/* Add the forces from enforced rotation potential to the local forces.
* Should be called after the SR forces have been evaluated */
-real add_rot_forces(gmx_enfrot* er, rvec f[], const t_commrec* cr, int64_t step, real t)
+real add_rot_forces(gmx_enfrot* er, gmx::ArrayRef<gmx::RVec> force, const t_commrec* cr, int64_t step, real t)
{
real Vrot = 0.0; /* If more than one rotation group is present, Vrot
assembles the local parts from all groups */
/* Get the right index of the local force */
int ii = localRotationGroupIndex[l];
/* Add */
- rvec_inc(f[ii], erg->f_rot_loc[l]);
+ rvec_inc(force[ii], erg->f_rot_loc[l]);
}
}
}
-static real do_flex2_lowlevel(gmx_enfrotgrp* erg,
- real sigma, /* The Gaussian width sigma */
- rvec x[],
- gmx_bool bOutstepRot,
- gmx_bool bOutstepSlab,
- const matrix box)
+static real do_flex2_lowlevel(gmx_enfrotgrp* erg,
+ real sigma, /* The Gaussian width sigma */
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx_bool bOutstepRot,
+ gmx_bool bOutstepSlab,
+ const matrix box)
{
int count, ii, iigrp;
rvec xj; /* position in the i-sum */
* Note that erg->xc_center contains the center of mass in case the flex2-t
* potential was chosen. For the flex2 potential erg->xc_center must be
* zero. */
- rvec_sub(x[ii], erg->xc_center, xj);
+ rvec_sub(coords[ii], erg->xc_center, xj);
/* Shift this atom such that it is near its reference */
shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
static real do_flex_lowlevel(gmx_enfrotgrp* erg,
- real sigma, /* The Gaussian width sigma */
- rvec x[],
- gmx_bool bOutstepRot,
- gmx_bool bOutstepSlab,
- const matrix box)
+ real sigma, /* The Gaussian width sigma */
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx_bool bOutstepRot,
+ gmx_bool bOutstepSlab,
+ const matrix box)
{
int count, iigrp;
rvec xj, yj0; /* current and reference position */
* Note that erg->xc_center contains the center of mass in case the flex-t
* potential was chosen. For the flex potential erg->xc_center must be
* zero. */
- rvec_sub(x[ii], erg->xc_center, xj);
+ rvec_sub(coords[ii], erg->xc_center, xj);
/* Shift this atom such that it is near its reference */
shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
static void do_flexible(gmx_bool bMaster,
gmx_enfrot* enfrot, /* Other rotation data */
gmx_enfrotgrp* erg,
- rvec x[], /* The local positions */
- const matrix box,
- double t, /* Time in picoseconds */
- gmx_bool bOutstepRot, /* Output to main rotation output file */
- gmx_bool bOutstepSlab) /* Output per-slab data */
+ gmx::ArrayRef<const gmx::RVec> coords, /* The local positions */
+ const matrix box,
+ double t, /* Time in picoseconds */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
{
int nslabs;
real sigma; /* The Gaussian width sigma */
if (erg->rotg->eType == EnforcedRotationGroupType::Flex
|| erg->rotg->eType == EnforcedRotationGroupType::Flext)
{
- erg->V = do_flex_lowlevel(erg, sigma, x, bOutstepRot, bOutstepSlab, box);
+ erg->V = do_flex_lowlevel(erg, sigma, coords, bOutstepRot, bOutstepSlab, box);
}
else if (erg->rotg->eType == EnforcedRotationGroupType::Flex2
|| erg->rotg->eType == EnforcedRotationGroupType::Flex2t)
{
- erg->V = do_flex2_lowlevel(erg, sigma, x, bOutstepRot, bOutstepSlab, box);
+ erg->V = do_flex2_lowlevel(erg, sigma, coords, bOutstepRot, bOutstepSlab, box);
}
else
{
/* Calculate the radial motion pivot-free potential and forces */
-static void do_radial_motion_pf(gmx_enfrotgrp* erg,
- rvec x[], /* The positions */
- const matrix box, /* The simulation box */
- gmx_bool bOutstepRot, /* Output to main rotation output file */
- gmx_bool bOutstepSlab) /* Output per-slab data */
+static void do_radial_motion_pf(gmx_enfrotgrp* erg,
+ gmx::ArrayRef<const gmx::RVec> coords, /* The positions */
+ const matrix box, /* The simulation box */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
{
rvec xj; /* Current position */
rvec xj_xc; /* xj - xc */
wj = N_M * mj;
/* Current position of this atom: x[ii][XX/YY/ZZ] */
- copy_rvec(x[ii], xj);
+ copy_rvec(coords[ii], xj);
/* Shift this atom such that it is near its reference */
shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
/* Calculate the radial motion 2 potential and forces */
-static void do_radial_motion2(gmx_enfrotgrp* erg,
- rvec x[], /* The positions */
- const matrix box, /* The simulation box */
+static void do_radial_motion2(gmx_enfrotgrp* erg,
+ gmx::ArrayRef<const gmx::RVec> coords, /* The positions */
+ const matrix box, /* The simulation box */
gmx_bool bOutstepRot, /* Output to main rotation output file */
gmx_bool bOutstepSlab) /* Output per-slab data */
{
mj = erg->mc[iigrp];
/* Current position of this atom: x[ii] */
- copy_rvec(x[ii], xj);
+ copy_rvec(coords[ii], xj);
/* Shift this atom such that it is near its reference */
shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
/* Select the PBC representation for each local x position and store that
* for later usage. We assume the right PBC image of an x is the one nearest to
* its rotated reference */
-static void choose_pbc_image(rvec x[], gmx_enfrotgrp* erg, const matrix box, int npbcdim)
+static void choose_pbc_image(gmx::ArrayRef<const gmx::RVec> coords, gmx_enfrotgrp* erg, const matrix box, int npbcdim)
{
const auto& localRotationGroupIndex = erg->atomSet->localIndex();
for (gmx::index i = 0; i < localRotationGroupIndex.ssize(); i++)
copy_rvec(erg->xr_loc[i], xref);
rvec_inc(xref, erg->xc_ref_center);
- copy_correct_pbc_image(x[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
+ copy_correct_pbc_image(coords[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
}
}
-void do_rotation(const t_commrec* cr, gmx_enfrot* er, const matrix box, rvec x[], real t, int64_t step, gmx_bool bNS)
+void do_rotation(const t_commrec* cr,
+ gmx_enfrot* er,
+ const matrix box,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ real t,
+ int64_t step,
+ gmx_bool bNS)
{
gmx_bool outstep_slab, outstep_rot;
gmx_bool bColl;
erg->xc_shifts,
erg->xc_eshifts,
bNS,
- x,
+ as_rvec_array(coords.data()),
rotg->nat,
erg->atomSet->numAtomsLocal(),
erg->atomSet->localIndex().data(),
/* Choose the nearest PBC images of the group atoms with respect
* to the rotated reference positions */
- choose_pbc_image(x, erg, box, 3);
+ choose_pbc_image(coords, erg, box, 3);
/* Get the center of the rotation group */
if ((rotg->eType == EnforcedRotationGroupType::Isopf)
do_radial_motion(erg, outstep_rot, outstep_slab);
break;
case EnforcedRotationGroupType::Rmpf:
- do_radial_motion_pf(erg, x, box, outstep_rot, outstep_slab);
+ do_radial_motion_pf(erg, coords, box, outstep_rot, outstep_slab);
break;
case EnforcedRotationGroupType::Rm2:
case EnforcedRotationGroupType::Rm2pf:
- do_radial_motion2(erg, x, box, outstep_rot, outstep_slab);
+ do_radial_motion2(erg, coords, box, outstep_rot, outstep_slab);
break;
case EnforcedRotationGroupType::Flext:
case EnforcedRotationGroupType::Flex2t:
get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
svmul(-1.0, erg->xc_center, transvec);
translate_x(erg->xc, rotg->nat, transvec);
- do_flexible(MASTER(cr), er, erg, x, box, t, outstep_rot, outstep_slab);
+ do_flexible(MASTER(cr), er, erg, coords, box, t, outstep_rot, outstep_slab);
break;
case EnforcedRotationGroupType::Flex:
case EnforcedRotationGroupType::Flex2:
/* Do NOT subtract the center of mass in the low level routines! */
clear_rvec(erg->xc_center);
- do_flexible(MASTER(cr), er, erg, x, box, t, outstep_rot, outstep_slab);
+ do_flexible(MASTER(cr), er, erg, coords, box, t, outstep_rot, outstep_slab);
break;
default: gmx_fatal(FARGS, "No such rotation potential.");
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff