/*
+ * 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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*
- * For more info, check our website at http://www.gromacs.org
+ * 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
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "string2.h"
-#include <stdio.h>
#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gen_vsite.h"
-#include "smalloc.h"
#include "resall.h"
#include "add_par.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "toputil.h"
-#include "physics.h"
-#include "index.h"
-#include "names.h"
-#include "futil.h"
+#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/utility/futil.h"
#include "gpp_atomtype.h"
#include "fflibutil.h"
-#include "macros.h"
+
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define MAXNAME 32
#define OPENDIR '[' /* starting sign for directive */
*nvsiteconf = nvsite;
*nvsitetop = ntop;
- ffclose(ddb);
+ gmx_ffclose(ddb);
}
static int nitrogen_is_planar(t_vsiteconf vsiteconflist[], int nvsiteconf, char atomtype[])
}
static int get_atype(int atom, t_atoms *at, int nrtp, t_restp rtp[],
- gmx_residuetype_t rt)
+ gmx_residuetype_t *rt)
{
int type;
gmx_bool bNterm;
}
static real get_amass(int atom, t_atoms *at, int nrtp, t_restp rtp[],
- gmx_residuetype_t rt)
+ gmx_residuetype_t *rt)
{
real mass;
gmx_bool bNterm;
static int gen_vsites_6ring(t_atoms *at, int *vsite_type[], t_params plist[],
int nrfound, int *ats, real bond_cc, real bond_ch,
- real xcom, real ycom, gmx_bool bDoZ)
+ real xcom, gmx_bool bDoZ)
{
/* these MUST correspond to the atnms array in do_vsite_aromatics! */
enum {
int nrfound, int *ats, t_vsitetop *vsitetop, int nvsitetop)
{
real bond_cc, bond_ch;
- real xcom, ycom, mtot;
+ real xcom, mtot;
int i;
/* these MUST correspond to the atnms array in do_vsite_aromatics! */
enum {
x[atHZ] = x[atCZ]+bond_ch;
y[atHZ] = 0;
- xcom = ycom = mtot = 0;
+ xcom = mtot = 0;
for (i = 0; i < atNR; i++)
{
xcom += x[i]*at->atom[ats[i]].m;
- ycom += y[i]*at->atom[ats[i]].m;
mtot += at->atom[ats[i]].m;
}
xcom /= mtot;
- ycom /= mtot;
- return gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, ycom, TRUE);
+ return gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, TRUE);
}
static void calc_vsite3_param(real xd, real yd, real xi, real yi, real xj, real yj,
for (j = 0; j < NMASS; j++)
{
sprintf(name, "MW%d", j+1);
- (*newatomname) [atM[j]] = put_symtab(symtab, name);
- (*newatom) [atM[j]].m = (*newatom)[atM[j]].mB = mM[j];
- (*newatom) [atM[j]].q = (*newatom)[atM[j]].qB = 0.0;
- (*newatom) [atM[j]].type = (*newatom)[atM[j]].typeB = tpM;
- (*newatom) [atM[j]].ptype = eptAtom;
- (*newatom) [atM[j]].resind = at->atom[i0].resind;
- (*newvsite_type)[atM[j]] = NOTSET;
- (*newcgnr) [atM[j]] = (*cgnr)[i0];
+ (*newatomname) [atM[j]] = put_symtab(symtab, name);
+ (*newatom) [atM[j]].m = (*newatom)[atM[j]].mB = mM[j];
+ (*newatom) [atM[j]].q = (*newatom)[atM[j]].qB = 0.0;
+ (*newatom) [atM[j]].type = (*newatom)[atM[j]].typeB = tpM;
+ (*newatom) [atM[j]].ptype = eptAtom;
+ (*newatom) [atM[j]].resind = at->atom[i0].resind;
+ (*newatom) [atM[j]].elem[0] = 'M';
+ (*newatom) [atM[j]].elem[1] = '\0';
+ (*newvsite_type)[atM[j]] = NOTSET;
+ (*newcgnr) [atM[j]] = (*cgnr)[i0];
}
/* renumber cgnr: */
for (i = i0; i < at->nr; i++)
int nvsite, i, i0, j, atM, tpM;
real dCGCE, dCEOH, dCGM, tmp1, a, b;
real bond_cc, bond_ch, bond_co, bond_oh, angle_coh;
- real xcom, ycom, mtot;
+ real xcom, mtot;
real vmass, vdist, mM;
rvec r1;
char name[10];
xi[atOH] = xi[atCZ]+bond_co;
yi[atOH] = 0;
- xcom = ycom = mtot = 0;
+ xcom = mtot = 0;
for (i = 0; i < atOH; i++)
{
xcom += xi[i]*at->atom[ats[i]].m;
- ycom += yi[i]*at->atom[ats[i]].m;
mtot += at->atom[ats[i]].m;
}
xcom /= mtot;
- ycom /= mtot;
/* first do 6 ring as default,
except CZ (we'll do that different) and HZ (we don't have that): */
- nvsite = gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, ycom, FALSE);
+ nvsite = gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, FALSE);
/* then construct CZ from the 2nd triangle */
/* vsite3 construction: r_d = r_i + a r_ij + b r_ik */
rvec_add(r1, x[ats[atHH]], (*newx)[atM]);
strcpy(name, "MW1");
- (*newatomname) [atM] = put_symtab(symtab, name);
- (*newatom) [atM].m = (*newatom)[atM].mB = mM;
- (*newatom) [atM].q = (*newatom)[atM].qB = 0.0;
- (*newatom) [atM].type = (*newatom)[atM].typeB = tpM;
- (*newatom) [atM].ptype = eptAtom;
- (*newatom) [atM].resind = at->atom[i0].resind;
- (*newvsite_type)[atM] = NOTSET;
- (*newcgnr) [atM] = (*cgnr)[i0];
+ (*newatomname) [atM] = put_symtab(symtab, name);
+ (*newatom) [atM].m = (*newatom)[atM].mB = mM;
+ (*newatom) [atM].q = (*newatom)[atM].qB = 0.0;
+ (*newatom) [atM].type = (*newatom)[atM].typeB = tpM;
+ (*newatom) [atM].ptype = eptAtom;
+ (*newatom) [atM].resind = at->atom[i0].resind;
+ (*newatom) [atM].elem[0] = 'M';
+ (*newatom) [atM].elem[1] = '\0';
+ (*newvsite_type)[atM] = NOTSET;
+ (*newcgnr) [atM] = (*cgnr)[i0];
/* renumber cgnr: */
for (i = i0; i < at->nr; i++)
{
char **db;
int nvsiteconf, nvsitetop, cmplength;
gmx_bool isN, planarN, bFound;
- gmx_residuetype_t rt;
+ gmx_residuetype_t*rt;
t_vsiteconf *vsiteconflist;
/* pointer to a list of CH3/NH3/NH2 configuration entries.
{
name[k+1] = (*at->atomname[Heavy])[k];
}
- name[k+1] = atomnamesuffix[j];
- name[k+2] = '\0';
- newatomname[ni0+j] = put_symtab(symtab, name);
- newatom[ni0+j].m = newatom[ni0+j].mB = mtot/NMASS;
- newatom[ni0+j].q = newatom[ni0+j].qB = 0.0;
- newatom[ni0+j].type = newatom[ni0+j].typeB = tpM;
- newatom[ni0+j].ptype = eptAtom;
- newatom[ni0+j].resind = at->atom[i0].resind;
- newvsite_type[ni0+j] = NOTSET;
- newcgnr[ni0+j] = (*cgnr)[i0];
+ name[k+1] = atomnamesuffix[j];
+ name[k+2] = '\0';
+ newatomname[ni0+j] = put_symtab(symtab, name);
+ newatom[ni0+j].m = newatom[ni0+j].mB = mtot/NMASS;
+ newatom[ni0+j].q = newatom[ni0+j].qB = 0.0;
+ newatom[ni0+j].type = newatom[ni0+j].typeB = tpM;
+ newatom[ni0+j].ptype = eptAtom;
+ newatom[ni0+j].resind = at->atom[i0].resind;
+ newatom[ni0+j].elem[0] = 'M';
+ newatom[ni0+j].elem[1] = '\0';
+ newvsite_type[ni0+j] = NOTSET;
+ newcgnr[ni0+j] = (*cgnr)[i0];
}
/* add constraints between dummy masses and to heavies[0] */
/* 'add_shift' says which atoms won't be renumbered afterwards */
{
if (debug)
{
- fprintf(debug, " [%u -> %u]", params->param[i].a[j],
+ fprintf(debug, " [%d -> %d]", params->param[i].a[j],
params->param[i].a[j]-add_shift);
}
params->param[i].a[j] = params->param[i].a[j]-add_shift;
{
if (debug)
{
- fprintf(debug, " [%u -> %d]", params->param[i].a[j],
+ fprintf(debug, " [%d -> %d]", params->param[i].a[j],
o2n[params->param[i].a[j]]);
}
params->param[i].a[j] = o2n[params->param[i].a[j]];
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff