/*
- *
- * 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.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* 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.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <stdio.h>
#include <math.h>
-#include "typedefs.h"
-#include "vec.h"
-#include "gmxcomplex.h"
-#include "smalloc.h"
-#include "futil.h"
-#include "gmx_fatal.h"
-#include "physics.h"
-#include "coulomb.h"
-#include "macros.h"
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define TOL 2e-5
struct ewald_tab
{
- int nx,ny,nz,kmax;
- cvec **eir;
+ int nx, ny, nz, kmax;
+ cvec **eir;
t_complex *tab_xy, *tab_qxyz;
-};
+};
/* TODO: fix thread-safety */
/* the other routines are in complex.h */
-static t_complex conjmul(t_complex a,t_complex b)
+static t_complex conjmul(t_complex a, t_complex b)
{
- t_complex c;
-
- c.re = a.re*b.re + a.im*b.im;
- c.im = a.im*b.re - a.re*b.im;
-
- return c;
+ t_complex c;
+
+ c.re = a.re*b.re + a.im*b.im;
+ c.im = a.im*b.re - a.re*b.im;
+
+ return c;
}
-
-
-static void tabulate_eir(int natom,rvec x[],int kmax,cvec **eir,rvec lll)
+
+
+static void tabulate_eir(int natom, rvec x[], int kmax, cvec **eir, rvec lll)
{
- int i,j,m;
-
- if (kmax < 1) {
- printf("Go away! kmax = %d\n",kmax);
- exit(1);
- }
-
- for(i=0; (i<natom); i++) {
- for(m=0; (m<3); m++) {
- eir[0][i][m].re = 1;
- eir[0][i][m].im = 0;
+ int i, j, m;
+
+ if (kmax < 1)
+ {
+ printf("Go away! kmax = %d\n", kmax);
+ exit(1);
}
-
- for(m=0; (m<3); m++) {
- eir[1][i][m].re = cos(x[i][m]*lll[m]);
- eir[1][i][m].im = sin(x[i][m]*lll[m]);
+
+ for (i = 0; (i < natom); i++)
+ {
+ for (m = 0; (m < 3); m++)
+ {
+ eir[0][i][m].re = 1;
+ eir[0][i][m].im = 0;
+ }
+
+ for (m = 0; (m < 3); m++)
+ {
+ eir[1][i][m].re = cos(x[i][m]*lll[m]);
+ eir[1][i][m].im = sin(x[i][m]*lll[m]);
+ }
+ for (j = 2; (j < kmax); j++)
+ {
+ for (m = 0; (m < 3); m++)
+ {
+ eir[j][i][m] = cmul(eir[j-1][i][m], eir[1][i][m]);
+ }
+ }
}
- for(j=2; (j<kmax); j++)
- for(m=0; (m<3); m++)
- eir[j][i][m] = cmul(eir[j-1][i][m],eir[1][i][m]);
- }
}
-void init_ewald_tab(ewald_tab_t *et, const t_commrec *cr, const t_inputrec *ir,
- FILE *fp)
+void init_ewald_tab(ewald_tab_t *et, const t_inputrec *ir, FILE *fp)
{
int n;
snew(*et, 1);
if (fp)
- fprintf(fp,"Will do ordinary reciprocal space Ewald sum.\n");
-
- (*et)->nx = ir->nkx+1;
- (*et)->ny = ir->nky+1;
- (*et)->nz = ir->nkz+1;
- (*et)->kmax = max((*et)->nx,max((*et)->ny,(*et)->nz));
- (*et)->eir = NULL;
- (*et)->tab_xy = NULL;
+ {
+ fprintf(fp, "Will do ordinary reciprocal space Ewald sum.\n");
+ }
+
+ (*et)->nx = ir->nkx+1;
+ (*et)->ny = ir->nky+1;
+ (*et)->nz = ir->nkz+1;
+ (*et)->kmax = max((*et)->nx, max((*et)->ny, (*et)->nz));
+ (*et)->eir = NULL;
+ (*et)->tab_xy = NULL;
(*et)->tab_qxyz = NULL;
}
-real do_ewald(FILE *log, gmx_bool bVerbose,
- t_inputrec *ir,
- rvec x[], rvec f[],
- real chargeA[], real chargeB[],
- rvec box,
- t_commrec *cr, int natoms,
- matrix lrvir, real ewaldcoeff,
- real lambda, real *dvdlambda,
+real do_ewald(t_inputrec *ir,
+ rvec x[], rvec f[],
+ real chargeA[], real chargeB[],
+ rvec box,
+ t_commrec *cr, int natoms,
+ matrix lrvir, real ewaldcoeff,
+ real lambda, real *dvdlambda,
ewald_tab_t et)
{
- real factor=-1.0/(4*ewaldcoeff*ewaldcoeff);
- real scaleRecip =4.0*M_PI/(box[XX]*box[YY]*box[ZZ])*ONE_4PI_EPS0/ir->epsilon_r; /* 1/(Vol*e0) */
- real *charge,energy_AB[2],energy;
- rvec lll;
- int lowiy,lowiz,ix,iy,iz,n,q;
- real tmp,cs,ss,ak,akv,mx,my,mz,m2,scale;
- gmx_bool bFreeEnergy;
-
- if (cr != NULL)
+ real factor = -1.0/(4*ewaldcoeff*ewaldcoeff);
+ real scaleRecip = 4.0*M_PI/(box[XX]*box[YY]*box[ZZ])*ONE_4PI_EPS0/ir->epsilon_r; /* 1/(Vol*e0) */
+ real *charge, energy_AB[2], energy;
+ rvec lll;
+ int lowiy, lowiz, ix, iy, iz, n, q;
+ real tmp, cs, ss, ak, akv, mx, my, mz, m2, scale;
+ gmx_bool bFreeEnergy;
+
+ if (cr != NULL)
{
if (PAR(cr))
- {
- gmx_fatal(FARGS,"No parallel Ewald. Use PME instead.\n");
- }
+ {
+ gmx_fatal(FARGS, "No parallel Ewald. Use PME instead.\n");
+ }
}
- if (!et->eir) /* allocate if we need to */
- {
- snew(et->eir,et->kmax);
- for(n=0;n<et->kmax;n++)
- snew(et->eir[n],natoms);
- snew(et->tab_xy,natoms);
- snew(et->tab_qxyz,natoms);
- }
-
- bFreeEnergy = (ir->efep != efepNO);
-
- clear_mat(lrvir);
-
- calc_lll(box,lll);
- /* make tables for the structure factor parts */
- tabulate_eir(natoms,x,et->kmax,et->eir,lll);
-
- for(q=0; q<(bFreeEnergy ? 2 : 1); q++) {
- if (!bFreeEnergy) {
- charge = chargeA;
- scale = 1.0;
- } else if (q==0) {
- charge = chargeA;
- scale = 1.0 - lambda;
- } else {
- charge = chargeB;
- scale = lambda;
+ if (!et->eir) /* allocate if we need to */
+ {
+ snew(et->eir, et->kmax);
+ for (n = 0; n < et->kmax; n++)
+ {
+ snew(et->eir[n], natoms);
+ }
+ snew(et->tab_xy, natoms);
+ snew(et->tab_qxyz, natoms);
}
- lowiy=0;
- lowiz=1;
- energy_AB[q]=0;
- for(ix=0;ix<et->nx;ix++) {
- mx=ix*lll[XX];
- for(iy=lowiy;iy<et->ny;iy++) {
- my=iy*lll[YY];
- if(iy>=0)
- for(n=0;n<natoms;n++)
- et->tab_xy[n]=cmul(et->eir[ix][n][XX],et->eir[iy][n][YY]);
- else
- for(n=0;n<natoms;n++)
- et->tab_xy[n]=conjmul(et->eir[ix][n][XX],et->eir[-iy][n][YY]);
- for(iz=lowiz;iz<et->nz;iz++) {
- mz=iz*lll[ZZ];
- m2=mx*mx+my*my+mz*mz;
- ak=exp(m2*factor)/m2;
- akv=2.0*ak*(1.0/m2-factor);
- if(iz>=0)
- for(n=0;n<natoms;n++)
- et->tab_qxyz[n]=rcmul(charge[n],cmul(et->tab_xy[n],
- et->eir[iz][n][ZZ]));
- else
- for(n=0;n<natoms;n++)
- et->tab_qxyz[n]=rcmul(charge[n],conjmul(et->tab_xy[n],
- et->eir[-iz][n][ZZ]));
-
- cs=ss=0;
- for(n=0;n<natoms;n++) {
- cs+=et->tab_qxyz[n].re;
- ss+=et->tab_qxyz[n].im;
- }
- energy_AB[q]+=ak*(cs*cs+ss*ss);
- tmp=scale*akv*(cs*cs+ss*ss);
- lrvir[XX][XX]-=tmp*mx*mx;
- lrvir[XX][YY]-=tmp*mx*my;
- lrvir[XX][ZZ]-=tmp*mx*mz;
- lrvir[YY][YY]-=tmp*my*my;
- lrvir[YY][ZZ]-=tmp*my*mz;
- lrvir[ZZ][ZZ]-=tmp*mz*mz;
- for(n=0;n<natoms;n++) {
- /*tmp=scale*ak*(cs*tab_qxyz[n].im-ss*tab_qxyz[n].re);*/
- tmp=scale*ak*(cs*et->tab_qxyz[n].im-ss*et->tab_qxyz[n].re);
- f[n][XX]+=tmp*mx*2*scaleRecip;
- f[n][YY]+=tmp*my*2*scaleRecip;
- f[n][ZZ]+=tmp*mz*2*scaleRecip;
+
+ bFreeEnergy = (ir->efep != efepNO);
+
+ clear_mat(lrvir);
+
+ calc_lll(box, lll);
+ /* make tables for the structure factor parts */
+ tabulate_eir(natoms, x, et->kmax, et->eir, lll);
+
+ for (q = 0; q < (bFreeEnergy ? 2 : 1); q++)
+ {
+ if (!bFreeEnergy)
+ {
+ charge = chargeA;
+ scale = 1.0;
+ }
+ else if (q == 0)
+ {
+ charge = chargeA;
+ scale = 1.0 - lambda;
+ }
+ else
+ {
+ charge = chargeB;
+ scale = lambda;
+ }
+ lowiy = 0;
+ lowiz = 1;
+ energy_AB[q] = 0;
+ for (ix = 0; ix < et->nx; ix++)
+ {
+ mx = ix*lll[XX];
+ for (iy = lowiy; iy < et->ny; iy++)
+ {
+ my = iy*lll[YY];
+ if (iy >= 0)
+ {
+ for (n = 0; n < natoms; n++)
+ {
+ et->tab_xy[n] = cmul(et->eir[ix][n][XX], et->eir[iy][n][YY]);
+ }
+ }
+ else
+ {
+ for (n = 0; n < natoms; n++)
+ {
+ et->tab_xy[n] = conjmul(et->eir[ix][n][XX], et->eir[-iy][n][YY]);
+ }
+ }
+ for (iz = lowiz; iz < et->nz; iz++)
+ {
+ mz = iz*lll[ZZ];
+ m2 = mx*mx+my*my+mz*mz;
+ ak = exp(m2*factor)/m2;
+ akv = 2.0*ak*(1.0/m2-factor);
+ if (iz >= 0)
+ {
+ for (n = 0; n < natoms; n++)
+ {
+ et->tab_qxyz[n] = rcmul(charge[n], cmul(et->tab_xy[n],
+ et->eir[iz][n][ZZ]));
+ }
+ }
+ else
+ {
+ for (n = 0; n < natoms; n++)
+ {
+ et->tab_qxyz[n] = rcmul(charge[n], conjmul(et->tab_xy[n],
+ et->eir[-iz][n][ZZ]));
+ }
+ }
+
+ cs = ss = 0;
+ for (n = 0; n < natoms; n++)
+ {
+ cs += et->tab_qxyz[n].re;
+ ss += et->tab_qxyz[n].im;
+ }
+ energy_AB[q] += ak*(cs*cs+ss*ss);
+ tmp = scale*akv*(cs*cs+ss*ss);
+ lrvir[XX][XX] -= tmp*mx*mx;
+ lrvir[XX][YY] -= tmp*mx*my;
+ lrvir[XX][ZZ] -= tmp*mx*mz;
+ lrvir[YY][YY] -= tmp*my*my;
+ lrvir[YY][ZZ] -= tmp*my*mz;
+ lrvir[ZZ][ZZ] -= tmp*mz*mz;
+ for (n = 0; n < natoms; n++)
+ {
+ /*tmp=scale*ak*(cs*tab_qxyz[n].im-ss*tab_qxyz[n].re);*/
+ tmp = scale*ak*(cs*et->tab_qxyz[n].im-ss*et->tab_qxyz[n].re);
+ f[n][XX] += tmp*mx*2*scaleRecip;
+ f[n][YY] += tmp*my*2*scaleRecip;
+ f[n][ZZ] += tmp*mz*2*scaleRecip;
#if 0
- f[n][XX]+=tmp*mx;
- f[n][YY]+=tmp*my;
- f[n][ZZ]+=tmp*mz;
+ f[n][XX] += tmp*mx;
+ f[n][YY] += tmp*my;
+ f[n][ZZ] += tmp*mz;
#endif
- }
- lowiz=1-et->nz;
- }
- lowiy=1-et->ny;
- }
+ }
+ lowiz = 1-et->nz;
+ }
+ lowiy = 1-et->ny;
+ }
+ }
}
- }
-
- if (!bFreeEnergy) {
- energy = energy_AB[0];
- } else {
- energy = (1.0 - lambda)*energy_AB[0] + lambda*energy_AB[1];
- *dvdlambda += scaleRecip*(energy_AB[1] - energy_AB[0]);
- }
-
- lrvir[XX][XX]=-0.5*scaleRecip*(lrvir[XX][XX]+energy);
- lrvir[XX][YY]=-0.5*scaleRecip*(lrvir[XX][YY]);
- lrvir[XX][ZZ]=-0.5*scaleRecip*(lrvir[XX][ZZ]);
- lrvir[YY][YY]=-0.5*scaleRecip*(lrvir[YY][YY]+energy);
- lrvir[YY][ZZ]=-0.5*scaleRecip*(lrvir[YY][ZZ]);
- lrvir[ZZ][ZZ]=-0.5*scaleRecip*(lrvir[ZZ][ZZ]+energy);
-
- lrvir[YY][XX]=lrvir[XX][YY];
- lrvir[ZZ][XX]=lrvir[XX][ZZ];
- lrvir[ZZ][YY]=lrvir[YY][ZZ];
-
- energy*=scaleRecip;
-
- return energy;
+
+ if (!bFreeEnergy)
+ {
+ energy = energy_AB[0];
+ }
+ else
+ {
+ energy = (1.0 - lambda)*energy_AB[0] + lambda*energy_AB[1];
+ *dvdlambda += scaleRecip*(energy_AB[1] - energy_AB[0]);
+ }
+
+ lrvir[XX][XX] = -0.5*scaleRecip*(lrvir[XX][XX]+energy);
+ lrvir[XX][YY] = -0.5*scaleRecip*(lrvir[XX][YY]);
+ lrvir[XX][ZZ] = -0.5*scaleRecip*(lrvir[XX][ZZ]);
+ lrvir[YY][YY] = -0.5*scaleRecip*(lrvir[YY][YY]+energy);
+ lrvir[YY][ZZ] = -0.5*scaleRecip*(lrvir[YY][ZZ]);
+ lrvir[ZZ][ZZ] = -0.5*scaleRecip*(lrvir[ZZ][ZZ]+energy);
+
+ lrvir[YY][XX] = lrvir[XX][YY];
+ lrvir[ZZ][XX] = lrvir[XX][ZZ];
+ lrvir[ZZ][YY] = lrvir[YY][ZZ];
+
+ energy *= scaleRecip;
+
+ return energy;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff