-/* -*- 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.
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+ * If you want to redistribute modifications to GROMACS, 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
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- * GROwing Monsters And Cloning Shrimps
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "pbc.h"
-#include "txtdump.h"
-#include "vec.h"
-#include "nrnb.h"
-#include "constr.h"
+
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
typedef struct gmx_shakedata
{
}
int vec_shakef(FILE *fplog, gmx_shakedata_t shaked,
- int natoms, real invmass[], int ncon,
+ real invmass[], int ncon,
t_iparams ip[], t_iatom *iatom,
real tol, rvec x[], rvec prime[], real omega,
gmx_bool bFEP, real lambda, real lagr[],
}
gmx_bool bshakef(FILE *log, gmx_shakedata_t shaked,
- int natoms, real invmass[], int nblocks, int sblock[],
+ real invmass[], int nblocks, int sblock[],
t_idef *idef, t_inputrec *ir, rvec x_s[], rvec prime[],
t_nrnb *nrnb, real *lagr, real lambda, real *dvdlambda,
real invdt, rvec *v, gmx_bool bCalcVir, tensor vir_r_m_dr,
{
blen = (sblock[i+1]-sblock[i]);
blen /= 3;
- n0 = vec_shakef(log, shaked, natoms, invmass, blen, idef->iparams,
+ n0 = vec_shakef(log, shaked, invmass, blen, idef->iparams,
iatoms, ir->shake_tol, x_s, prime, shaked->omega,
ir->efep != efepNO, lambda, lam, invdt, v, bCalcVir, vir_r_m_dr,
econq, vetavar);
{
if (ir->efep != efepNO)
{
+ real bondA, bondB;
dt_2 = 1/sqr(ir->delta_t);
dvdl = 0;
for (i = 0; i < ncons; i++)
{
type = idef->il[F_CONSTR].iatoms[3*i];
- dvdl += lagr[i]*dt_2*
- (idef->iparams[type].constr.dB-idef->iparams[type].constr.dA);
+
+ /* dh/dl contribution from constraint force is dh/dr (constraint force) dot dr/dl */
+ /* constraint force is -\sum_i lagr_i* d(constraint)/dr, with constrant = r^2-d^2 */
+ /* constraint force is -\sum_i lagr_i* 2 r */
+ /* so dh/dl = -\sum_i lagr_i* 2 r * dr/dl */
+ /* However, by comparison with lincs and with
+ comparison with a full thermodynamics cycle (see
+ redmine issue #1255), this is off by a factor of
+ two -- the 2r should apparently just be r. Further
+ investigation should be done at some point to
+ understand why and see if there is something deeper
+ we are missing */
+
+ bondA = idef->iparams[type].constr.dA;
+ bondB = idef->iparams[type].constr.dB;
+ dvdl += lagr[i] * dt_2 * ((1.0-lambda)*bondA + lambda*bondB) * (bondB-bondA);
}
*dvdlambda += dvdl;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff