k */
+{
+ /* 41 FLOPS */
+ real th;
+
+ *t1 = pbc_rvec_sub(pbc, xi, xj, r_ij); /* 3 */
+ *t2 = pbc_rvec_sub(pbc, xk, xj, r_kj); /* 3 */
+
+ *costh = cos_angle(r_ij, r_kj); /* 25 */
+ th = acos(*costh); /* 10 */
+ /* 41 TOTAL */
+ return th;
+}
+
+real angles(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ 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); )
+ for (i = 0; i < nbonds; )
{
type = forceatoms[i++];
ai = forceatoms[i++];
- pr = &forceparams[type];
-
- for(m=0; m<DIM; m++)
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+
+ theta = bond_angle(x[ai], x[aj], x[ak], pbc,
+ r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
+
+ *dvdlambda += harmonic(forceparams[type].harmonic.krA,
+ forceparams[type].harmonic.krB,
+ forceparams[type].harmonic.rA*DEG2RAD,
+ forceparams[type].harmonic.rB*DEG2RAD,
+ theta, lambda, &va, &dVdt); /* 21 */
+ vtot += va;
+
+ cos_theta2 = sqr(cos_theta);
+ if (cos_theta2 < 1)
{
- posA = forceparams[type].posres.pos0A[m];
- posB = forceparams[type].posres.pos0B[m];
- if (m < npbcdim)
+ int m;
+ real st, sth;
+ real cik, cii, ckk;
+ real nrkj2, nrij2;
+ real nrkj_1, nrij_1;
+ rvec f_i, f_j, f_k;
+
+ st = dVdt*gmx_invsqrt(1 - cos_theta2); /* 12 */
+ sth = st*cos_theta; /* 1 */
+#ifdef DEBUG
+ if (debug)
{
- switch (refcoord_scaling)
- {
- case erscNO:
- ref = 0;
- rdist[m] = L1*posA + lambda*posB;
- dpdl[m] = posB - posA;
- break;
- case erscALL:
- /* Box relative coordinates are stored for dimensions with pbc */
- posA *= pbc->box[m][m];
- posB *= pbc->box[m][m];
- for(d=m+1; d<npbcdim; d++)
- {
- posA += forceparams[type].posres.pos0A[d]*pbc->box[d][m];
- posB += forceparams[type].posres.pos0B[d]*pbc->box[d][m];
- }
- ref = L1*posA + lambda*posB;
- rdist[m] = 0;
- dpdl[m] = posB - posA;
- break;
- case erscCOM:
- ref = L1*comA_sc[m] + lambda*comB_sc[m];
- rdist[m] = L1*posA + lambda*posB;
- dpdl[m] = comB_sc[m] - comA_sc[m] + posB - posA;
- break;
- }
+ fprintf(debug, "ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
+ theta*RAD2DEG, va, dVdt);
+ }
+#endif
+ nrij2 = iprod(r_ij, r_ij); /* 5 */
+ nrkj2 = iprod(r_kj, r_kj); /* 5 */
+
+ nrij_1 = gmx_invsqrt(nrij2); /* 10 */
+ nrkj_1 = gmx_invsqrt(nrkj2); /* 10 */
+
+ cik = st*nrij_1*nrkj_1; /* 2 */
+ cii = sth*nrij_1*nrij_1; /* 2 */
+ ckk = sth*nrkj_1*nrkj_1; /* 2 */
+
+ for (m = 0; m < DIM; m++)
+ { /* 39 */
+ f_i[m] = -(cik*r_kj[m] - cii*r_ij[m]);
+ f_k[m] = -(cik*r_ij[m] - ckk*r_kj[m]);
+ f_j[m] = -f_i[m] - f_k[m];
+ f[ai][m] += f_i[m];
+ f[aj][m] += f_j[m];
+ f[ak][m] += f_k[m];
}
- else
+ if (g != NULL)
{
- ref = L1*posA + lambda*posB;
- rdist[m] = 0;
- dpdl[m] = posB - posA;
+ 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);
+ } /* 161 TOTAL */
+ }
+
+ return vtot;
+}
+
+#ifdef GMX_SIMD_HAVE_REAL
+
+/* As angles, but using SIMD to calculate many dihedrals at once.
+ * This routines does not calculate energies and shift forces.
+ */
+static gmx_inline void
+angles_noener_simd(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const t_pbc *pbc, const t_graph gmx_unused *g,
+ real gmx_unused lambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ const int nfa1 = 4;
+ int i, iu, s, m;
+ int type, ai[GMX_SIMD_REAL_WIDTH], aj[GMX_SIMD_REAL_WIDTH];
+ int ak[GMX_SIMD_REAL_WIDTH];
+ real coeff_array[2*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *coeff;
+ real dr_array[2*DIM*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *dr;
+ real f_buf_array[6*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *f_buf;
+ gmx_simd_real_t k_S, theta0_S;
+ gmx_simd_real_t rijx_S, rijy_S, rijz_S;
+ gmx_simd_real_t rkjx_S, rkjy_S, rkjz_S;
+ gmx_simd_real_t one_S;
+ gmx_simd_real_t min_one_plus_eps_S;
+ gmx_simd_real_t rij_rkj_S;
+ gmx_simd_real_t nrij2_S, nrij_1_S;
+ gmx_simd_real_t nrkj2_S, nrkj_1_S;
+ gmx_simd_real_t cos_S, invsin_S;
+ gmx_simd_real_t theta_S;
+ gmx_simd_real_t st_S, sth_S;
+ gmx_simd_real_t cik_S, cii_S, ckk_S;
+ gmx_simd_real_t f_ix_S, f_iy_S, f_iz_S;
+ gmx_simd_real_t f_kx_S, f_ky_S, f_kz_S;
+ pbc_simd_t pbc_simd;
+
+ /* Ensure register memory alignment */
+ coeff = gmx_simd_align_r(coeff_array);
+ dr = gmx_simd_align_r(dr_array);
+ f_buf = gmx_simd_align_r(f_buf_array);
+
+ set_pbc_simd(pbc, &pbc_simd);
+
+ one_S = gmx_simd_set1_r(1.0);
+
+ /* The smallest number > -1 */
+ min_one_plus_eps_S = gmx_simd_set1_r(-1.0 + 2*GMX_REAL_EPS);
+
+ /* nbonds is the number of angles times nfa1, here we step GMX_SIMD_REAL_WIDTH angles */
+ for (i = 0; (i < nbonds); i += GMX_SIMD_REAL_WIDTH*nfa1)
+ {
+ /* Collect atoms for GMX_SIMD_REAL_WIDTH angles.
+ * iu indexes into forceatoms, we should not let iu go beyond nbonds.
+ */
+ iu = i;
+ for (s = 0; s < GMX_SIMD_REAL_WIDTH; s++)
+ {
+ type = forceatoms[iu];
+ ai[s] = forceatoms[iu+1];
+ aj[s] = forceatoms[iu+2];
+ ak[s] = forceatoms[iu+3];
- /* We do pbc_dx with ref+rdist,
- * since with only ref we can be up to half a box vector wrong.
+ coeff[s] = forceparams[type].harmonic.krA;
+ coeff[GMX_SIMD_REAL_WIDTH+s] = forceparams[type].harmonic.rA*DEG2RAD;
+
+ /* If you can't use pbc_dx_simd below for PBC, e.g. because
+ * you can't round in SIMD, use pbc_rvec_sub here.
*/
- pos[m] = ref + rdist[m];
+ /* Store the non PBC corrected distances packed and aligned */
+ for (m = 0; m < DIM; m++)
+ {
+ dr[s + m *GMX_SIMD_REAL_WIDTH] = x[ai[s]][m] - x[aj[s]][m];
+ dr[s + (DIM+m)*GMX_SIMD_REAL_WIDTH] = x[ak[s]][m] - x[aj[s]][m];
+ }
+
+ /* At the end fill the arrays with identical entries */
+ if (iu + nfa1 < nbonds)
+ {
+ iu += nfa1;
+ }
}
- if (pbc)
+ k_S = gmx_simd_load_r(coeff);
+ theta0_S = gmx_simd_load_r(coeff+GMX_SIMD_REAL_WIDTH);
+
+ rijx_S = gmx_simd_load_r(dr + 0*GMX_SIMD_REAL_WIDTH);
+ rijy_S = gmx_simd_load_r(dr + 1*GMX_SIMD_REAL_WIDTH);
+ rijz_S = gmx_simd_load_r(dr + 2*GMX_SIMD_REAL_WIDTH);
+ rkjx_S = gmx_simd_load_r(dr + 3*GMX_SIMD_REAL_WIDTH);
+ rkjy_S = gmx_simd_load_r(dr + 4*GMX_SIMD_REAL_WIDTH);
+ rkjz_S = gmx_simd_load_r(dr + 5*GMX_SIMD_REAL_WIDTH);
+
+ pbc_dx_simd(&rijx_S, &rijy_S, &rijz_S, &pbc_simd);
+ pbc_dx_simd(&rkjx_S, &rkjy_S, &rkjz_S, &pbc_simd);
+
+ rij_rkj_S = gmx_simd_iprod_r(rijx_S, rijy_S, rijz_S,
+ rkjx_S, rkjy_S, rkjz_S);
+
+ nrij2_S = gmx_simd_norm2_r(rijx_S, rijy_S, rijz_S);
+ nrkj2_S = gmx_simd_norm2_r(rkjx_S, rkjy_S, rkjz_S);
+
+ nrij_1_S = gmx_simd_invsqrt_r(nrij2_S);
+ nrkj_1_S = gmx_simd_invsqrt_r(nrkj2_S);
+
+ cos_S = gmx_simd_mul_r(rij_rkj_S, gmx_simd_mul_r(nrij_1_S, nrkj_1_S));
+
+ /* To allow for 180 degrees, we take the max of cos and -1 + 1bit,
+ * so we can safely get the 1/sin from 1/sqrt(1 - cos^2).
+ * This also ensures that rounding errors would cause the argument
+ * of gmx_simd_acos_r to be < -1.
+ * Note that we do not take precautions for cos(0)=1, so the outer
+ * atoms in an angle should not be on top of each other.
+ */
+ cos_S = gmx_simd_max_r(cos_S, min_one_plus_eps_S);
+
+ theta_S = gmx_simd_acos_r(cos_S);
+
+ invsin_S = gmx_simd_invsqrt_r(gmx_simd_sub_r(one_S, gmx_simd_mul_r(cos_S, cos_S)));
+
+ st_S = gmx_simd_mul_r(gmx_simd_mul_r(k_S, gmx_simd_sub_r(theta0_S, theta_S)),
+ invsin_S);
+ sth_S = gmx_simd_mul_r(st_S, cos_S);
+
+ cik_S = gmx_simd_mul_r(st_S, gmx_simd_mul_r(nrij_1_S, nrkj_1_S));
+ cii_S = gmx_simd_mul_r(sth_S, gmx_simd_mul_r(nrij_1_S, nrij_1_S));
+ ckk_S = gmx_simd_mul_r(sth_S, gmx_simd_mul_r(nrkj_1_S, nrkj_1_S));
+
+ f_ix_S = gmx_simd_mul_r(cii_S, rijx_S);
+ f_ix_S = gmx_simd_fnmadd_r(cik_S, rkjx_S, f_ix_S);
+ f_iy_S = gmx_simd_mul_r(cii_S, rijy_S);
+ f_iy_S = gmx_simd_fnmadd_r(cik_S, rkjy_S, f_iy_S);
+ f_iz_S = gmx_simd_mul_r(cii_S, rijz_S);
+ f_iz_S = gmx_simd_fnmadd_r(cik_S, rkjz_S, f_iz_S);
+ f_kx_S = gmx_simd_mul_r(ckk_S, rkjx_S);
+ f_kx_S = gmx_simd_fnmadd_r(cik_S, rijx_S, f_kx_S);
+ f_ky_S = gmx_simd_mul_r(ckk_S, rkjy_S);
+ f_ky_S = gmx_simd_fnmadd_r(cik_S, rijy_S, f_ky_S);
+ f_kz_S = gmx_simd_mul_r(ckk_S, rkjz_S);
+ f_kz_S = gmx_simd_fnmadd_r(cik_S, rijz_S, f_kz_S);
+
+ gmx_simd_store_r(f_buf + 0*GMX_SIMD_REAL_WIDTH, f_ix_S);
+ gmx_simd_store_r(f_buf + 1*GMX_SIMD_REAL_WIDTH, f_iy_S);
+ gmx_simd_store_r(f_buf + 2*GMX_SIMD_REAL_WIDTH, f_iz_S);
+ gmx_simd_store_r(f_buf + 3*GMX_SIMD_REAL_WIDTH, f_kx_S);
+ gmx_simd_store_r(f_buf + 4*GMX_SIMD_REAL_WIDTH, f_ky_S);
+ gmx_simd_store_r(f_buf + 5*GMX_SIMD_REAL_WIDTH, f_kz_S);
+
+ iu = i;
+ s = 0;
+ do
{
- pbc_dx(pbc,x[ai],pos,dx);
+ for (m = 0; m < DIM; m++)
+ {
+ f[ai[s]][m] += f_buf[s + m*GMX_SIMD_REAL_WIDTH];
+ f[aj[s]][m] -= f_buf[s + m*GMX_SIMD_REAL_WIDTH] + f_buf[s + (DIM+m)*GMX_SIMD_REAL_WIDTH];
+ f[ak[s]][m] += f_buf[s + (DIM+m)*GMX_SIMD_REAL_WIDTH];
+ }
+ s++;
+ iu += nfa1;
}
- else
+ while (s < GMX_SIMD_REAL_WIDTH && iu < nbonds);
+ }
+}
+
+#endif /* GMX_SIMD_HAVE_REAL */
+
+real linear_angles(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ 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;
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+
+ kA = forceparams[type].linangle.klinA;
+ kB = forceparams[type].linangle.klinB;
+ klin = L1*kA + lambda*kB;
+
+ aA = forceparams[type].linangle.aA;
+ aB = forceparams[type].linangle.aB;
+ a = L1*aA+lambda*aB;
+ b = 1-a;
+
+ t1 = pbc_rvec_sub(pbc, x[ai], x[aj], r_ij);
+ t2 = pbc_rvec_sub(pbc, x[ak], x[aj], r_kj);
+ rvec_sub(r_ij, r_kj, r_ik);
+
+ dr2 = 0;
+ for (m = 0; (m < DIM); m++)
{
- rvec_sub(x[ai],pos,dx);
+ dr = -a * r_ij[m] - b * r_kj[m];
+ dr2 += dr*dr;
+ dx[m] = dr;
+ f_i[m] = a*klin*dr;
+ f_k[m] = b*klin*dr;
+ f_j[m] = -(f_i[m]+f_k[m]);
+ f[ai][m] += f_i[m];
+ f[aj][m] += f_j[m];
+ f[ak][m] += f_k[m];
}
+ va = 0.5*klin*dr2;
+ *dvdlambda += 0.5*(kB-kA)*dr2 + klin*(aB-aA)*iprod(dx, r_ik);
- for (m=0; (m<DIM); m++)
+ vtot += va;
+
+ if (g)
{
- kk = L1*pr->posres.fcA[m] + lambda*pr->posres.fcB[m];
- fm = -kk*dx[m];
- f[ai][m] += fm;
- vtot += 0.5*kk*dx[m]*dx[m];
- *dvdlambda +=
- 0.5*(pr->posres.fcB[m] - pr->posres.fcA[m])*dx[m]*dx[m]
- -fm*dpdl[m];
+ copy_ivec(SHIFT_IVEC(g, aj), jt);
- /* Here we correct for the pbc_dx which included rdist */
- vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm;
+ 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);
+ } /* 57 TOTAL */
return vtot;
}
-static real low_angres(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- gmx_bool bZAxis)
-{
- int i,m,type,ai,aj,ak,al;
- int t1,t2;
- real phi,cos_phi,cos_phi2,vid,vtot,dVdphi;
- 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;
- ak=al=0; /* to avoid warnings */
- for(i=0; i<nbonds; ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- t1 = pbc_rvec_sub(pbc,x[aj],x[ai],r_ij); /* 3 */
- if (!bZAxis) {
- ak = forceatoms[i++];
- al = forceatoms[i++];
- t2 = pbc_rvec_sub(pbc,x[al],x[ak],r_kl); /* 3 */
- } else {
- r_kl[XX] = 0;
- r_kl[YY] = 0;
- r_kl[ZZ] = 1;
- }
-
- cos_phi = cos_angle(r_ij,r_kl); /* 25 */
- phi = acos(cos_phi); /* 10 */
-
- *dvdlambda += dopdihs_min(forceparams[type].pdihs.cpA,
- forceparams[type].pdihs.cpB,
- forceparams[type].pdihs.phiA,
- forceparams[type].pdihs.phiB,
- forceparams[type].pdihs.mult,
- phi,lambda,&vid,&dVdphi); /* 40 */
-
- vtot += vid;
-
- cos_phi2 = sqr(cos_phi); /* 1 */
- if (cos_phi2 < 1) {
- st = -dVdphi*gmx_invsqrt(1 - cos_phi2); /* 12 */
- sth = st*cos_phi; /* 1 */
- nrij2 = iprod(r_ij,r_ij); /* 5 */
- nrkl2 = iprod(r_kl,r_kl); /* 5 */
-
- c = st*gmx_invsqrt(nrij2*nrkl2); /* 11 */
- cij = sth/nrij2; /* 10 */
- ckl = sth/nrkl2; /* 10 */
-
- for (m=0; m<DIM; m++) { /* 18+18 */
- f_i[m] = (c*r_kl[m]-cij*r_ij[m]);
- f[ai][m] += f_i[m];
- f[aj][m] -= f_i[m];
- if (!bZAxis) {
- f_k[m] = (c*r_ij[m]-ckl*r_kl[m]);
- f[ak][m] += f_k[m];
- f[al][m] -= f_k[m];
- }
- }
-
- 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);
- }
- }
- }
-
- return vtot; /* 184 / 157 (bZAxis) total */
-}
-
-real angres(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
+real urey_bradley(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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(nbonds,forceatoms,forceparams,x,f,fshift,pbc,g,
- lambda,dvdlambda,FALSE);
-}
+ int i, m, ai, aj, ak, t1, t2, type, ki;
+ rvec r_ij, r_kj, r_ik;
+ 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;
-real angresz(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- return low_angres(nbonds,forceatoms,forceparams,x,f,fshift,pbc,g,
- lambda,dvdlambda,TRUE);
-}
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ th0A = forceparams[type].u_b.thetaA*DEG2RAD;
+ kthA = forceparams[type].u_b.kthetaA;
+ r13A = forceparams[type].u_b.r13A;
+ kUBA = forceparams[type].u_b.kUBA;
+ th0B = forceparams[type].u_b.thetaB*DEG2RAD;
+ kthB = forceparams[type].u_b.kthetaB;
+ r13B = forceparams[type].u_b.r13B;
+ kUBB = forceparams[type].u_b.kUBB;
+
+ theta = bond_angle(x[ai], x[aj], x[ak], pbc,
+ r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
+
+ *dvdlambda += harmonic(kthA, kthB, th0A, th0B, theta, lambda, &va, &dVdt); /* 21 */
+ vtot += va;
+
+ ki = pbc_rvec_sub(pbc, x[ai], x[ak], r_ik); /* 3 */
+ dr2 = iprod(r_ik, r_ik); /* 5 */
+ dr = dr2*gmx_invsqrt(dr2); /* 10 */
+
+ *dvdlambda += harmonic(kUBA, kUBB, r13A, r13B, dr, lambda, &vbond, &fbond); /* 19 */
+
+ cos_theta2 = sqr(cos_theta); /* 1 */
+ if (cos_theta2 < 1)
+ {
+ real st, sth;
+ real cik, cii, ckk;
+ real nrkj2, nrij2;
+ rvec f_i, f_j, f_k;
+ st = dVdt*gmx_invsqrt(1 - cos_theta2); /* 12 */
+ sth = st*cos_theta; /* 1 */
+#ifdef DEBUG
+ if (debug)
+ {
+ fprintf(debug, "ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
+ theta*RAD2DEG, va, dVdt);
+ }
+#endif
+ nrkj2 = iprod(r_kj, r_kj); /* 5 */
+ nrij2 = iprod(r_ij, r_ij);
-real unimplemented(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- gmx_impl("*** you are using a not implemented function");
+ cik = st*gmx_invsqrt(nrkj2*nrij2); /* 12 */
+ cii = sth/nrij2; /* 10 */
+ ckk = sth/nrkj2; /* 10 */
- return 0.0; /* To make the compiler happy */
-}
+ for (m = 0; (m < DIM); m++) /* 39 */
+ {
+ f_i[m] = -(cik*r_kj[m]-cii*r_ij[m]);
+ f_k[m] = -(cik*r_ij[m]-ckk*r_kj[m]);
+ f_j[m] = -f_i[m]-f_k[m];
+ f[ai][m] += f_i[m];
+ f[aj][m] += f_j[m];
+ f[ak][m] += f_k[m];
+ }
+ if (g)
+ {
+ copy_ivec(SHIFT_IVEC(g, aj), jt);
-real rbdihs(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- const real c0=0.0,c1=1.0,c2=2.0,c3=3.0,c4=4.0,c5=5.0;
- int type,ai,aj,ak,al,i,j;
- int t1,t2,t3;
- rvec r_ij,r_kj,r_kl,m,n;
- real parmA[NR_RBDIHS];
- real parmB[NR_RBDIHS];
- real parm[NR_RBDIHS];
- real cos_phi,phi,rbp,rbpBA;
- real v,sign,ddphi,sin_phi;
- real cosfac,vtot;
- real L1 = 1.0-lambda;
- real dvdl=0;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
- al = forceatoms[i++];
-
- phi=dih_angle(x[ai],x[aj],x[ak],x[al],pbc,r_ij,r_kj,r_kl,m,n,
- &sign,&t1,&t2,&t3); /* 84 */
-
- /* Change to polymer convention */
- if (phi < c0)
- phi += M_PI;
- else
- phi -= M_PI; /* 1 */
-
- cos_phi = cos(phi);
- /* Beware of accuracy loss, cannot use 1-sqrt(cos^2) ! */
- sin_phi = sin(phi);
-
- for(j=0; (j<NR_RBDIHS); j++) {
- parmA[j] = forceparams[type].rbdihs.rbcA[j];
- parmB[j] = forceparams[type].rbdihs.rbcB[j];
- parm[j] = L1*parmA[j]+lambda*parmB[j];
- }
- /* Calculate cosine powers */
- /* Calculate the energy */
- /* Calculate the derivative */
-
- v = parm[0];
- dvdl += (parmB[0]-parmA[0]);
- ddphi = c0;
- cosfac = c1;
-
- rbp = parm[1];
- rbpBA = parmB[1]-parmA[1];
- ddphi += rbp*cosfac;
- cosfac *= cos_phi;
- v += cosfac*rbp;
- dvdl += cosfac*rbpBA;
- rbp = parm[2];
- rbpBA = parmB[2]-parmA[2];
- ddphi += c2*rbp*cosfac;
- cosfac *= cos_phi;
- v += cosfac*rbp;
- dvdl += cosfac*rbpBA;
- rbp = parm[3];
- rbpBA = parmB[3]-parmA[3];
- ddphi += c3*rbp*cosfac;
- cosfac *= cos_phi;
- v += cosfac*rbp;
- dvdl += cosfac*rbpBA;
- rbp = parm[4];
- rbpBA = parmB[4]-parmA[4];
- ddphi += c4*rbp*cosfac;
- cosfac *= cos_phi;
- v += cosfac*rbp;
- dvdl += cosfac*rbpBA;
- rbp = parm[5];
- rbpBA = parmB[5]-parmA[5];
- ddphi += c5*rbp*cosfac;
- cosfac *= cos_phi;
- v += cosfac*rbp;
- dvdl += cosfac*rbpBA;
-
- ddphi = -ddphi*sin_phi; /* 11 */
-
- 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 */
- vtot += v;
- }
- *dvdlambda += dvdl;
-
- return vtot;
-}
+ 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);
+ } /* 161 TOTAL */
+ /* Time for the bond calculations */
+ if (dr2 == 0.0)
+ {
+ continue;
+ }
-int cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
-{
- int im1, ip1, ip2;
-
- if(ip<0)
- {
- ip = ip + grid_spacing - 1;
- }
- else if(ip > grid_spacing)
- {
- ip = ip - grid_spacing - 1;
- }
-
- im1 = ip - 1;
- ip1 = ip + 1;
- ip2 = ip + 2;
-
- if(ip == 0)
- {
- im1 = grid_spacing - 1;
- }
- else if(ip == grid_spacing-2)
- {
- ip2 = 0;
- }
- else if(ip == grid_spacing-1)
- {
- ip1 = 0;
- ip2 = 1;
- }
-
- *ipm1 = im1;
- *ipp1 = ip1;
- *ipp2 = ip2;
-
- return ip;
-
+ vtot += vbond; /* 1*/
+ fbond *= gmx_invsqrt(dr2); /* 6 */
+
+ if (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];
+ f[ai][m] += fik;
+ f[ak][m] -= fik;
+ fshift[ki][m] += fik;
+ fshift[CENTRAL][m] -= fik;
+ }
+ }
+ return vtot;
}
-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 lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,j,k,n,idx;
- int ai,aj,ak,al,am;
- int a1i,a1j,a1k,a1l,a2i,a2j,a2k,a2l;
- int type,cmapA;
- 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;
-
- 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 ra21,rb21,rg21,rg1,rgr1,ra2r1,rb2r1,rabr1;
- real ra22,rb22,rg22,rg2,rgr2,ra2r2,rb2r2,rabr2;
- real fg1,hg1,fga1,hgb1,gaa1,gbb1;
- real fg2,hg2,fga2,hgb2,gaa2,gbb2;
- real fac;
-
- rvec r1_ij, r1_kj, r1_kl,m1,n1;
- rvec r2_ij, r2_kj, r2_kl,m2,n2;
- rvec f1_i,f1_j,f1_k,f1_l;
- rvec f2_i,f2_j,f2_k,f2_l;
- 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;
+real quartic_angles(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ 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, 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;
- const real *cmapd;
-
- int loop_index[4][4] = {
- {0,4,8,12},
- {1,5,9,13},
- {2,6,10,14},
- {3,7,11,15}
- };
-
- /* Total CMAP energy */
- vtot = 0;
-
- for(n=0;n<nbonds; )
- {
- /* Five atoms are involved in the two torsions */
- type = forceatoms[n++];
- ai = forceatoms[n++];
- aj = forceatoms[n++];
- ak = forceatoms[n++];
- al = forceatoms[n++];
- am = forceatoms[n++];
-
- /* Which CMAP type is this */
- cmapA = forceparams[type].cmap.cmapA;
- cmapd = cmap_grid->cmapdata[cmapA].cmap;
-
- /* First torsion */
- a1i = ai;
- a1j = aj;
- a1k = ak;
- a1l = al;
-
- phi1 = dih_angle(x[a1i], x[a1j], x[a1k], x[a1l], pbc, r1_ij, r1_kj, r1_kl, m1, n1,
- &sign1, &t11, &t21, &t31); /* 84 */
-
- cos_phi1 = cos(phi1);
-
- a1[0] = r1_ij[1]*r1_kj[2]-r1_ij[2]*r1_kj[1];
- a1[1] = r1_ij[2]*r1_kj[0]-r1_ij[0]*r1_kj[2];
- a1[2] = r1_ij[0]*r1_kj[1]-r1_ij[1]*r1_kj[0]; /* 9 */
-
- b1[0] = r1_kl[1]*r1_kj[2]-r1_kl[2]*r1_kj[1];
- 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);
-
- ra21 = iprod(a1,a1); /* 5 */
- rb21 = iprod(b1,b1); /* 5 */
- rg21 = iprod(r1_kj,r1_kj); /* 5 */
- rg1 = sqrt(rg21);
-
- rgr1 = 1.0/rg1;
- ra2r1 = 1.0/ra21;
- rb2r1 = 1.0/rb21;
- rabr1 = sqrt(ra2r1*rb2r1);
-
- sin_phi1 = rg1 * rabr1 * iprod(a1,h1) * (-1);
-
- if(cos_phi1 < -0.5 || cos_phi1 > 0.5)
- {
- phi1 = asin(sin_phi1);
-
- if(cos_phi1 < 0)
- {
- if(phi1 > 0)
- {
- phi1 = M_PI - phi1;
- }
- else
- {
- phi1 = -M_PI - phi1;
- }
- }
- }
- else
- {
- phi1 = acos(cos_phi1);
-
- if(sin_phi1 < 0)
- {
- phi1 = -phi1;
- }
- }
-
- xphi1 = phi1 + M_PI; /* 1 */
-
- /* Second torsion */
- a2i = aj;
- a2j = ak;
- a2k = al;
- a2l = am;
-
- phi2 = dih_angle(x[a2i], x[a2j], x[a2k], x[a2l], pbc, r2_ij, r2_kj, r2_kl, m2, n2,
- &sign2, &t12, &t22, &t32); /* 84 */
-
- cos_phi2 = cos(phi2);
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
- a2[0] = r2_ij[1]*r2_kj[2]-r2_ij[2]*r2_kj[1];
- a2[1] = r2_ij[2]*r2_kj[0]-r2_ij[0]*r2_kj[2];
- a2[2] = r2_ij[0]*r2_kj[1]-r2_ij[1]*r2_kj[0]; /* 9 */
-
- b2[0] = r2_kl[1]*r2_kj[2]-r2_kl[2]*r2_kj[1];
- 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);
-
- ra22 = iprod(a2,a2); /* 5 */
- rb22 = iprod(b2,b2); /* 5 */
- rg22 = iprod(r2_kj,r2_kj); /* 5 */
- rg2 = sqrt(rg22);
-
- rgr2 = 1.0/rg2;
- ra2r2 = 1.0/ra22;
- rb2r2 = 1.0/rb22;
- rabr2 = sqrt(ra2r2*rb2r2);
-
- sin_phi2 = rg2 * rabr2 * iprod(a2,h2) * (-1);
-
- if(cos_phi2 < -0.5 || cos_phi2 > 0.5)
- {
- phi2 = asin(sin_phi2);
-
- if(cos_phi2 < 0)
- {
- if(phi2 > 0)
- {
- phi2 = M_PI - phi2;
- }
- else
- {
- phi2 = -M_PI - phi2;
- }
- }
- }
- else
- {
- phi2 = acos(cos_phi2);
-
- if(sin_phi2 < 0)
- {
- phi2 = -phi2;
- }
- }
-
- xphi2 = phi2 + M_PI; /* 1 */
-
- /* Range mangling */
- if(xphi1<0)
- {
- xphi1 = xphi1 + 2*M_PI;
- }
- else if(xphi1>=2*M_PI)
- {
- xphi1 = xphi1 - 2*M_PI;
- }
-
- if(xphi2<0)
- {
- xphi2 = xphi2 + 2*M_PI;
- }
- else if(xphi2>=2*M_PI)
- {
- xphi2 = xphi2 - 2*M_PI;
- }
-
- /* Number of grid points */
- dx = 2*M_PI / cmap_grid->grid_spacing;
-
- /* Where on the grid are we */
- iphi1 = (int)(xphi1/dx);
- iphi2 = (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);
-
- pos1 = iphi1*cmap_grid->grid_spacing+iphi2;
- pos2 = ip1p1*cmap_grid->grid_spacing+iphi2;
- pos3 = ip1p1*cmap_grid->grid_spacing+ip2p1;
- pos4 = iphi1*cmap_grid->grid_spacing+ip2p1;
-
- ty[0] = cmapd[pos1*4];
- ty[1] = cmapd[pos2*4];
- ty[2] = cmapd[pos3*4];
- ty[3] = cmapd[pos4*4];
-
- ty1[0] = cmapd[pos1*4+1];
- ty1[1] = cmapd[pos2*4+1];
- ty1[2] = cmapd[pos3*4+1];
- ty1[3] = cmapd[pos4*4+1];
-
- ty2[0] = cmapd[pos1*4+2];
- ty2[1] = cmapd[pos2*4+2];
- ty2[2] = cmapd[pos3*4+2];
- ty2[3] = cmapd[pos4*4+2];
-
- ty12[0] = cmapd[pos1*4+3];
- ty12[1] = cmapd[pos2*4+3];
- ty12[2] = cmapd[pos3*4+3];
- ty12[3] = cmapd[pos4*4+3];
-
- /* Switch to degrees */
- dx = 360.0 / cmap_grid->grid_spacing;
- xphi1 = xphi1 * RAD2DEG;
- xphi2 = xphi2 * RAD2DEG;
-
- for(i=0;i<4;i++) /* 16 */
- {
- tx[i] = ty[i];
- tx[i+4] = ty1[i]*dx;
- tx[i+8] = ty2[i]*dx;
- tx[i+12] = ty12[i]*dx*dx;
- }
-
- idx=0;
- for(i=0;i<4;i++) /* 1056 */
- {
- for(j=0;j<4;j++)
- {
- xx = 0;
- for(k=0;k<16;k++)
- {
- xx = xx + cmap_coeff_matrix[k*16+idx]*tx[k];
- }
-
- idx++;
- tc[i*4+j]=xx;
- }
- }
-
- tt = (xphi1-iphi1*dx)/dx;
- tu = (xphi2-iphi2*dx)/dx;
-
- e = 0;
- df1 = 0;
- df2 = 0;
- ddf1 = 0;
- ddf2 = 0;
- ddf12 = 0;
-
- for(i=3;i>=0;i--)
- {
- l1 = loop_index[i][3];
- l2 = loop_index[i][2];
- l3 = loop_index[i][1];
-
- 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;
-
- /* Do forces - first torsion */
- fg1 = iprod(r1_ij,r1_kj);
- hg1 = iprod(r1_kl,r1_kj);
- fga1 = fg1*ra2r1*rgr1;
- hgb1 = hg1*rb2r1*rgr1;
- gaa1 = -ra2r1*rg1;
- gbb1 = rb2r1*rg1;
-
- for(i=0;i<DIM;i++)
- {
- dtf1[i] = gaa1 * a1[i];
- dtg1[i] = fga1 * a1[i] - hgb1 * b1[i];
- dth1[i] = gbb1 * b1[i];
-
- f1[i] = df1 * dtf1[i];
- g1[i] = df1 * dtg1[i];
- h1[i] = df1 * dth1[i];
-
- f1_i[i] = f1[i];
- f1_j[i] = -f1[i] - g1[i];
- f1_k[i] = h1[i] + g1[i];
- f1_l[i] = -h1[i];
-
- f[a1i][i] = f[a1i][i] + f1_i[i];
- f[a1j][i] = f[a1j][i] + f1_j[i]; /* - f1[i] - g1[i] */
- f[a1k][i] = f[a1k][i] + f1_k[i]; /* h1[i] + g1[i] */
- f[a1l][i] = f[a1l][i] + f1_l[i]; /* h1[i] */
- }
-
- /* Do forces - second torsion */
- fg2 = iprod(r2_ij,r2_kj);
- hg2 = iprod(r2_kl,r2_kj);
- fga2 = fg2*ra2r2*rgr2;
- hgb2 = hg2*rb2r2*rgr2;
- gaa2 = -ra2r2*rg2;
- gbb2 = rb2r2*rg2;
-
- for(i=0;i<DIM;i++)
- {
- dtf2[i] = gaa2 * a2[i];
- dtg2[i] = fga2 * a2[i] - hgb2 * b2[i];
- dth2[i] = gbb2 * b2[i];
-
- f2[i] = df2 * dtf2[i];
- g2[i] = df2 * dtg2[i];
- h2[i] = df2 * dth2[i];
-
- f2_i[i] = f2[i];
- f2_j[i] = -f2[i] - g2[i];
- f2_k[i] = h2[i] + g2[i];
- f2_l[i] = -h2[i];
-
- f[a2i][i] = f[a2i][i] + f2_i[i]; /* f2[i] */
- f[a2j][i] = f[a2j][i] + f2_j[i]; /* - f2[i] - g2[i] */
- f[a2k][i] = f[a2k][i] + f2_k[i]; /* h2[i] + g2[i] */
- f[a2l][i] = f[a2l][i] + f2_l[i]; /* - h2[i] */
- }
-
- /* Shift forces */
- 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)
- {
- t31 = pbc_rvec_sub(pbc,x[a1l],x[a1j],h1);
- t32 = pbc_rvec_sub(pbc,x[a2l],x[a2j],h2);
- }
- else
- {
- t31 = CENTRAL;
- t32 = CENTRAL;
- }
-
- rvec_inc(fshift[t11],f1_i);
- rvec_inc(fshift[CENTRAL],f1_j);
- rvec_inc(fshift[t21],f1_k);
- rvec_inc(fshift[t31],f1_l);
-
- rvec_inc(fshift[t21],f2_i);
- rvec_inc(fshift[CENTRAL],f2_j);
- rvec_inc(fshift[t22],f2_k);
- rvec_inc(fshift[t32],f2_l);
- }
- return vtot;
-}
+ theta = bond_angle(x[ai], x[aj], x[ak], pbc,
+ r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
+ dt = theta - forceparams[type].qangle.theta*DEG2RAD; /* 2 */
+ dVdt = 0;
+ va = forceparams[type].qangle.c[0];
+ dtp = 1.0;
+ for (j = 1; j <= 4; j++)
+ {
+ c = forceparams[type].qangle.c[j];
+ dVdt -= j*c*dtp;
+ dtp *= dt;
+ va += c*dtp;
+ }
+ /* 20 */
-/***********************************************************
- *
- * G R O M O S 9 6 F U N C T I O N S
- *
- ***********************************************************/
-real g96harmonic(real kA,real kB,real xA,real xB,real x,real lambda,
- real *V,real *F)
-{
- const real half=0.5;
- real L1,kk,x0,dx,dx2;
- real v,f,dvdl;
-
- L1 = 1.0-lambda;
- kk = L1*kA+lambda*kB;
- x0 = L1*xA+lambda*xB;
-
- dx = x-x0;
- dx2 = dx*dx;
-
- f = -kk*dx;
- v = half*kk*dx2;
- dvdl = half*(kB-kA)*dx2 + (xA-xB)*kk*dx;
-
- *F = f;
- *V = v;
-
- return dvdl;
-
- /* That was 21 flops */
-}
+ vtot += va;
-real g96bonds(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,m,ki,ai,aj,type;
- real dr2,fbond,vbond,fij,vtot;
- rvec dx;
- ivec dt;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
-
- ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx); /* 3 */
- dr2 = iprod(dx,dx); /* 5 */
-
- *dvdlambda += g96harmonic(forceparams[type].harmonic.krA,
- forceparams[type].harmonic.krB,
- forceparams[type].harmonic.rA,
- forceparams[type].harmonic.rB,
- dr2,lambda,&vbond,&fbond);
-
- vtot += 0.5*vbond; /* 1*/
+ cos_theta2 = sqr(cos_theta); /* 1 */
+ if (cos_theta2 < 1)
+ {
+ int m;
+ real st, sth;
+ real cik, cii, ckk;
+ real nrkj2, nrij2;
+ rvec f_i, f_j, f_k;
+
+ st = dVdt*gmx_invsqrt(1 - cos_theta2); /* 12 */
+ sth = st*cos_theta; /* 1 */
#ifdef DEBUG
- if (debug)
- fprintf(debug,"G96-BONDS: dr = %10g vbond = %10g fbond = %10g\n",
- sqrt(dr2),vbond,fbond);
+ if (debug)
+ {
+ fprintf(debug, "ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
+ theta*RAD2DEG, va, dVdt);
+ }
#endif
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
- ki=IVEC2IS(dt);
- }
- for (m=0; (m<DIM); m++) { /* 15 */
- fij=fbond*dx[m];
- f[ai][m]+=fij;
- f[aj][m]-=fij;
- fshift[ki][m]+=fij;
- fshift[CENTRAL][m]-=fij;
+ nrkj2 = iprod(r_kj, r_kj); /* 5 */
+ nrij2 = iprod(r_ij, r_ij);
+
+ cik = st*gmx_invsqrt(nrkj2*nrij2); /* 12 */
+ cii = sth/nrij2; /* 10 */
+ ckk = sth/nrkj2; /* 10 */
+
+ for (m = 0; (m < DIM); m++) /* 39 */
+ {
+ f_i[m] = -(cik*r_kj[m]-cii*r_ij[m]);
+ f_k[m] = -(cik*r_ij[m]-ckk*r_kj[m]);
+ f_j[m] = -f_i[m]-f_k[m];
+ f[ai][m] += f_i[m];
+ f[aj][m] += f_j[m];
+ f[ak][m] += f_k[m];
+ }
+ 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);
+ } /* 153 TOTAL */
}
- } /* 44 TOTAL */
- return vtot;
+ return vtot;
}
-real g96bond_angle(const rvec xi,const rvec xj,const rvec xk,const t_pbc *pbc,
- rvec r_ij,rvec r_kj,
- int *t1,int *t2)
-/* Return value is the angle between the bonds i-j and j-k */
+real dih_angle(const rvec xi, const rvec xj, const rvec xk, const rvec xl,
+ const t_pbc *pbc,
+ rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n,
+ real *sign, int *t1, int *t2, int *t3)
{
- real costh;
-
- *t1 = pbc_rvec_sub(pbc,xi,xj,r_ij); /* 3 */
- *t2 = pbc_rvec_sub(pbc,xk,xj,r_kj); /* 3 */
-
- costh=cos_angle(r_ij,r_kj); /* 25 */
- /* 41 TOTAL */
- return costh;
+ real ipr, phi;
+
+ *t1 = pbc_rvec_sub(pbc, xi, xj, r_ij); /* 3 */
+ *t2 = pbc_rvec_sub(pbc, xk, xj, r_kj); /* 3 */
+ *t3 = pbc_rvec_sub(pbc, xk, xl, r_kl); /* 3 */
+
+ cprod(r_ij, r_kj, m); /* 9 */
+ cprod(r_kj, r_kl, n); /* 9 */
+ phi = gmx_angle(m, n); /* 49 (assuming 25 for atan2) */
+ ipr = iprod(r_ij, n); /* 5 */
+ (*sign) = (ipr < 0.0) ? -1.0 : 1.0;
+ phi = (*sign)*phi; /* 1 */
+ /* 82 TOTAL */
+ return phi;
}
-real g96angles(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,ai,aj,ak,type,m,t1,t2;
- rvec r_ij,r_kj;
- 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); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
-
- cos_theta = g96bond_angle(x[ai],x[aj],x[ak],pbc,r_ij,r_kj,&t1,&t2);
-
- *dvdlambda += g96harmonic(forceparams[type].harmonic.krA,
- forceparams[type].harmonic.krB,
- forceparams[type].harmonic.rA,
- forceparams[type].harmonic.rB,
- cos_theta,lambda,&va,&dVdt);
- vtot += va;
-
- rij_1 = gmx_invsqrt(iprod(r_ij,r_ij));
- rkj_1 = gmx_invsqrt(iprod(r_kj,r_kj));
- rij_2 = rij_1*rij_1;
- rkj_2 = rkj_1*rkj_1;
- rijrkj_1 = rij_1*rkj_1; /* 23 */
-
-#ifdef DEBUG
- if (debug)
- fprintf(debug,"G96ANGLES: costheta = %10g vth = %10g dV/dct = %10g\n",
- cos_theta,va,dVdt);
-#endif
- for (m=0; (m<DIM); m++) { /* 42 */
- f_i[m]=dVdt*(r_kj[m]*rijrkj_1 - r_ij[m]*rij_2*cos_theta);
- f_k[m]=dVdt*(r_ij[m]*rijrkj_1 - r_kj[m]*rkj_2*cos_theta);
- f_j[m]=-f_i[m]-f_k[m];
- f[ai][m]+=f_i[m];
- f[aj][m]+=f_j[m];
- f[ak][m]+=f_k[m];
- }
-
- 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 */
- /* 163 TOTAL */
- }
- return vtot;
-}
-real cross_bond_bond(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- /* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
- * pp. 842-847
- */
- int i,ai,aj,ak,type,m,t1,t2;
- 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); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
- r1e = forceparams[type].cross_bb.r1e;
- r2e = forceparams[type].cross_bb.r2e;
- krr = forceparams[type].cross_bb.krr;
-
- /* 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);
-
- /* ... and their lengths */
- r1 = norm(r_ij);
- r2 = norm(r_kj);
-
- /* Deviations from ideality */
- s1 = r1-r1e;
- s2 = r2-r2e;
-
- /* Energy (can be negative!) */
- vrr = krr*s1*s2;
- vtot += vrr;
-
- /* Forces */
- svmul(-krr*s2/r1,r_ij,f_i);
- svmul(-krr*s1/r2,r_kj,f_k);
-
- for (m=0; (m<DIM); m++) { /* 12 */
- f_j[m] = -f_i[m] - f_k[m];
- f[ai][m] += f_i[m];
- f[aj][m] += f_j[m];
- f[ak][m] += f_k[m];
- }
-
- /* Virial stuff */
- 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 */
- /* 163 TOTAL */
- }
- return vtot;
-}
+#ifdef GMX_SIMD_HAVE_REAL
-real cross_bond_angle(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- /* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
- * pp. 842-847
- */
- int i,ai,aj,ak,type,m,t1,t2,t3;
- 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); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
- r1e = forceparams[type].cross_ba.r1e;
- r2e = forceparams[type].cross_ba.r2e;
- r3e = forceparams[type].cross_ba.r3e;
- krt = forceparams[type].cross_ba.krt;
-
- /* 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);
-
- /* ... and their lengths */
- r1 = norm(r_ij);
- r2 = norm(r_kj);
- r3 = norm(r_ik);
-
- /* Deviations from ideality */
- s1 = r1-r1e;
- s2 = r2-r2e;
- s3 = r3-r3e;
-
- /* Energy (can be negative!) */
- vrt = krt*s3*(s1+s2);
- vtot += vrt;
-
- /* Forces */
- k1 = -krt*(s3/r1);
- k2 = -krt*(s3/r2);
- k3 = -krt*(s1+s2)/r3;
- for(m=0; (m<DIM); m++) {
- f_i[m] = k1*r_ij[m] + k3*r_ik[m];
- f_k[m] = k2*r_kj[m] - k3*r_ik[m];
- f_j[m] = -f_i[m] - f_k[m];
- }
-
- for (m=0; (m<DIM); m++) { /* 12 */
- f[ai][m] += f_i[m];
- f[aj][m] += f_j[m];
- f[ak][m] += f_k[m];
- }
-
- /* Virial stuff */
- 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 */
- /* 163 TOTAL */
- }
- return vtot;
-}
-
-static real bonded_tab(const char *type,int table_nr,
- const bondedtable_t *table,real kA,real kB,real r,
- real lambda,real *V,real *F)
-{
- real k,tabscale,*VFtab,rt,eps,eps2,Yt,Ft,Geps,Heps2,Fp,VV,FF;
- int n0,nnn;
- real v,f,dvdl;
-
- k = (1.0 - lambda)*kA + lambda*kB;
-
- tabscale = table->scale;
- VFtab = table->tab;
-
- rt = r*tabscale;
- n0 = 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",
- type,table_nr,r,n0,n0+1,table->n);
- }
- eps = rt - n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Yt = VFtab[nnn];
- Ft = VFtab[nnn+1];
- Geps = VFtab[nnn+2]*eps;
- Heps2 = VFtab[nnn+3]*eps2;
- Fp = Ft + Geps + Heps2;
- VV = Yt + Fp*eps;
- FF = Fp + Geps + 2.0*Heps2;
-
- *F = -k*FF*tabscale;
- *V = k*VV;
- dvdl = (kB - kA)*VV;
-
- return dvdl;
-
- /* That was 22 flops */
-}
+/* As dih_angle above, but calculates 4 dihedral angles at once using SIMD,
+ * also calculates the pre-factor required for the dihedral force update.
+ * Note that bv and buf should be register aligned.
+ */
+static gmx_inline void
+dih_angle_simd(const rvec *x,
+ const int *ai, const int *aj, const int *ak, const int *al,
+ const pbc_simd_t *pbc,
+ real *dr,
+ gmx_simd_real_t *phi_S,
+ gmx_simd_real_t *mx_S, gmx_simd_real_t *my_S, gmx_simd_real_t *mz_S,
+ gmx_simd_real_t *nx_S, gmx_simd_real_t *ny_S, gmx_simd_real_t *nz_S,
+ gmx_simd_real_t *nrkj_m2_S,
+ gmx_simd_real_t *nrkj_n2_S,
+ real *p,
+ real *q)
+{
+ int s, m;
+ gmx_simd_real_t rijx_S, rijy_S, rijz_S;
+ gmx_simd_real_t rkjx_S, rkjy_S, rkjz_S;
+ gmx_simd_real_t rklx_S, rkly_S, rklz_S;
+ gmx_simd_real_t cx_S, cy_S, cz_S;
+ gmx_simd_real_t cn_S;
+ gmx_simd_real_t s_S;
+ gmx_simd_real_t ipr_S;
+ gmx_simd_real_t iprm_S, iprn_S;
+ gmx_simd_real_t nrkj2_S, nrkj_1_S, nrkj_2_S, nrkj_S;
+ gmx_simd_real_t toler_S;
+ gmx_simd_real_t p_S, q_S;
+ gmx_simd_real_t nrkj2_min_S;
+ gmx_simd_real_t real_eps_S;
+
+ /* Used to avoid division by zero.
+ * We take into acount that we multiply the result by real_eps_S.
+ */
+ nrkj2_min_S = gmx_simd_set1_r(GMX_REAL_MIN/(2*GMX_REAL_EPS));
-real tab_bonds(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,m,ki,ai,aj,type,table;
- real dr,dr2,fbond,vbond,fij,vtot;
- rvec dx;
- ivec dt;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
-
- ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx); /* 3 */
- dr2 = iprod(dx,dx); /* 5 */
- dr = dr2*gmx_invsqrt(dr2); /* 10 */
-
- table = forceparams[type].tab.table;
-
- *dvdlambda += bonded_tab("bond",table,
- &fcd->bondtab[table],
- forceparams[type].tab.kA,
- forceparams[type].tab.kB,
- dr,lambda,&vbond,&fbond); /* 22 */
-
- if (dr2 == 0.0)
- continue;
-
-
- vtot += vbond;/* 1*/
- fbond *= gmx_invsqrt(dr2); /* 6 */
-#ifdef DEBUG
- if (debug)
- fprintf(debug,"TABBONDS: dr = %10g vbond = %10g fbond = %10g\n",
- dr,vbond,fbond);
-#endif
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
- ki=IVEC2IS(dt);
- }
- for (m=0; (m<DIM); m++) { /* 15 */
- fij=fbond*dx[m];
- f[ai][m]+=fij;
- f[aj][m]-=fij;
- fshift[ki][m]+=fij;
- fshift[CENTRAL][m]-=fij;
+ /* The value of the last significant bit (GMX_REAL_EPS is half of that) */
+ real_eps_S = gmx_simd_set1_r(2*GMX_REAL_EPS);
+
+ for (s = 0; s < GMX_SIMD_REAL_WIDTH; s++)
+ {
+ /* If you can't use pbc_dx_simd below for PBC, e.g. because
+ * you can't round in SIMD, use pbc_rvec_sub here.
+ */
+ for (m = 0; m < DIM; m++)
+ {
+ dr[s + (0*DIM + m)*GMX_SIMD_REAL_WIDTH] = x[ai[s]][m] - x[aj[s]][m];
+ dr[s + (1*DIM + m)*GMX_SIMD_REAL_WIDTH] = x[ak[s]][m] - x[aj[s]][m];
+ dr[s + (2*DIM + m)*GMX_SIMD_REAL_WIDTH] = x[ak[s]][m] - x[al[s]][m];
+ }
}
- } /* 62 TOTAL */
- return vtot;
-}
-real tab_angles(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- 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); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
-
- theta = bond_angle(x[ai],x[aj],x[ak],pbc,
- r_ij,r_kj,&cos_theta,&t1,&t2); /* 41 */
-
- table = forceparams[type].tab.table;
-
- *dvdlambda += bonded_tab("angle",table,
- &fcd->angletab[table],
- forceparams[type].tab.kA,
- forceparams[type].tab.kB,
- theta,lambda,&va,&dVdt); /* 22 */
- vtot += va;
-
- cos_theta2 = sqr(cos_theta); /* 1 */
- if (cos_theta2 < 1) {
- int m;
- real snt,st,sth;
- real cik,cii,ckk;
- real nrkj2,nrij2;
- rvec f_i,f_j,f_k;
-
- st = dVdt*gmx_invsqrt(1 - cos_theta2); /* 12 */
- sth = st*cos_theta; /* 1 */
-#ifdef DEBUG
- if (debug)
- fprintf(debug,"ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
- theta*RAD2DEG,va,dVdt);
-#endif
- nrkj2=iprod(r_kj,r_kj); /* 5 */
- nrij2=iprod(r_ij,r_ij);
-
- cik=st*gmx_invsqrt(nrkj2*nrij2); /* 12 */
- cii=sth/nrij2; /* 10 */
- ckk=sth/nrkj2; /* 10 */
-
- for (m=0; (m<DIM); m++) { /* 39 */
- f_i[m]=-(cik*r_kj[m]-cii*r_ij[m]);
- f_k[m]=-(cik*r_ij[m]-ckk*r_kj[m]);
- f_j[m]=-f_i[m]-f_k[m];
- f[ai][m]+=f_i[m];
- f[aj][m]+=f_j[m];
- f[ak][m]+=f_k[m];
- }
- 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);
- } /* 169 TOTAL */
- }
- return vtot;
-}
+ rijx_S = gmx_simd_load_r(dr + 0*GMX_SIMD_REAL_WIDTH);
+ rijy_S = gmx_simd_load_r(dr + 1*GMX_SIMD_REAL_WIDTH);
+ rijz_S = gmx_simd_load_r(dr + 2*GMX_SIMD_REAL_WIDTH);
+ rkjx_S = gmx_simd_load_r(dr + 3*GMX_SIMD_REAL_WIDTH);
+ rkjy_S = gmx_simd_load_r(dr + 4*GMX_SIMD_REAL_WIDTH);
+ rkjz_S = gmx_simd_load_r(dr + 5*GMX_SIMD_REAL_WIDTH);
+ rklx_S = gmx_simd_load_r(dr + 6*GMX_SIMD_REAL_WIDTH);
+ rkly_S = gmx_simd_load_r(dr + 7*GMX_SIMD_REAL_WIDTH);
+ rklz_S = gmx_simd_load_r(dr + 8*GMX_SIMD_REAL_WIDTH);
-real tab_dihs(int nbonds,
- const t_iatom forceatoms[],const t_iparams forceparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real lambda,real *dvdlambda,
- const t_mdatoms *md,t_fcdata *fcd,
- int *global_atom_index)
-{
- int i,type,ai,aj,ak,al,table;
- int t1,t2,t3;
- rvec r_ij,r_kj,r_kl,m,n;
- real phi,sign,ddphi,vpd,vtot;
-
- vtot = 0.0;
- for(i=0; (i<nbonds); ) {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- aj = forceatoms[i++];
- ak = forceatoms[i++];
- al = forceatoms[i++];
-
- phi=dih_angle(x[ai],x[aj],x[ak],x[al],pbc,r_ij,r_kj,r_kl,m,n,
- &sign,&t1,&t2,&t3); /* 84 */
-
- table = forceparams[type].tab.table;
-
- /* Hopefully phi+M_PI never results in values < 0 */
- *dvdlambda += bonded_tab("dihedral",table,
- &fcd->dihtab[table],
- forceparams[type].tab.kA,
- forceparams[type].tab.kB,
- phi+M_PI,lambda,&vpd,&ddphi);
-
- vtot += vpd;
- 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 */
+ pbc_dx_simd(&rijx_S, &rijy_S, &rijz_S, pbc);
+ pbc_dx_simd(&rkjx_S, &rkjy_S, &rkjz_S, pbc);
+ pbc_dx_simd(&rklx_S, &rkly_S, &rklz_S, pbc);
-#ifdef DEBUG
- fprintf(debug,"pdih: (%d,%d,%d,%d) phi=%g\n",
- ai,aj,ak,al,phi);
-#endif
- } /* 227 TOTAL */
+ gmx_simd_cprod_r(rijx_S, rijy_S, rijz_S,
+ rkjx_S, rkjy_S, rkjz_S,
+ mx_S, my_S, mz_S);
- return vtot;
-}
+ gmx_simd_cprod_r(rkjx_S, rkjy_S, rkjz_S,
+ rklx_S, rkly_S, rklz_S,
+ nx_S, ny_S, nz_S);
-void calc_bonds(FILE *fplog,const gmx_multisim_t *ms,
- const t_idef *idef,
- rvec x[],history_t *hist,
- rvec f[],t_forcerec *fr,
- const t_pbc *pbc,const 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 *atype, gmx_genborn_t *born,
- gmx_bool bPrintSepPot,gmx_large_int_t step)
-{
- int ftype,nbonds,ind,nat1;
- real *epot,v,dvdl;
- const t_pbc *pbc_null;
- char buf[22];
+ gmx_simd_cprod_r(*mx_S, *my_S, *mz_S,
+ *nx_S, *ny_S, *nz_S,
+ &cx_S, &cy_S, &cz_S);
- if (fr->bMolPBC)
- pbc_null = pbc;
- else
- pbc_null = NULL;
+ cn_S = gmx_simd_sqrt_r(gmx_simd_norm2_r(cx_S, cy_S, cz_S));
- if (bPrintSepPot)
- fprintf(fplog,"Step %s: bonded V and dVdl for this node\n",
- gmx_step_str(step,buf));
+ s_S = gmx_simd_iprod_r(*mx_S, *my_S, *mz_S, *nx_S, *ny_S, *nz_S);
-#ifdef DEBUG
- if (g && debug)
- p_graph(debug,"Bondage is fun",g);
-#endif
-
- epot = enerd->term;
-
- /* Do pre force calculation stuff which might require communication */
- if (idef->il[F_ORIRES].nr) {
- epot[F_ORIRESDEV] = calc_orires_dev(ms,idef->il[F_ORIRES].nr,
- idef->il[F_ORIRES].iatoms,
- idef->iparams,md,(const rvec*)x,
- pbc_null,fcd,hist);
- }
- if (idef->il[F_DISRES].nr) {
- calc_disres_R_6(ms,idef->il[F_DISRES].nr,
- idef->il[F_DISRES].iatoms,
- idef->iparams,(const rvec*)x,pbc_null,
- fcd,hist);
- }
-
- /* Loop over all bonded force types to calculate the bonded forces */
- for(ftype=0; (ftype<F_NRE); ftype++) {
- if(ftype<F_GB12 || ftype>F_GB14) {
- if ((interaction_function[ftype].flags & IF_BOND) &&
- !(ftype == F_CONNBONDS || ftype == F_POSRES)) {
- nbonds=idef->il[ftype].nr;
- if (nbonds > 0) {
- ind = interaction_function[ftype].nrnb_ind;
- nat1 = interaction_function[ftype].nratoms + 1;
- dvdl = 0;
- if (ftype < F_LJ14 || ftype > F_LJC_PAIRS_NB) {
- if(ftype==F_CMAP)
- {
- v = cmap_dihs(nbonds,idef->il[ftype].iatoms,
- idef->iparams,&idef->cmap_grid,
- (const rvec*)x,f,fr->fshift,
- pbc_null,g,lambda,&dvdl,md,fcd,
- global_atom_index);
- }
- else
- {
- v =
- interaction_function[ftype].ifunc(nbonds,idef->il[ftype].iatoms,
- idef->iparams,
- (const rvec*)x,f,fr->fshift,
- pbc_null,g,lambda,&dvdl,md,fcd,
- global_atom_index);
- }
-
- if (bPrintSepPot) {
- fprintf(fplog," %-23s #%4d V %12.5e dVdl %12.5e\n",
- interaction_function[ftype].longname,nbonds/nat1,v,dvdl);
- }
- } else {
- v = do_listed_vdw_q(ftype,nbonds,idef->il[ftype].iatoms,
- idef->iparams,
- (const rvec*)x,f,fr->fshift,
- pbc_null,g,
- lambda,&dvdl,
- md,fr,&enerd->grpp,global_atom_index);
- if (bPrintSepPot) {
- fprintf(fplog," %-5s + %-15s #%4d dVdl %12.5e\n",
- interaction_function[ftype].longname,
- interaction_function[F_COUL14].longname,nbonds/nat1,dvdl);
- }
- }
- if (ind != -1)
- inc_nrnb(nrnb,ind,nbonds/nat1);
- epot[ftype] += v;
- enerd->dvdl_nonlin += dvdl;
- }
- }
- }
- }
- /* Copy the sum of violations for the distance restraints from fcd */
- if (fcd)
- epot[F_DISRESVIOL] = fcd->disres.sumviol;
+ /* Determine the dihedral angle, the sign might need correction */
+ *phi_S = gmx_simd_atan2_r(cn_S, s_S);
+
+ ipr_S = gmx_simd_iprod_r(rijx_S, rijy_S, rijz_S,
+ *nx_S, *ny_S, *nz_S);
+
+ iprm_S = gmx_simd_norm2_r(*mx_S, *my_S, *mz_S);
+ iprn_S = gmx_simd_norm2_r(*nx_S, *ny_S, *nz_S);
+
+ nrkj2_S = gmx_simd_norm2_r(rkjx_S, rkjy_S, rkjz_S);
+
+ /* Avoid division by zero. When zero, the result is multiplied by 0
+ * anyhow, so the 3 max below do not affect the final result.
+ */
+ nrkj2_S = gmx_simd_max_r(nrkj2_S, nrkj2_min_S);
+ nrkj_1_S = gmx_simd_invsqrt_r(nrkj2_S);
+ nrkj_2_S = gmx_simd_mul_r(nrkj_1_S, nrkj_1_S);
+ nrkj_S = gmx_simd_mul_r(nrkj2_S, nrkj_1_S);
+
+ toler_S = gmx_simd_mul_r(nrkj2_S, real_eps_S);
+
+ /* Here the plain-C code uses a conditional, but we can't do that in SIMD.
+ * So we take a max with the tolerance instead. Since we multiply with
+ * m or n later, the max does not affect the results.
+ */
+ iprm_S = gmx_simd_max_r(iprm_S, toler_S);
+ iprn_S = gmx_simd_max_r(iprn_S, toler_S);
+ *nrkj_m2_S = gmx_simd_mul_r(nrkj_S, gmx_simd_inv_r(iprm_S));
+ *nrkj_n2_S = gmx_simd_mul_r(nrkj_S, gmx_simd_inv_r(iprn_S));
+
+ /* Set sign of phi_S with the sign of ipr_S; phi_S is currently positive */
+ *phi_S = gmx_simd_xor_sign_r(*phi_S, ipr_S);
+ p_S = gmx_simd_iprod_r(rijx_S, rijy_S, rijz_S,
+ rkjx_S, rkjy_S, rkjz_S);
+ p_S = gmx_simd_mul_r(p_S, nrkj_2_S);
+
+ q_S = gmx_simd_iprod_r(rklx_S, rkly_S, rklz_S,
+ rkjx_S, rkjy_S, rkjz_S);
+ q_S = gmx_simd_mul_r(q_S, nrkj_2_S);
+
+ gmx_simd_store_r(p, p_S);
+ gmx_simd_store_r(q, q_S);
}
-void calc_bonds_lambda(FILE *fplog,
- const t_idef *idef,
- rvec x[],
- t_forcerec *fr,
- const t_pbc *pbc,const t_graph *g,
- gmx_enerdata_t *enerd,t_nrnb *nrnb,
- real lambda,
- const t_mdatoms *md,
- t_fcdata *fcd,int *global_atom_index)
-{
- int ftype,nbonds_np,nbonds,ind, nat1;
- real *epot,v,dvdl;
- rvec *f,*fshift_orig;
- const t_pbc *pbc_null;
- t_iatom *iatom_fe;
-
- if (fr->bMolPBC)
- pbc_null = pbc;
- else
- pbc_null = NULL;
-
- epot = enerd->term;
-
- snew(f,fr->natoms_force);
- /* We want to preserve the fshift array in forcerec */
- fshift_orig = fr->fshift;
- snew(fr->fshift,SHIFTS);
-
- /* Loop over all bonded force types to calculate the bonded forces */
- for(ftype=0; (ftype<F_NRE); ftype++) {
- if(ftype<F_GB12 || ftype>F_GB14) {
-
- if ((interaction_function[ftype].flags & IF_BOND) &&
- !(ftype == F_CONNBONDS || ftype == F_POSRES))
- {
- nbonds_np = idef->il[ftype].nr_nonperturbed;
- nbonds = idef->il[ftype].nr - nbonds_np;
- nat1 = interaction_function[ftype].nratoms + 1;
- if (nbonds > 0) {
- ind = interaction_function[ftype].nrnb_ind;
- iatom_fe = idef->il[ftype].iatoms + nbonds_np;
- dvdl = 0;
- if (ftype < F_LJ14 || ftype > F_LJC_PAIRS_NB) {
- v =
- interaction_function[ftype].ifunc(nbonds,iatom_fe,
- idef->iparams,
- (const rvec*)x,f,fr->fshift,
- pbc_null,g,lambda,&dvdl,md,fcd,
- global_atom_index);
- } else {
- v = do_listed_vdw_q(ftype,nbonds,iatom_fe,
- idef->iparams,
- (const rvec*)x,f,fr->fshift,
- pbc_null,g,
- lambda,&dvdl,
- md,fr,&enerd->grpp,global_atom_index);
- }
- if (ind != -1)
- inc_nrnb(nrnb,ind,nbonds/nat1);
- epot[ftype] += v;
- }
- }
- }
- }
-
- sfree(fr->fshift);
- fr->fshift = fshift_orig;
- sfree(f);
+#endif /* GMX_SIMD_HAVE_REAL */
+
+
+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, rvec f[], rvec fshift[],
+ const t_pbc *pbc, const t_graph *g,
+ 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 */
+ nrkj2 = iprod(r_kj, r_kj); /* 5 */
+ toler = nrkj2*GMX_REAL_EPS;
+ if ((iprm > toler) && (iprn > toler))
+ {
+ nrkj_1 = gmx_invsqrt(nrkj2); /* 10 */
+ nrkj_2 = nrkj_1*nrkj_1; /* 1 */
+ nrkj = nrkj2*nrkj_1; /* 1 */
+ a = -ddphi*nrkj/iprm; /* 11 */
+ svmul(a, m, f_i); /* 3 */
+ b = ddphi*nrkj/iprn; /* 11 */
+ svmul(b, n, f_l); /* 3 */
+ p = iprod(r_ij, r_kj); /* 5 */
+ p *= nrkj_2; /* 1 */
+ q = iprod(r_kl, r_kj); /* 5 */
+ q *= nrkj_2; /* 1 */
+ svmul(p, f_i, uvec); /* 3 */
+ svmul(q, f_l, vvec); /* 3 */
+ rvec_sub(uvec, vvec, svec); /* 3 */
+ rvec_sub(f_i, svec, f_j); /* 3 */
+ rvec_add(f_l, svec, f_k); /* 3 */
+ rvec_inc(f[i], f_i); /* 3 */
+ rvec_dec(f[j], f_j); /* 3 */
+ rvec_dec(f[k], f_k); /* 3 */
+ rvec_inc(f[l], f_l); /* 3 */
+
+ 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)
+ {
+ t3 = pbc_rvec_sub(pbc, x[l], x[j], dx_jl);
+ }
+ else
+ {
+ t3 = CENTRAL;
+ }
+
+ rvec_inc(fshift[t1], f_i);
+ rvec_dec(fshift[CENTRAL], f_j);
+ rvec_dec(fshift[t2], f_k);
+ rvec_inc(fshift[t3], f_l);
+ }
+ /* 112 TOTAL */
+}
+
+/* As do_dih_fup above, but without shift forces */
+static void
+do_dih_fup_noshiftf(int i, int j, int k, int l, real ddphi,
+ rvec r_ij, rvec r_kj, rvec r_kl,
+ rvec m, rvec n, rvec f[])
+{
+ 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 */
+ nrkj2 = iprod(r_kj, r_kj); /* 5 */
+ toler = nrkj2*GMX_REAL_EPS;
+ if ((iprm > toler) && (iprn > toler))
+ {
+ nrkj_1 = gmx_invsqrt(nrkj2); /* 10 */
+ nrkj_2 = nrkj_1*nrkj_1; /* 1 */
+ nrkj = nrkj2*nrkj_1; /* 1 */
+ a = -ddphi*nrkj/iprm; /* 11 */
+ svmul(a, m, f_i); /* 3 */
+ b = ddphi*nrkj/iprn; /* 11 */
+ svmul(b, n, f_l); /* 3 */
+ p = iprod(r_ij, r_kj); /* 5 */
+ p *= nrkj_2; /* 1 */
+ q = iprod(r_kl, r_kj); /* 5 */
+ q *= nrkj_2; /* 1 */
+ svmul(p, f_i, uvec); /* 3 */
+ svmul(q, f_l, vvec); /* 3 */
+ rvec_sub(uvec, vvec, svec); /* 3 */
+ rvec_sub(f_i, svec, f_j); /* 3 */
+ rvec_add(f_l, svec, f_k); /* 3 */
+ rvec_inc(f[i], f_i); /* 3 */
+ rvec_dec(f[j], f_j); /* 3 */
+ rvec_dec(f[k], f_k); /* 3 */
+ rvec_inc(f[l], f_l); /* 3 */
+ }
+}
+
+/* As do_dih_fup_noshiftf above, but with pre-calculated pre-factors */
+static gmx_inline void
+do_dih_fup_noshiftf_precalc(int i, int j, int k, int l,
+ real p, real q,
+ real f_i_x, real f_i_y, real f_i_z,
+ real mf_l_x, real mf_l_y, real mf_l_z,
+ rvec f[])
+{
+ rvec f_i, f_j, f_k, f_l;
+ rvec uvec, vvec, svec;
+
+ f_i[XX] = f_i_x;
+ f_i[YY] = f_i_y;
+ f_i[ZZ] = f_i_z;
+ f_l[XX] = -mf_l_x;
+ f_l[YY] = -mf_l_y;
+ f_l[ZZ] = -mf_l_z;
+ svmul(p, f_i, uvec);
+ svmul(q, f_l, vvec);
+ rvec_sub(uvec, vvec, svec);
+ rvec_sub(f_i, svec, f_j);
+ rvec_add(f_l, svec, f_k);
+ rvec_inc(f[i], f_i);
+ rvec_dec(f[j], f_j);
+ rvec_dec(f[k], f_k);
+ rvec_inc(f[l], f_l);
+}
+
+
+real dopdihs(real cpA, real cpB, real phiA, real phiB, int mult,
+ real phi, real lambda, real *V, real *F)
+{
+ real v, dvdlambda, mdphi, v1, sdphi, ddphi;
+ real L1 = 1.0 - lambda;
+ real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD;
+ real dph0 = (phiB - phiA)*DEG2RAD;
+ real cp = L1*cpA + lambda*cpB;
+
+ mdphi = mult*phi - ph0;
+ sdphi = sin(mdphi);
+ ddphi = -cp*mult*sdphi;
+ v1 = 1.0 + cos(mdphi);
+ v = cp*v1;
+
+ dvdlambda = (cpB - cpA)*v1 + cp*dph0*sdphi;
+
+ *V = v;
+ *F = ddphi;
+
+ return dvdlambda;
+
+ /* That was 40 flops */
+}
+
+static void
+dopdihs_noener(real cpA, real cpB, real phiA, real phiB, int mult,
+ real phi, real lambda, real *F)
+{
+ real mdphi, sdphi, ddphi;
+ real L1 = 1.0 - lambda;
+ real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD;
+ real cp = L1*cpA + lambda*cpB;
+
+ mdphi = mult*phi - ph0;
+ sdphi = sin(mdphi);
+ ddphi = -cp*mult*sdphi;
+
+ *F = ddphi;
+
+ /* That was 20 flops */
+}
+
+static void
+dopdihs_mdphi(real cpA, real cpB, real phiA, real phiB, int mult,
+ real phi, real lambda, real *cp, real *mdphi)
+{
+ real L1 = 1.0 - lambda;
+ real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD;
+
+ *cp = L1*cpA + lambda*cpB;
+
+ *mdphi = mult*phi - ph0;
+}
+
+static real dopdihs_min(real cpA, real cpB, real phiA, real phiB, int mult,
+ real phi, real lambda, real *V, real *F)
+/* similar to dopdihs, except for a minus sign *
+ * and a different treatment of mult/phi0 */
+{
+ real v, dvdlambda, mdphi, v1, sdphi, ddphi;
+ real L1 = 1.0 - lambda;
+ real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD;
+ real dph0 = (phiB - phiA)*DEG2RAD;
+ real cp = L1*cpA + lambda*cpB;
+
+ mdphi = mult*(phi-ph0);
+ sdphi = sin(mdphi);
+ ddphi = cp*mult*sdphi;
+ v1 = 1.0-cos(mdphi);
+ v = cp*v1;
+
+ dvdlambda = (cpB-cpA)*v1 + cp*dph0*sdphi;
+
+ *V = v;
+ *F = ddphi;
+
+ return dvdlambda;
+
+ /* That was 40 flops */
+}
+
+real pdihs(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ int i, type, ai, aj, ak, al;
+ int t1, t2, t3;
+ rvec r_ij, r_kj, r_kl, m, n;
+ real phi, sign, ddphi, vpd, vtot;
+
+ vtot = 0.0;
+
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ al = forceatoms[i++];
+
+ phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
+ &sign, &t1, &t2, &t3); /* 84 */
+ *dvdlambda += dopdihs(forceparams[type].pdihs.cpA,
+ forceparams[type].pdihs.cpB,
+ forceparams[type].pdihs.phiA,
+ forceparams[type].pdihs.phiB,
+ forceparams[type].pdihs.mult,
+ phi, lambda, &vpd, &ddphi);
+
+ vtot += vpd;
+ 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 */
+
+#ifdef DEBUG
+ fprintf(debug, "pdih: (%d,%d,%d,%d) phi=%g\n",
+ ai, aj, ak, al, phi);
+#endif
+ } /* 223 TOTAL */
+
+ return vtot;
+}
+
+void make_dp_periodic(real *dp) /* 1 flop? */
+{
+ /* dp cannot be outside (-pi,pi) */
+ if (*dp >= M_PI)
+ {
+ *dp -= 2*M_PI;
+ }
+ else if (*dp < -M_PI)
+ {
+ *dp += 2*M_PI;
+ }
+ return;
+}
+
+/* As pdihs above, but without calculating energies and shift forces */
+static void
+pdihs_noener(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const t_pbc gmx_unused *pbc, const t_graph gmx_unused *g,
+ real lambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ int i, type, ai, aj, ak, al;
+ int t1, t2, t3;
+ rvec r_ij, r_kj, r_kl, m, n;
+ real phi, sign, ddphi_tot, ddphi;
+
+ for (i = 0; (i < nbonds); )
+ {
+ ai = forceatoms[i+1];
+ aj = forceatoms[i+2];
+ ak = forceatoms[i+3];
+ al = forceatoms[i+4];
+
+ phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
+ &sign, &t1, &t2, &t3);
+
+ ddphi_tot = 0;
+
+ /* Loop over dihedrals working on the same atoms,
+ * so we avoid recalculating angles and force distributions.
+ */
+ do
+ {
+ type = forceatoms[i];
+ dopdihs_noener(forceparams[type].pdihs.cpA,
+ forceparams[type].pdihs.cpB,
+ forceparams[type].pdihs.phiA,
+ forceparams[type].pdihs.phiB,
+ forceparams[type].pdihs.mult,
+ phi, lambda, &ddphi);
+ ddphi_tot += ddphi;
+
+ i += 5;
+ }
+ while (i < nbonds &&
+ forceatoms[i+1] == ai &&
+ forceatoms[i+2] == aj &&
+ forceatoms[i+3] == ak &&
+ forceatoms[i+4] == al);
+
+ do_dih_fup_noshiftf(ai, aj, ak, al, ddphi_tot, r_ij, r_kj, r_kl, m, n, f);
+ }
+}
+
+
+#ifdef GMX_SIMD_HAVE_REAL
+
+/* As pdihs_noner above, but using SIMD to calculate many dihedrals at once */
+static void
+pdihs_noener_simd(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const t_pbc *pbc, const t_graph gmx_unused *g,
+ real gmx_unused lambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ 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;
+ 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;
+ gmx_simd_real_t nrkj_m2_S, nrkj_n2_S;
+ gmx_simd_real_t cp_S, mdphi_S, mult_S;
+ gmx_simd_real_t sin_S, cos_S;
+ gmx_simd_real_t mddphi_S;
+ gmx_simd_real_t sf_i_S, msf_l_S;
+ pbc_simd_t pbc_simd;
+
+ /* Ensure SIMD register alignment */
+ dr = gmx_simd_align_r(dr_array);
+ buf = gmx_simd_align_r(buf_array);
+
+ /* Extract aligned pointer for parameters and variables */
+ cp = buf + 0*GMX_SIMD_REAL_WIDTH;
+ phi0 = buf + 1*GMX_SIMD_REAL_WIDTH;
+ 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);
+
+ /* nbonds is the number of dihedrals times nfa1, here we step GMX_SIMD_REAL_WIDTH dihs */
+ for (i = 0; (i < nbonds); i += GMX_SIMD_REAL_WIDTH*nfa1)
+ {
+ /* Collect atoms quadruplets for GMX_SIMD_REAL_WIDTH dihedrals.
+ * iu indexes into forceatoms, we should not let iu go beyond nbonds.
+ */
+ iu = i;
+ for (s = 0; s < GMX_SIMD_REAL_WIDTH; s++)
+ {
+ type = forceatoms[iu];
+ ai[s] = forceatoms[iu+1];
+ aj[s] = forceatoms[iu+2];
+ ak[s] = forceatoms[iu+3];
+ al[s] = forceatoms[iu+4];
+
+ cp[s] = forceparams[type].pdihs.cpA;
+ phi0[s] = forceparams[type].pdihs.phiA*DEG2RAD;
+ mult[s] = forceparams[type].pdihs.mult;
+
+ /* At the end fill the arrays with identical entries */
+ if (iu + nfa1 < nbonds)
+ {
+ iu += nfa1;
+ }
+ }
+
+ /* Caclulate GMX_SIMD_REAL_WIDTH dihedral angles at once */
+ dih_angle_simd(x, ai, aj, ak, al, &pbc_simd,
+ dr,
+ &phi_S,
+ &mx_S, &my_S, &mz_S,
+ &nx_S, &ny_S, &nz_S,
+ &nrkj_m2_S,
+ &nrkj_n2_S,
+ p, q);
+
+ cp_S = gmx_simd_load_r(cp);
+ phi0_S = gmx_simd_load_r(phi0);
+ mult_S = gmx_simd_load_r(mult);
+
+ mdphi_S = gmx_simd_sub_r(gmx_simd_mul_r(mult_S, phi_S), phi0_S);
+
+ /* Calculate GMX_SIMD_REAL_WIDTH sines at once */
+ gmx_simd_sincos_r(mdphi_S, &sin_S, &cos_S);
+ mddphi_S = gmx_simd_mul_r(gmx_simd_mul_r(cp_S, mult_S), sin_S);
+ sf_i_S = gmx_simd_mul_r(mddphi_S, nrkj_m2_S);
+ msf_l_S = gmx_simd_mul_r(mddphi_S, nrkj_n2_S);
+
+ /* After this m?_S will contain f[i] */
+ mx_S = gmx_simd_mul_r(sf_i_S, mx_S);
+ my_S = gmx_simd_mul_r(sf_i_S, my_S);
+ mz_S = gmx_simd_mul_r(sf_i_S, mz_S);
+
+ /* After this m?_S will contain -f[l] */
+ nx_S = gmx_simd_mul_r(msf_l_S, nx_S);
+ ny_S = gmx_simd_mul_r(msf_l_S, ny_S);
+ nz_S = gmx_simd_mul_r(msf_l_S, nz_S);
+
+ gmx_simd_store_r(dr + 0*GMX_SIMD_REAL_WIDTH, mx_S);
+ gmx_simd_store_r(dr + 1*GMX_SIMD_REAL_WIDTH, my_S);
+ gmx_simd_store_r(dr + 2*GMX_SIMD_REAL_WIDTH, mz_S);
+ gmx_simd_store_r(dr + 3*GMX_SIMD_REAL_WIDTH, nx_S);
+ gmx_simd_store_r(dr + 4*GMX_SIMD_REAL_WIDTH, ny_S);
+ gmx_simd_store_r(dr + 5*GMX_SIMD_REAL_WIDTH, nz_S);
+
+ iu = i;
+ s = 0;
+ do
+ {
+ do_dih_fup_noshiftf_precalc(ai[s], aj[s], ak[s], al[s],
+ p[s], q[s],
+ dr[ XX *GMX_SIMD_REAL_WIDTH+s],
+ dr[ YY *GMX_SIMD_REAL_WIDTH+s],
+ dr[ ZZ *GMX_SIMD_REAL_WIDTH+s],
+ dr[(DIM+XX)*GMX_SIMD_REAL_WIDTH+s],
+ dr[(DIM+YY)*GMX_SIMD_REAL_WIDTH+s],
+ dr[(DIM+ZZ)*GMX_SIMD_REAL_WIDTH+s],
+ f);
+ s++;
+ iu += nfa1;
+ }
+ while (s < GMX_SIMD_REAL_WIDTH && iu < nbonds);
+ }
+}
+
+/* This is mostly a copy of pdihs_noener_simd above, but with using
+ * the RB potential instead of a harmonic potential.
+ * This function can replace rbdihs() when no energy and virial are needed.
+ */
+static void
+rbdihs_noener_simd(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const t_pbc *pbc, const t_graph gmx_unused *g,
+ real gmx_unused lambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ 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;
+
+ gmx_simd_real_t phi_S;
+ gmx_simd_real_t ddphi_S, cosfac_S;
+ gmx_simd_real_t mx_S, my_S, mz_S;
+ gmx_simd_real_t nx_S, ny_S, nz_S;
+ gmx_simd_real_t nrkj_m2_S, nrkj_n2_S;
+ gmx_simd_real_t parm_S, c_S;
+ gmx_simd_real_t sin_S, cos_S;
+ gmx_simd_real_t sf_i_S, msf_l_S;
+ pbc_simd_t pbc_simd;
+
+ gmx_simd_real_t pi_S = gmx_simd_set1_r(M_PI);
+ gmx_simd_real_t one_S = gmx_simd_set1_r(1.0);
+
+ /* Ensure SIMD register alignment */
+ dr = gmx_simd_align_r(dr_array);
+ buf = gmx_simd_align_r(buf_array);
+
+ /* Extract aligned pointer for parameters and variables */
+ 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);
+
+ /* nbonds is the number of dihedrals times nfa1, here we step GMX_SIMD_REAL_WIDTH dihs */
+ for (i = 0; (i < nbonds); i += GMX_SIMD_REAL_WIDTH*nfa1)
+ {
+ /* Collect atoms quadruplets for GMX_SIMD_REAL_WIDTH dihedrals.
+ * iu indexes into forceatoms, we should not let iu go beyond nbonds.
+ */
+ iu = i;
+ for (s = 0; s < GMX_SIMD_REAL_WIDTH; s++)
+ {
+ type = forceatoms[iu];
+ ai[s] = forceatoms[iu+1];
+ aj[s] = forceatoms[iu+2];
+ ak[s] = forceatoms[iu+3];
+ al[s] = forceatoms[iu+4];
+
+ /* We don't need the first parameter, since that's a constant
+ * which only affects the energies, not the forces.
+ */
+ for (j = 1; j < NR_RBDIHS; j++)
+ {
+ parm[j*GMX_SIMD_REAL_WIDTH + s] =
+ forceparams[type].rbdihs.rbcA[j];
+ }
+
+ /* At the end fill the arrays with identical entries */
+ if (iu + nfa1 < nbonds)
+ {
+ iu += nfa1;
+ }
+ }
+
+ /* Caclulate GMX_SIMD_REAL_WIDTH dihedral angles at once */
+ dih_angle_simd(x, ai, aj, ak, al, &pbc_simd,
+ dr,
+ &phi_S,
+ &mx_S, &my_S, &mz_S,
+ &nx_S, &ny_S, &nz_S,
+ &nrkj_m2_S,
+ &nrkj_n2_S,
+ p, q);
+
+ /* Change to polymer convention */
+ phi_S = gmx_simd_sub_r(phi_S, pi_S);
+
+ gmx_simd_sincos_r(phi_S, &sin_S, &cos_S);
+
+ ddphi_S = gmx_simd_setzero_r();
+ c_S = one_S;
+ cosfac_S = one_S;
+ for (j = 1; j < NR_RBDIHS; j++)
+ {
+ parm_S = gmx_simd_load_r(parm + j*GMX_SIMD_REAL_WIDTH);
+ ddphi_S = gmx_simd_fmadd_r(gmx_simd_mul_r(c_S, parm_S), cosfac_S, ddphi_S);
+ cosfac_S = gmx_simd_mul_r(cosfac_S, cos_S);
+ c_S = gmx_simd_add_r(c_S, one_S);
+ }
+
+ /* Note that here we do not use the minus sign which is present
+ * in the normal RB code. This is corrected for through (m)sf below.
+ */
+ ddphi_S = gmx_simd_mul_r(ddphi_S, sin_S);
+
+ sf_i_S = gmx_simd_mul_r(ddphi_S, nrkj_m2_S);
+ msf_l_S = gmx_simd_mul_r(ddphi_S, nrkj_n2_S);
+
+ /* After this m?_S will contain f[i] */
+ mx_S = gmx_simd_mul_r(sf_i_S, mx_S);
+ my_S = gmx_simd_mul_r(sf_i_S, my_S);
+ mz_S = gmx_simd_mul_r(sf_i_S, mz_S);
+
+ /* After this m?_S will contain -f[l] */
+ nx_S = gmx_simd_mul_r(msf_l_S, nx_S);
+ ny_S = gmx_simd_mul_r(msf_l_S, ny_S);
+ nz_S = gmx_simd_mul_r(msf_l_S, nz_S);
+
+ gmx_simd_store_r(dr + 0*GMX_SIMD_REAL_WIDTH, mx_S);
+ gmx_simd_store_r(dr + 1*GMX_SIMD_REAL_WIDTH, my_S);
+ gmx_simd_store_r(dr + 2*GMX_SIMD_REAL_WIDTH, mz_S);
+ gmx_simd_store_r(dr + 3*GMX_SIMD_REAL_WIDTH, nx_S);
+ gmx_simd_store_r(dr + 4*GMX_SIMD_REAL_WIDTH, ny_S);
+ gmx_simd_store_r(dr + 5*GMX_SIMD_REAL_WIDTH, nz_S);
+
+ iu = i;
+ s = 0;
+ do
+ {
+ do_dih_fup_noshiftf_precalc(ai[s], aj[s], ak[s], al[s],
+ p[s], q[s],
+ dr[ XX *GMX_SIMD_REAL_WIDTH+s],
+ dr[ YY *GMX_SIMD_REAL_WIDTH+s],
+ dr[ ZZ *GMX_SIMD_REAL_WIDTH+s],
+ dr[(DIM+XX)*GMX_SIMD_REAL_WIDTH+s],
+ dr[(DIM+YY)*GMX_SIMD_REAL_WIDTH+s],
+ dr[(DIM+ZZ)*GMX_SIMD_REAL_WIDTH+s],
+ f);
+ s++;
+ iu += nfa1;
+ }
+ while (s < GMX_SIMD_REAL_WIDTH && iu < nbonds);
+ }
+}
+
+#endif /* GMX_SIMD_HAVE_REAL */
+
+
+real idihs(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ int i, type, ai, aj, ak, al;
+ int t1, t2, t3;
+ real phi, phi0, dphi0, ddphi, sign, vtot;
+ rvec r_ij, r_kj, r_kl, m, n;
+ real L1, kk, dp, dp2, kA, kB, pA, pB, dvdl_term;
+
+ L1 = 1.0-lambda;
+ dvdl_term = 0;
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ al = forceatoms[i++];
+
+ phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
+ &sign, &t1, &t2, &t3); /* 84 */
+
+ /* phi can jump if phi0 is close to Pi/-Pi, which will cause huge
+ * force changes if we just apply a normal harmonic.
+ * Instead, we first calculate phi-phi0 and take it modulo (-Pi,Pi).
+ * This means we will never have the periodicity problem, unless
+ * the dihedral is Pi away from phiO, which is very unlikely due to
+ * the potential.
+ */
+ kA = forceparams[type].harmonic.krA;
+ kB = forceparams[type].harmonic.krB;
+ pA = forceparams[type].harmonic.rA;
+ pB = forceparams[type].harmonic.rB;
+
+ kk = L1*kA + lambda*kB;
+ phi0 = (L1*pA + lambda*pB)*DEG2RAD;
+ dphi0 = (pB - pA)*DEG2RAD;
+
+ dp = phi-phi0;
+
+ make_dp_periodic(&dp);
+
+ dp2 = dp*dp;
+
+ vtot += 0.5*kk*dp2;
+ ddphi = -kk*dp;
+
+ 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,
+ f, fshift, pbc, g, x, t1, t2, t3); /* 112 */
+ /* 218 TOTAL */
+#ifdef DEBUG
+ if (debug)
+ {
+ fprintf(debug, "idih: (%d,%d,%d,%d) phi=%g\n",
+ ai, aj, ak, al, phi);
+ }
+#endif
+ }
+
+ *dvdlambda += dvdl_term;
+ return vtot;
+}
+
+
+/*! \brief returns dx, rdist, and dpdl for functions posres() and fbposres()
+ */
+static void posres_dx(const rvec x, const rvec pos0A, const rvec pos0B,
+ const rvec comA_sc, const rvec comB_sc,
+ real lambda,
+ t_pbc *pbc, int refcoord_scaling, int npbcdim,
+ rvec dx, rvec rdist, rvec dpdl)
+{
+ int m, d;
+ real posA, posB, L1, ref = 0.;
+ rvec pos;
+
+ L1 = 1.0-lambda;
+
+ for (m = 0; m < DIM; m++)
+ {
+ posA = pos0A[m];
+ posB = pos0B[m];
+ if (m < npbcdim)
+ {
+ switch (refcoord_scaling)
+ {
+ case erscNO:
+ ref = 0;
+ rdist[m] = L1*posA + lambda*posB;
+ dpdl[m] = posB - posA;
+ break;
+ case erscALL:
+ /* Box relative coordinates are stored for dimensions with pbc */
+ posA *= pbc->box[m][m];
+ posB *= pbc->box[m][m];
+ assert(npbcdim <= DIM);
+ for (d = m+1; d < npbcdim; d++)
+ {
+ posA += pos0A[d]*pbc->box[d][m];
+ posB += pos0B[d]*pbc->box[d][m];
+ }
+ ref = L1*posA + lambda*posB;
+ rdist[m] = 0;
+ dpdl[m] = posB - posA;
+ break;
+ case erscCOM:
+ ref = L1*comA_sc[m] + lambda*comB_sc[m];
+ rdist[m] = L1*posA + lambda*posB;
+ dpdl[m] = comB_sc[m] - comA_sc[m] + posB - posA;
+ break;
+ default:
+ gmx_fatal(FARGS, "No such scaling method implemented");
+ }
+ }
+ else
+ {
+ ref = L1*posA + lambda*posB;
+ rdist[m] = 0;
+ dpdl[m] = posB - posA;
+ }
+
+ /* We do pbc_dx with ref+rdist,
+ * since with only ref we can be up to half a box vector wrong.
+ */
+ pos[m] = ref + rdist[m];
+ }
+
+ if (pbc)
+ {
+ pbc_dx(pbc, x, pos, dx);
+ }
+ else
+ {
+ rvec_sub(x, pos, dx);
+ }
+}
+
+/*! \brief Adds forces of flat-bottomed positions restraints to f[]
+ * and fixes vir_diag. Returns the flat-bottomed potential. */
+real fbposres(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec vir_diag,
+ t_pbc *pbc,
+ int refcoord_scaling, int ePBC, rvec com)
+/* compute flat-bottomed positions restraints */
+{
+ 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;
+ gmx_bool bInvert;
+
+ npbcdim = ePBC2npbcdim(ePBC);
+
+ if (refcoord_scaling == erscCOM)
+ {
+ clear_rvec(com_sc);
+ for (m = 0; m < npbcdim; m++)
+ {
+ assert(npbcdim <= DIM);
+ for (d = m; d < npbcdim; d++)
+ {
+ com_sc[m] += com[d]*pbc->box[d][m];
+ }
+ }
+ }
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ pr = &forceparams[type];
+
+ /* same calculation as for normal posres, but with identical A and B states, and lambda==0 */
+ posres_dx(x[ai], forceparams[type].fbposres.pos0, forceparams[type].fbposres.pos0,
+ com_sc, com_sc, 0.0,
+ pbc, refcoord_scaling, npbcdim,
+ dx, rdist, dpdl);
+
+ clear_rvec(fm);
+ v = 0.0;
+
+ kk = pr->fbposres.k;
+ rfb = pr->fbposres.r;
+ rfb2 = sqr(rfb);
+
+ /* with rfb<0, push particle out of the sphere/cylinder/layer */
+ bInvert = FALSE;
+ if (rfb < 0.)
+ {
+ bInvert = TRUE;
+ rfb = -rfb;
+ }
+
+ switch (pr->fbposres.geom)
+ {
+ case efbposresSPHERE:
+ /* spherical flat-bottom posres */
+ dr2 = norm2(dx);
+ if (dr2 > 0.0 &&
+ ( (dr2 > rfb2 && bInvert == FALSE ) || (dr2 < rfb2 && bInvert == TRUE ) )
+ )
+ {
+ dr = sqrt(dr2);
+ v = 0.5*kk*sqr(dr - rfb);
+ fact = -kk*(dr-rfb)/dr; /* Force pointing to the center pos0 */
+ svmul(fact, dx, fm);
+ }
+ 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;
+ }
+ break;
+ case efbposresX: /* fbdim=XX */
+ case efbposresY: /* fbdim=YY */
+ case efbposresZ: /* fbdim=ZZ */
+ /* 1D flat-bottom potential */
+ fbdim = pr->fbposres.geom - efbposresX;
+ dr = dx[fbdim];
+ if ( ( dr > rfb && bInvert == FALSE ) || ( 0 < dr && dr < rfb && bInvert == TRUE ) )
+ {
+ v = 0.5*kk*sqr(dr - rfb);
+ fm[fbdim] = -kk*(dr - rfb);
+ }
+ else if ( (dr < (-rfb) && bInvert == FALSE ) || ( (-rfb) < dr && dr < 0 && bInvert == TRUE ))
+ {
+ v = 0.5*kk*sqr(dr + rfb);
+ fm[fbdim] = -kk*(dr + rfb);
+ }
+ break;
+ }
+
+ vtot += v;
+
+ for (m = 0; (m < DIM); m++)
+ {
+ f[ai][m] += fm[m];
+ /* Here we correct for the pbc_dx which included rdist */
+ vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];
+ }
+ }
+
+ return vtot;
+}
+
+
+real posres(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec vir_diag,
+ t_pbc *pbc,
+ real lambda, real *dvdlambda,
+ int refcoord_scaling, int ePBC, rvec comA, rvec comB)
+{
+ int i, ai, m, d, type, ki, 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;
+ gmx_bool bForceValid = TRUE;
+
+ if ((f == NULL) || (vir_diag == NULL)) /* should both be null together! */
+ {
+ bForceValid = FALSE;
+ }
+
+ npbcdim = ePBC2npbcdim(ePBC);
+
+ if (refcoord_scaling == erscCOM)
+ {
+ clear_rvec(comA_sc);
+ clear_rvec(comB_sc);
+ for (m = 0; m < npbcdim; m++)
+ {
+ assert(npbcdim <= DIM);
+ for (d = m; d < npbcdim; d++)
+ {
+ comA_sc[m] += comA[d]*pbc->box[d][m];
+ comB_sc[m] += comB[d]*pbc->box[d][m];
+ }
+ }
+ }
+
+ L1 = 1.0 - lambda;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ pr = &forceparams[type];
+
+ /* return dx, rdist, and dpdl */
+ posres_dx(x[ai], forceparams[type].posres.pos0A, forceparams[type].posres.pos0B,
+ comA_sc, comB_sc, lambda,
+ pbc, refcoord_scaling, npbcdim,
+ dx, rdist, dpdl);
+
+ for (m = 0; (m < DIM); m++)
+ {
+ kk = L1*pr->posres.fcA[m] + lambda*pr->posres.fcB[m];
+ fm = -kk*dx[m];
+ vtot += 0.5*kk*dx[m]*dx[m];
+ *dvdlambda +=
+ 0.5*(pr->posres.fcB[m] - pr->posres.fcA[m])*dx[m]*dx[m]
+ + fm*dpdl[m];
+
+ /* Here we correct for the pbc_dx which included rdist */
+ if (bForceValid)
+ {
+ f[ai][m] += fm;
+ vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm;
+ }
+ }
+ }
+
+ return vtot;
+}
+
+static real low_angres(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const t_pbc *pbc, const t_graph *g,
+ real lambda, real *dvdlambda,
+ gmx_bool bZAxis)
+{
+ int i, m, type, ai, aj, ak, al;
+ int t1, t2;
+ real phi, cos_phi, cos_phi2, vid, vtot, dVdphi;
+ 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;
+ ak = al = 0; /* to avoid warnings */
+ for (i = 0; i < nbonds; )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ t1 = pbc_rvec_sub(pbc, x[aj], x[ai], r_ij); /* 3 */
+ if (!bZAxis)
+ {
+ ak = forceatoms[i++];
+ al = forceatoms[i++];
+ t2 = pbc_rvec_sub(pbc, x[al], x[ak], r_kl); /* 3 */
+ }
+ else
+ {
+ r_kl[XX] = 0;
+ r_kl[YY] = 0;
+ r_kl[ZZ] = 1;
+ }
+
+ cos_phi = cos_angle(r_ij, r_kl); /* 25 */
+ phi = acos(cos_phi); /* 10 */
+
+ *dvdlambda += dopdihs_min(forceparams[type].pdihs.cpA,
+ forceparams[type].pdihs.cpB,
+ forceparams[type].pdihs.phiA,
+ forceparams[type].pdihs.phiB,
+ forceparams[type].pdihs.mult,
+ phi, lambda, &vid, &dVdphi); /* 40 */
+
+ vtot += vid;
+
+ cos_phi2 = sqr(cos_phi); /* 1 */
+ if (cos_phi2 < 1)
+ {
+ st = -dVdphi*gmx_invsqrt(1 - cos_phi2); /* 12 */
+ sth = st*cos_phi; /* 1 */
+ nrij2 = iprod(r_ij, r_ij); /* 5 */
+ nrkl2 = iprod(r_kl, r_kl); /* 5 */
+
+ c = st*gmx_invsqrt(nrij2*nrkl2); /* 11 */
+ cij = sth/nrij2; /* 10 */
+ ckl = sth/nrkl2; /* 10 */
+
+ for (m = 0; m < DIM; m++) /* 18+18 */
+ {
+ f_i[m] = (c*r_kl[m]-cij*r_ij[m]);
+ f[ai][m] += f_i[m];
+ f[aj][m] -= f_i[m];
+ if (!bZAxis)
+ {
+ f_k[m] = (c*r_ij[m]-ckl*r_kl[m]);
+ f[ak][m] += f_k[m];
+ f[al][m] -= f_k[m];
+ }
+ }
+
+ 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);
+ }
+ }
+ }
+
+ return vtot; /* 184 / 157 (bZAxis) total */
+}
+
+real angres(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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(nbonds, forceatoms, forceparams, x, f, fshift, pbc, g,
+ lambda, dvdlambda, FALSE);
+}
+
+real angresz(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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(nbonds, forceatoms, forceparams, x, f, fshift, pbc, g,
+ lambda, dvdlambda, TRUE);
+}
+
+real dihres(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ 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;
+ rvec r_ij, r_kj, r_kl, m, n;
+
+ L1 = 1.0-lambda;
+
+ d2r = DEG2RAD;
+ k = 0;
+
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ al = forceatoms[i++];
+
+ phi0A = forceparams[type].dihres.phiA*d2r;
+ dphiA = forceparams[type].dihres.dphiA*d2r;
+ kfacA = forceparams[type].dihres.kfacA;
+
+ phi0B = forceparams[type].dihres.phiB*d2r;
+ dphiB = forceparams[type].dihres.dphiB*d2r;
+ kfacB = forceparams[type].dihres.kfacB;
+
+ phi0 = L1*phi0A + lambda*phi0B;
+ dphi = L1*dphiA + lambda*dphiB;
+ kfac = L1*kfacA + lambda*kfacB;
+
+ phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
+ &sign, &t1, &t2, &t3);
+ /* 84 flops */
+
+ if (debug)
+ {
+ fprintf(debug, "dihres[%d]: %d %d %d %d : phi=%f, dphi=%f, kfac=%f\n",
+ k++, ai, aj, ak, al, phi0, dphi, kfac);
+ }
+ /* phi can jump if phi0 is close to Pi/-Pi, which will cause huge
+ * force changes if we just apply a normal harmonic.
+ * Instead, we first calculate phi-phi0 and take it modulo (-Pi,Pi).
+ * This means we will never have the periodicity problem, unless
+ * the dihedral is Pi away from phiO, which is very unlikely due to
+ * the potential.
+ */
+ dp = phi-phi0;
+ make_dp_periodic(&dp);
+
+ if (dp > dphi)
+ {
+ ddp = dp-dphi;
+ }
+ else if (dp < -dphi)
+ {
+ ddp = dp+dphi;
+ }
+ else
+ {
+ ddp = 0;
+ }
+
+ if (ddp != 0.0)
+ {
+ ddp2 = ddp*ddp;
+ vtot += 0.5*kfac*ddp2;
+ ddphi = kfac*ddp;
+
+ *dvdlambda += 0.5*(kfacB - kfacA)*ddp2;
+ /* lambda dependence from changing restraint distances */
+ if (ddp > 0)
+ {
+ *dvdlambda -= kfac*ddp*((dphiB - dphiA)+(phi0B - phi0A));
+ }
+ else if (ddp < 0)
+ {
+ *dvdlambda += kfac*ddp*((dphiB - dphiA)-(phi0B - phi0A));
+ }
+ 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 */
+ }
+ }
+ return vtot;
+}
+
+
+real unimplemented(int gmx_unused nbonds,
+ const t_iatom gmx_unused forceatoms[], const t_iparams gmx_unused forceparams[],
+ const rvec gmx_unused x[], rvec 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, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ gmx_impl("*** you are using a not implemented function");
+
+ return 0.0; /* To make the compiler happy */
+}
+
+real restrangles(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ 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, 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;
+ real prefactor, ratio_ante, ratio_post;
+ rvec delta_ante, delta_post, vec_temp;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+
+ 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_post);
+
+
+ /* This function computes factors needed for restricted angle potential.
+ * The restricted angle potential is used in coarse-grained simulations to avoid singularities
+ * when three particles align and the dihedral angle and dihedral potential
+ * cannot be calculated. This potential is calculated using the formula:
+ real restrangles(int nbonds,
+ const t_iatom forceatoms[],const t_iparams forceparams[],
+ 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, 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;
+ real prefactor, ratio_ante, ratio_post;
+ rvec delta_ante, delta_post, vec_temp;
+
+ vtot = 0.0;
+ for(i=0; (i<nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+
+ * \f[V_{\rm ReB}(\theta_i) = \frac{1}{2} k_{\theta} \frac{(\cos\theta_i - \cos\theta_0)^2}
+ * {\sin^2\theta_i}\f] ({eq:ReB} and ref \cite{MonicaGoga2013} from the manual).
+ * For more explanations see comments file "restcbt.h". */
+
+ compute_factors_restangles(type, forceparams, delta_ante, delta_post,
+ &prefactor, &ratio_ante, &ratio_post, &v);
+
+ /* Forces are computed per component */
+ for (d = 0; d < DIM; d++)
+ {
+ f_i[d] = prefactor * (ratio_ante * delta_ante[d] - delta_post[d]);
+ f_j[d] = prefactor * ((ratio_post + 1.0) * delta_post[d] - (ratio_ante + 1.0) * delta_ante[d]);
+ f_k[d] = prefactor * (delta_ante[d] - ratio_post * delta_post[d]);
+ }
+
+ /* Computation of potential energy */
+
+ vtot += v;
+
+ /* Update forces */
+
+ for (m = 0; (m < DIM); m++)
+ {
+ f[ai][m] += f_i[m];
+ f[aj][m] += f_j[m];
+ f[ak][m] += f_k[m];
+ }
+
+ 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);
+ }
+ return vtot;
+}
+
+
+real restrdihs(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
+{
+ 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;
+ real factor_phi_ai_ante, factor_phi_ai_crnt, factor_phi_ai_post;
+ real factor_phi_aj_ante, factor_phi_aj_crnt, factor_phi_aj_post;
+ real factor_phi_ak_ante, factor_phi_ak_crnt, factor_phi_ak_post;
+ real factor_phi_al_ante, factor_phi_al_crnt, factor_phi_al_post;
+ real prefactor_phi;
+
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ al = forceatoms[i++];
+
+ 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[al], x[ak], delta_post);
+
+ /* This function computes factors needed for restricted angle potential.
+ * The restricted angle potential is used in coarse-grained simulations to avoid singularities
+ * when three particles align and the dihedral angle and dihedral potential cannot be calculated.
+ * This potential is calculated using the formula:
+ * \f[V_{\rm ReB}(\theta_i) = \frac{1}{2} k_{\theta}
+ * \frac{(\cos\theta_i - \cos\theta_0)^2}{\sin^2\theta_i}\f]
+ * ({eq:ReB} and ref \cite{MonicaGoga2013} from the manual).
+ * For more explanations see comments file "restcbt.h" */
+
+ compute_factors_restrdihs(type, forceparams,
+ delta_ante, delta_crnt, delta_post,
+ &factor_phi_ai_ante, &factor_phi_ai_crnt, &factor_phi_ai_post,
+ &factor_phi_aj_ante, &factor_phi_aj_crnt, &factor_phi_aj_post,
+ &factor_phi_ak_ante, &factor_phi_ak_crnt, &factor_phi_ak_post,
+ &factor_phi_al_ante, &factor_phi_al_crnt, &factor_phi_al_post,
+ &prefactor_phi, &v);
+
+
+ /* Computation of forces per component */
+ for (d = 0; d < DIM; d++)
+ {
+ f_i[d] = prefactor_phi * (factor_phi_ai_ante * delta_ante[d] + factor_phi_ai_crnt * delta_crnt[d] + factor_phi_ai_post * delta_post[d]);
+ f_j[d] = prefactor_phi * (factor_phi_aj_ante * delta_ante[d] + factor_phi_aj_crnt * delta_crnt[d] + factor_phi_aj_post * delta_post[d]);
+ f_k[d] = prefactor_phi * (factor_phi_ak_ante * delta_ante[d] + factor_phi_ak_crnt * delta_crnt[d] + factor_phi_ak_post * delta_post[d]);
+ f_l[d] = prefactor_phi * (factor_phi_al_ante * delta_ante[d] + factor_phi_al_crnt * delta_crnt[d] + factor_phi_al_post * delta_post[d]);
+ }
+ /* Computation of the energy */
+
+ vtot += v;
+
+
+
+ /* Updating the forces */
+
+ rvec_inc(f[ai], f_i);
+ rvec_inc(f[aj], f_j);
+ rvec_inc(f[ak], f_k);
+ rvec_inc(f[al], f_l);
+
+
+ /* Updating the fshift forces for the pressure coupling */
+ 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)
+ {
+ t3 = pbc_rvec_sub(pbc, x[al], x[aj], dx_jl);
+ }
+ else
+ {
+ t3 = CENTRAL;
+ }
+
+ rvec_inc(fshift[t1], f_i);
+ rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[t2], f_k);
+ rvec_inc(fshift[t3], f_l);
+
+ }
+
+ return vtot;
+}
+
+
+real cbtdihs(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ 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 type, ai, aj, ak, al, i, d;
+ int t1, t2, t3;
+ 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;
+ rvec f_theta_ante_ai, f_theta_ante_aj, f_theta_ante_ak;
+ rvec f_theta_post_aj, f_theta_post_ak, f_theta_post_al;
+
+
+
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ al = forceatoms[i++];
+
+
+ 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], 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[al], x[ak], delta_post);
+
+ /* \brief Compute factors for CBT potential
+ * The combined bending-torsion potential goes to zero in a very smooth manner, eliminating the numerical
+ * instabilities, when three coarse-grained particles align and the dihedral angle and standard
+ * dihedral potentials cannot be calculated. The CBT potential is calculated using the formula:
+ * \f[V_{\rm CBT}(\theta_{i-1}, \theta_i, \phi_i) = k_{\phi} \sin^3\theta_{i-1} \sin^3\theta_{i}
+ * \sum_{n=0}^4 { a_n \cos^n\phi_i}\f] ({eq:CBT} and ref \cite{MonicaGoga2013} from the manual).
+ * It contains in its expression not only the dihedral angle \f$\phi\f$
+ * but also \f[\theta_{i-1}\f] (theta_ante bellow) and \f[\theta_{i}\f] (theta_post bellow)
+ * --- the adjacent bending angles.
+ * For more explanations see comments file "restcbt.h". */
+
+ compute_factors_cbtdihs(type, forceparams, delta_ante, delta_crnt, delta_post,
+ f_phi_ai, f_phi_aj, f_phi_ak, f_phi_al,
+ f_theta_ante_ai, f_theta_ante_aj, f_theta_ante_ak,
+ f_theta_post_aj, f_theta_post_ak, f_theta_post_al,
+ &v);
+
+
+ /* Acumulate the resuts per beads */
+ for (d = 0; d < DIM; d++)
+ {
+ f_i[d] = f_phi_ai[d] + f_theta_ante_ai[d];
+ f_j[d] = f_phi_aj[d] + f_theta_ante_aj[d] + f_theta_post_aj[d];
+ f_k[d] = f_phi_ak[d] + f_theta_ante_ak[d] + f_theta_post_ak[d];
+ f_l[d] = f_phi_al[d] + f_theta_post_al[d];
+ }
+
+ /* Compute the potential energy */
+
+ vtot += v;
+
+
+ /* Updating the forces */
+ rvec_inc(f[ai], f_i);
+ rvec_inc(f[aj], f_j);
+ rvec_inc(f[ak], f_k);
+ rvec_inc(f[al], f_l);
+
+
+ /* Updating the fshift forces for the pressure coupling */
+ 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)
+ {
+ t3 = pbc_rvec_sub(pbc, x[al], x[aj], dx_jl);
+ }
+ else
+ {
+ t3 = CENTRAL;
+ }
+
+ rvec_inc(fshift[t1], f_i);
+ rvec_inc(fshift[CENTRAL], f_j);
+ rvec_inc(fshift[t2], f_k);
+ rvec_inc(fshift[t3], f_l);
+ }
+
+ return vtot;
+}
+
+real rbdihs(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ const real c0 = 0.0, c1 = 1.0, c2 = 2.0, c3 = 3.0, c4 = 4.0, c5 = 5.0;
+ int type, ai, aj, ak, al, i, j;
+ int t1, t2, t3;
+ rvec r_ij, r_kj, r_kl, m, n;
+ real parmA[NR_RBDIHS];
+ real parmB[NR_RBDIHS];
+ real parm[NR_RBDIHS];
+ real cos_phi, phi, rbp, rbpBA;
+ real v, sign, ddphi, sin_phi;
+ real cosfac, vtot;
+ real L1 = 1.0-lambda;
+ real dvdl_term = 0;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ al = forceatoms[i++];
+
+ phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
+ &sign, &t1, &t2, &t3); /* 84 */
+
+ /* Change to polymer convention */
+ if (phi < c0)
+ {
+ phi += M_PI;
+ }
+ else
+ {
+ phi -= M_PI; /* 1 */
+
+ }
+ cos_phi = cos(phi);
+ /* Beware of accuracy loss, cannot use 1-sqrt(cos^2) ! */
+ sin_phi = sin(phi);
+
+ for (j = 0; (j < NR_RBDIHS); j++)
+ {
+ parmA[j] = forceparams[type].rbdihs.rbcA[j];
+ parmB[j] = forceparams[type].rbdihs.rbcB[j];
+ parm[j] = L1*parmA[j]+lambda*parmB[j];
+ }
+ /* Calculate cosine powers */
+ /* Calculate the energy */
+ /* Calculate the derivative */
+
+ v = parm[0];
+ dvdl_term += (parmB[0]-parmA[0]);
+ ddphi = c0;
+ cosfac = c1;
+
+ rbp = parm[1];
+ rbpBA = parmB[1]-parmA[1];
+ ddphi += rbp*cosfac;
+ cosfac *= cos_phi;
+ v += cosfac*rbp;
+ dvdl_term += cosfac*rbpBA;
+ rbp = parm[2];
+ rbpBA = parmB[2]-parmA[2];
+ ddphi += c2*rbp*cosfac;
+ cosfac *= cos_phi;
+ v += cosfac*rbp;
+ dvdl_term += cosfac*rbpBA;
+ rbp = parm[3];
+ rbpBA = parmB[3]-parmA[3];
+ ddphi += c3*rbp*cosfac;
+ cosfac *= cos_phi;
+ v += cosfac*rbp;
+ dvdl_term += cosfac*rbpBA;
+ rbp = parm[4];
+ rbpBA = parmB[4]-parmA[4];
+ ddphi += c4*rbp*cosfac;
+ cosfac *= cos_phi;
+ v += cosfac*rbp;
+ dvdl_term += cosfac*rbpBA;
+ rbp = parm[5];
+ rbpBA = parmB[5]-parmA[5];
+ ddphi += c5*rbp*cosfac;
+ cosfac *= cos_phi;
+ v += cosfac*rbp;
+ dvdl_term += cosfac*rbpBA;
+
+ ddphi = -ddphi*sin_phi; /* 11 */
+
+ 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 */
+ vtot += v;
+ }
+ *dvdlambda += dvdl_term;
+
+ return vtot;
+}
+
+int cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
+{
+ int im1, ip1, ip2;
+
+ if (ip < 0)
+ {
+ ip = ip + grid_spacing - 1;
+ }
+ else if (ip > grid_spacing)
+ {
+ ip = ip - grid_spacing - 1;
+ }
+
+ im1 = ip - 1;
+ ip1 = ip + 1;
+ ip2 = ip + 2;
+
+ if (ip == 0)
+ {
+ im1 = grid_spacing - 1;
+ }
+ else if (ip == grid_spacing-2)
+ {
+ ip2 = 0;
+ }
+ else if (ip == grid_spacing-1)
+ {
+ ip1 = 0;
+ ip2 = 1;
+ }
+
+ *ipm1 = im1;
+ *ipp1 = ip1;
+ *ipp2 = ip2;
+
+ return ip;
+
+}
+
+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 a1i, a1j, a1k, a1l, a2i, a2j, a2k, a2l;
+ int type, cmapA;
+ 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;
+
+ 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 ra21, rb21, rg21, rg1, rgr1, ra2r1, rb2r1, rabr1;
+ real ra22, rb22, rg22, rg2, rgr2, ra2r2, rb2r2, rabr2;
+ real fg1, hg1, fga1, hgb1, gaa1, gbb1;
+ real fg2, hg2, fga2, hgb2, gaa2, gbb2;
+ real fac;
+
+ rvec r1_ij, r1_kj, r1_kl, m1, n1;
+ rvec r2_ij, r2_kj, r2_kl, m2, n2;
+ rvec f1_i, f1_j, f1_k, f1_l;
+ rvec f2_i, f2_j, f2_k, f2_l;
+ 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;
+
+ const real *cmapd;
+
+ int loop_index[4][4] = {
+ {0, 4, 8, 12},
+ {1, 5, 9, 13},
+ {2, 6, 10, 14},
+ {3, 7, 11, 15}
+ };
+
+ /* Total CMAP energy */
+ vtot = 0;
+
+ for (n = 0; n < nbonds; )
+ {
+ /* Five atoms are involved in the two torsions */
+ type = forceatoms[n++];
+ ai = forceatoms[n++];
+ aj = forceatoms[n++];
+ ak = forceatoms[n++];
+ al = forceatoms[n++];
+ am = forceatoms[n++];
+
+ /* Which CMAP type is this */
+ cmapA = forceparams[type].cmap.cmapA;
+ cmapd = cmap_grid->cmapdata[cmapA].cmap;
+
+ /* First torsion */
+ a1i = ai;
+ a1j = aj;
+ a1k = ak;
+ a1l = al;
+
+ phi1 = dih_angle(x[a1i], x[a1j], x[a1k], x[a1l], pbc, r1_ij, r1_kj, r1_kl, m1, n1,
+ &sign1, &t11, &t21, &t31); /* 84 */
+
+ cos_phi1 = cos(phi1);
+
+ a1[0] = r1_ij[1]*r1_kj[2]-r1_ij[2]*r1_kj[1];
+ a1[1] = r1_ij[2]*r1_kj[0]-r1_ij[0]*r1_kj[2];
+ a1[2] = r1_ij[0]*r1_kj[1]-r1_ij[1]*r1_kj[0]; /* 9 */
+
+ b1[0] = r1_kl[1]*r1_kj[2]-r1_kl[2]*r1_kj[1];
+ 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);
+
+ ra21 = iprod(a1, a1); /* 5 */
+ rb21 = iprod(b1, b1); /* 5 */
+ rg21 = iprod(r1_kj, r1_kj); /* 5 */
+ rg1 = sqrt(rg21);
+
+ rgr1 = 1.0/rg1;
+ ra2r1 = 1.0/ra21;
+ rb2r1 = 1.0/rb21;
+ rabr1 = sqrt(ra2r1*rb2r1);
+
+ sin_phi1 = rg1 * rabr1 * iprod(a1, h1) * (-1);
+
+ if (cos_phi1 < -0.5 || cos_phi1 > 0.5)
+ {
+ phi1 = asin(sin_phi1);
+
+ if (cos_phi1 < 0)
+ {
+ if (phi1 > 0)
+ {
+ phi1 = M_PI - phi1;
+ }
+ else
+ {
+ phi1 = -M_PI - phi1;
+ }
+ }
+ }
+ else
+ {
+ phi1 = acos(cos_phi1);
+
+ if (sin_phi1 < 0)
+ {
+ phi1 = -phi1;
+ }
+ }
+
+ xphi1 = phi1 + M_PI; /* 1 */
+
+ /* Second torsion */
+ a2i = aj;
+ a2j = ak;
+ a2k = al;
+ a2l = am;
+
+ phi2 = dih_angle(x[a2i], x[a2j], x[a2k], x[a2l], pbc, r2_ij, r2_kj, r2_kl, m2, n2,
+ &sign2, &t12, &t22, &t32); /* 84 */
+
+ cos_phi2 = cos(phi2);
+
+ a2[0] = r2_ij[1]*r2_kj[2]-r2_ij[2]*r2_kj[1];
+ a2[1] = r2_ij[2]*r2_kj[0]-r2_ij[0]*r2_kj[2];
+ a2[2] = r2_ij[0]*r2_kj[1]-r2_ij[1]*r2_kj[0]; /* 9 */
+
+ b2[0] = r2_kl[1]*r2_kj[2]-r2_kl[2]*r2_kj[1];
+ 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);
+
+ ra22 = iprod(a2, a2); /* 5 */
+ rb22 = iprod(b2, b2); /* 5 */
+ rg22 = iprod(r2_kj, r2_kj); /* 5 */
+ rg2 = sqrt(rg22);
+
+ rgr2 = 1.0/rg2;
+ ra2r2 = 1.0/ra22;
+ rb2r2 = 1.0/rb22;
+ rabr2 = sqrt(ra2r2*rb2r2);
+
+ sin_phi2 = rg2 * rabr2 * iprod(a2, h2) * (-1);
+
+ if (cos_phi2 < -0.5 || cos_phi2 > 0.5)
+ {
+ phi2 = asin(sin_phi2);
+
+ if (cos_phi2 < 0)
+ {
+ if (phi2 > 0)
+ {
+ phi2 = M_PI - phi2;
+ }
+ else
+ {
+ phi2 = -M_PI - phi2;
+ }
+ }
+ }
+ else
+ {
+ phi2 = acos(cos_phi2);
+
+ if (sin_phi2 < 0)
+ {
+ phi2 = -phi2;
+ }
+ }
+
+ xphi2 = phi2 + M_PI; /* 1 */
+
+ /* Range mangling */
+ if (xphi1 < 0)
+ {
+ xphi1 = xphi1 + 2*M_PI;
+ }
+ else if (xphi1 >= 2*M_PI)
+ {
+ xphi1 = xphi1 - 2*M_PI;
+ }
+
+ if (xphi2 < 0)
+ {
+ xphi2 = xphi2 + 2*M_PI;
+ }
+ else if (xphi2 >= 2*M_PI)
+ {
+ xphi2 = xphi2 - 2*M_PI;
+ }
+
+ /* Number of grid points */
+ dx = 2*M_PI / cmap_grid->grid_spacing;
+
+ /* Where on the grid are we */
+ iphi1 = (int)(xphi1/dx);
+ iphi2 = (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);
+
+ pos1 = iphi1*cmap_grid->grid_spacing+iphi2;
+ pos2 = ip1p1*cmap_grid->grid_spacing+iphi2;
+ pos3 = ip1p1*cmap_grid->grid_spacing+ip2p1;
+ pos4 = iphi1*cmap_grid->grid_spacing+ip2p1;
+
+ ty[0] = cmapd[pos1*4];
+ ty[1] = cmapd[pos2*4];
+ ty[2] = cmapd[pos3*4];
+ ty[3] = cmapd[pos4*4];
+
+ ty1[0] = cmapd[pos1*4+1];
+ ty1[1] = cmapd[pos2*4+1];
+ ty1[2] = cmapd[pos3*4+1];
+ ty1[3] = cmapd[pos4*4+1];
+
+ ty2[0] = cmapd[pos1*4+2];
+ ty2[1] = cmapd[pos2*4+2];
+ ty2[2] = cmapd[pos3*4+2];
+ ty2[3] = cmapd[pos4*4+2];
+
+ ty12[0] = cmapd[pos1*4+3];
+ ty12[1] = cmapd[pos2*4+3];
+ ty12[2] = cmapd[pos3*4+3];
+ ty12[3] = cmapd[pos4*4+3];
+
+ /* Switch to degrees */
+ dx = 360.0 / cmap_grid->grid_spacing;
+ xphi1 = xphi1 * RAD2DEG;
+ xphi2 = xphi2 * RAD2DEG;
+
+ for (i = 0; i < 4; i++) /* 16 */
+ {
+ tx[i] = ty[i];
+ tx[i+4] = ty1[i]*dx;
+ tx[i+8] = ty2[i]*dx;
+ tx[i+12] = ty12[i]*dx*dx;
+ }
+
+ idx = 0;
+ for (i = 0; i < 4; i++) /* 1056 */
+ {
+ for (j = 0; j < 4; j++)
+ {
+ xx = 0;
+ for (k = 0; k < 16; k++)
+ {
+ xx = xx + cmap_coeff_matrix[k*16+idx]*tx[k];
+ }
+
+ idx++;
+ tc[i*4+j] = xx;
+ }
+ }
+
+ tt = (xphi1-iphi1*dx)/dx;
+ tu = (xphi2-iphi2*dx)/dx;
+
+ e = 0;
+ df1 = 0;
+ df2 = 0;
+ ddf1 = 0;
+ ddf2 = 0;
+ ddf12 = 0;
+
+ for (i = 3; i >= 0; i--)
+ {
+ l1 = loop_index[i][3];
+ l2 = loop_index[i][2];
+ l3 = loop_index[i][1];
+
+ 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;
+
+ /* Do forces - first torsion */
+ fg1 = iprod(r1_ij, r1_kj);
+ hg1 = iprod(r1_kl, r1_kj);
+ fga1 = fg1*ra2r1*rgr1;
+ hgb1 = hg1*rb2r1*rgr1;
+ gaa1 = -ra2r1*rg1;
+ gbb1 = rb2r1*rg1;
+
+ for (i = 0; i < DIM; i++)
+ {
+ dtf1[i] = gaa1 * a1[i];
+ dtg1[i] = fga1 * a1[i] - hgb1 * b1[i];
+ dth1[i] = gbb1 * b1[i];
+
+ f1[i] = df1 * dtf1[i];
+ g1[i] = df1 * dtg1[i];
+ h1[i] = df1 * dth1[i];
+
+ f1_i[i] = f1[i];
+ f1_j[i] = -f1[i] - g1[i];
+ f1_k[i] = h1[i] + g1[i];
+ f1_l[i] = -h1[i];
+
+ f[a1i][i] = f[a1i][i] + f1_i[i];
+ f[a1j][i] = f[a1j][i] + f1_j[i]; /* - f1[i] - g1[i] */
+ f[a1k][i] = f[a1k][i] + f1_k[i]; /* h1[i] + g1[i] */
+ f[a1l][i] = f[a1l][i] + f1_l[i]; /* h1[i] */
+ }
+
+ /* Do forces - second torsion */
+ fg2 = iprod(r2_ij, r2_kj);
+ hg2 = iprod(r2_kl, r2_kj);
+ fga2 = fg2*ra2r2*rgr2;
+ hgb2 = hg2*rb2r2*rgr2;
+ gaa2 = -ra2r2*rg2;
+ gbb2 = rb2r2*rg2;
+
+ for (i = 0; i < DIM; i++)
+ {
+ dtf2[i] = gaa2 * a2[i];
+ dtg2[i] = fga2 * a2[i] - hgb2 * b2[i];
+ dth2[i] = gbb2 * b2[i];
+
+ f2[i] = df2 * dtf2[i];
+ g2[i] = df2 * dtg2[i];
+ h2[i] = df2 * dth2[i];
+
+ f2_i[i] = f2[i];
+ f2_j[i] = -f2[i] - g2[i];
+ f2_k[i] = h2[i] + g2[i];
+ f2_l[i] = -h2[i];
+
+ f[a2i][i] = f[a2i][i] + f2_i[i]; /* f2[i] */
+ f[a2j][i] = f[a2j][i] + f2_j[i]; /* - f2[i] - g2[i] */
+ f[a2k][i] = f[a2k][i] + f2_k[i]; /* h2[i] + g2[i] */
+ f[a2l][i] = f[a2l][i] + f2_l[i]; /* - h2[i] */
+ }
+
+ /* Shift forces */
+ 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)
+ {
+ t31 = pbc_rvec_sub(pbc, x[a1l], x[a1j], h1);
+ t32 = pbc_rvec_sub(pbc, x[a2l], x[a2j], h2);
+ }
+ else
+ {
+ t31 = CENTRAL;
+ t32 = CENTRAL;
+ }
+
+ rvec_inc(fshift[t11], f1_i);
+ rvec_inc(fshift[CENTRAL], f1_j);
+ rvec_inc(fshift[t21], f1_k);
+ rvec_inc(fshift[t31], f1_l);
+
+ rvec_inc(fshift[t21], f2_i);
+ rvec_inc(fshift[CENTRAL], f2_j);
+ rvec_inc(fshift[t22], f2_k);
+ rvec_inc(fshift[t32], f2_l);
+ }
+ return vtot;
+}
+
+
+
+/***********************************************************
+ *
+ * G R O M O S 9 6 F U N C T I O N S
+ *
+ ***********************************************************/
+real g96harmonic(real kA, real kB, real xA, real xB, real x, real lambda,
+ real *V, real *F)
+{
+ const real half = 0.5;
+ real L1, kk, x0, dx, dx2;
+ real v, f, dvdlambda;
+
+ L1 = 1.0-lambda;
+ kk = L1*kA+lambda*kB;
+ x0 = L1*xA+lambda*xB;
+
+ dx = x-x0;
+ dx2 = dx*dx;
+
+ f = -kk*dx;
+ v = half*kk*dx2;
+ dvdlambda = half*(kB-kA)*dx2 + (xA-xB)*kk*dx;
+
+ *F = f;
+ *V = v;
+
+ return dvdlambda;
+
+ /* That was 21 flops */
+}
+
+real g96bonds(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ int i, m, ki, ai, aj, type;
+ real dr2, fbond, vbond, fij, vtot;
+ rvec dx;
+ ivec dt;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+
+ ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
+ dr2 = iprod(dx, dx); /* 5 */
+
+ *dvdlambda += g96harmonic(forceparams[type].harmonic.krA,
+ forceparams[type].harmonic.krB,
+ forceparams[type].harmonic.rA,
+ forceparams[type].harmonic.rB,
+ dr2, lambda, &vbond, &fbond);
+
+ vtot += 0.5*vbond; /* 1*/
+#ifdef DEBUG
+ if (debug)
+ {
+ fprintf(debug, "G96-BONDS: dr = %10g vbond = %10g fbond = %10g\n",
+ sqrt(dr2), vbond, fbond);
+ }
+#endif
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ ki = IVEC2IS(dt);
+ }
+ for (m = 0; (m < DIM); m++) /* 15 */
+ {
+ fij = fbond*dx[m];
+ f[ai][m] += fij;
+ f[aj][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
+ }
+ } /* 44 TOTAL */
+ return vtot;
+}
+
+real g96bond_angle(const rvec xi, const rvec xj, const rvec xk, const t_pbc *pbc,
+ rvec r_ij, rvec r_kj,
+ int *t1, int *t2)
+/* Return value is the angle between the bonds i-j and j-k */
+{
+ real costh;
+
+ *t1 = pbc_rvec_sub(pbc, xi, xj, r_ij); /* 3 */
+ *t2 = pbc_rvec_sub(pbc, xk, xj, r_kj); /* 3 */
+
+ costh = cos_angle(r_ij, r_kj); /* 25 */
+ /* 41 TOTAL */
+ return costh;
+}
+
+real g96angles(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec 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)
+{
+ int i, ai, aj, ak, type, m, t1, t2;
+ rvec r_ij, r_kj;
+ 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); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+
+ cos_theta = g96bond_angle(x[ai], x[aj], x[ak], pbc, r_ij, r_kj, &t1, &t2);
+
+ *dvdlambda += g96harmonic(forceparams[type].harmonic.krA,
+ forceparams[type].harmonic.krB,
+ forceparams[type].harmonic.rA,
+ forceparams[type].harmonic.rB,
+ cos_theta, lambda, &va, &dVdt);
+ vtot += va;
+
+ rij_1 = gmx_invsqrt(iprod(r_ij, r_ij));
+ rkj_1 = gmx_invsqrt(iprod(r_kj, r_kj));
+ rij_2 = rij_1*rij_1;
+ rkj_2 = rkj_1*rkj_1;
+ rijrkj_1 = rij_1*rkj_1; /* 23 */
+
+#ifdef DEBUG
+ if (debug)
+ {
+ fprintf(debug, "G96ANGLES: costheta = %10g vth = %10g dV/dct = %10g\n",
+ cos_theta, va, dVdt);
+ }
+#endif
+ for (m = 0; (m < DIM); m++) /* 42 */
+ {
+ f_i[m] = dVdt*(r_kj[m]*rijrkj_1 - r_ij[m]*rij_2*cos_theta);
+ f_k[m] = dVdt*(r_ij[m]*rijrkj_1 - r_kj[m]*rkj_2*cos_theta);
+ f_j[m] = -f_i[m]-f_k[m];
+ f[ai][m] += f_i[m];
+ f[aj][m] += f_j[m];
+ f[ak][m] += f_k[m];
+ }
+
+ 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 */
+ /* 163 TOTAL */
+ }
+ return vtot;
+}
+
+real cross_bond_bond(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ 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)
+{
+ /* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
+ * pp. 842-847
+ */
+ int i, ai, aj, ak, type, m, t1, t2;
+ 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); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ r1e = forceparams[type].cross_bb.r1e;
+ r2e = forceparams[type].cross_bb.r2e;
+ krr = forceparams[type].cross_bb.krr;
+
+ /* 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);
+
+ /* ... and their lengths */
+ r1 = norm(r_ij);
+ r2 = norm(r_kj);
+
+ /* Deviations from ideality */
+ s1 = r1-r1e;
+ s2 = r2-r2e;
+
+ /* Energy (can be negative!) */
+ vrr = krr*s1*s2;
+ vtot += vrr;
+
+ /* Forces */
+ svmul(-krr*s2/r1, r_ij, f_i);
+ svmul(-krr*s1/r2, r_kj, f_k);
+
+ for (m = 0; (m < DIM); m++) /* 12 */
+ {
+ f_j[m] = -f_i[m] - f_k[m];
+ f[ai][m] += f_i[m];
+ f[aj][m] += f_j[m];
+ f[ak][m] += f_k[m];
+ }
+
+ /* Virial stuff */
+ 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 */
+ /* 163 TOTAL */
+ }
+ return vtot;
+}
+
+real cross_bond_angle(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ 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)
+{
+ /* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
+ * pp. 842-847
+ */
+ int i, ai, aj, ak, type, m, t1, t2, t3;
+ 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); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ r1e = forceparams[type].cross_ba.r1e;
+ r2e = forceparams[type].cross_ba.r2e;
+ r3e = forceparams[type].cross_ba.r3e;
+ krt = forceparams[type].cross_ba.krt;
+
+ /* 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);
+
+ /* ... and their lengths */
+ r1 = norm(r_ij);
+ r2 = norm(r_kj);
+ r3 = norm(r_ik);
+
+ /* Deviations from ideality */
+ s1 = r1-r1e;
+ s2 = r2-r2e;
+ s3 = r3-r3e;
+
+ /* Energy (can be negative!) */
+ vrt = krt*s3*(s1+s2);
+ vtot += vrt;
+
+ /* Forces */
+ k1 = -krt*(s3/r1);
+ k2 = -krt*(s3/r2);
+ k3 = -krt*(s1+s2)/r3;
+ for (m = 0; (m < DIM); m++)
+ {
+ f_i[m] = k1*r_ij[m] + k3*r_ik[m];
+ f_k[m] = k2*r_kj[m] - k3*r_ik[m];
+ f_j[m] = -f_i[m] - f_k[m];
+ }
+
+ for (m = 0; (m < DIM); m++) /* 12 */
+ {
+ f[ai][m] += f_i[m];
+ f[aj][m] += f_j[m];
+ f[ak][m] += f_k[m];
+ }
+
+ /* Virial stuff */
+ 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 */
+ /* 163 TOTAL */
+ }
+ return vtot;
+}
+
+static real bonded_tab(const char *type, int table_nr,
+ const bondedtable_t *table, real kA, real kB, real r,
+ real lambda, real *V, real *F)
+{
+ real k, tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps2, Fp, VV, FF;
+ int n0, nnn;
+ real v, f, dvdlambda;
+
+ k = (1.0 - lambda)*kA + lambda*kB;
+
+ tabscale = table->scale;
+ VFtab = table->data;
+
+ rt = r*tabscale;
+ n0 = 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",
+ type, table_nr, r, n0, n0+1, table->n);
+ }
+ eps = rt - n0;
+ eps2 = eps*eps;
+ nnn = 4*n0;
+ Yt = VFtab[nnn];
+ Ft = VFtab[nnn+1];
+ Geps = VFtab[nnn+2]*eps;
+ Heps2 = VFtab[nnn+3]*eps2;
+ Fp = Ft + Geps + Heps2;
+ VV = Yt + Fp*eps;
+ FF = Fp + Geps + 2.0*Heps2;
+
+ *F = -k*FF*tabscale;
+ *V = k*VV;
+ dvdlambda = (kB - kA)*VV;
+
+ return dvdlambda;
+
+ /* That was 22 flops */
+}
+
+real tab_bonds(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const t_pbc *pbc, const t_graph *g,
+ real lambda, real *dvdlambda,
+ const t_mdatoms gmx_unused *md, t_fcdata *fcd,
+ int gmx_unused *global_atom_index)
+{
+ int i, m, ki, ai, aj, type, table;
+ real dr, dr2, fbond, vbond, fij, vtot;
+ rvec dx;
+ ivec dt;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+
+ ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
+ dr2 = iprod(dx, dx); /* 5 */
+ dr = dr2*gmx_invsqrt(dr2); /* 10 */
+
+ table = forceparams[type].tab.table;
+
+ *dvdlambda += bonded_tab("bond", table,
+ &fcd->bondtab[table],
+ forceparams[type].tab.kA,
+ forceparams[type].tab.kB,
+ dr, lambda, &vbond, &fbond); /* 22 */
+
+ if (dr2 == 0.0)
+ {
+ continue;
+ }
+
+
+ vtot += vbond; /* 1*/
+ fbond *= gmx_invsqrt(dr2); /* 6 */
+#ifdef DEBUG
+ if (debug)
+ {
+ fprintf(debug, "TABBONDS: dr = %10g vbond = %10g fbond = %10g\n",
+ dr, vbond, fbond);
+ }
+#endif
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ ki = IVEC2IS(dt);
+ }
+ for (m = 0; (m < DIM); m++) /* 15 */
+ {
+ fij = fbond*dx[m];
+ f[ai][m] += fij;
+ f[aj][m] -= fij;
+ fshift[ki][m] += fij;
+ fshift[CENTRAL][m] -= fij;
+ }
+ } /* 62 TOTAL */
+ return vtot;
+}
+
+real tab_angles(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const t_pbc *pbc, const t_graph *g,
+ real lambda, real *dvdlambda,
+ const t_mdatoms gmx_unused *md, t_fcdata *fcd,
+ int gmx_unused *global_atom_index)
+{
+ 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); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+
+ theta = bond_angle(x[ai], x[aj], x[ak], pbc,
+ r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
+
+ table = forceparams[type].tab.table;
+
+ *dvdlambda += bonded_tab("angle", table,
+ &fcd->angletab[table],
+ forceparams[type].tab.kA,
+ forceparams[type].tab.kB,
+ theta, lambda, &va, &dVdt); /* 22 */
+ vtot += va;
+
+ cos_theta2 = sqr(cos_theta); /* 1 */
+ if (cos_theta2 < 1)
+ {
+ int m;
+ real snt, st, sth;
+ real cik, cii, ckk;
+ real nrkj2, nrij2;
+ rvec f_i, f_j, f_k;
+
+ st = dVdt*gmx_invsqrt(1 - cos_theta2); /* 12 */
+ sth = st*cos_theta; /* 1 */
+#ifdef DEBUG
+ if (debug)
+ {
+ fprintf(debug, "ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
+ theta*RAD2DEG, va, dVdt);
+ }
+#endif
+ nrkj2 = iprod(r_kj, r_kj); /* 5 */
+ nrij2 = iprod(r_ij, r_ij);
+
+ cik = st*gmx_invsqrt(nrkj2*nrij2); /* 12 */
+ cii = sth/nrij2; /* 10 */
+ ckk = sth/nrkj2; /* 10 */
+
+ for (m = 0; (m < DIM); m++) /* 39 */
+ {
+ f_i[m] = -(cik*r_kj[m]-cii*r_ij[m]);
+ f_k[m] = -(cik*r_ij[m]-ckk*r_kj[m]);
+ f_j[m] = -f_i[m]-f_k[m];
+ f[ai][m] += f_i[m];
+ f[aj][m] += f_j[m];
+ f[ak][m] += f_k[m];
+ }
+ 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);
+ } /* 169 TOTAL */
+ }
+ return vtot;
+}
+
+real tab_dihs(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const t_pbc *pbc, const t_graph *g,
+ real lambda, real *dvdlambda,
+ const t_mdatoms gmx_unused *md, t_fcdata *fcd,
+ int gmx_unused *global_atom_index)
+{
+ int i, type, ai, aj, ak, al, table;
+ int t1, t2, t3;
+ rvec r_ij, r_kj, r_kl, m, n;
+ real phi, sign, ddphi, vpd, vtot;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ aj = forceatoms[i++];
+ ak = forceatoms[i++];
+ al = forceatoms[i++];
+
+ phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
+ &sign, &t1, &t2, &t3); /* 84 */
+
+ table = forceparams[type].tab.table;
+
+ /* Hopefully phi+M_PI never results in values < 0 */
+ *dvdlambda += bonded_tab("dihedral", table,
+ &fcd->dihtab[table],
+ forceparams[type].tab.kA,
+ forceparams[type].tab.kB,
+ phi+M_PI, lambda, &vpd, &ddphi);
+
+ vtot += vpd;
+ 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 */
+
+#ifdef DEBUG
+ fprintf(debug, "pdih: (%d,%d,%d,%d) phi=%g\n",
+ ai, aj, ak, al, phi);
+#endif
+ } /* 227 TOTAL */
+
+ 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)
+{
+ return
+ (interaction_function[ftype].flags & IF_BOND) &&
+ !(ftype == F_CONNBONDS || ftype == F_POSRES || ftype == F_FBPOSRES) &&
+ (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));
+ }
+}
+
+static void zero_thread_forces(f_thread_t *f_t, int n,
+ int nblock, int blocksize)
+{
+ int b, a0, a1, a, i, j;
+
+ if (n > f_t->f_nalloc)
+ {
+ f_t->f_nalloc = over_alloc_large(n);
+ srenew(f_t->f, f_t->f_nalloc);
+ }
+
+ if (f_t->red_mask != 0)
+ {
+ for (b = 0; b < nblock; b++)
+ {
+ if (f_t->red_mask && (1U<<b))
+ {
+ a0 = b*blocksize;
+ a1 = min((b+1)*blocksize, n);
+ for (a = a0; a < a1; a++)
+ {
+ clear_rvec(f_t->f[a]);
+ }
+ }
+ }
+ }
+ for (i = 0; i < SHIFTS; i++)
+ {
+ clear_rvec(f_t->fshift[i]);
+ }
+ for (i = 0; i < F_NRE; i++)
+ {
+ f_t->ener[i] = 0;
+ }
+ for (i = 0; i < egNR; i++)
+ {
+ for (j = 0; j < f_t->grpp.nener; j++)
+ {
+ f_t->grpp.ener[i][j] = 0;
+ }
+ }
+ for (i = 0; i < efptNR; i++)
+ {
+ f_t->dvdl[i] = 0;
+ }
+}
+
+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)
+ {
+ gmx_fatal(FARGS, "Can not reduce bonded forces on more than %d threads",
+ MAX_BONDED_THREADS);
+ }
+
+ /* This reduction can run on any number of threads,
+ * independently of nthreads.
+ */
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+ for (b = 0; b < nblock; b++)
+ {
+ rvec *fp[MAX_BONDED_THREADS];
+ int nfb, ft, fb;
+ int a0, a1, a;
+
+ /* Determine which threads contribute to this block */
+ nfb = 0;
+ for (ft = 1; ft < nthreads; ft++)
+ {
+ if (f_t[ft].red_mask & (1U<<b))
+ {
+ fp[nfb++] = f_t[ft].f;
+ }
+ }
+ if (nfb > 0)
+ {
+ /* Reduce force buffers for threads that contribute */
+ a0 = b *block_size;
+ a1 = (b+1)*block_size;
+ a1 = min(a1, n);
+ for (a = a0; a < a1; a++)
+ {
+ for (fb = 0; fb < nfb; fb++)
+ {
+ rvec_inc(f[a], fp[fb][a]);
+ }
+ }
+ }
+ }
+}
+
+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,
+ int nblock, int block_size,
+ gmx_bool bCalcEnerVir,
+ gmx_bool bDHDL)
+{
+ if (nblock > 0)
+ {
+ /* Reduce the bonded force buffer */
+ reduce_thread_force_buffer(n, f, nthreads, f_t, nblock, block_size);
+ }
+
+ /* When necessary, reduce energy and virial using one thread only */
+ if (bCalcEnerVir)
+ {
+ int t, i, j;
+
+ for (i = 0; i < SHIFTS; i++)
+ {
+ for (t = 1; t < nthreads; t++)
+ {
+ rvec_inc(fshift[i], f_t[t].fshift[i]);
+ }
+ }
+ for (i = 0; i < F_NRE; i++)
+ {
+ for (t = 1; t < nthreads; t++)
+ {
+ ener[i] += f_t[t].ener[i];
+ }
+ }
+ for (i = 0; i < egNR; i++)
+ {
+ for (j = 0; j < f_t[1].grpp.nener; j++)
+ {
+ for (t = 1; t < nthreads; t++)
+ {
+
+ grpp->ener[i][j] += f_t[t].grpp.ener[i][j];
+ }
+ }
+ }
+ if (bDHDL)
+ {
+ for (i = 0; i < efptNR; i++)
+ {
+
+ for (t = 1; t < nthreads; t++)
+ {
+ dvdl[i] += f_t[t].dvdl[i];
+ }
+ }
+ }
+ }
+}
+
+static real calc_one_bond(FILE *fplog, int thread,
+ int ftype, const t_idef *idef,
+ rvec x[], rvec f[], rvec fshift[],
+ t_forcerec *fr,
+ const t_pbc *pbc, const t_graph *g,
+ gmx_grppairener_t *grpp,
+ t_nrnb *nrnb,
+ real *lambda, real *dvdl,
+ const t_mdatoms *md, t_fcdata *fcd,
+ gmx_bool bCalcEnerVir,
+ int *global_atom_index, gmx_bool bPrintSepPot)
+{
+ int nat1, nbonds, efptFTYPE;
+ real v = 0;
+ t_iatom *iatoms;
+ int nb0, nbn;
+
+ if (IS_RESTRAINT_TYPE(ftype))
+ {
+ efptFTYPE = efptRESTRAINT;
+ }
+ else
+ {
+ efptFTYPE = efptBONDED;
+ }
+
+ nat1 = interaction_function[ftype].nratoms + 1;
+ nbonds = idef->il[ftype].nr/nat1;
+ iatoms = idef->il[ftype].iatoms;
+
+ nb0 = idef->il_thread_division[ftype*(idef->nthreads+1)+thread];
+ nbn = idef->il_thread_division[ftype*(idef->nthreads+1)+thread+1] - nb0;
+
+ if (!IS_LISTED_LJ_C(ftype))
+ {
+ if (ftype == F_CMAP)
+ {
+ v = cmap_dihs(nbn, iatoms+nb0,
+ idef->iparams, &idef->cmap_grid,
+ (const rvec*)x, f, fshift,
+ pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
+ md, fcd, global_atom_index);
+ }
+#ifdef GMX_SIMD_HAVE_REAL
+ else if (ftype == F_ANGLES &&
+ !bCalcEnerVir && fr->efep == efepNO)
+ {
+ /* No energies, shift forces, dvdl */
+ angles_noener_simd(nbn, idef->il[ftype].iatoms+nb0,
+ idef->iparams,
+ (const rvec*)x, f,
+ pbc, g, lambda[efptFTYPE], md, fcd,
+ global_atom_index);
+ v = 0;
+ }
+#endif
+ else if (ftype == F_PDIHS &&
+ !bCalcEnerVir && fr->efep == efepNO)
+ {
+ /* No energies, shift forces, dvdl */
+#ifdef GMX_SIMD_HAVE_REAL
+ pdihs_noener_simd
+#else
+ pdihs_noener
+#endif
+ (nbn, idef->il[ftype].iatoms+nb0,
+ idef->iparams,
+ (const rvec*)x, f,
+ pbc, g, lambda[efptFTYPE], md, fcd,
+ global_atom_index);
+ v = 0;
+ }
+#ifdef GMX_SIMD_HAVE_REAL
+ else if (ftype == F_RBDIHS &&
+ !bCalcEnerVir && fr->efep == efepNO)
+ {
+ /* No energies, shift forces, dvdl */
+ rbdihs_noener_simd(nbn, idef->il[ftype].iatoms+nb0,
+ idef->iparams,
+ (const rvec*)x, f,
+ pbc, g, lambda[efptFTYPE], md, fcd,
+ global_atom_index);
+ v = 0;
+ }
+#endif
+ else
+ {
+ v = interaction_function[ftype].ifunc(nbn, iatoms+nb0,
+ idef->iparams,
+ (const rvec*)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,
+ 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)
+ {
+ inc_nrnb(nrnb, interaction_function[ftype].nrnb_ind, nbonds);
+ }
+
+ return v;
+}
+
+void calc_bonds(FILE *fplog, const gmx_multisim_t *ms,
+ const t_idef *idef,
+ rvec x[], history_t *hist,
+ rvec f[], t_forcerec *fr,
+ const t_pbc *pbc, const 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)
+{
+ 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
+ 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);
+
+ bCalcEnerVir = (force_flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY));
+
+ for (i = 0; i < efptNR; i++)
+ {
+ dvdl[i] = 0.0;
+ }
+ if (fr->bMolPBC)
+ {
+ pbc_null = pbc;
+ }
+ else
+ {
+ 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)
+ {
+ p_graph(debug, "Bondage is fun", g);
+ }
+#endif
+
+ /* Do pre force calculation stuff which might require communication */
+ if (idef->il[F_ORIRES].nr)
+ {
+ enerd->term[F_ORIRESDEV] =
+ calc_orires_dev(ms, idef->il[F_ORIRES].nr,
+ idef->il[F_ORIRES].iatoms,
+ idef->iparams, md, (const rvec*)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,
+ fcd, hist);
+#ifdef GMX_MPI
+ if (fcd->disres.nsystems > 1)
+ {
+ gmx_sum_sim(2*fcd->disres.nres, fcd->disres.Rt_6, ms);
+ }
+#endif
+ }
+
+#pragma omp parallel for num_threads(fr->nthreads) schedule(static)
+ for (thread = 0; thread < fr->nthreads; thread++)
+ {
+ int ftype;
+ real *epot, v;
+ /* thread stuff */
+ rvec *ft, *fshift;
+ real *dvdlt;
+ gmx_grppairener_t *grpp;
+
+ if (thread == 0)
+ {
+ ft = f;
+ fshift = fr->fshift;
+ epot = enerd->term;
+ grpp = &enerd->grpp;
+ dvdlt = dvdl;
+ }
+ else
+ {
+ zero_thread_forces(&fr->f_t[thread], fr->natoms_force,
+ fr->red_nblock, 1<<fr->red_ashift);
+
+ ft = fr->f_t[thread].f;
+ fshift = fr->f_t[thread].fshift;
+ epot = fr->f_t[thread].ener;
+ grpp = &fr->f_t[thread].grpp;
+ dvdlt = fr->f_t[thread].dvdl;
+ }
+ /* Loop over all bonded force types to calculate the bonded forces */
+ for (ftype = 0; (ftype < F_NRE); ftype++)
+ {
+ if (idef->il[ftype].nr > 0 && ftype_is_bonded_potential(ftype))
+ {
+ v = calc_one_bond(fplog, thread, ftype, idef, x,
+ ft, fshift, fr, pbc_null, g, grpp,
+ nrnb, lambda, dvdlt,
+ md, fcd, bCalcEnerVir,
+ global_atom_index, bPrintSepPot);
+ epot[ftype] += v;
+ }
+ }
+ }
+ if (fr->nthreads > 1)
+ {
+ reduce_thread_forces(fr->natoms_force, f, fr->fshift,
+ enerd->term, &enerd->grpp, dvdl,
+ fr->nthreads, fr->f_t,
+ fr->red_nblock, 1<<fr->red_ashift,
+ bCalcEnerVir,
+ force_flags & GMX_FORCE_DHDL);
+ }
+ if (force_flags & GMX_FORCE_DHDL)
+ {
+ for (i = 0; i < efptNR; i++)
+ {
+ enerd->dvdl_nonlin[i] += dvdl[i];
+ }
+ }
+
+ /* Copy the sum of violations for the distance restraints from fcd */
+ if (fcd)
+ {
+ enerd->term[F_DISRESVIOL] = fcd->disres.sumviol;
+
+ }
+}
+
+void calc_bonds_lambda(FILE *fplog,
+ const t_idef *idef,
+ rvec x[],
+ t_forcerec *fr,
+ const t_pbc *pbc, const 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;
+ real v;
+ real dvdl_dum[efptNR];
+ rvec *f, *fshift;
+ const t_pbc *pbc_null;
+ t_idef idef_fe;
+
+ if (fr->bMolPBC)
+ {
+ pbc_null = pbc;
+ }
+ else
+ {
+ pbc_null = NULL;
+ }
+
+ /* Copy the whole idef, so we can modify the contents locally */
+ idef_fe = *idef;
+ idef_fe.nthreads = 1;
+ snew(idef_fe.il_thread_division, F_NRE*(idef_fe.nthreads+1));
+
+ /* We already have the forces, so we use temp buffers here */
+ snew(f, fr->natoms_force);
+ snew(fshift, SHIFTS);
+
+ /* Loop over all bonded force types to calculate the bonded energies */
+ for (ftype = 0; (ftype < F_NRE); ftype++)
+ {
+ if (ftype_is_bonded_potential(ftype))
+ {
+ /* Set the work range of thread 0 to the perturbed bondeds only */
+ nr_nonperturbed = idef->il[ftype].nr_nonperturbed;
+ nr = idef->il[ftype].nr;
+ idef_fe.il_thread_division[ftype*2+0] = nr_nonperturbed;
+ idef_fe.il_thread_division[ftype*2+1] = nr;
+
+ /* This is only to get the flop count correct */
+ idef_fe.il[ftype].nr = nr - nr_nonperturbed;
+
+ if (nr - nr_nonperturbed > 0)
+ {
+ v = calc_one_bond(fplog, 0, ftype, &idef_fe,
+ x, f, fshift, fr, pbc_null, g,
+ grpp, nrnb, lambda, dvdl_dum,
+ md, fcd, TRUE,
+ global_atom_index, FALSE);
+ epot[ftype] += v;
+ }
+ }
+ }
+
+ sfree(fshift);
+ sfree(f);
+
+ sfree(idef_fe.il_thread_division);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff