-/* -*- 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,
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-
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- * 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.
+ *
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/vsite.h"
#include <stdio.h>
-#include "typedefs.h"
-#include "vsite.h"
-#include "macros.h"
-#include "smalloc.h"
-#include "nrnb.h"
-#include "vec.h"
-#include "mvdata.h"
-#include "network.h"
-#include "mshift.h"
-#include "pbc.h"
-#include "domdec.h"
-#include "partdec.h"
-#include "mtop_util.h"
-#include "gmx_omp_nthreads.h"
-#include "gmx_omp.h"
+
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
/* Routines to send/recieve coordinates and force
- * of constructing atoms.
- */
+ * of constructing atoms.
+ */
-static void move_construct_x(t_comm_vsites *vsitecomm, rvec x[], t_commrec *cr)
+static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
{
- rvec *sendbuf;
- rvec *recvbuf;
- int i,ia;
-
- sendbuf = vsitecomm->send_buf;
- recvbuf = vsitecomm->recv_buf;
-
-
- /* Prepare pulse left by copying to send buffer */
- for(i=0;i<vsitecomm->left_export_nconstruct;i++)
- {
- ia = vsitecomm->left_export_construct[i];
- copy_rvec(x[ia],sendbuf[i]);
- }
-
- /* Pulse coordinates left */
- gmx_tx_rx_real(cr,GMX_LEFT,(real *)sendbuf,3*vsitecomm->left_export_nconstruct,GMX_RIGHT,(real *)recvbuf,3*vsitecomm->right_import_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for(i=0;i<vsitecomm->right_import_nconstruct;i++)
- {
- ia = vsitecomm->right_import_construct[i];
- copy_rvec(recvbuf[i],x[ia]);
- }
-
- /* Prepare pulse right by copying to send buffer */
- for(i=0;i<vsitecomm->right_export_nconstruct;i++)
- {
- ia = vsitecomm->right_export_construct[i];
- copy_rvec(x[ia],sendbuf[i]);
- }
-
- /* Pulse coordinates right */
- gmx_tx_rx_real(cr,GMX_RIGHT,(real *)sendbuf,3*vsitecomm->right_export_nconstruct,GMX_LEFT,(real *)recvbuf,3*vsitecomm->left_import_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for(i=0;i<vsitecomm->left_import_nconstruct;i++)
- {
- ia = vsitecomm->left_import_construct[i];
- copy_rvec(recvbuf[i],x[ia]);
- }
+ if (pbc)
+ {
+ return pbc_dx_aiuc(pbc, xi, xj, dx);
+ }
+ else
+ {
+ rvec_sub(xi, xj, dx);
+ return CENTRAL;
+ }
}
+/* Vsite construction routines */
-static void move_construct_f(t_comm_vsites *vsitecomm, rvec f[], t_commrec *cr)
+static void constr_vsite2(rvec xi, rvec xj, rvec x, real a, t_pbc *pbc)
{
- rvec *sendbuf;
- rvec *recvbuf;
- int i,ia;
-
- sendbuf = vsitecomm->send_buf;
- recvbuf = vsitecomm->recv_buf;
-
- /* Prepare pulse right by copying to send buffer */
- for(i=0;i<vsitecomm->right_import_nconstruct;i++)
- {
- ia = vsitecomm->right_import_construct[i];
- copy_rvec(f[ia],sendbuf[i]);
- clear_rvec(f[ia]); /* Zero it here after moving, just to simplify debug book-keeping... */
- }
-
- /* Pulse forces right */
- gmx_tx_rx_real(cr,GMX_RIGHT,(real *)sendbuf,3*vsitecomm->right_import_nconstruct,GMX_LEFT,(real *)recvbuf,3*vsitecomm->left_export_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for(i=0;i<vsitecomm->left_export_nconstruct;i++)
- {
- ia = vsitecomm->left_export_construct[i];
- rvec_inc(f[ia],recvbuf[i]);
- }
-
- /* Prepare pulse left by copying to send buffer */
- for(i=0;i<vsitecomm->left_import_nconstruct;i++)
- {
- ia = vsitecomm->left_import_construct[i];
- copy_rvec(f[ia],sendbuf[i]);
- clear_rvec(f[ia]); /* Zero it here after moving, just to simplify debug book-keeping... */
- }
-
- /* Pulse coordinates left */
- gmx_tx_rx_real(cr,GMX_LEFT,(real *)sendbuf,3*vsitecomm->left_import_nconstruct,GMX_RIGHT,(real *)recvbuf,3*vsitecomm->right_export_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for(i=0;i<vsitecomm->right_export_nconstruct;i++)
- {
- ia = vsitecomm->right_export_construct[i];
- rvec_inc(f[ia],recvbuf[i]);
- }
-
- /* All forces are now on the home processors */
-}
+ real b;
+ rvec dx;
-
-static void
-pd_clear_nonlocal_constructs(t_comm_vsites *vsitecomm, rvec f[])
-{
- int i,ia;
-
- for(i=0;i<vsitecomm->left_import_nconstruct;i++)
- {
- ia = vsitecomm->left_import_construct[i];
- clear_rvec(f[ia]);
- }
- for(i=0;i<vsitecomm->right_import_nconstruct;i++)
- {
- ia = vsitecomm->right_import_construct[i];
- clear_rvec(f[ia]);
- }
-}
+ b = 1.0-a;
+ /* 1 flop */
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, xj, xi, dx);
+ x[XX] = xi[XX] + a*dx[XX];
+ x[YY] = xi[YY] + a*dx[YY];
+ x[ZZ] = xi[ZZ] + a*dx[ZZ];
+ }
+ else
+ {
+ x[XX] = b*xi[XX] + a*xj[XX];
+ x[YY] = b*xi[YY] + a*xj[YY];
+ x[ZZ] = b*xi[ZZ] + a*xj[ZZ];
+ /* 9 Flops */
+ }
+ /* TOTAL: 10 flops */
+}
-static int pbc_rvec_sub(const t_pbc *pbc,const rvec xi,const rvec xj,rvec dx)
+static void constr_vsite3(rvec xi, rvec xj, rvec xk, rvec x, real a, real b,
+ t_pbc *pbc)
{
- if (pbc) {
- return pbc_dx_aiuc(pbc,xi,xj,dx);
- }
- else {
- rvec_sub(xi,xj,dx);
- return CENTRAL;
- }
-}
+ real c;
+ rvec dxj, dxk;
-/* Vsite construction routines */
+ c = 1.0-a-b;
+ /* 2 flops */
-static void constr_vsite2(rvec xi,rvec xj,rvec x,real a,t_pbc *pbc)
-{
- real b;
- rvec dx;
-
- b=1.0-a;
- /* 1 flop */
-
- if (pbc) {
- pbc_dx_aiuc(pbc,xj,xi,dx);
- x[XX] = xi[XX] + a*dx[XX];
- x[YY] = xi[YY] + a*dx[YY];
- x[ZZ] = xi[ZZ] + a*dx[ZZ];
- } else {
- x[XX] = b*xi[XX] + a*xj[XX];
- x[YY] = b*xi[YY] + a*xj[YY];
- x[ZZ] = b*xi[ZZ] + a*xj[ZZ];
- /* 9 Flops */
- }
-
- /* TOTAL: 10 flops */
-}
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, xj, xi, dxj);
+ pbc_dx_aiuc(pbc, xk, xi, dxk);
+ x[XX] = xi[XX] + a*dxj[XX] + b*dxk[XX];
+ x[YY] = xi[YY] + a*dxj[YY] + b*dxk[YY];
+ x[ZZ] = xi[ZZ] + a*dxj[ZZ] + b*dxk[ZZ];
+ }
+ else
+ {
+ x[XX] = c*xi[XX] + a*xj[XX] + b*xk[XX];
+ x[YY] = c*xi[YY] + a*xj[YY] + b*xk[YY];
+ x[ZZ] = c*xi[ZZ] + a*xj[ZZ] + b*xk[ZZ];
+ /* 15 Flops */
+ }
-static void constr_vsite3(rvec xi,rvec xj,rvec xk,rvec x,real a,real b,
- t_pbc *pbc)
-{
- real c;
- rvec dxj,dxk;
-
- c=1.0-a-b;
- /* 2 flops */
-
- if (pbc) {
- pbc_dx_aiuc(pbc,xj,xi,dxj);
- pbc_dx_aiuc(pbc,xk,xi,dxk);
- x[XX] = xi[XX] + a*dxj[XX] + b*dxk[XX];
- x[YY] = xi[YY] + a*dxj[YY] + b*dxk[YY];
- x[ZZ] = xi[ZZ] + a*dxj[ZZ] + b*dxk[ZZ];
- } else {
- x[XX] = c*xi[XX] + a*xj[XX] + b*xk[XX];
- x[YY] = c*xi[YY] + a*xj[YY] + b*xk[YY];
- x[ZZ] = c*xi[ZZ] + a*xj[ZZ] + b*xk[ZZ];
- /* 15 Flops */
- }
-
- /* TOTAL: 17 flops */
+ /* TOTAL: 17 flops */
}
-static void constr_vsite3FD(rvec xi,rvec xj,rvec xk,rvec x,real a,real b,
- t_pbc *pbc)
+static void constr_vsite3FD(rvec xi, rvec xj, rvec xk, rvec x, real a, real b,
+ t_pbc *pbc)
{
- rvec xij,xjk,temp;
- real c;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xj,xjk);
- /* 6 flops */
-
- /* temp goes from i to a point on the line jk */
- temp[XX] = xij[XX] + a*xjk[XX];
- temp[YY] = xij[YY] + a*xjk[YY];
- temp[ZZ] = xij[ZZ] + a*xjk[ZZ];
- /* 6 flops */
-
- c=b*gmx_invsqrt(iprod(temp,temp));
- /* 6 + 10 flops */
-
- x[XX] = xi[XX] + c*temp[XX];
- x[YY] = xi[YY] + c*temp[YY];
- x[ZZ] = xi[ZZ] + c*temp[ZZ];
- /* 6 Flops */
-
- /* TOTAL: 34 flops */
+ rvec xij, xjk, temp;
+ real c;
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xj, xjk);
+ /* 6 flops */
+
+ /* temp goes from i to a point on the line jk */
+ temp[XX] = xij[XX] + a*xjk[XX];
+ temp[YY] = xij[YY] + a*xjk[YY];
+ temp[ZZ] = xij[ZZ] + a*xjk[ZZ];
+ /* 6 flops */
+
+ c = b*gmx_invsqrt(iprod(temp, temp));
+ /* 6 + 10 flops */
+
+ x[XX] = xi[XX] + c*temp[XX];
+ x[YY] = xi[YY] + c*temp[YY];
+ x[ZZ] = xi[ZZ] + c*temp[ZZ];
+ /* 6 Flops */
+
+ /* TOTAL: 34 flops */
}
-static void constr_vsite3FAD(rvec xi,rvec xj,rvec xk,rvec x,real a,real b, t_pbc *pbc)
+static void constr_vsite3FAD(rvec xi, rvec xj, rvec xk, rvec x, real a, real b, t_pbc *pbc)
{
- rvec xij,xjk,xp;
- real a1,b1,c1,invdij;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xj,xjk);
- /* 6 flops */
-
- invdij = gmx_invsqrt(iprod(xij,xij));
- c1 = invdij * invdij * iprod(xij,xjk);
- xp[XX] = xjk[XX] - c1*xij[XX];
- xp[YY] = xjk[YY] - c1*xij[YY];
- xp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
- a1 = a*invdij;
- b1 = b*gmx_invsqrt(iprod(xp,xp));
- /* 45 */
-
- x[XX] = xi[XX] + a1*xij[XX] + b1*xp[XX];
- x[YY] = xi[YY] + a1*xij[YY] + b1*xp[YY];
- x[ZZ] = xi[ZZ] + a1*xij[ZZ] + b1*xp[ZZ];
- /* 12 Flops */
-
- /* TOTAL: 63 flops */
+ rvec xij, xjk, xp;
+ real a1, b1, c1, invdij;
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xj, xjk);
+ /* 6 flops */
+
+ invdij = gmx_invsqrt(iprod(xij, xij));
+ c1 = invdij * invdij * iprod(xij, xjk);
+ xp[XX] = xjk[XX] - c1*xij[XX];
+ xp[YY] = xjk[YY] - c1*xij[YY];
+ xp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
+ a1 = a*invdij;
+ b1 = b*gmx_invsqrt(iprod(xp, xp));
+ /* 45 */
+
+ x[XX] = xi[XX] + a1*xij[XX] + b1*xp[XX];
+ x[YY] = xi[YY] + a1*xij[YY] + b1*xp[YY];
+ x[ZZ] = xi[ZZ] + a1*xij[ZZ] + b1*xp[ZZ];
+ /* 12 Flops */
+
+ /* TOTAL: 63 flops */
}
-static void constr_vsite3OUT(rvec xi,rvec xj,rvec xk,rvec x,
- real a,real b,real c,t_pbc *pbc)
+static void constr_vsite3OUT(rvec xi, rvec xj, rvec xk, rvec x,
+ real a, real b, real c, t_pbc *pbc)
{
- rvec xij,xik,temp;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xi,xik);
- cprod(xij,xik,temp);
- /* 15 Flops */
-
- x[XX] = xi[XX] + a*xij[XX] + b*xik[XX] + c*temp[XX];
- x[YY] = xi[YY] + a*xij[YY] + b*xik[YY] + c*temp[YY];
- x[ZZ] = xi[ZZ] + a*xij[ZZ] + b*xik[ZZ] + c*temp[ZZ];
- /* 18 Flops */
-
- /* TOTAL: 33 flops */
+ rvec xij, xik, temp;
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xi, xik);
+ cprod(xij, xik, temp);
+ /* 15 Flops */
+
+ x[XX] = xi[XX] + a*xij[XX] + b*xik[XX] + c*temp[XX];
+ x[YY] = xi[YY] + a*xij[YY] + b*xik[YY] + c*temp[YY];
+ x[ZZ] = xi[ZZ] + a*xij[ZZ] + b*xik[ZZ] + c*temp[ZZ];
+ /* 18 Flops */
+
+ /* TOTAL: 33 flops */
}
-static void constr_vsite4FD(rvec xi,rvec xj,rvec xk,rvec xl,rvec x,
- real a,real b,real c,t_pbc *pbc)
+static void constr_vsite4FD(rvec xi, rvec xj, rvec xk, rvec xl, rvec x,
+ real a, real b, real c, t_pbc *pbc)
{
- rvec xij,xjk,xjl,temp;
- real d;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xj,xjk);
- pbc_rvec_sub(pbc,xl,xj,xjl);
- /* 9 flops */
-
- /* temp goes from i to a point on the plane jkl */
- temp[XX] = xij[XX] + a*xjk[XX] + b*xjl[XX];
- temp[YY] = xij[YY] + a*xjk[YY] + b*xjl[YY];
- temp[ZZ] = xij[ZZ] + a*xjk[ZZ] + b*xjl[ZZ];
- /* 12 flops */
-
- d=c*gmx_invsqrt(iprod(temp,temp));
- /* 6 + 10 flops */
-
- x[XX] = xi[XX] + d*temp[XX];
- x[YY] = xi[YY] + d*temp[YY];
- x[ZZ] = xi[ZZ] + d*temp[ZZ];
- /* 6 Flops */
-
- /* TOTAL: 43 flops */
+ rvec xij, xjk, xjl, temp;
+ real d;
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xj, xjk);
+ pbc_rvec_sub(pbc, xl, xj, xjl);
+ /* 9 flops */
+
+ /* temp goes from i to a point on the plane jkl */
+ temp[XX] = xij[XX] + a*xjk[XX] + b*xjl[XX];
+ temp[YY] = xij[YY] + a*xjk[YY] + b*xjl[YY];
+ temp[ZZ] = xij[ZZ] + a*xjk[ZZ] + b*xjl[ZZ];
+ /* 12 flops */
+
+ d = c*gmx_invsqrt(iprod(temp, temp));
+ /* 6 + 10 flops */
+
+ x[XX] = xi[XX] + d*temp[XX];
+ x[YY] = xi[YY] + d*temp[YY];
+ x[ZZ] = xi[ZZ] + d*temp[ZZ];
+ /* 6 Flops */
+
+ /* TOTAL: 43 flops */
}
-static void constr_vsite4FDN(rvec xi,rvec xj,rvec xk,rvec xl,rvec x,
- real a,real b,real c,t_pbc *pbc)
+static void constr_vsite4FDN(rvec xi, rvec xj, rvec xk, rvec xl, rvec x,
+ real a, real b, real c, t_pbc *pbc)
{
- rvec xij,xik,xil,ra,rb,rja,rjb,rm;
+ rvec xij, xik, xil, ra, rb, rja, rjb, rm;
real d;
-
- pbc_rvec_sub(pbc,xj,xi,xij);
- pbc_rvec_sub(pbc,xk,xi,xik);
- pbc_rvec_sub(pbc,xl,xi,xil);
+
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ pbc_rvec_sub(pbc, xk, xi, xik);
+ pbc_rvec_sub(pbc, xl, xi, xil);
/* 9 flops */
ra[XX] = a*xik[XX];
ra[YY] = a*xik[YY];
ra[ZZ] = a*xik[ZZ];
-
+
rb[XX] = b*xil[XX];
rb[YY] = b*xil[YY];
rb[ZZ] = b*xil[ZZ];
/* 6 flops */
- rvec_sub(ra,xij,rja);
- rvec_sub(rb,xij,rjb);
+ rvec_sub(ra, xij, rja);
+ rvec_sub(rb, xij, rjb);
/* 6 flops */
-
- cprod(rja,rjb,rm);
+
+ cprod(rja, rjb, rm);
/* 9 flops */
-
- d=c*gmx_invsqrt(norm2(rm));
+
+ d = c*gmx_invsqrt(norm2(rm));
/* 5+5+1 flops */
-
+
x[XX] = xi[XX] + d*rm[XX];
x[YY] = xi[YY] + d*rm[YY];
x[ZZ] = xi[ZZ] + d*rm[ZZ];
/* 6 Flops */
-
+
/* TOTAL: 47 flops */
}
static int constr_vsiten(t_iatom *ia, t_iparams ip[],
- rvec *x, t_pbc *pbc)
+ rvec *x, t_pbc *pbc)
{
- rvec xs,x1,dx;
- dvec dsum;
- int n3,av,ai,i;
- real a;
-
- n3 = 3*ip[ia[0]].vsiten.n;
- av = ia[1];
- ai = ia[2];
- copy_rvec(x[ai],x1);
- clear_dvec(dsum);
- for(i=3; i<n3; i+=3) {
- ai = ia[i+2];
- a = ip[ia[i]].vsiten.a;
- if (pbc) {
- pbc_dx_aiuc(pbc,x[ai],x1,dx);
- } else {
- rvec_sub(x[ai],x1,dx);
- }
- dsum[XX] += a*dx[XX];
- dsum[YY] += a*dx[YY];
- dsum[ZZ] += a*dx[ZZ];
- /* 9 Flops */
- }
+ rvec xs, x1, dx;
+ dvec dsum;
+ int n3, av, ai, i;
+ real a;
- x[av][XX] = x1[XX] + dsum[XX];
- x[av][YY] = x1[YY] + dsum[YY];
- x[av][ZZ] = x1[ZZ] + dsum[ZZ];
+ n3 = 3*ip[ia[0]].vsiten.n;
+ av = ia[1];
+ ai = ia[2];
+ copy_rvec(x[ai], x1);
+ clear_dvec(dsum);
+ for (i = 3; i < n3; i += 3)
+ {
+ ai = ia[i+2];
+ a = ip[ia[i]].vsiten.a;
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, x[ai], x1, dx);
+ }
+ else
+ {
+ rvec_sub(x[ai], x1, dx);
+ }
+ dsum[XX] += a*dx[XX];
+ dsum[YY] += a*dx[YY];
+ dsum[ZZ] += a*dx[ZZ];
+ /* 9 Flops */
+ }
+
+ x[av][XX] = x1[XX] + dsum[XX];
+ x[av][YY] = x1[YY] + dsum[YY];
+ x[av][ZZ] = x1[ZZ] + dsum[ZZ];
- return n3;
+ return n3;
}
void construct_vsites_thread(gmx_vsite_t *vsite,
- rvec x[],t_nrnb *nrnb,
- real dt,rvec *v,
- t_iparams ip[],t_ilist ilist[],
+ rvec x[],
+ real dt, rvec *v,
+ t_iparams ip[], t_ilist ilist[],
t_pbc *pbc_null)
{
- gmx_bool bPBCAll;
- rvec xpbc,xv,vv,dx;
- real a1,b1,c1,inv_dt;
- int i,inc,ii,nra,nr,tp,ftype;
- t_iatom avsite,ai,aj,ak,al,pbc_atom;
+ gmx_bool bPBCAll;
+ rvec xpbc, xv, vv, dx;
+ real a1, b1, c1, inv_dt;
+ int i, inc, ii, nra, nr, tp, ftype;
+ t_iatom avsite, ai, aj, ak, al, pbc_atom;
t_iatom *ia;
t_pbc *pbc_null2;
- int *vsite_pbc,ishift;
- rvec reftmp,vtmp,rtmp;
+ int *vsite_pbc, ishift;
+ rvec reftmp, vtmp, rtmp;
if (v != NULL)
{
pbc_null2 = NULL;
vsite_pbc = NULL;
- for(ftype=0; (ftype<F_NRE); ftype++)
+ for (ftype = 0; (ftype < F_NRE); ftype++)
{
if ((interaction_function[ftype].flags & IF_VSITE) &&
ilist[ftype].nr > 0)
vsite_pbc = vsite->vsite_pbc_loc[ftype-F_VSITE2];
}
- for(i=0; i<nr; )
+ for (i = 0; i < nr; )
{
tp = ia[0];
/* The vsite and constructing atoms */
avsite = ia[1];
- ai = ia[2];
- aj = ia[3];
+ ai = ia[2];
/* Constants for constructing vsites */
a1 = ip[tp].vsite.a;
{
/* No charge groups, vsite follows its own pbc */
pbc_atom = avsite;
- copy_rvec(x[avsite],xpbc);
+ copy_rvec(x[avsite], xpbc);
}
else if (vsite_pbc != NULL)
{
* single for single atom cg's pbc_atom
* is the vsite itself.
*/
- copy_rvec(x[pbc_atom],xpbc);
+ copy_rvec(x[pbc_atom], xpbc);
}
pbc_null2 = pbc_null;
}
pbc_atom = -2;
}
/* Copy the old position */
- copy_rvec(x[avsite],xv);
+ copy_rvec(x[avsite], xv);
/* Construct the vsite depending on type */
switch (ftype)
{
- case F_VSITE2:
- constr_vsite2(x[ai],x[aj],x[avsite],a1,pbc_null2);
- break;
- case F_VSITE3:
- ak = ia[4];
- b1 = ip[tp].vsite.b;
- constr_vsite3(x[ai],x[aj],x[ak],x[avsite],a1,b1,pbc_null2);
- break;
- case F_VSITE3FD:
- ak = ia[4];
- b1 = ip[tp].vsite.b;
- constr_vsite3FD(x[ai],x[aj],x[ak],x[avsite],a1,b1,pbc_null2);
- break;
- case F_VSITE3FAD:
- ak = ia[4];
- b1 = ip[tp].vsite.b;
- constr_vsite3FAD(x[ai],x[aj],x[ak],x[avsite],a1,b1,pbc_null2);
- break;
- case F_VSITE3OUT:
- ak = ia[4];
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- constr_vsite3OUT(x[ai],x[aj],x[ak],x[avsite],a1,b1,c1,pbc_null2);
- break;
- case F_VSITE4FD:
- ak = ia[4];
- al = ia[5];
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- constr_vsite4FD(x[ai],x[aj],x[ak],x[al],x[avsite],a1,b1,c1,
- pbc_null2);
- break;
- case F_VSITE4FDN:
- ak = ia[4];
- al = ia[5];
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- constr_vsite4FDN(x[ai],x[aj],x[ak],x[al],x[avsite],a1,b1,c1,
- pbc_null2);
- break;
- case F_VSITEN:
- inc = constr_vsiten(ia,ip,x,pbc_null2);
- break;
- default:
- gmx_fatal(FARGS,"No such vsite type %d in %s, line %d",
- ftype,__FILE__,__LINE__);
+ case F_VSITE2:
+ aj = ia[3];
+ constr_vsite2(x[ai], x[aj], x[avsite], a1, pbc_null2);
+ break;
+ case F_VSITE3:
+ aj = ia[3];
+ ak = ia[4];
+ b1 = ip[tp].vsite.b;
+ constr_vsite3(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ break;
+ case F_VSITE3FD:
+ aj = ia[3];
+ ak = ia[4];
+ b1 = ip[tp].vsite.b;
+ constr_vsite3FD(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ break;
+ case F_VSITE3FAD:
+ aj = ia[3];
+ ak = ia[4];
+ b1 = ip[tp].vsite.b;
+ constr_vsite3FAD(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ break;
+ case F_VSITE3OUT:
+ aj = ia[3];
+ ak = ia[4];
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ constr_vsite3OUT(x[ai], x[aj], x[ak], x[avsite], a1, b1, c1, pbc_null2);
+ break;
+ case F_VSITE4FD:
+ aj = ia[3];
+ ak = ia[4];
+ al = ia[5];
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ constr_vsite4FD(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1,
+ pbc_null2);
+ break;
+ case F_VSITE4FDN:
+ aj = ia[3];
+ ak = ia[4];
+ al = ia[5];
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ constr_vsite4FDN(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1,
+ pbc_null2);
+ break;
+ case F_VSITEN:
+ inc = constr_vsiten(ia, ip, x, pbc_null2);
+ break;
+ default:
+ gmx_fatal(FARGS, "No such vsite type %d in %s, line %d",
+ ftype, __FILE__, __LINE__);
}
if (pbc_atom >= 0)
{
/* Match the pbc of this vsite to the rest of its charge group */
- ishift = pbc_dx_aiuc(pbc_null,x[avsite],xpbc,dx);
+ ishift = pbc_dx_aiuc(pbc_null, x[avsite], xpbc, dx);
if (ishift != CENTRAL)
{
- rvec_add(xpbc,dx,x[avsite]);
+ rvec_add(xpbc, dx, x[avsite]);
}
}
if (v != NULL)
{
/* Calculate velocity of vsite... */
- rvec_sub(x[avsite],xv,vv);
- svmul(inv_dt,vv,v[avsite]);
+ rvec_sub(x[avsite], xv, vv);
+ svmul(inv_dt, vv, v[avsite]);
}
/* Increment loop variables */
}
}
-void construct_vsites(FILE *log,gmx_vsite_t *vsite,
- rvec x[],t_nrnb *nrnb,
- real dt,rvec *v,
- t_iparams ip[],t_ilist ilist[],
- int ePBC,gmx_bool bMolPBC,t_graph *graph,
- t_commrec *cr,matrix box)
+void construct_vsites(gmx_vsite_t *vsite,
+ rvec x[],
+ real dt, rvec *v,
+ t_iparams ip[], t_ilist ilist[],
+ int ePBC, gmx_bool bMolPBC,
+ t_commrec *cr, matrix box)
{
- t_pbc pbc,*pbc_null;
+ t_pbc pbc, *pbc_null;
gmx_bool bDomDec;
int nthreads;
bDomDec = cr && DOMAINDECOMP(cr);
-
+
/* We only need to do pbc when we have inter-cg vsites */
if (ePBC != epbcNONE && (bDomDec || bMolPBC) && vsite->n_intercg_vsite)
{
/* This is wasting some CPU time as we now do this multiple times
* per MD step. But how often do we have vsites with full pbc?
*/
- pbc_null = set_pbc_dd(&pbc,ePBC,cr!=NULL ? cr->dd : NULL,FALSE,box);
+ pbc_null = set_pbc_dd(&pbc, ePBC, cr != NULL ? cr->dd : NULL, FALSE, box);
}
else
{
pbc_null = NULL;
}
- if (cr)
+ if (bDomDec)
{
- if (bDomDec)
- {
- dd_move_x_vsites(cr->dd,box,x);
- }
- else if (vsite->bPDvsitecomm)
- {
- /* I'm not sure whether the periodicity and shift are guaranteed
- * to be consistent between different nodes when running e.g. polymers
- * in parallel. In this special case we thus unshift/shift,
- * but only when necessary. This is to make sure the coordinates
- * we move don't end up a box away...
- */
- if (graph != NULL)
- {
- unshift_self(graph,box,x);
- }
-
- move_construct_x(vsite->vsitecomm,x,cr);
-
- if (graph != NULL)
- {
- shift_self(graph,box,x);
- }
- }
+ dd_move_x_vsites(cr->dd, box, x);
}
if (vsite->nthreads == 1)
{
construct_vsites_thread(vsite,
- x,nrnb,dt,v,
- ip,ilist,
+ x, dt, v,
+ ip, ilist,
pbc_null);
}
else
#pragma omp parallel num_threads(vsite->nthreads)
{
construct_vsites_thread(vsite,
- x,nrnb,dt,v,
- ip,vsite->tdata[gmx_omp_get_thread_num()].ilist,
+ x, dt, v,
+ ip, vsite->tdata[gmx_omp_get_thread_num()].ilist,
pbc_null);
}
/* Now we can construct the vsites that might depend on other vsites */
construct_vsites_thread(vsite,
- x,nrnb,dt,v,
- ip,vsite->tdata[vsite->nthreads].ilist,
+ x, dt, v,
+ ip, vsite->tdata[vsite->nthreads].ilist,
pbc_null);
}
}
-static void spread_vsite2(t_iatom ia[],real a,
- rvec x[],rvec f[],rvec fshift[],
- t_pbc *pbc,t_graph *g)
+static void spread_vsite2(t_iatom ia[], real a,
+ rvec x[], rvec f[], rvec fshift[],
+ t_pbc *pbc, t_graph *g)
{
- rvec fi,fj,dx;
- t_iatom av,ai,aj;
- ivec di;
- real b;
- int siv,sij;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
-
- svmul(1-a,f[av],fi);
- svmul( a,f[av],fj);
- /* 7 flop */
-
- rvec_inc(f[ai],fi);
- rvec_inc(f[aj],fj);
- /* 6 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,av),di);
- siv = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),di);
- sij = IVEC2IS(di);
- } else if (pbc) {
- siv = pbc_dx_aiuc(pbc,x[ai],x[av],dx);
- sij = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
- } else {
- siv = CENTRAL;
- sij = CENTRAL;
- }
-
- if (fshift && (siv != CENTRAL || sij != CENTRAL)) {
- rvec_inc(fshift[siv],f[av]);
- rvec_dec(fshift[CENTRAL],fi);
- rvec_dec(fshift[sij],fj);
- }
-
- /* TOTAL: 13 flops */
+ rvec fi, fj, dx;
+ t_iatom av, ai, aj;
+ ivec di;
+ real b;
+ int siv, sij;
+
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+
+ svmul(1-a, f[av], fi);
+ svmul( a, f[av], fj);
+ /* 7 flop */
+
+ rvec_inc(f[ai], fi);
+ rvec_inc(f[aj], fj);
+ /* 6 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, av), di);
+ siv = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), di);
+ sij = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ siv = pbc_dx_aiuc(pbc, x[ai], x[av], dx);
+ sij = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
+ }
+ else
+ {
+ siv = CENTRAL;
+ sij = CENTRAL;
+ }
+
+ if (fshift && (siv != CENTRAL || sij != CENTRAL))
+ {
+ rvec_inc(fshift[siv], f[av]);
+ rvec_dec(fshift[CENTRAL], fi);
+ rvec_dec(fshift[sij], fj);
+ }
+
+ /* TOTAL: 13 flops */
}
-void construct_vsites_mtop(FILE *log,gmx_vsite_t *vsite,
- gmx_mtop_t *mtop,rvec x[])
+void construct_vsites_mtop(gmx_vsite_t *vsite,
+ gmx_mtop_t *mtop, rvec x[])
{
- int as,mb,mol;
- gmx_molblock_t *molb;
- gmx_moltype_t *molt;
-
- as = 0;
- for(mb=0; mb<mtop->nmolblock; mb++) {
- molb = &mtop->molblock[mb];
- molt = &mtop->moltype[molb->type];
- for(mol=0; mol<molb->nmol; mol++) {
- construct_vsites(log,vsite,x+as,NULL,0.0,NULL,
- mtop->ffparams.iparams,molt->ilist,
- epbcNONE,TRUE,NULL,NULL,NULL);
- as += molt->atoms.nr;
- }
- }
+ int as, mb, mol;
+ gmx_molblock_t *molb;
+ gmx_moltype_t *molt;
+
+ as = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ molt = &mtop->moltype[molb->type];
+ for (mol = 0; mol < molb->nmol; mol++)
+ {
+ construct_vsites(vsite, x+as, 0.0, NULL,
+ mtop->ffparams.iparams, molt->ilist,
+ epbcNONE, TRUE, NULL, NULL);
+ as += molt->atoms.nr;
+ }
+ }
}
-static void spread_vsite3(t_iatom ia[],real a,real b,
- rvec x[],rvec f[],rvec fshift[],
- t_pbc *pbc,t_graph *g)
+static void spread_vsite3(t_iatom ia[], real a, real b,
+ rvec x[], rvec f[], rvec fshift[],
+ t_pbc *pbc, t_graph *g)
{
- rvec fi,fj,fk,dx;
- atom_id av,ai,aj,ak;
- ivec di;
- int siv,sij,sik;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
-
- svmul(1-a-b,f[av],fi);
- svmul( a,f[av],fj);
- svmul( b,f[av],fk);
- /* 11 flops */
-
- rvec_inc(f[ai],fi);
- rvec_inc(f[aj],fj);
- rvec_inc(f[ak],fk);
- /* 9 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,ia[1]),di);
- siv = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),di);
- sij = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,ak),di);
- sik = IVEC2IS(di);
- } else if (pbc) {
- siv = pbc_dx_aiuc(pbc,x[ai],x[av],dx);
- sij = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
- sik = pbc_dx_aiuc(pbc,x[ai],x[ak],dx);
- } else {
- siv = CENTRAL;
- sij = CENTRAL;
- sik = CENTRAL;
- }
-
- if (fshift && (siv!=CENTRAL || sij!=CENTRAL || sik!=CENTRAL)) {
- rvec_inc(fshift[siv],f[av]);
- rvec_dec(fshift[CENTRAL],fi);
- rvec_dec(fshift[sij],fj);
- rvec_dec(fshift[sik],fk);
- }
-
- /* TOTAL: 20 flops */
+ rvec fi, fj, fk, dx;
+ atom_id av, ai, aj, ak;
+ ivec di;
+ int siv, sij, sik;
+
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
+
+ svmul(1-a-b, f[av], fi);
+ svmul( a, f[av], fj);
+ svmul( b, f[av], fk);
+ /* 11 flops */
+
+ rvec_inc(f[ai], fi);
+ rvec_inc(f[aj], fj);
+ rvec_inc(f[ak], fk);
+ /* 9 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, ia[1]), di);
+ siv = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), di);
+ sij = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, ak), di);
+ sik = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ siv = pbc_dx_aiuc(pbc, x[ai], x[av], dx);
+ sij = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
+ sik = pbc_dx_aiuc(pbc, x[ai], x[ak], dx);
+ }
+ else
+ {
+ siv = CENTRAL;
+ sij = CENTRAL;
+ sik = CENTRAL;
+ }
+
+ if (fshift && (siv != CENTRAL || sij != CENTRAL || sik != CENTRAL))
+ {
+ rvec_inc(fshift[siv], f[av]);
+ rvec_dec(fshift[CENTRAL], fi);
+ rvec_dec(fshift[sij], fj);
+ rvec_dec(fshift[sik], fk);
+ }
+
+ /* TOTAL: 20 flops */
}
-static void spread_vsite3FD(t_iatom ia[],real a,real b,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+static void spread_vsite3FD(t_iatom ia[], real a, real b,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
{
- real fx,fy,fz,c,invl,fproj,a1;
- rvec xvi,xij,xjk,xix,fv,temp;
- t_iatom av,ai,aj,ak;
- int svi,sji,skj,d;
- ivec di;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
- copy_rvec(f[av],fv);
-
- sji = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- skj = pbc_rvec_sub(pbc,x[ak],x[aj],xjk);
- /* 6 flops */
-
- /* xix goes from i to point x on the line jk */
- xix[XX]=xij[XX]+a*xjk[XX];
- xix[YY]=xij[YY]+a*xjk[YY];
- xix[ZZ]=xij[ZZ]+a*xjk[ZZ];
- /* 6 flops */
-
- invl=gmx_invsqrt(iprod(xix,xix));
- c=b*invl;
- /* 4 + ?10? flops */
-
- fproj=iprod(xix,fv)*invl*invl; /* = (xix . f)/(xix . xix) */
-
- temp[XX]=c*(fv[XX]-fproj*xix[XX]);
- temp[YY]=c*(fv[YY]-fproj*xix[YY]);
- temp[ZZ]=c*(fv[ZZ]-fproj*xix[ZZ]);
- /* 16 */
-
- /* c is already calculated in constr_vsite3FD
- storing c somewhere will save 26 flops! */
-
- a1=1-a;
- f[ai][XX] += fv[XX] - temp[XX];
- f[ai][YY] += fv[YY] - temp[YY];
- f[ai][ZZ] += fv[ZZ] - temp[ZZ];
- f[aj][XX] += a1*temp[XX];
- f[aj][YY] += a1*temp[YY];
- f[aj][ZZ] += a1*temp[ZZ];
- f[ak][XX] += a*temp[XX];
- f[ak][YY] += a*temp[YY];
- f[ak][ZZ] += a*temp[ZZ];
- /* 19 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ia[1]),SHIFT_IVEC(g,ai),di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,aj),di);
- skj = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
- svi = CENTRAL;
- }
-
- if (fshift && (svi!=CENTRAL || sji!=CENTRAL || skj!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
- fshift[CENTRAL][XX] += fv[XX] - (1 + a)*temp[XX];
- fshift[CENTRAL][YY] += fv[YY] - (1 + a)*temp[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - (1 + a)*temp[ZZ];
- fshift[ sji][XX] += temp[XX];
- fshift[ sji][YY] += temp[YY];
- fshift[ sji][ZZ] += temp[ZZ];
- fshift[ skj][XX] += a*temp[XX];
- fshift[ skj][YY] += a*temp[YY];
- fshift[ skj][ZZ] += a*temp[ZZ];
- }
+ real fx, fy, fz, c, invl, fproj, a1;
+ rvec xvi, xij, xjk, xix, fv, temp;
+ t_iatom av, ai, aj, ak;
+ int svi, sji, skj, d;
+ ivec di;
+
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
+ copy_rvec(f[av], fv);
+
+ sji = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ skj = pbc_rvec_sub(pbc, x[ak], x[aj], xjk);
+ /* 6 flops */
+
+ /* xix goes from i to point x on the line jk */
+ xix[XX] = xij[XX]+a*xjk[XX];
+ xix[YY] = xij[YY]+a*xjk[YY];
+ xix[ZZ] = xij[ZZ]+a*xjk[ZZ];
+ /* 6 flops */
+
+ invl = gmx_invsqrt(iprod(xix, xix));
+ c = b*invl;
+ /* 4 + ?10? flops */
+
+ fproj = iprod(xix, fv)*invl*invl; /* = (xix . f)/(xix . xix) */
+
+ temp[XX] = c*(fv[XX]-fproj*xix[XX]);
+ temp[YY] = c*(fv[YY]-fproj*xix[YY]);
+ temp[ZZ] = c*(fv[ZZ]-fproj*xix[ZZ]);
+ /* 16 */
+
+ /* c is already calculated in constr_vsite3FD
+ storing c somewhere will save 26 flops! */
+
+ a1 = 1-a;
+ f[ai][XX] += fv[XX] - temp[XX];
+ f[ai][YY] += fv[YY] - temp[YY];
+ f[ai][ZZ] += fv[ZZ] - temp[ZZ];
+ f[aj][XX] += a1*temp[XX];
+ f[aj][YY] += a1*temp[YY];
+ f[aj][ZZ] += a1*temp[ZZ];
+ f[ak][XX] += a*temp[XX];
+ f[ak][YY] += a*temp[YY];
+ f[ak][ZZ] += a*temp[ZZ];
+ /* 19 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
+ svi = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
+ sji = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, aj), di);
+ skj = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = CENTRAL;
+ }
+
+ if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[CENTRAL][XX] += fv[XX] - (1 + a)*temp[XX];
+ fshift[CENTRAL][YY] += fv[YY] - (1 + a)*temp[YY];
+ fshift[CENTRAL][ZZ] += fv[ZZ] - (1 + a)*temp[ZZ];
+ fshift[ sji][XX] += temp[XX];
+ fshift[ sji][YY] += temp[YY];
+ fshift[ sji][ZZ] += temp[ZZ];
+ fshift[ skj][XX] += a*temp[XX];
+ fshift[ skj][YY] += a*temp[YY];
+ fshift[ skj][ZZ] += a*temp[ZZ];
+ }
if (VirCorr)
{
* subtract (xv-xi)*fv and add (xj-xi)*fj + (xk-xi)*fk.
*/
rvec xiv;
- int i,j;
+ int i, j;
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
- for(i=0; i<DIM; i++)
+ for (i = 0; i < DIM; i++)
{
- for(j=0; j<DIM; j++)
+ for (j = 0; j < DIM; j++)
{
/* As xix is a linear combination of j and k, use that here */
dxdf[i][j] += -xiv[i]*fv[j] + xix[i]*temp[j];
}
}
- /* TOTAL: 61 flops */
+ /* TOTAL: 61 flops */
}
-static void spread_vsite3FAD(t_iatom ia[],real a,real b,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+static void spread_vsite3FAD(t_iatom ia[], real a, real b,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
{
- rvec xvi,xij,xjk,xperp,Fpij,Fppp,fv,f1,f2,f3;
- real a1,b1,c1,c2,invdij,invdij2,invdp,fproj;
- t_iatom av,ai,aj,ak;
- int svi,sji,skj,d;
- ivec di;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
- copy_rvec(f[ia[1]],fv);
-
- sji = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- skj = pbc_rvec_sub(pbc,x[ak],x[aj],xjk);
- /* 6 flops */
-
- invdij = gmx_invsqrt(iprod(xij,xij));
- invdij2 = invdij * invdij;
- c1 = iprod(xij,xjk) * invdij2;
- xperp[XX] = xjk[XX] - c1*xij[XX];
- xperp[YY] = xjk[YY] - c1*xij[YY];
- xperp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
- /* xperp in plane ijk, perp. to ij */
- invdp = gmx_invsqrt(iprod(xperp,xperp));
- a1 = a*invdij;
- b1 = b*invdp;
- /* 45 flops */
-
- /* a1, b1 and c1 are already calculated in constr_vsite3FAD
- storing them somewhere will save 45 flops! */
-
- fproj=iprod(xij ,fv)*invdij2;
- svmul(fproj, xij, Fpij); /* proj. f on xij */
- svmul(iprod(xperp,fv)*invdp*invdp,xperp,Fppp); /* proj. f on xperp */
- svmul(b1*fproj, xperp,f3);
- /* 23 flops */
-
- rvec_sub(fv,Fpij,f1); /* f1 = f - Fpij */
- rvec_sub(f1,Fppp,f2); /* f2 = f - Fpij - Fppp */
- for (d=0; (d<DIM); d++) {
- f1[d]*=a1;
- f2[d]*=b1;
- }
- /* 12 flops */
-
- c2=1+c1;
- f[ai][XX] += fv[XX] - f1[XX] + c1*f2[XX] + f3[XX];
- f[ai][YY] += fv[YY] - f1[YY] + c1*f2[YY] + f3[YY];
- f[ai][ZZ] += fv[ZZ] - f1[ZZ] + c1*f2[ZZ] + f3[ZZ];
- f[aj][XX] += f1[XX] - c2*f2[XX] - f3[XX];
- f[aj][YY] += f1[YY] - c2*f2[YY] - f3[YY];
- f[aj][ZZ] += f1[ZZ] - c2*f2[ZZ] - f3[ZZ];
- f[ak][XX] += f2[XX];
- f[ak][YY] += f2[YY];
- f[ak][ZZ] += f2[ZZ];
- /* 30 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ia[1]),SHIFT_IVEC(g,ai),di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,aj),di);
- skj = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
- svi = CENTRAL;
- }
-
- if (fshift && (svi!=CENTRAL || sji!=CENTRAL || skj!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
- fshift[CENTRAL][XX] += fv[XX] - f1[XX] - (1-c1)*f2[XX] + f3[XX];
- fshift[CENTRAL][YY] += fv[YY] - f1[YY] - (1-c1)*f2[YY] + f3[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - f1[ZZ] - (1-c1)*f2[ZZ] + f3[ZZ];
- fshift[ sji][XX] += f1[XX] - c1 *f2[XX] - f3[XX];
- fshift[ sji][YY] += f1[YY] - c1 *f2[YY] - f3[YY];
- fshift[ sji][ZZ] += f1[ZZ] - c1 *f2[ZZ] - f3[ZZ];
- fshift[ skj][XX] += f2[XX];
- fshift[ skj][YY] += f2[YY];
- fshift[ skj][ZZ] += f2[ZZ];
- }
+ rvec xvi, xij, xjk, xperp, Fpij, Fppp, fv, f1, f2, f3;
+ real a1, b1, c1, c2, invdij, invdij2, invdp, fproj;
+ t_iatom av, ai, aj, ak;
+ int svi, sji, skj, d;
+ ivec di;
+
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
+ copy_rvec(f[ia[1]], fv);
+
+ sji = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ skj = pbc_rvec_sub(pbc, x[ak], x[aj], xjk);
+ /* 6 flops */
+
+ invdij = gmx_invsqrt(iprod(xij, xij));
+ invdij2 = invdij * invdij;
+ c1 = iprod(xij, xjk) * invdij2;
+ xperp[XX] = xjk[XX] - c1*xij[XX];
+ xperp[YY] = xjk[YY] - c1*xij[YY];
+ xperp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
+ /* xperp in plane ijk, perp. to ij */
+ invdp = gmx_invsqrt(iprod(xperp, xperp));
+ a1 = a*invdij;
+ b1 = b*invdp;
+ /* 45 flops */
+
+ /* a1, b1 and c1 are already calculated in constr_vsite3FAD
+ storing them somewhere will save 45 flops! */
+
+ fproj = iprod(xij, fv)*invdij2;
+ svmul(fproj, xij, Fpij); /* proj. f on xij */
+ svmul(iprod(xperp, fv)*invdp*invdp, xperp, Fppp); /* proj. f on xperp */
+ svmul(b1*fproj, xperp, f3);
+ /* 23 flops */
+
+ rvec_sub(fv, Fpij, f1); /* f1 = f - Fpij */
+ rvec_sub(f1, Fppp, f2); /* f2 = f - Fpij - Fppp */
+ for (d = 0; (d < DIM); d++)
+ {
+ f1[d] *= a1;
+ f2[d] *= b1;
+ }
+ /* 12 flops */
+
+ c2 = 1+c1;
+ f[ai][XX] += fv[XX] - f1[XX] + c1*f2[XX] + f3[XX];
+ f[ai][YY] += fv[YY] - f1[YY] + c1*f2[YY] + f3[YY];
+ f[ai][ZZ] += fv[ZZ] - f1[ZZ] + c1*f2[ZZ] + f3[ZZ];
+ f[aj][XX] += f1[XX] - c2*f2[XX] - f3[XX];
+ f[aj][YY] += f1[YY] - c2*f2[YY] - f3[YY];
+ f[aj][ZZ] += f1[ZZ] - c2*f2[ZZ] - f3[ZZ];
+ f[ak][XX] += f2[XX];
+ f[ak][YY] += f2[YY];
+ f[ak][ZZ] += f2[ZZ];
+ /* 30 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
+ svi = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
+ sji = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, aj), di);
+ skj = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = CENTRAL;
+ }
+
+ if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[CENTRAL][XX] += fv[XX] - f1[XX] - (1-c1)*f2[XX] + f3[XX];
+ fshift[CENTRAL][YY] += fv[YY] - f1[YY] - (1-c1)*f2[YY] + f3[YY];
+ fshift[CENTRAL][ZZ] += fv[ZZ] - f1[ZZ] - (1-c1)*f2[ZZ] + f3[ZZ];
+ fshift[ sji][XX] += f1[XX] - c1 *f2[XX] - f3[XX];
+ fshift[ sji][YY] += f1[YY] - c1 *f2[YY] - f3[YY];
+ fshift[ sji][ZZ] += f1[ZZ] - c1 *f2[ZZ] - f3[ZZ];
+ fshift[ skj][XX] += f2[XX];
+ fshift[ skj][YY] += f2[YY];
+ fshift[ skj][ZZ] += f2[ZZ];
+ }
if (VirCorr)
{
rvec xiv;
- int i,j;
+ int i, j;
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
- for(i=0; i<DIM; i++)
+ for (i = 0; i < DIM; i++)
{
- for(j=0; j<DIM; j++)
+ for (j = 0; j < DIM; j++)
{
/* Note that xik=xij+xjk, so we have to add xij*f2 */
dxdf[i][j] +=
- - xiv[i]*fv[j]
+ -xiv[i]*fv[j]
+ xij[i]*(f1[j] + (1 - c2)*f2[j] - f3[j])
+ xjk[i]*f2[j];
}
}
}
-
- /* TOTAL: 113 flops */
+
+ /* TOTAL: 113 flops */
}
-static void spread_vsite3OUT(t_iatom ia[],real a,real b,real c,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+static void spread_vsite3OUT(t_iatom ia[], real a, real b, real c,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
{
- rvec xvi,xij,xik,fv,fj,fk;
- real cfx,cfy,cfz;
- atom_id av,ai,aj,ak;
- ivec di;
- int svi,sji,ski;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
-
- sji = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- ski = pbc_rvec_sub(pbc,x[ak],x[ai],xik);
- /* 6 Flops */
-
- copy_rvec(f[av],fv);
-
- cfx = c*fv[XX];
- cfy = c*fv[YY];
- cfz = c*fv[ZZ];
- /* 3 Flops */
-
- fj[XX] = a*fv[XX] - xik[ZZ]*cfy + xik[YY]*cfz;
- fj[YY] = xik[ZZ]*cfx + a*fv[YY] - xik[XX]*cfz;
- fj[ZZ] = -xik[YY]*cfx + xik[XX]*cfy + a*fv[ZZ];
-
- fk[XX] = b*fv[XX] + xij[ZZ]*cfy - xij[YY]*cfz;
- fk[YY] = -xij[ZZ]*cfx + b*fv[YY] + xij[XX]*cfz;
- fk[ZZ] = xij[YY]*cfx - xij[XX]*cfy + b*fv[ZZ];
- /* 30 Flops */
-
- f[ai][XX] += fv[XX] - fj[XX] - fk[XX];
- f[ai][YY] += fv[YY] - fj[YY] - fk[YY];
- f[ai][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
- rvec_inc(f[aj],fj);
- rvec_inc(f[ak],fk);
- /* 15 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ia[1]),SHIFT_IVEC(g,ai),di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,ai),di);
- ski = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
- svi = CENTRAL;
- }
-
- if (fshift && (svi!=CENTRAL || sji!=CENTRAL || ski!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
- fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX];
- fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
- rvec_inc(fshift[sji],fj);
- rvec_inc(fshift[ski],fk);
- }
+ rvec xvi, xij, xik, fv, fj, fk;
+ real cfx, cfy, cfz;
+ atom_id av, ai, aj, ak;
+ ivec di;
+ int svi, sji, ski;
+
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
+
+ sji = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ ski = pbc_rvec_sub(pbc, x[ak], x[ai], xik);
+ /* 6 Flops */
+
+ copy_rvec(f[av], fv);
+
+ cfx = c*fv[XX];
+ cfy = c*fv[YY];
+ cfz = c*fv[ZZ];
+ /* 3 Flops */
+
+ fj[XX] = a*fv[XX] - xik[ZZ]*cfy + xik[YY]*cfz;
+ fj[YY] = xik[ZZ]*cfx + a*fv[YY] - xik[XX]*cfz;
+ fj[ZZ] = -xik[YY]*cfx + xik[XX]*cfy + a*fv[ZZ];
+
+ fk[XX] = b*fv[XX] + xij[ZZ]*cfy - xij[YY]*cfz;
+ fk[YY] = -xij[ZZ]*cfx + b*fv[YY] + xij[XX]*cfz;
+ fk[ZZ] = xij[YY]*cfx - xij[XX]*cfy + b*fv[ZZ];
+ /* 30 Flops */
+
+ f[ai][XX] += fv[XX] - fj[XX] - fk[XX];
+ f[ai][YY] += fv[YY] - fj[YY] - fk[YY];
+ f[ai][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
+ rvec_inc(f[aj], fj);
+ rvec_inc(f[ak], fk);
+ /* 15 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
+ svi = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
+ sji = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, ai), di);
+ ski = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = CENTRAL;
+ }
+
+ if (fshift && (svi != CENTRAL || sji != CENTRAL || ski != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX];
+ fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY];
+ fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
+ rvec_inc(fshift[sji], fj);
+ rvec_inc(fshift[ski], fk);
+ }
if (VirCorr)
{
rvec xiv;
- int i,j;
+ int i, j;
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
- for(i=0; i<DIM; i++)
+ for (i = 0; i < DIM; i++)
{
- for(j=0; j<DIM; j++)
+ for (j = 0; j < DIM; j++)
{
dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j] + xik[i]*fk[j];
}
}
}
-
- /* TOTAL: 54 flops */
+
+ /* TOTAL: 54 flops */
}
-static void spread_vsite4FD(t_iatom ia[],real a,real b,real c,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+static void spread_vsite4FD(t_iatom ia[], real a, real b, real c,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
{
- real d,invl,fproj,a1;
- rvec xvi,xij,xjk,xjl,xix,fv,temp;
- atom_id av,ai,aj,ak,al;
- ivec di;
- int svi,sji,skj,slj,m;
-
- av = ia[1];
- ai = ia[2];
- aj = ia[3];
- ak = ia[4];
- al = ia[5];
-
- sji = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- skj = pbc_rvec_sub(pbc,x[ak],x[aj],xjk);
- slj = pbc_rvec_sub(pbc,x[al],x[aj],xjl);
- /* 9 flops */
-
- /* xix goes from i to point x on the plane jkl */
- for(m=0; m<DIM; m++)
- xix[m] = xij[m] + a*xjk[m] + b*xjl[m];
- /* 12 flops */
-
- invl=gmx_invsqrt(iprod(xix,xix));
- d=c*invl;
- /* 4 + ?10? flops */
-
- copy_rvec(f[av],fv);
-
- fproj=iprod(xix,fv)*invl*invl; /* = (xix . f)/(xix . xix) */
-
- for(m=0; m<DIM; m++)
- temp[m] = d*(fv[m] - fproj*xix[m]);
- /* 16 */
-
- /* c is already calculated in constr_vsite3FD
- storing c somewhere will save 35 flops! */
-
- a1 = 1 - a - b;
- for(m=0; m<DIM; m++) {
- f[ai][m] += fv[m] - temp[m];
- f[aj][m] += a1*temp[m];
- f[ak][m] += a*temp[m];
- f[al][m] += b*temp[m];
- }
- /* 26 Flops */
-
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ia[1]),SHIFT_IVEC(g,ai),di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,aj),di);
- skj = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,al),SHIFT_IVEC(g,aj),di);
- slj = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
- svi = CENTRAL;
- }
-
- if (fshift &&
- (svi!=CENTRAL || sji!=CENTRAL || skj!=CENTRAL || slj!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
- for(m=0; m<DIM; m++) {
- fshift[CENTRAL][m] += fv[m] - (1 + a + b)*temp[m];
- fshift[ sji][m] += temp[m];
- fshift[ skj][m] += a*temp[m];
- fshift[ slj][m] += b*temp[m];
- }
- }
+ real d, invl, fproj, a1;
+ rvec xvi, xij, xjk, xjl, xix, fv, temp;
+ atom_id av, ai, aj, ak, al;
+ ivec di;
+ int svi, sji, skj, slj, m;
+
+ av = ia[1];
+ ai = ia[2];
+ aj = ia[3];
+ ak = ia[4];
+ al = ia[5];
+
+ sji = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ skj = pbc_rvec_sub(pbc, x[ak], x[aj], xjk);
+ slj = pbc_rvec_sub(pbc, x[al], x[aj], xjl);
+ /* 9 flops */
+
+ /* xix goes from i to point x on the plane jkl */
+ for (m = 0; m < DIM; m++)
+ {
+ xix[m] = xij[m] + a*xjk[m] + b*xjl[m];
+ }
+ /* 12 flops */
+
+ invl = gmx_invsqrt(iprod(xix, xix));
+ d = c*invl;
+ /* 4 + ?10? flops */
+
+ copy_rvec(f[av], fv);
+
+ fproj = iprod(xix, fv)*invl*invl; /* = (xix . f)/(xix . xix) */
+
+ for (m = 0; m < DIM; m++)
+ {
+ temp[m] = d*(fv[m] - fproj*xix[m]);
+ }
+ /* 16 */
+
+ /* c is already calculated in constr_vsite3FD
+ storing c somewhere will save 35 flops! */
+
+ a1 = 1 - a - b;
+ for (m = 0; m < DIM; m++)
+ {
+ f[ai][m] += fv[m] - temp[m];
+ f[aj][m] += a1*temp[m];
+ f[ak][m] += a*temp[m];
+ f[al][m] += b*temp[m];
+ }
+ /* 26 Flops */
+
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
+ svi = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
+ sji = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, aj), di);
+ skj = IVEC2IS(di);
+ ivec_sub(SHIFT_IVEC(g, al), SHIFT_IVEC(g, aj), di);
+ slj = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = CENTRAL;
+ }
+
+ if (fshift &&
+ (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL || slj != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
+ for (m = 0; m < DIM; m++)
+ {
+ fshift[CENTRAL][m] += fv[m] - (1 + a + b)*temp[m];
+ fshift[ sji][m] += temp[m];
+ fshift[ skj][m] += a*temp[m];
+ fshift[ slj][m] += b*temp[m];
+ }
+ }
if (VirCorr)
{
rvec xiv;
- int i,j;
+ int i, j;
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
- for(i=0; i<DIM; i++)
+ for (i = 0; i < DIM; i++)
{
- for(j=0; j<DIM; j++)
+ for (j = 0; j < DIM; j++)
{
dxdf[i][j] += -xiv[i]*fv[j] + xix[i]*temp[j];
}
}
}
- /* TOTAL: 77 flops */
+ /* TOTAL: 77 flops */
}
-static void spread_vsite4FDN(t_iatom ia[],real a,real b,real c,
- rvec x[],rvec f[],rvec fshift[],
- gmx_bool VirCorr,matrix dxdf,
- t_pbc *pbc,t_graph *g)
+static void spread_vsite4FDN(t_iatom ia[], real a, real b, real c,
+ rvec x[], rvec f[], rvec fshift[],
+ gmx_bool VirCorr, matrix dxdf,
+ t_pbc *pbc, t_graph *g)
{
- rvec xvi,xij,xik,xil,ra,rb,rja,rjb,rab,rm,rt;
- rvec fv,fj,fk,fl;
- real invrm,denom;
- real cfx,cfy,cfz;
+ rvec xvi, xij, xik, xil, ra, rb, rja, rjb, rab, rm, rt;
+ rvec fv, fj, fk, fl;
+ real invrm, denom;
+ real cfx, cfy, cfz;
ivec di;
- int av,ai,aj,ak,al;
- int svi,sij,sik,sil;
+ int av, ai, aj, ak, al;
+ int svi, sij, sik, sil;
/* DEBUG: check atom indices */
av = ia[1];
ak = ia[4];
al = ia[5];
- copy_rvec(f[av],fv);
-
- sij = pbc_rvec_sub(pbc,x[aj],x[ai],xij);
- sik = pbc_rvec_sub(pbc,x[ak],x[ai],xik);
- sil = pbc_rvec_sub(pbc,x[al],x[ai],xil);
+ copy_rvec(f[av], fv);
+
+ sij = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ sik = pbc_rvec_sub(pbc, x[ak], x[ai], xik);
+ sil = pbc_rvec_sub(pbc, x[al], x[ai], xil);
/* 9 flops */
-
+
ra[XX] = a*xik[XX];
ra[YY] = a*xik[YY];
ra[ZZ] = a*xik[ZZ];
-
+
rb[XX] = b*xil[XX];
rb[YY] = b*xil[YY];
rb[ZZ] = b*xil[ZZ];
-
+
/* 6 flops */
-
- rvec_sub(ra,xij,rja);
- rvec_sub(rb,xij,rjb);
- rvec_sub(rb,ra,rab);
+
+ rvec_sub(ra, xij, rja);
+ rvec_sub(rb, xij, rjb);
+ rvec_sub(rb, ra, rab);
/* 9 flops */
-
- cprod(rja,rjb,rm);
+
+ cprod(rja, rjb, rm);
/* 9 flops */
- invrm=gmx_invsqrt(norm2(rm));
- denom=invrm*invrm;
+ invrm = gmx_invsqrt(norm2(rm));
+ denom = invrm*invrm;
/* 5+5+2 flops */
-
+
cfx = c*invrm*fv[XX];
cfy = c*invrm*fv[YY];
cfz = c*invrm*fv[ZZ];
/* 6 Flops */
-
- cprod(rm,rab,rt);
+
+ cprod(rm, rab, rt);
/* 9 flops */
rt[XX] *= denom;
rt[YY] *= denom;
rt[ZZ] *= denom;
/* 3flops */
-
+
fj[XX] = ( -rm[XX]*rt[XX]) * cfx + ( rab[ZZ]-rm[YY]*rt[XX]) * cfy + (-rab[YY]-rm[ZZ]*rt[XX]) * cfz;
fj[YY] = (-rab[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + ( rab[XX]-rm[ZZ]*rt[YY]) * cfz;
fj[ZZ] = ( rab[YY]-rm[XX]*rt[ZZ]) * cfx + (-rab[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
/* 30 flops */
-
- cprod(rjb,rm,rt);
+
+ cprod(rjb, rm, rt);
/* 9 flops */
rt[XX] *= denom*a;
rt[YY] *= denom*a;
rt[ZZ] *= denom*a;
/* 3flops */
-
+
fk[XX] = ( -rm[XX]*rt[XX]) * cfx + (-a*rjb[ZZ]-rm[YY]*rt[XX]) * cfy + ( a*rjb[YY]-rm[ZZ]*rt[XX]) * cfz;
fk[YY] = ( a*rjb[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + (-a*rjb[XX]-rm[ZZ]*rt[YY]) * cfz;
fk[ZZ] = (-a*rjb[YY]-rm[XX]*rt[ZZ]) * cfx + ( a*rjb[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
/* 36 flops */
-
- cprod(rm,rja,rt);
+
+ cprod(rm, rja, rt);
/* 9 flops */
-
+
rt[XX] *= denom*b;
rt[YY] *= denom*b;
rt[ZZ] *= denom*b;
/* 3flops */
-
+
fl[XX] = ( -rm[XX]*rt[XX]) * cfx + ( b*rja[ZZ]-rm[YY]*rt[XX]) * cfy + (-b*rja[YY]-rm[ZZ]*rt[XX]) * cfz;
fl[YY] = (-b*rja[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + ( b*rja[XX]-rm[ZZ]*rt[YY]) * cfz;
fl[ZZ] = ( b*rja[YY]-rm[XX]*rt[ZZ]) * cfx + (-b*rja[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
f[ai][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
f[ai][YY] += fv[YY] - fj[YY] - fk[YY] - fl[YY];
f[ai][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ] - fl[ZZ];
- rvec_inc(f[aj],fj);
- rvec_inc(f[ak],fk);
- rvec_inc(f[al],fl);
+ rvec_inc(f[aj], fj);
+ rvec_inc(f[ak], fk);
+ rvec_inc(f[al], fl);
/* 21 flops */
- if (g) {
- ivec_sub(SHIFT_IVEC(g,av),SHIFT_IVEC(g,ai),di);
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, av), SHIFT_IVEC(g, ai), di);
svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,aj),SHIFT_IVEC(g,ai),di);
+ ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
sij = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,ak),SHIFT_IVEC(g,ai),di);
+ ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, ai), di);
sik = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g,al),SHIFT_IVEC(g,ai),di);
+ ivec_sub(SHIFT_IVEC(g, al), SHIFT_IVEC(g, ai), di);
sil = IVEC2IS(di);
- } else if (pbc) {
- svi = pbc_rvec_sub(pbc,x[av],x[ai],xvi);
- } else {
+ }
+ else if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
svi = CENTRAL;
}
-
- if (fshift && (svi!=CENTRAL || sij!=CENTRAL || sik!=CENTRAL || sil!=CENTRAL)) {
- rvec_dec(fshift[svi],fv);
+
+ if (fshift && (svi != CENTRAL || sij != CENTRAL || sik != CENTRAL || sil != CENTRAL))
+ {
+ rvec_dec(fshift[svi], fv);
fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY] - fl[YY];
fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ] - fl[ZZ];
- rvec_inc(fshift[sij],fj);
- rvec_inc(fshift[sik],fk);
- rvec_inc(fshift[sil],fl);
+ rvec_inc(fshift[sij], fj);
+ rvec_inc(fshift[sik], fk);
+ rvec_inc(fshift[sil], fl);
}
if (VirCorr)
{
rvec xiv;
- int i,j;
+ int i, j;
- pbc_rvec_sub(pbc,x[av],x[ai],xiv);
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
- for(i=0; i<DIM; i++)
+ for (i = 0; i < DIM; i++)
{
- for(j=0; j<DIM; j++)
+ for (j = 0; j < DIM; j++)
{
dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j] + xik[i]*fk[j] + xil[i]*fl[j];
}
}
}
-
+
/* Total: 207 flops (Yuck!) */
}
-static int spread_vsiten(t_iatom ia[],t_iparams ip[],
- rvec x[],rvec f[],rvec fshift[],
- t_pbc *pbc,t_graph *g)
+static int spread_vsiten(t_iatom ia[], t_iparams ip[],
+ rvec x[], rvec f[], rvec fshift[],
+ t_pbc *pbc, t_graph *g)
{
- rvec xv,dx,fi;
- int n3,av,i,ai;
- real a;
- ivec di;
- int siv;
-
- n3 = 3*ip[ia[0]].vsiten.n;
- av = ia[1];
- copy_rvec(x[av],xv);
-
- for(i=0; i<n3; i+=3) {
- ai = ia[i+2];
- if (g) {
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,av),di);
- siv = IVEC2IS(di);
- } else if (pbc) {
- siv = pbc_dx_aiuc(pbc,x[ai],xv,dx);
- } else {
- siv = CENTRAL;
- }
- a = ip[ia[i]].vsiten.a;
- svmul(a,f[av],fi);
- rvec_inc(f[ai],fi);
- if (fshift && siv != CENTRAL) {
- rvec_inc(fshift[siv],fi);
- rvec_dec(fshift[CENTRAL],fi);
+ rvec xv, dx, fi;
+ int n3, av, i, ai;
+ real a;
+ ivec di;
+ int siv;
+
+ n3 = 3*ip[ia[0]].vsiten.n;
+ av = ia[1];
+ copy_rvec(x[av], xv);
+
+ for (i = 0; i < n3; i += 3)
+ {
+ ai = ia[i+2];
+ if (g)
+ {
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, av), di);
+ siv = IVEC2IS(di);
+ }
+ else if (pbc)
+ {
+ siv = pbc_dx_aiuc(pbc, x[ai], xv, dx);
+ }
+ else
+ {
+ siv = CENTRAL;
+ }
+ a = ip[ia[i]].vsiten.a;
+ svmul(a, f[av], fi);
+ rvec_inc(f[ai], fi);
+ if (fshift && siv != CENTRAL)
+ {
+ rvec_inc(fshift[siv], fi);
+ rvec_dec(fshift[CENTRAL], fi);
+ }
+ /* 6 Flops */
}
- /* 6 Flops */
- }
- return n3;
+ return n3;
}
-static int vsite_count(const t_ilist *ilist,int ftype)
+static int vsite_count(const t_ilist *ilist, int ftype)
{
if (ftype == F_VSITEN)
{
}
static void spread_vsite_f_thread(gmx_vsite_t *vsite,
- rvec x[],rvec f[],rvec *fshift,
- gmx_bool VirCorr,matrix dxdf,
- t_iparams ip[],t_ilist ilist[],
- t_graph *g,t_pbc *pbc_null)
+ rvec x[], rvec f[], rvec *fshift,
+ gmx_bool VirCorr, matrix dxdf,
+ t_iparams ip[], t_ilist ilist[],
+ t_graph *g, t_pbc *pbc_null)
{
- gmx_bool bPBCAll;
- real a1,b1,c1;
- int i,inc,m,nra,nr,tp,ftype;
+ gmx_bool bPBCAll;
+ real a1, b1, c1;
+ int i, inc, m, nra, nr, tp, ftype;
t_iatom *ia;
t_pbc *pbc_null2;
int *vsite_pbc;
}
bPBCAll = (pbc_null != NULL && !vsite->bHaveChargeGroups);
-
+
/* this loop goes backwards to be able to build *
* higher type vsites from lower types */
pbc_null2 = NULL;
vsite_pbc = NULL;
- for(ftype=F_NRE-1; (ftype>=0); ftype--)
+ for (ftype = F_NRE-1; (ftype >= 0); ftype--)
{
if ((interaction_function[ftype].flags & IF_VSITE) &&
ilist[ftype].nr > 0)
vsite_pbc = vsite->vsite_pbc_loc[ftype-F_VSITE2];
}
- for(i=0; i<nr; )
+ for (i = 0; i < nr; )
{
if (vsite_pbc != NULL)
{
tp = ia[0];
/* Constants for constructing */
- a1 = ip[tp].vsite.a;
+ a1 = ip[tp].vsite.a;
/* Construct the vsite depending on type */
switch (ftype)
{
- case F_VSITE2:
- spread_vsite2(ia,a1,x,f,fshift,pbc_null2,g);
- break;
- case F_VSITE3:
- b1 = ip[tp].vsite.b;
- spread_vsite3(ia,a1,b1,x,f,fshift,pbc_null2,g);
- break;
- case F_VSITE3FD:
- b1 = ip[tp].vsite.b;
- spread_vsite3FD(ia,a1,b1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- break;
- case F_VSITE3FAD:
- b1 = ip[tp].vsite.b;
- spread_vsite3FAD(ia,a1,b1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- break;
- case F_VSITE3OUT:
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- spread_vsite3OUT(ia,a1,b1,c1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- break;
- case F_VSITE4FD:
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- spread_vsite4FD(ia,a1,b1,c1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- break;
- case F_VSITE4FDN:
- b1 = ip[tp].vsite.b;
- c1 = ip[tp].vsite.c;
- spread_vsite4FDN(ia,a1,b1,c1,x,f,fshift,VirCorr,dxdf,pbc_null2,g);
- break;
- case F_VSITEN:
- inc = spread_vsiten(ia,ip,x,f,fshift,pbc_null2,g);
- break;
- default:
- gmx_fatal(FARGS,"No such vsite type %d in %s, line %d",
- ftype,__FILE__,__LINE__);
+ case F_VSITE2:
+ spread_vsite2(ia, a1, x, f, fshift, pbc_null2, g);
+ break;
+ case F_VSITE3:
+ b1 = ip[tp].vsite.b;
+ spread_vsite3(ia, a1, b1, x, f, fshift, pbc_null2, g);
+ break;
+ case F_VSITE3FD:
+ b1 = ip[tp].vsite.b;
+ spread_vsite3FD(ia, a1, b1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITE3FAD:
+ b1 = ip[tp].vsite.b;
+ spread_vsite3FAD(ia, a1, b1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITE3OUT:
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ spread_vsite3OUT(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITE4FD:
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ spread_vsite4FD(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITE4FDN:
+ b1 = ip[tp].vsite.b;
+ c1 = ip[tp].vsite.c;
+ spread_vsite4FDN(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ break;
+ case F_VSITEN:
+ inc = spread_vsiten(ia, ip, x, f, fshift, pbc_null2, g);
+ break;
+ default:
+ gmx_fatal(FARGS, "No such vsite type %d in %s, line %d",
+ ftype, __FILE__, __LINE__);
}
clear_rvec(f[ia[1]]);
}
}
-void spread_vsite_f(FILE *log,gmx_vsite_t *vsite,
- rvec x[],rvec f[],rvec *fshift,
- gmx_bool VirCorr,matrix vir,
- t_nrnb *nrnb,t_idef *idef,
- int ePBC,gmx_bool bMolPBC,t_graph *g,matrix box,
+void spread_vsite_f(gmx_vsite_t *vsite,
+ rvec x[], rvec f[], rvec *fshift,
+ gmx_bool VirCorr, matrix vir,
+ t_nrnb *nrnb, t_idef *idef,
+ int ePBC, gmx_bool bMolPBC, t_graph *g, matrix box,
t_commrec *cr)
{
- t_pbc pbc,*pbc_null;
+ t_pbc pbc, *pbc_null;
int th;
/* We only need to do pbc when we have inter-cg vsites */
/* This is wasting some CPU time as we now do this multiple times
* per MD step. But how often do we have vsites with full pbc?
*/
- pbc_null = set_pbc_dd(&pbc,ePBC,cr->dd,FALSE,box);
+ pbc_null = set_pbc_dd(&pbc, ePBC, cr->dd, FALSE, box);
}
else
{
pbc_null = NULL;
}
-
- if (DOMAINDECOMP(cr))
- {
- dd_clear_f_vsites(cr->dd,f);
- }
- else if (PARTDECOMP(cr) && vsite->vsitecomm != NULL)
+
+ if (DOMAINDECOMP(cr))
{
- pd_clear_nonlocal_constructs(vsite->vsitecomm,f);
+ dd_clear_f_vsites(cr->dd, f);
}
if (vsite->nthreads == 1)
{
spread_vsite_f_thread(vsite,
- x,f,fshift,
- VirCorr,vsite->tdata[0].dxdf,
- idef->iparams,idef->il,
- g,pbc_null);
+ x, f, fshift,
+ VirCorr, vsite->tdata[0].dxdf,
+ idef->iparams, idef->il,
+ g, pbc_null);
}
else
{
/* First spread the vsites that might depend on other vsites */
spread_vsite_f_thread(vsite,
- x,f,fshift,
- VirCorr,vsite->tdata[vsite->nthreads].dxdf,
+ x, f, fshift,
+ VirCorr, vsite->tdata[vsite->nthreads].dxdf,
idef->iparams,
vsite->tdata[vsite->nthreads].ilist,
- g,pbc_null);
+ g, pbc_null);
#pragma omp parallel num_threads(vsite->nthreads)
{
- int thread;
+ int thread;
rvec *fshift_t;
thread = gmx_omp_get_thread_num();
}
else
{
+ int i;
+
fshift_t = vsite->tdata[thread].fshift;
+
+ for (i = 0; i < SHIFTS; i++)
+ {
+ clear_rvec(fshift_t[i]);
+ }
}
spread_vsite_f_thread(vsite,
- x,f,fshift_t,
- VirCorr,vsite->tdata[thread].dxdf,
+ x, f, fshift_t,
+ VirCorr, vsite->tdata[thread].dxdf,
idef->iparams,
vsite->tdata[thread].ilist,
- g,pbc_null);
+ g, pbc_null);
}
if (fshift != NULL)
{
int i;
- for(th=1; th<vsite->nthreads; th++)
+ for (th = 1; th < vsite->nthreads; th++)
{
- for(i=0; i<SHIFTS; i++)
+ for (i = 0; i < SHIFTS; i++)
{
- rvec_inc(fshift[i],vsite->tdata[th].fshift[i]);
+ rvec_inc(fshift[i], vsite->tdata[th].fshift[i]);
}
}
}
if (VirCorr)
{
- int i,j;
+ int i, j;
- for(th=0; th<(vsite->nthreads==1 ? 1 : vsite->nthreads+1); th++)
+ for (th = 0; th < (vsite->nthreads == 1 ? 1 : vsite->nthreads+1); th++)
{
- for(i=0; i<DIM; i++)
+ for (i = 0; i < DIM; i++)
{
- for(j=0; j<DIM; j++)
+ for (j = 0; j < DIM; j++)
{
vir[i][j] += -0.5*vsite->tdata[th].dxdf[i][j];
}
if (DOMAINDECOMP(cr))
{
- dd_move_f_vsites(cr->dd,f,fshift);
- }
- else if (vsite->bPDvsitecomm)
- {
- /* We only move forces here, and they are independent of shifts */
- move_construct_f(vsite->vsitecomm,f,cr);
+ dd_move_f_vsites(cr->dd, f, fshift);
}
- inc_nrnb(nrnb,eNR_VSITE2, vsite_count(idef->il,F_VSITE2));
- inc_nrnb(nrnb,eNR_VSITE3, vsite_count(idef->il,F_VSITE3));
- inc_nrnb(nrnb,eNR_VSITE3FD, vsite_count(idef->il,F_VSITE3FD));
- inc_nrnb(nrnb,eNR_VSITE3FAD,vsite_count(idef->il,F_VSITE3FAD));
- inc_nrnb(nrnb,eNR_VSITE3OUT,vsite_count(idef->il,F_VSITE3OUT));
- inc_nrnb(nrnb,eNR_VSITE4FD, vsite_count(idef->il,F_VSITE4FD));
- inc_nrnb(nrnb,eNR_VSITE4FDN,vsite_count(idef->il,F_VSITE4FDN));
- inc_nrnb(nrnb,eNR_VSITEN, vsite_count(idef->il,F_VSITEN));
+ inc_nrnb(nrnb, eNR_VSITE2, vsite_count(idef->il, F_VSITE2));
+ inc_nrnb(nrnb, eNR_VSITE3, vsite_count(idef->il, F_VSITE3));
+ inc_nrnb(nrnb, eNR_VSITE3FD, vsite_count(idef->il, F_VSITE3FD));
+ inc_nrnb(nrnb, eNR_VSITE3FAD, vsite_count(idef->il, F_VSITE3FAD));
+ inc_nrnb(nrnb, eNR_VSITE3OUT, vsite_count(idef->il, F_VSITE3OUT));
+ inc_nrnb(nrnb, eNR_VSITE4FD, vsite_count(idef->il, F_VSITE4FD));
+ inc_nrnb(nrnb, eNR_VSITE4FDN, vsite_count(idef->il, F_VSITE4FDN));
+ inc_nrnb(nrnb, eNR_VSITEN, vsite_count(idef->il, F_VSITEN));
}
static int *atom2cg(t_block *cgs)
{
- int *a2cg,cg,i;
-
- snew(a2cg,cgs->index[cgs->nr]);
- for(cg=0; cg<cgs->nr; cg++) {
- for(i=cgs->index[cg]; i<cgs->index[cg+1]; i++)
- a2cg[i] = cg;
- }
-
- return a2cg;
+ int *a2cg, cg, i;
+
+ snew(a2cg, cgs->index[cgs->nr]);
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ for (i = cgs->index[cg]; i < cgs->index[cg+1]; i++)
+ {
+ a2cg[i] = cg;
+ }
+ }
+
+ return a2cg;
}
static int count_intercg_vsite(gmx_mtop_t *mtop,
- gmx_bool *bHaveChargeGroups)
+ gmx_bool *bHaveChargeGroups)
{
- int mb,mt,ftype,nral,i,cg,a;
+ int mb, mt, ftype, nral, i, cg, a;
gmx_molblock_t *molb;
- gmx_moltype_t *molt;
- int *a2cg;
- t_ilist *il;
- t_iatom *ia;
- int n_intercg_vsite;
+ gmx_moltype_t *molt;
+ int *a2cg;
+ t_ilist *il;
+ t_iatom *ia;
+ int n_intercg_vsite;
*bHaveChargeGroups = FALSE;
n_intercg_vsite = 0;
- for(mb=0; mb<mtop->nmolblock; mb++)
+ for (mb = 0; mb < mtop->nmolblock; mb++)
{
molb = &mtop->molblock[mb];
molt = &mtop->moltype[molb->type];
}
a2cg = atom2cg(&molt->cgs);
- for(ftype=0; ftype<F_NRE; ftype++)
+ for (ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_VSITE)
{
nral = NRAL(ftype);
- il = &molt->ilist[ftype];
- ia = il->iatoms;
- for(i=0; i<il->nr; i+=1+nral)
+ il = &molt->ilist[ftype];
+ ia = il->iatoms;
+ for (i = 0; i < il->nr; i += 1+nral)
{
cg = a2cg[ia[1+i]];
- for(a=1; a<nral; a++)
+ for (a = 1; a < nral; a++)
{
- if (a2cg[ia[1+a]] != cg) {
+ if (a2cg[ia[1+a]] != cg)
+ {
n_intercg_vsite += molb->nmol;
break;
}
return n_intercg_vsite;
}
-static int **get_vsite_pbc(t_iparams *iparams,t_ilist *ilist,
- t_atom *atom,t_mdatoms *md,
- t_block *cgs,int *a2cg)
+static int **get_vsite_pbc(t_iparams *iparams, t_ilist *ilist,
+ t_atom *atom, t_mdatoms *md,
+ t_block *cgs, int *a2cg)
{
- int ftype,nral,i,j,vsi,vsite,cg_v,cg_c,a,nc3=0;
- t_ilist *il;
- t_iatom *ia;
- int **vsite_pbc,*vsite_pbc_f;
- char *pbc_set;
- gmx_bool bViteOnlyCG_and_FirstAtom;
-
- /* Make an array that tells if the pbc of an atom is set */
- snew(pbc_set,cgs->index[cgs->nr]);
- /* PBC is set for all non vsites */
- for(a=0; a<cgs->index[cgs->nr]; a++) {
- if ((atom && atom[a].ptype != eptVSite) ||
- (md && md->ptype[a] != eptVSite)) {
- pbc_set[a] = 1;
- }
- }
-
- snew(vsite_pbc,F_VSITEN-F_VSITE2+1);
-
- for(ftype=0; ftype<F_NRE; ftype++) {
- if (interaction_function[ftype].flags & IF_VSITE) {
- nral = NRAL(ftype);
- il = &ilist[ftype];
- ia = il->iatoms;
-
- snew(vsite_pbc[ftype-F_VSITE2],il->nr/(1+nral));
- vsite_pbc_f = vsite_pbc[ftype-F_VSITE2];
-
- i = 0;
- while (i < il->nr) {
- vsi = i/(1+nral);
- vsite = ia[i+1];
- cg_v = a2cg[vsite];
- /* A value of -2 signals that this vsite and its contructing
- * atoms are all within the same cg, so no pbc is required.
- */
- vsite_pbc_f[vsi] = -2;
- /* Check if constructing atoms are outside the vsite's cg */
- nc3 = 0;
- if (ftype == F_VSITEN) {
- nc3 = 3*iparams[ia[i]].vsiten.n;
- for(j=0; j<nc3; j+=3) {
- if (a2cg[ia[i+j+2]] != cg_v)
- vsite_pbc_f[vsi] = -1;
- }
- } else {
- for(a=1; a<nral; a++) {
- if (a2cg[ia[i+1+a]] != cg_v)
- vsite_pbc_f[vsi] = -1;
- }
- }
- if (vsite_pbc_f[vsi] == -1) {
- /* Check if this is the first processed atom of a vsite only cg */
- bViteOnlyCG_and_FirstAtom = TRUE;
- for(a=cgs->index[cg_v]; a<cgs->index[cg_v+1]; a++) {
- /* Non-vsites already have pbc set, so simply check for pbc_set */
- if (pbc_set[a]) {
- bViteOnlyCG_and_FirstAtom = FALSE;
- break;
- }
- }
- if (bViteOnlyCG_and_FirstAtom) {
- /* First processed atom of a vsite only charge group.
- * The pbc of the input coordinates to construct_vsites
- * should be preserved.
- */
- vsite_pbc_f[vsi] = vsite;
- } else if (cg_v != a2cg[ia[1+i+1]]) {
- /* This vsite has a different charge group index
- * than it's first constructing atom
- * and the charge group has more than one atom,
- * search for the first normal particle
- * or vsite that already had its pbc defined.
- * If nothing is found, use full pbc for this vsite.
- */
- for(a=cgs->index[cg_v]; a<cgs->index[cg_v+1]; a++) {
- if (a != vsite && pbc_set[a]) {
- vsite_pbc_f[vsi] = a;
- if (gmx_debug_at)
- fprintf(debug,"vsite %d match pbc with atom %d\n",
- vsite+1,a+1);
- break;
- }
- }
- if (gmx_debug_at)
- fprintf(debug,"vsite atom %d cg %d - %d pbc atom %d\n",
- vsite+1,cgs->index[cg_v]+1,cgs->index[cg_v+1],
- vsite_pbc_f[vsi]+1);
- }
- }
- if (ftype == F_VSITEN) {
- /* The other entries in vsite_pbc_f are not used for center vsites */
- i += nc3;
- } else {
- i += 1+nral;
- }
-
- /* This vsite now has its pbc defined */
- pbc_set[vsite] = 1;
- }
- }
- }
-
- sfree(pbc_set);
-
- return vsite_pbc;
+ int ftype, nral, i, j, vsi, vsite, cg_v, cg_c, a, nc3 = 0;
+ t_ilist *il;
+ t_iatom *ia;
+ int **vsite_pbc, *vsite_pbc_f;
+ char *pbc_set;
+ gmx_bool bViteOnlyCG_and_FirstAtom;
+
+ /* Make an array that tells if the pbc of an atom is set */
+ snew(pbc_set, cgs->index[cgs->nr]);
+ /* PBC is set for all non vsites */
+ for (a = 0; a < cgs->index[cgs->nr]; a++)
+ {
+ if ((atom && atom[a].ptype != eptVSite) ||
+ (md && md->ptype[a] != eptVSite))
+ {
+ pbc_set[a] = 1;
+ }
+ }
+
+ snew(vsite_pbc, F_VSITEN-F_VSITE2+1);
+
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_VSITE)
+ {
+ nral = NRAL(ftype);
+ il = &ilist[ftype];
+ ia = il->iatoms;
+
+ snew(vsite_pbc[ftype-F_VSITE2], il->nr/(1+nral));
+ vsite_pbc_f = vsite_pbc[ftype-F_VSITE2];
+
+ i = 0;
+ while (i < il->nr)
+ {
+ vsi = i/(1+nral);
+ vsite = ia[i+1];
+ cg_v = a2cg[vsite];
+ /* A value of -2 signals that this vsite and its contructing
+ * atoms are all within the same cg, so no pbc is required.
+ */
+ vsite_pbc_f[vsi] = -2;
+ /* Check if constructing atoms are outside the vsite's cg */
+ nc3 = 0;
+ if (ftype == F_VSITEN)
+ {
+ nc3 = 3*iparams[ia[i]].vsiten.n;
+ for (j = 0; j < nc3; j += 3)
+ {
+ if (a2cg[ia[i+j+2]] != cg_v)
+ {
+ vsite_pbc_f[vsi] = -1;
+ }
+ }
+ }
+ else
+ {
+ for (a = 1; a < nral; a++)
+ {
+ if (a2cg[ia[i+1+a]] != cg_v)
+ {
+ vsite_pbc_f[vsi] = -1;
+ }
+ }
+ }
+ if (vsite_pbc_f[vsi] == -1)
+ {
+ /* Check if this is the first processed atom of a vsite only cg */
+ bViteOnlyCG_and_FirstAtom = TRUE;
+ for (a = cgs->index[cg_v]; a < cgs->index[cg_v+1]; a++)
+ {
+ /* Non-vsites already have pbc set, so simply check for pbc_set */
+ if (pbc_set[a])
+ {
+ bViteOnlyCG_and_FirstAtom = FALSE;
+ break;
+ }
+ }
+ if (bViteOnlyCG_and_FirstAtom)
+ {
+ /* First processed atom of a vsite only charge group.
+ * The pbc of the input coordinates to construct_vsites
+ * should be preserved.
+ */
+ vsite_pbc_f[vsi] = vsite;
+ }
+ else if (cg_v != a2cg[ia[1+i+1]])
+ {
+ /* This vsite has a different charge group index
+ * than it's first constructing atom
+ * and the charge group has more than one atom,
+ * search for the first normal particle
+ * or vsite that already had its pbc defined.
+ * If nothing is found, use full pbc for this vsite.
+ */
+ for (a = cgs->index[cg_v]; a < cgs->index[cg_v+1]; a++)
+ {
+ if (a != vsite && pbc_set[a])
+ {
+ vsite_pbc_f[vsi] = a;
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "vsite %d match pbc with atom %d\n",
+ vsite+1, a+1);
+ }
+ break;
+ }
+ }
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "vsite atom %d cg %d - %d pbc atom %d\n",
+ vsite+1, cgs->index[cg_v]+1, cgs->index[cg_v+1],
+ vsite_pbc_f[vsi]+1);
+ }
+ }
+ }
+ if (ftype == F_VSITEN)
+ {
+ /* The other entries in vsite_pbc_f are not used for center vsites */
+ i += nc3;
+ }
+ else
+ {
+ i += 1+nral;
+ }
+
+ /* This vsite now has its pbc defined */
+ pbc_set[vsite] = 1;
+ }
+ }
+ }
+
+ sfree(pbc_set);
+
+ return vsite_pbc;
}
-gmx_vsite_t *init_vsite(gmx_mtop_t *mtop,t_commrec *cr,
+gmx_vsite_t *init_vsite(gmx_mtop_t *mtop, t_commrec *cr,
gmx_bool bSerial_NoPBC)
{
- int nvsite,i;
- int *a2cg,cg;
- gmx_vsite_t *vsite;
- int mt;
+ int nvsite, i;
+ int *a2cg, cg;
+ gmx_vsite_t *vsite;
+ int mt;
gmx_moltype_t *molt;
- int nthreads;
+ int nthreads;
/* check if there are vsites */
nvsite = 0;
- for(i=0; i<F_NRE; i++)
+ for (i = 0; i < F_NRE; i++)
{
if (interaction_function[i].flags & IF_VSITE)
{
- nvsite += gmx_mtop_ftype_count(mtop,i);
+ nvsite += gmx_mtop_ftype_count(mtop, i);
}
}
return NULL;
}
- snew(vsite,1);
+ snew(vsite, 1);
vsite->n_intercg_vsite = count_intercg_vsite(mtop,
&vsite->bHaveChargeGroups);
vsite->n_intercg_vsite > 0 && DOMAINDECOMP(cr))
{
vsite->nvsite_pbc_molt = mtop->nmoltype;
- snew(vsite->vsite_pbc_molt,vsite->nvsite_pbc_molt);
- for(mt=0; mt<mtop->nmoltype; mt++)
+ snew(vsite->vsite_pbc_molt, vsite->nvsite_pbc_molt);
+ for (mt = 0; mt < mtop->nmoltype; mt++)
{
molt = &mtop->moltype[mt];
/* Make an atom to charge group index */
a2cg = atom2cg(&molt->cgs);
vsite->vsite_pbc_molt[mt] = get_vsite_pbc(mtop->ffparams.iparams,
molt->ilist,
- molt->atoms.atom,NULL,
- &molt->cgs,a2cg);
+ molt->atoms.atom, NULL,
+ &molt->cgs, a2cg);
sfree(a2cg);
}
-
- snew(vsite->vsite_pbc_loc_nalloc,F_VSITEN-F_VSITE2+1);
- snew(vsite->vsite_pbc_loc ,F_VSITEN-F_VSITE2+1);
+
+ snew(vsite->vsite_pbc_loc_nalloc, F_VSITEN-F_VSITE2+1);
+ snew(vsite->vsite_pbc_loc, F_VSITEN-F_VSITE2+1);
}
if (bSerial_NoPBC)
if (!bSerial_NoPBC)
{
/* We need one extra thread data structure for the overlap vsites */
- snew(vsite->tdata,vsite->nthreads+1);
+ snew(vsite->tdata, vsite->nthreads+1);
}
vsite->th_ind = NULL;
return vsite;
}
-static void prepare_vsite_thread(const t_ilist *ilist,
+static void prepare_vsite_thread(const t_ilist *ilist,
gmx_vsite_thread_t *vsite_th)
{
int ftype;
- for(ftype=0; ftype<F_NRE; ftype++)
+ for (ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_VSITE)
{
if (ilist[ftype].nr > vsite_th->ilist[ftype].nalloc)
{
vsite_th->ilist[ftype].nalloc = over_alloc_large(ilist[ftype].nr);
- srenew(vsite_th->ilist[ftype].iatoms,vsite_th->ilist[ftype].nalloc);
+ srenew(vsite_th->ilist[ftype].iatoms, vsite_th->ilist[ftype].nalloc);
}
vsite_th->ilist[ftype].nr = 0;
}
}
-void split_vsites_over_threads(const t_ilist *ilist,
+void split_vsites_over_threads(const t_ilist *ilist,
+ const t_iparams *ip,
const t_mdatoms *mdatoms,
- gmx_bool bLimitRange,
- gmx_vsite_t *vsite)
+ gmx_bool bLimitRange,
+ gmx_vsite_t *vsite)
{
- int th;
- int vsite_atom_range,natperthread;
- int *th_ind;
- int ftype;
+ int th;
+ int vsite_atom_range, natperthread;
+ int *th_ind;
+ int ftype;
t_iatom *iat;
t_ilist *il_th;
- int nral1,inc,i,j;
+ int nral1, inc, i, j;
if (vsite->nthreads == 1)
{
}
#pragma omp parallel for num_threads(vsite->nthreads) schedule(static)
- for(th=0; th<vsite->nthreads; th++)
+ for (th = 0; th < vsite->nthreads; th++)
{
- prepare_vsite_thread(ilist,&vsite->tdata[th]);
+ prepare_vsite_thread(ilist, &vsite->tdata[th]);
}
/* Master threads does the (potential) overlap vsites */
- prepare_vsite_thread(ilist,&vsite->tdata[vsite->nthreads]);
+ prepare_vsite_thread(ilist, &vsite->tdata[vsite->nthreads]);
/* The current way of distributing the vsites over threads in primitive.
* We divide the atom range 0 - natoms_in_vsite uniformly over threads,
if (bLimitRange)
{
vsite_atom_range = -1;
- for(ftype=0; ftype<F_NRE; ftype++)
+ for (ftype = 0; ftype < F_NRE; ftype++)
{
- if ((interaction_function[ftype].flags & IF_VSITE) &&
- ftype != F_VSITEN)
+ if (interaction_function[ftype].flags & IF_VSITE)
{
- nral1 = 1 + NRAL(ftype);
- iat = ilist[ftype].iatoms;
- for(i=0; i<ilist[ftype].nr; i+=nral1)
+ if (ftype != F_VSITEN)
{
- for(j=i+1; j<i+nral1; j++)
+ nral1 = 1 + NRAL(ftype);
+ iat = ilist[ftype].iatoms;
+ for (i = 0; i < ilist[ftype].nr; i += nral1)
{
- vsite_atom_range = max(vsite_atom_range,iat[j]);
+ for (j = i + 1; j < i + nral1; j++)
+ {
+ vsite_atom_range = max(vsite_atom_range, iat[j]);
+ }
+ }
+ }
+ else
+ {
+ int vs_ind_end;
+
+ iat = ilist[ftype].iatoms;
+
+ i = 0;
+ while (i < ilist[ftype].nr)
+ {
+ /* The 3 below is from 1+NRAL(ftype)=3 */
+ vs_ind_end = i + ip[iat[i]].vsiten.n*3;
+
+ vsite_atom_range = max(vsite_atom_range, iat[i+1]);
+ while (i < vs_ind_end)
+ {
+ vsite_atom_range = max(vsite_atom_range, iat[i+2]);
+ i += 3;
+ }
}
}
}
if (debug)
{
- fprintf(debug,"virtual site thread dist: natoms %d, range %d, natperthread %d\n",mdatoms->nr,vsite_atom_range,natperthread);
+ fprintf(debug, "virtual site thread dist: natoms %d, range %d, natperthread %d\n", mdatoms->nr, vsite_atom_range, natperthread);
}
/* To simplify the vsite assignment, we make an index which tells us
if (mdatoms->nr > vsite->th_ind_nalloc)
{
vsite->th_ind_nalloc = over_alloc_large(mdatoms->nr);
- srenew(vsite->th_ind,vsite->th_ind_nalloc);
+ srenew(vsite->th_ind, vsite->th_ind_nalloc);
}
th_ind = vsite->th_ind;
- th = 0;
- for(i=0; i<mdatoms->nr; i++)
+ th = 0;
+ for (i = 0; i < mdatoms->nr; i++)
{
if (mdatoms->ptype[i] == eptVSite)
{
}
}
- for(ftype=0; ftype<F_NRE; ftype++)
+ for (ftype = 0; ftype < F_NRE; ftype++)
{
- if ((interaction_function[ftype].flags & IF_VSITE) &&
- ftype != F_VSITEN)
+ if (interaction_function[ftype].flags & IF_VSITE)
{
nral1 = 1 + NRAL(ftype);
inc = nral1;
iat = ilist[ftype].iatoms;
- for(i=0; i<ilist[ftype].nr; )
+ for (i = 0; i < ilist[ftype].nr; )
{
th = iat[1+i]/natperthread;
/* We would like to assign this vsite the thread th,
*/
if (ftype != F_VSITEN)
{
- for(j=i+2; j<i+nral1; j++)
+ for (j = i + 2; j < i + nral1; j++)
{
if (th_ind[iat[j]] != th)
{
}
else
{
- inc = iat[i];
- for(j=i+2; j<i+inc; j+=3)
+ /* The 3 below is from 1+NRAL(ftype)=3 */
+ inc = ip[iat[i]].vsiten.n*3;
+ for (j = i + 2; j < i + inc; j += 3)
{
if (th_ind[iat[j]] != th)
{
}
/* Copy this vsite to the thread data struct of thread th */
il_th = &vsite->tdata[th].ilist[ftype];
- for(j=i; j<i+inc; j++)
+ for (j = i; j < i + inc; j++)
{
il_th->iatoms[il_th->nr++] = iat[j];
}
if (debug)
{
- for(ftype=0; ftype<F_NRE; ftype++)
+ for (ftype = 0; ftype < F_NRE; ftype++)
{
if ((interaction_function[ftype].flags & IF_VSITE) &&
- ilist[ftype].nr > 0)
+ ilist[ftype].nr > 0)
{
- fprintf(debug,"%-20s thread dist:",
+ fprintf(debug, "%-20s thread dist:",
interaction_function[ftype].longname);
- for(th=0; th<vsite->nthreads+1; th++)
+ for (th = 0; th < vsite->nthreads+1; th++)
{
- fprintf(debug," %4d",vsite->tdata[th].ilist[ftype].nr);
+ fprintf(debug, " %4d", vsite->tdata[th].ilist[ftype].nr);
}
- fprintf(debug,"\n");
+ fprintf(debug, "\n");
}
}
}
}
-void set_vsite_top(gmx_vsite_t *vsite,gmx_localtop_t *top,t_mdatoms *md,
+void set_vsite_top(gmx_vsite_t *vsite, gmx_localtop_t *top, t_mdatoms *md,
t_commrec *cr)
{
int *a2cg;
-
+
if (vsite->n_intercg_vsite > 0)
{
if (vsite->bHaveChargeGroups)
{
/* Make an atom to charge group index */
- a2cg = atom2cg(&top->cgs);
+ a2cg = atom2cg(&top->cgs);
vsite->vsite_pbc_loc = get_vsite_pbc(top->idef.iparams,
- top->idef.il,NULL,md,
- &top->cgs,a2cg);
+ top->idef.il, NULL, md,
+ &top->cgs, a2cg);
sfree(a2cg);
}
- if (PARTDECOMP(cr))
- {
- snew(vsite->vsitecomm,1);
- vsite->bPDvsitecomm =
- setup_parallel_vsites(&(top->idef),cr,vsite->vsitecomm);
- }
}
if (vsite->nthreads > 1)
{
- if (vsite->bHaveChargeGroups || PARTDECOMP(cr))
+ if (vsite->bHaveChargeGroups)
{
- gmx_incons("Can not use threads virtual sites combined with charge groups or particle decomposition");
+ gmx_fatal(FARGS, "The combination of threading, virtual sites and charge groups is not implemented");
}
- split_vsites_over_threads(top->idef.il,md,!DOMAINDECOMP(cr),vsite);
+ split_vsites_over_threads(top->idef.il, top->idef.iparams,
+ md, !DOMAINDECOMP(cr), vsite);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff