-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
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*
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+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
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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 "vec.h"
-#include "pbc.h"
-#include "smalloc.h"
-#include "gmx_fatal.h"
-#include "chargegroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/chargegroup.h"
-void calc_chargegroup_radii(const gmx_mtop_t *mtop,rvec *x,
- real *rvdw1,real *rvdw2,
- real *rcoul1,real *rcoul2)
+void calc_chargegroup_radii(const gmx_mtop_t *mtop, rvec *x,
+ real *rvdw1, real *rvdw2,
+ real *rcoul1, real *rcoul2)
{
- real r2v1,r2v2,r2c1,r2c2,r2;
- int ntype,i,j,mb,m,cg,a_mol,a0,a1,a;
- gmx_bool *bLJ;
+ real r2v1, r2v2, r2c1, r2c2, r2;
+ int ntype, i, j, mb, m, cg, a_mol, a0, a1, a;
+ gmx_bool *bLJ;
gmx_molblock_t *molb;
- gmx_moltype_t *molt;
- t_block *cgs;
- t_atom *atom;
- rvec cen;
+ gmx_moltype_t *molt;
+ t_block *cgs;
+ t_atom *atom;
+ rvec cen;
r2v1 = 0;
r2v2 = 0;
r2c2 = 0;
ntype = mtop->ffparams.atnr;
- snew(bLJ,ntype);
- for(i=0; i<ntype; i++)
+ snew(bLJ, ntype);
+ for (i = 0; i < ntype; i++)
{
bLJ[i] = FALSE;
- for(j=0; j<ntype; j++)
+ for (j = 0; j < ntype; j++)
{
if (mtop->ffparams.iparams[i*ntype+j].lj.c6 != 0 ||
mtop->ffparams.iparams[i*ntype+j].lj.c12 != 0)
}
a_mol = 0;
- for(mb=0; mb<mtop->nmolblock; mb++)
+ for (mb = 0; mb < mtop->nmolblock; mb++)
{
molb = &mtop->molblock[mb];
molt = &mtop->moltype[molb->type];
cgs = &molt->cgs;
atom = molt->atoms.atom;
- for(m=0; m<molb->nmol; m++)
+ for (m = 0; m < molb->nmol; m++)
{
- for(cg=0; cg<cgs->nr; cg++)
+ for (cg = 0; cg < cgs->nr; cg++)
{
a0 = cgs->index[cg];
a1 = cgs->index[cg+1];
if (a1 - a0 > 1)
{
clear_rvec(cen);
- for(a=a0; a<a1; a++)
+ for (a = a0; a < a1; a++)
{
- rvec_inc(cen,x[a_mol+a]);
+ rvec_inc(cen, x[a_mol+a]);
}
- svmul(1.0/(a1-a0),cen,cen);
- for(a=a0; a<a1; a++)
+ svmul(1.0/(a1-a0), cen, cen);
+ for (a = a0; a < a1; a++)
{
- r2 = distance2(cen,x[a_mol+a]);
+ r2 = distance2(cen, x[a_mol+a]);
if (r2 > r2v2 && (bLJ[atom[a].type ] ||
bLJ[atom[a].typeB]))
{
*rcoul2 = sqrt(r2c2);
}
-void calc_cgcm(FILE *fplog,int cg0,int cg1,t_block *cgs,
- rvec pos[],rvec cg_cm[])
+void calc_cgcm(FILE gmx_unused *fplog, int cg0, int cg1, t_block *cgs,
+ rvec pos[], rvec cg_cm[])
{
- int icg,k,k0,k1,d;
- rvec cg;
- real nrcg,inv_ncg;
+ int icg, k, k0, k1, d;
+ rvec cg;
+ real nrcg, inv_ncg;
atom_id *cgindex;
#ifdef DEBUG
- fprintf(fplog,"Calculating centre of geometry for charge groups %d to %d\n",
- cg0,cg1);
+ fprintf(fplog, "Calculating centre of geometry for charge groups %d to %d\n",
+ cg0, cg1);
#endif
cgindex = cgs->index;
/* Compute the center of geometry for all charge groups */
- for(icg=cg0; (icg<cg1); icg++) {
+ for (icg = cg0; (icg < cg1); icg++)
+ {
k0 = cgindex[icg];
k1 = cgindex[icg+1];
nrcg = k1-k0;
- if (nrcg == 1) {
- copy_rvec(pos[k0],cg_cm[icg]);
+ if (nrcg == 1)
+ {
+ copy_rvec(pos[k0], cg_cm[icg]);
}
- else {
+ else
+ {
inv_ncg = 1.0/nrcg;
clear_rvec(cg);
- for(k=k0; (k<k1); k++) {
- for(d=0; (d<DIM); d++)
+ for (k = k0; (k < k1); k++)
+ {
+ for (d = 0; (d < DIM); d++)
+ {
cg[d] += pos[k][d];
+ }
}
- for(d=0; (d<DIM); d++)
+ for (d = 0; (d < DIM); d++)
+ {
cg_cm[icg][d] = inv_ncg*cg[d];
+ }
}
}
}
-void put_charge_groups_in_box(FILE *fplog,int cg0,int cg1,
- int ePBC,matrix box,t_block *cgs,
- rvec pos[],rvec cg_cm[])
+void put_charge_groups_in_box(FILE gmx_unused *fplog, int cg0, int cg1,
+ int ePBC, matrix box, t_block *cgs,
+ rvec pos[], rvec cg_cm[])
-{
- int npbcdim,icg,k,k0,k1,d,e;
- rvec cg;
- real nrcg,inv_ncg;
+{
+ int npbcdim, icg, k, k0, k1, d, e;
+ rvec cg;
+ real nrcg, inv_ncg;
atom_id *cgindex;
gmx_bool bTric;
- if (ePBC == epbcNONE)
+ if (ePBC == epbcNONE)
+ {
gmx_incons("Calling put_charge_groups_in_box for a system without PBC");
+ }
#ifdef DEBUG
- fprintf(fplog,"Putting cgs %d to %d in box\n",cg0,cg1);
+ fprintf(fplog, "Putting cgs %d to %d in box\n", cg0, cg1);
#endif
cgindex = cgs->index;
if (ePBC == epbcXY)
+ {
npbcdim = 2;
+ }
else
+ {
npbcdim = 3;
+ }
bTric = TRICLINIC(box);
- for(icg=cg0; (icg<cg1); icg++) {
+ for (icg = cg0; (icg < cg1); icg++)
+ {
/* First compute the center of geometry for this charge group */
k0 = cgindex[icg];
k1 = cgindex[icg+1];
nrcg = k1-k0;
- if (nrcg == 1) {
- copy_rvec(pos[k0],cg_cm[icg]);
- } else {
+ if (nrcg == 1)
+ {
+ copy_rvec(pos[k0], cg_cm[icg]);
+ }
+ else
+ {
inv_ncg = 1.0/nrcg;
clear_rvec(cg);
- for(k=k0; (k<k1); k++) {
- for(d=0; d<DIM; d++)
+ for (k = k0; (k < k1); k++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
cg[d] += pos[k][d];
+ }
}
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
+ {
cg_cm[icg][d] = inv_ncg*cg[d];
+ }
}
/* Now check pbc for this cg */
- if (bTric) {
- for(d=npbcdim-1; d>=0; d--) {
- while(cg_cm[icg][d] < 0) {
- for(e=d; e>=0; e--) {
+ if (bTric)
+ {
+ for (d = npbcdim-1; d >= 0; d--)
+ {
+ while (cg_cm[icg][d] < 0)
+ {
+ for (e = d; e >= 0; e--)
+ {
cg_cm[icg][e] += box[d][e];
- for(k=k0; (k<k1); k++)
+ for (k = k0; (k < k1); k++)
+ {
pos[k][e] += box[d][e];
+ }
}
}
- while(cg_cm[icg][d] >= box[d][d]) {
- for(e=d; e>=0; e--) {
+ while (cg_cm[icg][d] >= box[d][d])
+ {
+ for (e = d; e >= 0; e--)
+ {
cg_cm[icg][e] -= box[d][e];
- for(k=k0; (k<k1); k++)
+ for (k = k0; (k < k1); k++)
+ {
pos[k][e] -= box[d][e];
+ }
}
}
}
- } else {
- for(d=0; d<npbcdim; d++) {
- while(cg_cm[icg][d] < 0) {
+ }
+ else
+ {
+ for (d = 0; d < npbcdim; d++)
+ {
+ while (cg_cm[icg][d] < 0)
+ {
cg_cm[icg][d] += box[d][d];
- for(k=k0; (k<k1); k++)
+ for (k = k0; (k < k1); k++)
+ {
pos[k][d] += box[d][d];
+ }
}
- while(cg_cm[icg][d] >= box[d][d]) {
+ while (cg_cm[icg][d] >= box[d][d])
+ {
cg_cm[icg][d] -= box[d][d];
- for(k=k0; (k<k1); k++)
+ for (k = k0; (k < k1); k++)
+ {
pos[k][d] -= box[d][d];
+ }
}
}
}
#ifdef DEBUG_PBC
- for(d=0; (d<npbcdim); d++) {
+ for (d = 0; (d < npbcdim); d++)
+ {
if ((cg_cm[icg][d] < 0) || (cg_cm[icg][d] >= box[d][d]))
- gmx_fatal(FARGS,"cg_cm[%d] = %15f %15f %15f\n"
+ {
+ gmx_fatal(FARGS, "cg_cm[%d] = %15f %15f %15f\n"
"box = %15f %15f %15f\n",
- icg,cg_cm[icg][XX],cg_cm[icg][YY],cg_cm[icg][ZZ],
- box[XX][XX],box[YY][YY],box[ZZ][ZZ]);
+ icg, cg_cm[icg][XX], cg_cm[icg][YY], cg_cm[icg][ZZ],
+ box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
+ }
}
#endif
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff