#include <stdlib.h>
#include <string.h>
+#include <cmath>
+
+#include <algorithm>
+
#include "gromacs/domdec/domdec.h"
#include "gromacs/legacyheaders/force.h"
#include "gromacs/legacyheaders/macros.h"
static int
round_up_to_simd_width(int length, int simd_width)
{
- int offset, newlength;
+ int offset;
offset = (simd_width > 0) ? length % simd_width : 0;
{
t_nblist *nl;
int homenr;
- int i, nn;
+ int i;
for (i = 0; (i < 2); i++)
{
*/
int maxsr, maxsr_wat, maxlr, maxlr_wat;
int ielec, ivdw, ielecmod, ivdwmod, type;
- int solvent;
int igeometry_def, igeometry_w, igeometry_ww;
int i;
gmx_bool bElecAndVdwSwitchDiffers;
* all the nlist arrays many times in a row.
* The numbers seem very accurate, but they are uncritical.
*/
- maxsr_wat = min(fr->nWatMol, (homenr+2)/3);
+ maxsr_wat = std::min(fr->nWatMol, (homenr+2)/3);
if (fr->bTwinRange)
{
maxlr = 50;
- maxlr_wat = min(maxsr_wat, maxlr);
+ maxlr_wat = std::min(maxsr_wat, maxlr);
}
else
{
static gmx_inline void new_i_nblist(t_nblist *nlist, atom_id i_atom, int shift, int gid)
{
- int i, k, nri, nshift;
-
- nri = nlist->nri;
+ int nri = nlist->nri;
/* Check whether we have to increase the i counter */
if ((nri == -1) ||
t_nblist * vdwc_ww = NULL;
t_nblist * coul_ww = NULL;
- int i, j, jcg, igid, gid, nbl_ind, ind_ij;
+ int i, j, jcg, igid, gid, nbl_ind;
atom_id jj, jj0, jj1, i_atom;
- int i0, nicg, len;
+ int i0, nicg;
int *cginfo;
int *type, *typeB;
real *charge, *chargeB;
- real qi, qiB, qq, rlj;
+ real qi, qiB;
gmx_bool bFreeEnergy, bFree, bFreeJ, bNotEx, *bPert;
gmx_bool bDoVdW_i, bDoCoul_i, bDoCoul_i_sol;
int iwater, jwater;
gmx_bool bLR,
gmx_bool bDoVdW,
gmx_bool bDoCoul,
- int solvent_opt)
+ int gmx_unused solvent_opt)
{
/* The a[] index has been removed,
* to put it back in i_atom should be a[i0] and jj should be a[jj].
t_nblist * vdwc_adress = NULL;
t_nblist * vdw_adress = NULL;
t_nblist * coul_adress = NULL;
- t_nblist * vdwc_ww = NULL;
- t_nblist * coul_ww = NULL;
int i, j, jcg, igid, gid, nbl_ind, nbl_ind_adress;
atom_id jj, jj0, jj1, i_atom;
- int i0, nicg, len;
+ int i0, nicg;
int *cginfo;
- int *type, *typeB;
- real *charge, *chargeB;
+ int *type;
+ real *charge;
real *wf;
- real qi, qiB, qq, rlj;
- gmx_bool bFreeEnergy, bFree, bFreeJ, bNotEx, *bPert;
- gmx_bool bDoVdW_i, bDoCoul_i, bDoCoul_i_sol;
+ real qi;
+ gmx_bool bNotEx;
+ gmx_bool bDoVdW_i, bDoCoul_i;
gmx_bool b_hybrid;
- gmx_bool j_all_atom;
- int iwater, jwater;
t_nblist *nlist, *nlist_adress;
gmx_bool bEnergyGroupCG;
/* Copy some pointers */
cginfo = fr->cginfo;
charge = md->chargeA;
- chargeB = md->chargeB;
type = md->typeA;
- typeB = md->typeB;
- bPert = md->bPerturbed;
wf = md->wf;
/* Get atom range */
/* Get the i charge group info */
igid = GET_CGINFO_GID(cginfo[icg]);
- iwater = (solvent_opt != esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
-
if (md->nPerturbed)
{
gmx_fatal(FARGS, "AdResS does not support free energy pertubation\n");
/* Perform NINT operation, using trunc operation, therefore
* we first add 2.5 then subtract 2 again
*/
- tz = dz*b_inv[ZZ] + h25;
+ tz = static_cast<int>(dz*b_inv[ZZ] + h25);
tz -= 2;
dz -= tz*box[ZZ][ZZ];
dy -= tz*box[ZZ][YY];
dx -= tz*box[ZZ][XX];
- ty = dy*b_inv[YY] + h25;
+ ty = static_cast<int>(dy*b_inv[YY] + h25);
ty -= 2;
dy -= ty*box[YY][YY];
dx -= ty*box[YY][XX];
- tx = dx*b_inv[XX]+h25;
+ tx = static_cast<int>(dx*b_inv[XX]+h25);
tx -= 2;
dx -= tx*box[XX][XX];
/* Perform NINT operation, using trunc operation, therefore
* we first add 1.5 then subtract 1 again
*/
- tx = dx*b_inv[XX] + h15;
- ty = dy*b_inv[YY] + h15;
- tz = dz*b_inv[ZZ] + h15;
+ tx = static_cast<int>(dx*b_inv[XX] + h15);
+ ty = static_cast<int>(dy*b_inv[YY] + h15);
+ tz = static_cast<int>(dz*b_inv[ZZ] + h15);
tx--;
ty--;
tz--;
return r2;
}
-static void add_simple(t_ns_buf *nsbuf, int nrj, atom_id cg_j,
+static void add_simple(t_ns_buf * nsbuf, int nrj, atom_id cg_j,
gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
int icg, int jgid, t_block *cgs, t_excl bexcl[],
int shift, t_forcerec *fr, put_in_list_t *put_in_list)
int j, nrj, jgid;
int *cginfo = fr->cginfo;
atom_id cg_j, *cgindex;
- t_ns_buf *nsbuf;
cgindex = cgs->index;
shift = CENTRAL;
int j, nrj, jgid;
int *cginfo = fr->cginfo;
atom_id cg_j, *cgindex;
- t_ns_buf *nsbuf;
cgindex = cgs->index;
if (bBox)
{
int naaj, k;
real rlist2;
- int nsearch, icg, jcg, igid, i0, nri, nn;
+ int nsearch, icg, igid, nn;
int *cginfo;
t_ns_buf *nsbuf;
/* atom_id *i_atoms; */
*rvdw2 = *rs2;
*rcoul2 = *rs2;
}
- *rm2 = min(*rvdw2, *rcoul2);
- *rl2 = max(*rvdw2, *rcoul2);
+ *rm2 = std::min(*rvdw2, *rcoul2);
+ *rl2 = std::max(*rvdw2, *rcoul2);
}
static void init_nsgrid_lists(t_forcerec *fr, int ngid, gmx_ns_t *ns)
#endif
int dx0, dx1, dy0, dy1, dz0, dz1;
int Nx, Ny, Nz, shift = -1, j, nrj, nns, nn = -1;
- real gridx, gridy, gridz, grid_x, grid_y, grid_z;
+ real gridx, gridy, gridz, grid_x, grid_y;
real *dcx2, *dcy2, *dcz2;
int zgi, ygi, xgi;
- int cg0, cg1, icg = -1, cgsnr, i0, igid, nri, naaj, max_jcg;
+ int cg0, cg1, icg = -1, cgsnr, i0, igid, naaj, max_jcg;
int jcg0, jcg1, jjcg, cgj0, jgid;
int *grida, *gridnra, *gridind;
gmx_bool rvdw_lt_rcoul, rcoul_lt_rvdw;
- rvec xi, *cgcm, grid_offset;
- real r2, rs2, rvdw2, rcoul2, rm2, rl2, XI, YI, ZI, dcx, dcy, dcz, tmp1, tmp2;
+ rvec *cgcm, grid_offset;
+ real r2, rs2, rvdw2, rcoul2, rm2, rl2, XI, YI, ZI, tmp1, tmp2;
int *i_egp_flags;
gmx_bool bDomDec, bTriclinicX, bTriclinicY;
ivec ncpddc;
gridz = grid->cell_size[ZZ];
grid_x = 1/gridx;
grid_y = 1/gridy;
- grid_z = 1/gridz;
copy_rvec(grid->cell_offset, grid_offset);
copy_ivec(grid->ncpddc, ncpddc);
dcx2 = grid->dcx2;
else
{
if (d == XX &&
- box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < sqrt(rl2))
+ box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < std::sqrt(rl2))
{
shp[d] = 2;
}
}
}
}
- /* setexcl(nri,i_atoms,&top->atoms.excl,FALSE,bexcl); */
setexcl(cgs->index[icg], cgs->index[icg+1], &top->excls, FALSE, bexcl);
}
/* No need to perform any left-over force calculations anymore (as we used to do here)
{
int mt, icg, nr_in_cg, maxcg, i, j, jcg, ngid, ncg;
t_block *cgs;
- char *ptr;
/* Compute largest charge groups size (# atoms) */
nr_in_cg = 1;
cgs = &mtop->moltype[mt].cgs;
for (icg = 0; (icg < cgs->nr); icg++)
{
- nr_in_cg = max(nr_in_cg, (int)(cgs->index[icg+1]-cgs->index[icg]));
+ nr_in_cg = std::max(nr_in_cg, (int)(cgs->index[icg+1]-cgs->index[icg]));
}
}
{
t_block *cgs = &(top->cgs);
rvec box_size, grid_x0, grid_x1;
- int i, j, m, ngid;
+ int m, ngid;
real min_size, grid_dens;
int nsearch;
gmx_bool bGrid;
- char *ptr;
- gmx_bool *i_egp_flags;
- int cg_start, cg_end, start, end;
+ int start, end;
gmx_ns_t *ns;
t_grid *grid;
gmx_domdec_zones_t *dd_zones;
}
if (!bGrid)
{
- min_size = min(box_size[XX], min(box_size[YY], box_size[ZZ]));
+ min_size = std::min(box_size[XX], std::min(box_size[YY], box_size[ZZ]));
if (2*fr->rlistlong >= min_size)
{
gmx_fatal(FARGS, "One of the box diagonal elements has become smaller than twice the cut-off length.");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
#include <stdio.h>
#include <stdlib.h>
+#include <cmath>
+
+#include <algorithm>
+
#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/legacyheaders/macros.h"
for (d = 0; d < DIM; d++)
{
av[d] = s1[d];
- stddev[d] = sqrt(s2[d] - s1[d]*s1[d]);
+ stddev[d] = std::sqrt(s2[d] - s1[d]*s1[d]);
}
}
{
int i, j;
gmx_bool bDD, bDDRect;
- rvec av, stddev;
rvec izones_size;
real inv_r_ideal, size, add_tric, radd;
}
/* Use the ideal number of cg's per cell to set the ideal cell size */
- inv_r_ideal = pow(grid_density/grid->ncg_ideal, 1.0/3.0);
+ inv_r_ideal = std::pow((real)(grid_density/grid->ncg_ideal), (real)(1.0/3.0));
if (rlist > 0 && inv_r_ideal*rlist < 1)
{
inv_r_ideal = 1/rlist;
/* Check if the cell boundary in this direction is
* perpendicular to the Cartesian axis.
+ * Since grid->npbcdim isan integer that in principle can take
+ * any value, we help the compiler avoid warnings and potentially
+ * optimize by ensuring that j < DIM here.
*/
- for (j = i+1; j < grid->npbcdim; j++)
+ for (j = i+1; j < grid->npbcdim && j < DIM; j++)
{
if (box[j][i] != 0)
{
t_grid *init_grid(FILE *fplog, t_forcerec *fr)
{
- int d, m;
char *ptr;
t_grid *grid;
real rlistlong, real grid_density)
{
int i, m;
- ivec cx;
set_grid_sizes(box, izones_x0, izones_x1, rlistlong, dd, ddbox, grid, grid_density);
}
}
- m = max(grid->n[XX], max(grid->n[YY], grid->n[ZZ]));
+ m = std::max(grid->n[XX], std::max(grid->n[YY], grid->n[ZZ]));
if (m > grid->dc_nalloc)
{
/* Allocate with double the initial size for box scaling */
int cg0, int cg1, rvec cg_cm[])
{
int *cell_index;
- int nrx, nry, nrz;
+ int nry, nrz;
rvec n_box, offset;
int zone, ccg0, ccg1, cg, d, not_used;
ivec shift0, useall, b0, b1, ind;
cell_index = grid->cell_index;
/* Initiate cell borders */
- nrx = grid->n[XX];
nry = grid->n[YY];
nrz = grid->n[ZZ];
for (d = 0; d < DIM; d++)
{
for (d = 0; d < DIM; d++)
{
- ind[d] = (cg_cm[cg][d] - offset[d])*n_box[d];
+ ind[d] = static_cast<int>((cg_cm[cg][d] - offset[d])*n_box[d]);
/* With pbc we should be done here.
* Without pbc cg's outside the grid
* should be assigned to the closest grid cell.
bUse = TRUE;
for (d = 0; d < DIM; d++)
{
- ind[d] = (cg_cm[cg][d] - offset[d])*n_box[d];
+ ind[d] = static_cast<int>((cg_cm[cg][d] - offset[d])*n_box[d]);
/* Here we have to correct for rounding problems,
* as this cg_cm to cell index operation is not necessarily
* binary identical to the operation for the DD zone assignment
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff