diff --git a/doc/src/Developer_updating.rst b/doc/src/Developer_updating.rst index 21980be3d8..ff914b2777 100644 --- a/doc/src/Developer_updating.rst +++ b/doc/src/Developer_updating.rst @@ -29,6 +29,7 @@ Available topics in mostly chronological order are: - `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_ - `Use Output::get_dump_by_id() instead of Output::find_dump()`_ - `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_ +- `FLERR as first argument to minimum image functions in Domain class`_ ---- @@ -610,3 +611,47 @@ KSpace solvers which use distributed FFT grids: - ``src/KSPACE/pppm.cpp`` This change is **required** or else the code will not compile. + +FLERR as first argument to minimum image functions in Domain class +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: TBD + +The ``Domain::minimum_image()`` and ``Domain::minimum_image_big()`` +functions were changed to take the ``FLERR`` macros as first argument. +This way the error message indicates *where* the function was called +instead of pointing to the implementation of the function. Example: + +Old: + +.. code-block:: c++ + + double delx1 = x[i1][0] - x[i2][0]; + double dely1 = x[i1][1] - x[i2][1]; + double delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1, dely1, delz1); + double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); + + double delx2 = x[i3][0] - x[i2][0]; + double dely2 = x[i3][1] - x[i2][1]; + double delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image_big(delx2, dely2, delz2); + double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); + +New: + +.. code-block:: c++ + + double delx1 = x[i1][0] - x[i2][0]; + double dely1 = x[i1][1] - x[i2][1]; + double delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(FLERR, delx1, dely1, delz1); + double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); + + double delx2 = x[i3][0] - x[i2][0]; + double dely2 = x[i3][1] - x[i2][1]; + double delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image_big(FLERR, delx2, dely2, delz2); + double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); + +This change is **required** or else the code will not compile. diff --git a/lib/atc/LammpsInterface.cpp b/lib/atc/LammpsInterface.cpp index 07b3ca6426..3912961b9d 100644 --- a/lib/atc/LammpsInterface.cpp +++ b/lib/atc/LammpsInterface.cpp @@ -561,7 +561,7 @@ bool LammpsInterface::region_bounds(const char * regionName, } void LammpsInterface::minimum_image(double & dx, double & dy, double & dz) const { - lammps_->domain->minimum_image(dx,dy,dz); + lammps_->domain->minimum_image(FLERR,dx,dy,dz); } void LammpsInterface::closest_image(const double * const xi, const double * const xj, double * const xjImage) const { diff --git a/src/AMOEBA/angle_amoeba.cpp b/src/AMOEBA/angle_amoeba.cpp index e2d26dd047..bf3bc179bc 100644 --- a/src/AMOEBA/angle_amoeba.cpp +++ b/src/AMOEBA/angle_amoeba.cpp @@ -834,13 +834,13 @@ double AngleAmoeba::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp index 284626464e..c47614afff 100644 --- a/src/BPM/bond_bpm.cpp +++ b/src/BPM/bond_bpm.cpp @@ -352,7 +352,7 @@ double BondBPM::equilibrium_distance(int /*i*/) delx = x[i][0] - x[j][0]; dely = x[i][1] - x[j][1]; delz = x[i][2] - x[j][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); r = sqrt(delx * delx + dely * dely + delz * delz); if (r > r0_max_estimate) r0_max_estimate = r; diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp index b1e6163d97..0e8f822a6d 100644 --- a/src/BPM/bond_bpm_rotational.cpp +++ b/src/BPM/bond_bpm_rotational.cpp @@ -177,7 +177,7 @@ void BondBPMRotational::store_data() } // Get closest image in case bonded with ghost - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); r = sqrt(delx * delx + dely * dely + delz * delz); rinv = 1.0 / r; diff --git a/src/BPM/bond_bpm_spring.cpp b/src/BPM/bond_bpm_spring.cpp index a5c31ea1b2..f5094ffbcb 100644 --- a/src/BPM/bond_bpm_spring.cpp +++ b/src/BPM/bond_bpm_spring.cpp @@ -140,7 +140,7 @@ void BondBPMSpring::store_data() delz = x[i][2] - x[j][2]; // Get closest image in case bonded with ghost - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); r = sqrt(delx * delx + dely * dely + delz * delz); fix_bond_history->update_atom_value(i, m, 0, r); diff --git a/src/BPM/bond_bpm_spring_plastic.cpp b/src/BPM/bond_bpm_spring_plastic.cpp index 21ef0f12fb..8ef8ef63c7 100644 --- a/src/BPM/bond_bpm_spring_plastic.cpp +++ b/src/BPM/bond_bpm_spring_plastic.cpp @@ -148,7 +148,7 @@ void BondBPMSpringPlastic::store_data() delz = x[i][2] - x[j][2]; // Get closest image in case bonded with ghost - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); r = sqrt(delx * delx + dely * dely + delz * delz); fix_bond_history->update_atom_value(i, m, 0, r); diff --git a/src/CG-SPICA/angle_spica.cpp b/src/CG-SPICA/angle_spica.cpp index 08e4217483..5f198f6d76 100644 --- a/src/CG-SPICA/angle_spica.cpp +++ b/src/CG-SPICA/angle_spica.cpp @@ -458,13 +458,13 @@ double AngleSPICA::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; @@ -479,7 +479,7 @@ double AngleSPICA::single(int type, int i1, int i2, int i3) double delx3 = x[i1][0] - x[i3][0]; double dely3 = x[i1][1] - x[i3][1]; double delz3 = x[i1][2] - x[i3][2]; - domain->minimum_image(delx3,dely3,delz3); + domain->minimum_image(FLERR, delx3,dely3,delz3); const int type1 = atom->type[i1]; const int type3 = atom->type[i3]; diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 04b7a9238c..7d345dac85 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -436,13 +436,13 @@ double AngleClass2::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/COLVARS/colvarproxy_lammps.cpp b/src/COLVARS/colvarproxy_lammps.cpp index c92d835cf6..29b9cbfcd0 100644 --- a/src/COLVARS/colvarproxy_lammps.cpp +++ b/src/COLVARS/colvarproxy_lammps.cpp @@ -188,7 +188,7 @@ cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1, double xtmp = pos2.x - pos1.x; double ytmp = pos2.y - pos1.y; double ztmp = pos2.z - pos1.z; - _lmp->domain->minimum_image_big(xtmp,ytmp,ztmp); + _lmp->domain->minimum_image_big(FLERR, xtmp,ytmp,ztmp); return {xtmp, ytmp, ztmp}; } diff --git a/src/DIELECTRIC/fix_polarize_functional.cpp b/src/DIELECTRIC/fix_polarize_functional.cpp index dd0c0eb648..2d2b1cb35e 100644 --- a/src/DIELECTRIC/fix_polarize_functional.cpp +++ b/src/DIELECTRIC/fix_polarize_functional.cpp @@ -652,7 +652,7 @@ void FixPolarizeFunctional::calculate_Rww_cutoff() double delx = xtmp - x[k][0]; double dely = ytmp - x[k][1]; double delz = ztmp - x[k][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); int mk = tag2mat[tag[k]]; // G1ww[mi][mk] = calculate_greens_ewald(delx, dely, delz); @@ -861,7 +861,7 @@ void FixPolarizeFunctional::calculate_qiRqw_cutoff() delx = xtmp - x[k][0]; dely = ytmp - x[k][1]; delz = ztmp - x[k][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); r = sqrt(delx * delx + dely * dely + delz * delz); int mk = tag2mat[tag[k]]; @@ -902,7 +902,7 @@ void FixPolarizeFunctional::calculate_qiRqw_cutoff() delx = x[i][0] - xtmp; dely = x[i][1] - ytmp; delz = x[i][2] - ztmp; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); int mi = tag2mat_ions[tag[i]]; //ion_idx[i]; diff --git a/src/DIPOLE/angle_dipole.cpp b/src/DIPOLE/angle_dipole.cpp index 530f23f844..00e55bbbcc 100644 --- a/src/DIPOLE/angle_dipole.cpp +++ b/src/DIPOLE/angle_dipole.cpp @@ -251,7 +251,7 @@ double AngleDipole::single(int type, int iRef, int iDip, int /*iDummy*/) double dely = x[iRef][1] - x[iDip][1]; double delz = x[iRef][2] - x[iDip][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); double r = sqrt(delx * delx + dely * dely + delz * delz); if (r < SMALL) return 0.0; diff --git a/src/EXTRA-COMPUTE/compute_born_matrix.cpp b/src/EXTRA-COMPUTE/compute_born_matrix.cpp index 26dcedcf55..c9967f9a46 100644 --- a/src/EXTRA-COMPUTE/compute_born_matrix.cpp +++ b/src/EXTRA-COMPUTE/compute_born_matrix.cpp @@ -764,7 +764,7 @@ void ComputeBornMatrix::compute_bonds() dx = x[atom2][0] - x[atom1][0]; dy = x[atom2][1] - x[atom1][1]; dz = x[atom2][2] - x[atom1][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); rsq = dx * dx + dy * dy + dz * dz; rij[0] = dx; rij[1] = dy; @@ -870,7 +870,7 @@ void ComputeBornMatrix::compute_angles() delx1 = x[atom1][0] - x[atom2][0]; dely1 = x[atom1][1] - x[atom2][1]; delz1 = x[atom1][2] - x[atom2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); del1[0] = delx1; del1[1] = dely1; del1[2] = delz1; @@ -882,7 +882,7 @@ void ComputeBornMatrix::compute_angles() delx2 = x[atom3][0] - x[atom2][0]; dely2 = x[atom3][1] - x[atom2][1]; delz2 = x[atom3][2] - x[atom2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); del2[0] = delx2; del2[1] = dely2; del2[2] = delz2; @@ -1046,7 +1046,7 @@ void ComputeBornMatrix::compute_dihedrals() vb1x = x[atom2][0] - x[atom1][0]; vb1y = x[atom2][1] - x[atom1][1]; vb1z = x[atom2][2] - x[atom1][2]; - domain->minimum_image(vb1x, vb1y, vb1z); + domain->minimum_image(FLERR, vb1x, vb1y, vb1z); b1[0] = vb1x; b1[1] = vb1y; b1[2] = vb1z; @@ -1055,7 +1055,7 @@ void ComputeBornMatrix::compute_dihedrals() vb2x = x[atom3][0] - x[atom2][0]; vb2y = x[atom3][1] - x[atom2][1]; vb2z = x[atom3][2] - x[atom2][2]; - domain->minimum_image(vb2x, vb2y, vb2z); + domain->minimum_image(FLERR, vb2x, vb2y, vb2z); b2[0] = vb2x; b2[1] = vb2y; b2[2] = vb2z; @@ -1064,7 +1064,7 @@ void ComputeBornMatrix::compute_dihedrals() vb3x = x[atom4][0] - x[atom3][0]; vb3y = x[atom4][1] - x[atom3][1]; vb3z = x[atom4][2] - x[atom3][2]; - domain->minimum_image(vb3x, vb3y, vb3z); + domain->minimum_image(FLERR, vb3x, vb3y, vb3z); b3[0] = vb3x; b3[1] = vb3y; b3[2] = vb3z; diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp index 9d3bcb92ca..5a59c7a175 100644 --- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp @@ -480,7 +480,7 @@ void ComputeStressCartesian::compute_pressure(double fpair, double xi, double yi tmp1[dir1] = (bin1 + 1) * bin_width1 - xi; else tmp1[dir1] = bin1 * bin_width1 - xi; - domain->minimum_image(tmp1[0],tmp1[1],tmp1[2]); + domain->minimum_image(FLERR, tmp1[0],tmp1[1],tmp1[2]); l1 = tmp1[dir1] / rij1; double l2; @@ -489,7 +489,7 @@ void ComputeStressCartesian::compute_pressure(double fpair, double xi, double yi tmp2[dir2] = (bin2 + 1) * bin_width2 - yi; else tmp2[dir2] = bin2 * bin_width2 - yi; - domain->minimum_image(tmp2[0],tmp2[1],tmp2[2]); + domain->minimum_image(FLERR, tmp2[0],tmp2[1],tmp2[2]); l2 = tmp2[dir2] / rij2; if ((dims == 1 || l1 < l2 || l2 < lb + SMALL) && l1 <= 1.0 && l1 > lb) { diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp index 6f96debd40..d362fe657d 100644 --- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp @@ -82,7 +82,7 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) : Compute( error->warning(FLERR, "The specified initial plane lies outside of the simulation box"); double dx[3] = {0.0, 0.0, 0.0}; dx[dir] = pos - 0.5 * (domain->boxhi[dir] + domain->boxlo[dir]); - domain->minimum_image(dx[0], dx[1], dx[2]); + domain->minimum_image(FLERR, dx[0], dx[1], dx[2]); pos = 0.5 * (domain->boxhi[dir] + domain->boxlo[dir]) + dx[dir]; if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir])) @@ -478,7 +478,7 @@ void ComputeStressMop::compute_pairs() // minimum image of xi with respect to the plane xi[dir] -= pos; - domain->minimum_image(xi[0], xi[1], xi[2]); + domain->minimum_image(FLERR, xi[0], xi[1], xi[2]); xi[dir] += pos; //velocities at t @@ -601,7 +601,7 @@ void ComputeStressMop::compute_bonds() dx[1] = x[atom1][1]; dx[2] = x[atom1][2]; dx[dir] -= pos; - domain->minimum_image(dx[0], dx[1], dx[2]); + domain->minimum_image(FLERR, dx[0], dx[1], dx[2]); x_bond_1[0] = dx[0]; x_bond_1[1] = dx[1]; x_bond_1[2] = dx[2]; @@ -612,7 +612,7 @@ void ComputeStressMop::compute_bonds() dx[0] = x[atom2][0] - x_bond_1[0]; dx[1] = x[atom2][1] - x_bond_1[1]; dx[2] = x[atom2][2] - x_bond_1[2]; - domain->minimum_image(dx[0], dx[1], dx[2]); + domain->minimum_image(FLERR, dx[0], dx[1], dx[2]); x_bond_2[0] = x_bond_1[0] + dx[0]; x_bond_2[1] = x_bond_1[1] + dx[1]; x_bond_2[2] = x_bond_1[2] + dx[2]; @@ -728,7 +728,7 @@ void ComputeStressMop::compute_angles() dx[1] = x[atom1][1]; dx[2] = x[atom1][2]; dx[dir] -= pos; - domain->minimum_image(dx[0], dx[1], dx[2]); + domain->minimum_image(FLERR, dx[0], dx[1], dx[2]); x_angle_left[0] = dx[0]; x_angle_left[1] = dx[1]; x_angle_left[2] = dx[2]; @@ -739,7 +739,7 @@ void ComputeStressMop::compute_angles() dx_left[0] = x[atom2][0] - x_angle_left[0]; dx_left[1] = x[atom2][1] - x_angle_left[1]; dx_left[2] = x[atom2][2] - x_angle_left[2]; - domain->minimum_image(dx_left[0], dx_left[1], dx_left[2]); + domain->minimum_image(FLERR, dx_left[0], dx_left[1], dx_left[2]); x_angle_middle[0] = x_angle_left[0] + dx_left[0]; x_angle_middle[1] = x_angle_left[1] + dx_left[1]; x_angle_middle[2] = x_angle_left[2] + dx_left[2]; @@ -749,7 +749,7 @@ void ComputeStressMop::compute_angles() dx_right[0] = x[atom3][0] - x_angle_middle[0]; dx_right[1] = x[atom3][1] - x_angle_middle[1]; dx_right[2] = x[atom3][2] - x_angle_middle[2]; - domain->minimum_image(dx_right[0], dx_right[1], dx_right[2]); + domain->minimum_image(FLERR, dx_right[0], dx_right[1], dx_right[2]); x_angle_right[0] = x_angle_middle[0] + dx_right[0]; x_angle_right[1] = x_angle_middle[1] + dx_right[1]; x_angle_right[2] = x_angle_middle[2] + dx_right[2]; @@ -920,14 +920,14 @@ void ComputeStressMop::compute_dihedrals() x_atom_1[1] = x[atom1][1]; x_atom_1[2] = x[atom1][2]; x_atom_1[dir] -= pos; - domain->minimum_image(x_atom_1[0], x_atom_1[1], x_atom_1[2]); + domain->minimum_image(FLERR, x_atom_1[0], x_atom_1[1], x_atom_1[2]); x_atom_1[dir] += pos; // minimum image of atom2 with respect to atom1 diffx[0] = x[atom2][0] - x_atom_1[0]; diffx[1] = x[atom2][1] - x_atom_1[1]; diffx[2] = x[atom2][2] - x_atom_1[2]; - domain->minimum_image(diffx[0], diffx[1], diffx[2]); + domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]); x_atom_2[0] = x_atom_1[0] + diffx[0]; x_atom_2[1] = x_atom_1[1] + diffx[1]; x_atom_2[2] = x_atom_1[2] + diffx[2]; @@ -936,7 +936,7 @@ void ComputeStressMop::compute_dihedrals() diffx[0] = x[atom3][0] - x_atom_2[0]; diffx[1] = x[atom3][1] - x_atom_2[1]; diffx[2] = x[atom3][2] - x_atom_2[2]; - domain->minimum_image(diffx[0], diffx[1], diffx[2]); + domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]); x_atom_3[0] = x_atom_2[0] + diffx[0]; x_atom_3[1] = x_atom_2[1] + diffx[1]; x_atom_3[2] = x_atom_2[2] + diffx[2]; @@ -945,7 +945,7 @@ void ComputeStressMop::compute_dihedrals() diffx[0] = x[atom4][0] - x_atom_3[0]; diffx[1] = x[atom4][1] - x_atom_3[1]; diffx[2] = x[atom4][2] - x_atom_3[2]; - domain->minimum_image(diffx[0], diffx[1], diffx[2]); + domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]); x_atom_4[0] = x_atom_3[0] + diffx[0]; x_atom_4[1] = x_atom_3[1] + diffx[1]; x_atom_4[2] = x_atom_3[2] + diffx[2]; diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp index c8087b60a9..a6bf661a9e 100644 --- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp +++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp @@ -537,14 +537,14 @@ void ComputeStressMopProfile::compute_pairs() // minimum image of xi with respect to the plane xi[dir] -= pos; - domain->minimum_image(xi[0], xi[1], xi[2]); + domain->minimum_image(FLERR, xi[0], xi[1], xi[2]); xi[dir] += pos; // minimum image of xj with respect to xi xj[0] -= xi[0]; xj[1] -= xi[1]; xj[2] -= xi[2]; - domain->minimum_image(xi[0], xi[1], xi[2]); + domain->minimum_image(FLERR, xj[0], xj[1], xj[2]); xj[0] += xi[0]; xj[1] += xi[1]; xj[2] += xi[2]; @@ -649,7 +649,7 @@ void ComputeStressMopProfile::compute_bonds() dx[1] = x[atom1][1]; dx[2] = x[atom1][2]; dx[dir] -= pos; - domain->minimum_image(dx[0], dx[1], dx[2]); + domain->minimum_image(FLERR, dx[0], dx[1], dx[2]); x_bond_1[0] = dx[0]; x_bond_1[1] = dx[1]; x_bond_1[2] = dx[2]; @@ -660,7 +660,7 @@ void ComputeStressMopProfile::compute_bonds() dx[0] = x[atom2][0] - x_bond_1[0]; dx[1] = x[atom2][1] - x_bond_1[1]; dx[2] = x[atom2][2] - x_bond_1[2]; - domain->minimum_image(dx[0], dx[1], dx[2]); + domain->minimum_image(FLERR, dx[0], dx[1], dx[2]); x_bond_2[0] = x_bond_1[0] + dx[0]; x_bond_2[1] = x_bond_1[1] + dx[1]; x_bond_2[2] = x_bond_1[2] + dx[2]; @@ -783,7 +783,7 @@ void ComputeStressMopProfile::compute_angles() dx[1] = x[atom1][1]; dx[2] = x[atom1][2]; dx[dir] -= pos; - domain->minimum_image(dx[0], dx[1], dx[2]); + domain->minimum_image(FLERR, dx[0], dx[1], dx[2]); x_angle_left[0] = dx[0]; x_angle_left[1] = dx[1]; x_angle_left[2] = dx[2]; @@ -793,7 +793,7 @@ void ComputeStressMopProfile::compute_angles() dx_left[0] = x[atom2][0] - x_angle_left[0]; dx_left[1] = x[atom2][1] - x_angle_left[1]; dx_left[2] = x[atom2][2] - x_angle_left[2]; - domain->minimum_image(dx_left[0], dx_left[1], dx_left[2]); + domain->minimum_image(FLERR, dx_left[0], dx_left[1], dx_left[2]); x_angle_middle[0] = x_angle_left[0] + dx_left[0]; x_angle_middle[1] = x_angle_left[1] + dx_left[1]; x_angle_middle[2] = x_angle_left[2] + dx_left[2]; @@ -802,7 +802,7 @@ void ComputeStressMopProfile::compute_angles() dx_right[0] = x[atom3][0] - x_angle_middle[0]; dx_right[1] = x[atom3][1] - x_angle_middle[1]; dx_right[2] = x[atom3][2] - x_angle_middle[2]; - domain->minimum_image(dx_right[0], dx_right[1], dx_right[2]); + domain->minimum_image(FLERR, dx_right[0], dx_right[1], dx_right[2]); x_angle_right[0] = x_angle_middle[0] + dx_right[0]; x_angle_right[1] = x_angle_middle[1] + dx_right[1]; x_angle_right[2] = x_angle_middle[2] + dx_right[2]; @@ -971,14 +971,14 @@ void ComputeStressMopProfile::compute_dihedrals() x_atom_1[1] = x[atom1][1]; x_atom_1[2] = x[atom1][2]; x_atom_1[dir] -= pos; - domain->minimum_image(x_atom_1[0], x_atom_1[1], x_atom_1[2]); + domain->minimum_image(FLERR, x_atom_1[0], x_atom_1[1], x_atom_1[2]); x_atom_1[dir] += pos; // minimum image of atom2 with respect to atom1 diffx[0] = x[atom2][0] - x_atom_1[0]; diffx[1] = x[atom2][1] - x_atom_1[1]; diffx[2] = x[atom2][2] - x_atom_1[2]; - domain->minimum_image(diffx[0], diffx[1], diffx[2]); + domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]); x_atom_2[0] = x_atom_1[0] + diffx[0]; x_atom_2[1] = x_atom_1[1] + diffx[1]; x_atom_2[2] = x_atom_1[2] + diffx[2]; @@ -987,7 +987,7 @@ void ComputeStressMopProfile::compute_dihedrals() diffx[0] = x[atom3][0] - x_atom_2[0]; diffx[1] = x[atom3][1] - x_atom_2[1]; diffx[2] = x[atom3][2] - x_atom_2[2]; - domain->minimum_image(diffx[0], diffx[1], diffx[2]); + domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]); x_atom_3[0] = x_atom_2[0] + diffx[0]; x_atom_3[1] = x_atom_2[1] + diffx[1]; x_atom_3[2] = x_atom_2[2] + diffx[2]; @@ -996,7 +996,7 @@ void ComputeStressMopProfile::compute_dihedrals() diffx[0] = x[atom4][0] - x_atom_3[0]; diffx[1] = x[atom4][1] - x_atom_3[1]; diffx[2] = x[atom4][2] - x_atom_3[2]; - domain->minimum_image(diffx[0], diffx[1], diffx[2]); + domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]); x_atom_4[0] = x_atom_3[0] + diffx[0]; x_atom_4[1] = x_atom_3[1] + diffx[1]; x_atom_4[2] = x_atom_3[2] + diffx[2]; diff --git a/src/EXTRA-FIX/fix_drag.cpp b/src/EXTRA-FIX/fix_drag.cpp index 45143fb665..d45342e07b 100644 --- a/src/EXTRA-FIX/fix_drag.cpp +++ b/src/EXTRA-FIX/fix_drag.cpp @@ -114,7 +114,7 @@ void FixDrag::post_force(int /*vflag*/) if (!xflag) dx = 0.0; if (!yflag) dy = 0.0; if (!zflag) dz = 0.0; - domain->minimum_image(dx,dy,dz); + domain->minimum_image(FLERR, dx,dy,dz); r = sqrt(dx*dx + dy*dy + dz*dz); if (r > delta) { prefactor = f_mag/r; diff --git a/src/EXTRA-FIX/fix_filter_corotate.cpp b/src/EXTRA-FIX/fix_filter_corotate.cpp index 872ebd1772..24376448a3 100644 --- a/src/EXTRA-FIX/fix_filter_corotate.cpp +++ b/src/EXTRA-FIX/fix_filter_corotate.cpp @@ -547,17 +547,17 @@ void FixFilterCorotate::pre_neighbor() del1[0] = x[atom1][0]-x[oxy][0]; del1[1] = x[atom1][1]-x[oxy][1]; del1[2] = x[atom1][2]-x[oxy][2]; - domain->minimum_image(del1); + domain->minimum_image(FLERR, del1); del2[0] = x[atom2][0]-x[atom1][0]; del2[1] = x[atom2][1]-x[atom1][1]; del2[2] = x[atom2][2]-x[atom1][2]; - domain->minimum_image(del2); + domain->minimum_image(FLERR, del2); del3[0] = x[atom3][0]-x[atom1][0]; del3[1] = x[atom3][1]-x[atom1][1]; del3[2] = x[atom3][2]-x[atom1][2]; - domain->minimum_image(del3); + domain->minimum_image(FLERR, del3); double a = (del2[1])*(del3[2]) - (del2[2])*(del3[1]); double b = (del2[2])*(del3[0]) - (del2[0])*(del3[2]); @@ -620,17 +620,17 @@ void FixFilterCorotate::pre_neighbor() del1[0] = x[atom1][0]-x[oxy][0]; del1[1] = x[atom1][1]-x[oxy][1]; del1[2] = x[atom1][2]-x[oxy][2]; - domain->minimum_image(del1); + domain->minimum_image(FLERR, del1); del2[0] = x[atom2][0]-x[atom1][0]; del2[1] = x[atom2][1]-x[atom1][1]; del2[2] = x[atom2][2]-x[atom1][2]; - domain->minimum_image(del2); + domain->minimum_image(FLERR, del2); del3[0] = x[atom3][0]-x[atom1][0]; del3[1] = x[atom3][1]-x[atom1][1]; del3[2] = x[atom3][2]-x[atom1][2]; - domain->minimum_image(del3); + domain->minimum_image(FLERR, del3); double a = (del2[1])*(del3[2]) - (del2[2])*(del3[1]); double b = (del2[2])*(del3[0]) - (del2[0])*(del3[2]); @@ -1414,7 +1414,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) del[i][0] = x[list_cluster[i]][0] - x[list_cluster[0]][0]; del[i][1] = x[list_cluster[i]][1] - x[list_cluster[0]][1]; del[i][2] = x[list_cluster[i]][2] - x[list_cluster[0]][2]; - domain->minimum_image(del[i]); + domain->minimum_image(FLERR, del[i]); r[i] = 1.0/sqrt(del[i][0]*del[i][0]+del[i][1]*del[i][1]+ del[i][2]*del[i][2]); } diff --git a/src/EXTRA-FIX/fix_pafi.cpp b/src/EXTRA-FIX/fix_pafi.cpp index 05ee6b90da..fb39e2e48d 100644 --- a/src/EXTRA-FIX/fix_pafi.cpp +++ b/src/EXTRA-FIX/fix_pafi.cpp @@ -261,7 +261,7 @@ void FixPAFI::post_force(int /*vflag*/) deviation[0] = x[i][0]-path[i][0]; // x-path deviation[1] = x[i][1]-path[i][1]; // x-path deviation[2] = x[i][2]-path[i][2]; // x-path - domain->minimum_image(deviation); + domain->minimum_image(FLERR, deviation); proj[3] += path[i][6]*deviation[0]; // (x-path).dn/nn = psi proj[3] += path[i][7]*deviation[1]; // (x-path).dn/nn = psi @@ -424,7 +424,7 @@ void FixPAFI::min_post_force(int /*vflag*/) deviation[0] = x[i][0]-path[i][0]; // x-path deviation[1] = x[i][1]-path[i][1]; // x-path deviation[2] = x[i][2]-path[i][2]; // x-path - domain->minimum_image(deviation); + domain->minimum_image(FLERR, deviation); proj[3] += path[i][6]*deviation[0]; // (x-path).dn/nn = psi proj[3] += path[i][7]*deviation[1]; // (x-path).dn/nn = psi diff --git a/src/EXTRA-MOLECULE/angle_cosine_delta.cpp b/src/EXTRA-MOLECULE/angle_cosine_delta.cpp index 56dd6da88d..43092876dc 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_delta.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_delta.cpp @@ -155,13 +155,13 @@ double AngleCosineDelta::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; @@ -185,13 +185,13 @@ void AngleCosineDelta::born_matrix(int type, int i1, int i2, int i3, double &du, double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp b/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp index e0e7f31f39..c0ae868576 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp @@ -284,13 +284,13 @@ double AngleCosinePeriodic::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; @@ -311,13 +311,13 @@ void AngleCosinePeriodic::born_matrix(int type, int i1, int i2, int i3, double & double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/EXTRA-MOLECULE/angle_cosine_shift.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift.cpp index 14640a5e12..9ac6fb9ba3 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_shift.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_shift.cpp @@ -258,13 +258,13 @@ double AngleCosineShift::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp index 185adea37d..34768652d9 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp @@ -297,13 +297,13 @@ double AngleCosineShiftExp::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp b/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp index 37003b5b05..6c8a27d13d 100644 --- a/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp +++ b/src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp @@ -242,13 +242,13 @@ double AngleCosineSquaredRestricted::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; @@ -272,13 +272,13 @@ void AngleCosineSquaredRestricted::born_matrix(int type, int i1, int i2, int i3, double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; diff --git a/src/EXTRA-MOLECULE/angle_fourier.cpp b/src/EXTRA-MOLECULE/angle_fourier.cpp index f6cd9f4c80..ca643bd57b 100644 --- a/src/EXTRA-MOLECULE/angle_fourier.cpp +++ b/src/EXTRA-MOLECULE/angle_fourier.cpp @@ -263,13 +263,13 @@ double AngleFourier::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; @@ -291,13 +291,13 @@ void AngleFourier::born_matrix(int type, int i1, int i2, int i3, double &du, dou double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/EXTRA-MOLECULE/angle_fourier_simple.cpp b/src/EXTRA-MOLECULE/angle_fourier_simple.cpp index e3497b5e81..0dc6cbad04 100644 --- a/src/EXTRA-MOLECULE/angle_fourier_simple.cpp +++ b/src/EXTRA-MOLECULE/angle_fourier_simple.cpp @@ -269,13 +269,13 @@ double AngleFourierSimple::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; @@ -297,13 +297,13 @@ void AngleFourierSimple::born_matrix(int type, int i1, int i2, int i3, double &d double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/EXTRA-MOLECULE/angle_gaussian.cpp b/src/EXTRA-MOLECULE/angle_gaussian.cpp index 1272ada0bb..17a3cb3b29 100644 --- a/src/EXTRA-MOLECULE/angle_gaussian.cpp +++ b/src/EXTRA-MOLECULE/angle_gaussian.cpp @@ -325,13 +325,13 @@ double AngleGaussian::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; diff --git a/src/EXTRA-MOLECULE/angle_mwlc.cpp b/src/EXTRA-MOLECULE/angle_mwlc.cpp index 804627cfa3..0853708e24 100644 --- a/src/EXTRA-MOLECULE/angle_mwlc.cpp +++ b/src/EXTRA-MOLECULE/angle_mwlc.cpp @@ -260,13 +260,13 @@ double AngleMWLC::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; @@ -289,12 +289,12 @@ void AngleMWLC::born_matrix(int type, int i1, int i2, int i3, double &du, double double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; c /= sqrt((delx1 * delx1 + dely1 * dely1 + delz1 * delz1) * diff --git a/src/EXTRA-MOLECULE/angle_quartic.cpp b/src/EXTRA-MOLECULE/angle_quartic.cpp index 92e84e79a5..87e3d6a662 100644 --- a/src/EXTRA-MOLECULE/angle_quartic.cpp +++ b/src/EXTRA-MOLECULE/angle_quartic.cpp @@ -269,13 +269,13 @@ double AngleQuartic::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; @@ -299,13 +299,13 @@ void AngleQuartic::born_matrix(int type, int i1, int i2, int i3, double &du, dou double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp b/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp index 2a9a1e4e7f..0fc9f5d981 100644 --- a/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp +++ b/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp @@ -74,7 +74,7 @@ void BondHarmonicRestrain::compute(int eflag, int vflag) delx = x0[i1][0] - x0[i2][0]; dely = x0[i1][1] - x0[i2][1]; delz = x0[i1][2] - x0[i2][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); rsq = delx * delx + dely * dely + delz * delz; r0 = sqrt(rsq); @@ -235,7 +235,7 @@ double BondHarmonicRestrain::single(int type, double rsq, int i, int j, double & double delx = x0[i][0] - x0[j][0]; double dely = x0[i][1] - x0[j][1]; double delz = x0[i][2] - x0[j][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); double r0 = sqrt(delx * delx + dely * dely + delz * delz); double r = sqrt(rsq); diff --git a/src/EXTRA-MOLECULE/dihedral_spherical.cpp b/src/EXTRA-MOLECULE/dihedral_spherical.cpp index 15e403ef03..0d66a6bbf0 100644 --- a/src/EXTRA-MOLECULE/dihedral_spherical.cpp +++ b/src/EXTRA-MOLECULE/dihedral_spherical.cpp @@ -110,9 +110,9 @@ static double Phi(double const *x1, //array holding x,y,z coords atom 1 } //Consider periodic boundary conditions: - domain->minimum_image(vb12[0], vb12[1], vb12[2]); - domain->minimum_image(vb23[0], vb23[1], vb23[2]); - domain->minimum_image(vb34[0], vb34[1], vb34[2]); + domain->minimum_image(FLERR, vb12[0], vb12[1], vb12[2]); + domain->minimum_image(FLERR, vb23[0], vb23[1], vb23[2]); + domain->minimum_image(FLERR, vb34[0], vb34[1], vb34[2]); //--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 --- diff --git a/src/EXTRA-MOLECULE/improper_distance.cpp b/src/EXTRA-MOLECULE/improper_distance.cpp index ec55abaf2b..de9a8f9a7b 100644 --- a/src/EXTRA-MOLECULE/improper_distance.cpp +++ b/src/EXTRA-MOLECULE/improper_distance.cpp @@ -94,31 +94,31 @@ void ImproperDistance::compute(int eflag, int vflag) xab = x[i2][0] - x[i1][0]; yab = x[i2][1] - x[i1][1]; zab = x[i2][2] - x[i1][2]; - domain->minimum_image(xab,yab,zab); + domain->minimum_image(FLERR, xab,yab,zab); // bond 1->3 xac = x[i3][0] - x[i1][0]; yac = x[i3][1] - x[i1][1]; zac = x[i3][2] - x[i1][2]; - domain->minimum_image(xac,yac,zac); + domain->minimum_image(FLERR, xac,yac,zac); // bond 1->4 xad = x[i4][0] - x[i1][0]; yad = x[i4][1] - x[i1][1]; zad = x[i4][2] - x[i1][2]; - domain->minimum_image(xad,yad,zad); + domain->minimum_image(FLERR, xad,yad,zad); // bond 2-3 xbc = x[i3][0] - x[i2][0]; ybc = x[i3][1] - x[i2][1]; zbc = x[i3][2] - x[i2][2]; - domain->minimum_image(xbc,ybc,zbc); + domain->minimum_image(FLERR, xbc,ybc,zbc); // bond 2-4 xbd = x[i4][0] - x[i2][0]; ybd = x[i4][1] - x[i2][1]; zbd = x[i4][2] - x[i2][2]; - domain->minimum_image(xbd,ybd,zbd); + domain->minimum_image(FLERR, xbd,ybd,zbd); xna = ybc*zbd - zbc*ybd; yna = -(xbc*zbd - zbc*xbd); diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 65cc356739..2d4090ea53 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -540,7 +540,7 @@ void FixPour::pre_exchange() delx = coords[m][0] - xnear[i][0]; dely = coords[m][1] - xnear[i][1]; delz = coords[m][2] - xnear[i][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); rsq = delx * delx + dely * dely + delz * delz; radsum = coords[m][3] + xnear[i][3]; if (rsq <= radsum * radsum) break; @@ -781,7 +781,7 @@ int FixPour::overlap(int i) double delx = x[0] - xc; double dely = x[1] - yc; double delz = 0.0; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); double rsq = delx * delx + dely * dely; double r = rc + delta; if (rsq > r * r) return 0; diff --git a/src/KOKKOS/fix_minimize_kokkos.cpp b/src/KOKKOS/fix_minimize_kokkos.cpp index 585c357992..f1bd218bfa 100644 --- a/src/KOKKOS/fix_minimize_kokkos.cpp +++ b/src/KOKKOS/fix_minimize_kokkos.cpp @@ -121,7 +121,7 @@ void FixMinimizeKokkos::reset_coords() double dx = dx0; double dy = dy0; double dz = dz0; - // domain->minimum_image(dx,dy,dz); + // domain->minimum_image(FLERR, dx,dy,dz); { if (triclinic == 0) { if (xperiodic) { @@ -175,7 +175,7 @@ void FixMinimizeKokkos::reset_coords() } } } - } // end domain->minimum_image(dx,dy,dz); + } // end domain->minimum_image(FLERR, dx,dy,dz); if (dx != dx0) l_x0[n] = l_x(i,0) - dx; if (dy != dy0) l_x0[n+1] = l_x(i,1) - dy; if (dz != dz0) l_x0[n+2] = l_x(i,2) - dz; diff --git a/src/LEPTON/angle_lepton.cpp b/src/LEPTON/angle_lepton.cpp index 4907086ab1..08d1ea9a83 100644 --- a/src/LEPTON/angle_lepton.cpp +++ b/src/LEPTON/angle_lepton.cpp @@ -395,13 +395,13 @@ double AngleLepton::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; diff --git a/src/LEPTON/dihedral_lepton.cpp b/src/LEPTON/dihedral_lepton.cpp index 2cee9fba8a..912896254b 100644 --- a/src/LEPTON/dihedral_lepton.cpp +++ b/src/LEPTON/dihedral_lepton.cpp @@ -508,9 +508,9 @@ double DihedralLepton::get_phi(double const *x1, //array holding x,y,z coords } //Consider periodic boundary conditions: - domain->minimum_image(vb12[0], vb12[1], vb12[2]); - domain->minimum_image(vb23[0], vb23[1], vb23[2]); - domain->minimum_image(vb34[0], vb34[1], vb34[2]); + domain->minimum_image(FLERR, vb12[0], vb12[1], vb12[2]); + domain->minimum_image(FLERR, vb23[0], vb23[1], vb23[2]); + domain->minimum_image(FLERR, vb34[0], vb34[1], vb34[2]); //--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 --- diff --git a/src/MACHDYN/pair_smd_hertz.cpp b/src/MACHDYN/pair_smd_hertz.cpp index fcdaae76bd..0c2444618f 100644 --- a/src/MACHDYN/pair_smd_hertz.cpp +++ b/src/MACHDYN/pair_smd_hertz.cpp @@ -145,7 +145,7 @@ void PairHertz::compute(int eflag, int vflag) { dely0 = x0[j][1] - x0[i][1]; delz0 = x0[j][2] - x0[i][2]; if (periodic) { - domain->minimum_image(delx0, dely0, delz0); + domain->minimum_image(FLERR, delx0, dely0, delz0); } rSq0 = delx0 * delx0 + dely0 * dely0 + delz0 * delz0; // initial distance sphCut = sph_radius[i] + sph_radius[j]; diff --git a/src/MACHDYN/pair_smd_tlsph.cpp b/src/MACHDYN/pair_smd_tlsph.cpp index 72ea1b4d5f..4c2f56eb48 100644 --- a/src/MACHDYN/pair_smd_tlsph.cpp +++ b/src/MACHDYN/pair_smd_tlsph.cpp @@ -220,7 +220,7 @@ void PairTlsph::PreCompute() { dx = xj - xi; if (periodic) - domain->minimum_image(dx0(0), dx0(1), dx0(2)); + domain->minimum_image(FLERR, dx0(0), dx0(1), dx0(2)); r0Sq = dx0.squaredNorm(); h = irad + radius[j]; @@ -488,7 +488,7 @@ void PairTlsph::ComputeForces(int eflag, int vflag) { } if (periodic) - domain->minimum_image(dx0(0), dx0(1), dx0(2)); + domain->minimum_image(FLERR, dx0(0), dx0(1), dx0(2)); // check that distance between i and j (in the reference config) is less than cutoff dx0 = x0j - x0i; diff --git a/src/MACHDYN/pair_smd_triangulated_surface.cpp b/src/MACHDYN/pair_smd_triangulated_surface.cpp index c50b7700f6..cded66e644 100644 --- a/src/MACHDYN/pair_smd_triangulated_surface.cpp +++ b/src/MACHDYN/pair_smd_triangulated_surface.cpp @@ -154,7 +154,7 @@ void PairTriSurf::compute(int eflag, int vflag) { x4(2) = x[particle][2]; dx = x_center - x4; // if (periodic) { - domain->minimum_image(dx(0), dx(1), dx(2)); + domain->minimum_image(FLERR, dx(0), dx(1), dx(2)); } rsq = dx.squaredNorm(); diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index ff90b81695..1e0b20a2d7 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -723,7 +723,7 @@ double FixBondSwap::dist_rsq(int i, int j) double delx = x[i][0] - x[j][0]; double dely = x[i][1] - x[j][1]; double delz = x[i][2] - x[j][2]; - domain->minimum_image(delx,dely,delz); + domain->minimum_image(FLERR, delx,dely,delz); return (delx*delx + dely*dely + delz*delz); } diff --git a/src/MDI/fix_mdi_qmmm.cpp b/src/MDI/fix_mdi_qmmm.cpp index dc5653bfce..d14c837cba 100644 --- a/src/MDI/fix_mdi_qmmm.cpp +++ b/src/MDI/fix_mdi_qmmm.cpp @@ -687,7 +687,7 @@ void FixMDIQMMM::pre_force(int vflag) double delx = xqm[i][0] - xqm[j][0]; double dely = xqm[i][1] - xqm[j][1]; double delz = xqm[i][2] - xqm[j][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); rsq = delx * delx + dely * dely + delz * delz; qpotential_mine[i] -= qqrd2e * qqm[j] / sqrt(rsq); } diff --git a/src/MESONT/angle_mesocnt.cpp b/src/MESONT/angle_mesocnt.cpp index 1394edc4c1..0e2ec7aa10 100644 --- a/src/MESONT/angle_mesocnt.cpp +++ b/src/MESONT/angle_mesocnt.cpp @@ -371,13 +371,13 @@ double AngleMesoCNT::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; diff --git a/src/MISC/fix_ipi.cpp b/src/MISC/fix_ipi.cpp index a571066b35..a713b9844b 100644 --- a/src/MISC/fix_ipi.cpp +++ b/src/MISC/fix_ipi.cpp @@ -399,7 +399,7 @@ void FixIPI::initial_integrate(int /*vflag*/) auto dely = x[i][1] - xhold[i][1]; auto delz = x[i][2] - xhold[i][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); x[i][0] = xhold[i][0] + delx; x[i][1] = xhold[i][1] + dely; diff --git a/src/MOFFF/angle_class2_p6.cpp b/src/MOFFF/angle_class2_p6.cpp index d7cedb0bcf..15a10eebcc 100644 --- a/src/MOFFF/angle_class2_p6.cpp +++ b/src/MOFFF/angle_class2_p6.cpp @@ -453,13 +453,13 @@ double AngleClass2P6::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/MOFFF/angle_cosine_buck6d.cpp b/src/MOFFF/angle_cosine_buck6d.cpp index bf7390a6f8..bc6b8eb51a 100644 --- a/src/MOFFF/angle_cosine_buck6d.cpp +++ b/src/MOFFF/angle_cosine_buck6d.cpp @@ -365,13 +365,13 @@ double AngleCosineBuck6d::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index 92f4d65723..78ce011d73 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -282,19 +282,19 @@ double AngleCharmm::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double delxUB = x[i3][0] - x[i1][0]; double delyUB = x[i3][1] - x[i1][1]; double delzUB = x[i3][2] - x[i1][2]; - domain->minimum_image(delxUB, delyUB, delzUB); + domain->minimum_image(FLERR, delxUB, delyUB, delzUB); double rUB = sqrt(delxUB * delxUB + delyUB * delyUB + delzUB * delzUB); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 6a6d838bc0..1faabfa5d7 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -222,13 +222,13 @@ double AngleCosine::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index 2074b822eb..3f48eb712b 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -245,13 +245,13 @@ double AngleCosineSquared::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; @@ -273,13 +273,13 @@ void AngleCosineSquared::born_matrix(int type, int i1, int i2, int i3, double &d double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index e04cecfe0d..db134de357 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -248,13 +248,13 @@ double AngleHarmonic::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; @@ -276,13 +276,13 @@ void AngleHarmonic::born_matrix(int type, int i1, int i2, int i3, double &du, do double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index b1984a6918..3923231690 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -330,13 +330,13 @@ double AngleTable::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; diff --git a/src/MOLECULE/dihedral_table.cpp b/src/MOLECULE/dihedral_table.cpp index a731a03b5e..eae7c36eeb 100644 --- a/src/MOLECULE/dihedral_table.cpp +++ b/src/MOLECULE/dihedral_table.cpp @@ -381,9 +381,9 @@ static double Phi(double const *x1, //array holding x,y,z coords atom 1 } //Consider periodic boundary conditions: - domain->minimum_image(vb12[0],vb12[1],vb12[2]); - domain->minimum_image(vb23[0],vb23[1],vb23[2]); - domain->minimum_image(vb34[0],vb34[1],vb34[2]); + domain->minimum_image(FLERR, vb12[0],vb12[1],vb12[2]); + domain->minimum_image(FLERR, vb23[0],vb23[1],vb23[2]); + domain->minimum_image(FLERR, vb34[0],vb34[1],vb34[2]); //--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 --- diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index 2de43b6215..4ec45b16cb 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -162,14 +162,14 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag) delr1[0] = x[i][0] - x[k][0]; delr1[1] = x[i][1] - x[k][1]; delr1[2] = x[i][2] - x[k][2]; - domain->minimum_image(delr1); + domain->minimum_image(FLERR, delr1); rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; r1 = sqrt(rsq1); delr2[0] = x[j][0] - x[k][0]; delr2[1] = x[j][1] - x[k][1]; delr2[2] = x[j][2] - x[k][2]; - domain->minimum_image(delr2); + domain->minimum_image(FLERR, delr2); rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; r2 = sqrt(rsq2); @@ -540,14 +540,14 @@ double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype, delr1[0] = x[i][0] - x[k][0]; delr1[1] = x[i][1] - x[k][1]; delr1[2] = x[i][2] - x[k][2]; - domain->minimum_image(delr1); + domain->minimum_image(FLERR, delr1); rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; r1 = sqrt(rsq1); delr2[0] = x[j][0] - x[k][0]; delr2[1] = x[j][1] - x[k][1]; delr2[2] = x[j][2] - x[k][2]; - domain->minimum_image(delr2); + domain->minimum_image(FLERR, delr2); rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; r2 = sqrt(rsq2); diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index c5465a076a..f238087f30 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -129,14 +129,14 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag) delr1[0] = x[i][0] - x[k][0]; delr1[1] = x[i][1] - x[k][1]; delr1[2] = x[i][2] - x[k][2]; - domain->minimum_image(delr1); + domain->minimum_image(FLERR, delr1); rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; r1 = sqrt(rsq1); delr2[0] = x[j][0] - x[k][0]; delr2[1] = x[j][1] - x[k][1]; delr2[2] = x[j][2] - x[k][2]; - domain->minimum_image(delr2); + domain->minimum_image(FLERR, delr2); rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; r2 = sqrt(rsq2); @@ -434,14 +434,14 @@ double PairHbondDreidingMorse::single(int i, int j, int itype, int jtype, delr1[0] = x[i][0] - x[k][0]; delr1[1] = x[i][1] - x[k][1]; delr1[2] = x[i][2] - x[k][2]; - domain->minimum_image(delr1); + domain->minimum_image(FLERR, delr1); rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; r1 = sqrt(rsq1); delr2[0] = x[j][0] - x[k][0]; delr2[1] = x[j][1] - x[k][1]; delr2[2] = x[j][2] - x[k][2]; - domain->minimum_image(delr2); + domain->minimum_image(FLERR, delr2); rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; r2 = sqrt(rsq2); diff --git a/src/OPENMP/dihedral_table_omp.cpp b/src/OPENMP/dihedral_table_omp.cpp index df1ca292c9..5a815a4cc6 100644 --- a/src/OPENMP/dihedral_table_omp.cpp +++ b/src/OPENMP/dihedral_table_omp.cpp @@ -64,9 +64,9 @@ static double Phi(double const *x1, //array holding x,y,z coords atom 1 } //Consider periodic boundary conditions: - domain->minimum_image(vb12[0],vb12[1],vb12[2]); - domain->minimum_image(vb23[0],vb23[1],vb23[2]); - domain->minimum_image(vb34[0],vb34[1],vb34[2]); + domain->minimum_image(FLERR, vb12[0],vb12[1],vb12[2]); + domain->minimum_image(FLERR, vb23[0],vb23[1],vb23[2]); + domain->minimum_image(FLERR, vb34[0],vb34[1],vb34[2]); //--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 --- diff --git a/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp b/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp index 60ec8938fe..933b18a732 100644 --- a/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp +++ b/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp @@ -201,14 +201,14 @@ void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr) delr1[0] = xtmp - x[k].x; delr1[1] = ytmp - x[k].y; delr1[2] = ztmp - x[k].z; - domain->minimum_image(delr1); + domain->minimum_image(FLERR, delr1); rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; r1 = sqrt(rsq1); delr2[0] = x[j].x - x[k].x; delr2[1] = x[j].y - x[k].y; delr2[2] = x[j].z - x[k].z; - domain->minimum_image(delr2); + domain->minimum_image(FLERR, delr2); rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; r2 = sqrt(rsq2); diff --git a/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp b/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp index 7772ea69fa..1626988f75 100644 --- a/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp +++ b/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp @@ -202,14 +202,14 @@ void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr) delr1[0] = xtmp - x[k].x; delr1[1] = ytmp - x[k].y; delr1[2] = ztmp - x[k].z; - domain->minimum_image(delr1); + domain->minimum_image(FLERR, delr1); rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; r1 = sqrt(rsq1); delr2[0] = x[j].x - x[k].x; delr2[1] = x[j].y - x[k].y; delr2[2] = x[j].z - x[k].z; - domain->minimum_image(delr2); + domain->minimum_image(FLERR, delr2); rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; r2 = sqrt(rsq2); diff --git a/src/OPENMP/pair_peri_lps_omp.cpp b/src/OPENMP/pair_peri_lps_omp.cpp index c34f3ac236..2a4289fdf2 100644 --- a/src/OPENMP/pair_peri_lps_omp.cpp +++ b/src/OPENMP/pair_peri_lps_omp.cpp @@ -161,7 +161,7 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr) delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0; jtype = type[j]; @@ -285,12 +285,12 @@ void PairPeriLPSOMP::eval(int iifrom, int iito, ThrData * const thr) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - if (periodic) domain->minimum_image(delx,dely,delz); + if (periodic) domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); jtype = type[j]; delta = cut[itype][jtype]; r = sqrt(rsq); diff --git a/src/OPENMP/pair_peri_pmb_omp.cpp b/src/OPENMP/pair_peri_pmb_omp.cpp index 0b903272fa..eb5911b294 100644 --- a/src/OPENMP/pair_peri_pmb_omp.cpp +++ b/src/OPENMP/pair_peri_pmb_omp.cpp @@ -156,7 +156,7 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr) delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0; jtype = type[j]; @@ -244,7 +244,7 @@ void PairPeriPMBOMP::eval(int iifrom, int iito, ThrData * const thr) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - if (periodic) domain->minimum_image(delx,dely,delz); + if (periodic) domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; jtype = type[j]; delta = cut[itype][jtype]; diff --git a/src/PERI/pair_peri.cpp b/src/PERI/pair_peri.cpp index 6606f36c6f..da761952fe 100644 --- a/src/PERI/pair_peri.cpp +++ b/src/PERI/pair_peri.cpp @@ -189,12 +189,12 @@ void PairPeri::compute_dilatation(int ifrom, int ito) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - if (periodic) domain->minimum_image(delx, dely, delz); + if (periodic) domain->minimum_image(FLERR, delx, dely, delz); rsq = delx * delx + dely * dely + delz * delz; delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0, dely0, delz0); + if (periodic) domain->minimum_image(FLERR, delx0, dely0, delz0); r = sqrt(rsq); dr = r - r0[i][jj]; diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index c0732d48e4..11d9ee646b 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -124,7 +124,7 @@ void PairPeriEPS::compute(int eflag, int vflag) delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0; jtype = type[j]; @@ -262,12 +262,12 @@ void PairPeriEPS::compute(int eflag, int vflag) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - if (periodic) domain->minimum_image(delx,dely,delz); + if (periodic) domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); jtype = type[j]; delta = cut[itype][jtype]; r = sqrt(rsq); @@ -514,12 +514,12 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - if (periodic) domain->minimum_image(delx,dely,delz); + if (periodic) domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); r = sqrt(rsq); dr = r - r0[i][jj]; if (fabs(dr) < NEAR_ZERO) dr = 0.0; diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index b7b7e6577a..bd0eb9651f 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -116,7 +116,7 @@ void PairPeriLPS::compute(int eflag, int vflag) delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0; jtype = type[j]; @@ -225,12 +225,12 @@ void PairPeriLPS::compute(int eflag, int vflag) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - if (periodic) domain->minimum_image(delx,dely,delz); + if (periodic) domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); jtype = type[j]; delta = cut[itype][jtype]; r = sqrt(rsq); diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index 0bacb3a2f0..c17336b8cf 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -110,7 +110,7 @@ void PairPeriPMB::compute(int eflag, int vflag) delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0; jtype = type[j]; @@ -189,7 +189,7 @@ void PairPeriPMB::compute(int eflag, int vflag) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - if (periodic) domain->minimum_image(delx,dely,delz); + if (periodic) domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; jtype = type[j]; delta = cut[itype][jtype]; @@ -361,7 +361,7 @@ double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq, dely0 = x0[i][1] - x0[j][1]; delz0 = x0[i][2] - x0[j][2]; int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0; d_ij = MIN(0.9*sqrt(rsq0),1.35*lc); diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index d814ce6f05..be9967436e 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -121,7 +121,7 @@ void PairPeriVES::compute(int eflag, int vflag) delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0; jtype = type[j]; @@ -233,12 +233,12 @@ void PairPeriVES::compute(int eflag, int vflag) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - if (periodic) domain->minimum_image(delx,dely,delz); + if (periodic) domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; delx0 = xtmp0 - x0[j][0]; dely0 = ytmp0 - x0[j][1]; delz0 = ztmp0 - x0[j][2]; - if (periodic) domain->minimum_image(delx0,dely0,delz0); + if (periodic) domain->minimum_image(FLERR, delx0,dely0,delz0); jtype = type[j]; delta = cut[itype][jtype]; r = sqrt(rsq); diff --git a/src/PHONON/fix_phonon.cpp b/src/PHONON/fix_phonon.cpp index 37f84b6f12..4669253401 100644 --- a/src/PHONON/fix_phonon.cpp +++ b/src/PHONON/fix_phonon.cpp @@ -400,7 +400,7 @@ void FixPhonon::end_of_step() ndim = sysdim; for (i = 1; i < nucell; ++i) { for (idim = 0; idim < sysdim; ++idim) dist2orig[idim] = Rnow[idx][ndim++] - Rnow[idx][idim]; - domain->minimum_image_big(dist2orig); + domain->minimum_image_big(FLERR, dist2orig); for (idim = 0; idim < sysdim; ++idim) basis[i][idim] += dist2orig[idim]; } } diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index b70092296f..6ba6954541 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -1190,7 +1190,7 @@ void FixBondReact::far_partner() delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - domain->minimum_image(delx,dely,delz); // ghost location fix + domain->minimum_image(FLERR, delx,dely,delz); // ghost location fix rsq = delx*delx + dely*dely + delz*delz; if (var_flag[RMIN][rxnID]) { @@ -1260,7 +1260,7 @@ void FixBondReact::close_partner() delx = x[i1][0] - x[i2][0]; dely = x[i1][1] - x[i2][1]; delz = x[i1][2] - x[i2][2]; - domain->minimum_image(delx,dely,delz); // ghost location fix + domain->minimum_image(FLERR, delx,dely,delz); // ghost location fix rsq = delx*delx + dely*dely + delz*delz; if (var_flag[RMIN][rxnID]) { @@ -1972,7 +1972,7 @@ int FixBondReact::check_constraints() delx = x1[0] - x2[0]; dely = x1[1] - x2[1]; delz = x1[2] - x2[2]; - domain->minimum_image(delx,dely,delz); // ghost location fix + domain->minimum_image(FLERR, delx,dely,delz); // ghost location fix rsq = delx*delx + dely*dely + delz*delz; if (rsq < constraints[i][rxnID].par[0] || rsq > constraints[i][rxnID].par[1]) satisfied[i] = 0; } else if (constraints[i][rxnID].type == ANGLE) { @@ -1984,7 +1984,7 @@ int FixBondReact::check_constraints() delx1 = x1[0] - x2[0]; dely1 = x1[1] - x2[1]; delz1 = x1[2] - x2[2]; - domain->minimum_image(delx1,dely1,delz1); // ghost location fix + domain->minimum_image(FLERR, delx1,dely1,delz1); // ghost location fix rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; r1 = sqrt(rsq1); @@ -1992,7 +1992,7 @@ int FixBondReact::check_constraints() delx2 = x3[0] - x2[0]; dely2 = x3[1] - x2[1]; delz2 = x3[2] - x2[2]; - domain->minimum_image(delx2,dely2,delz2); // ghost location fix + domain->minimum_image(FLERR, delx2,dely2,delz2); // ghost location fix rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; r2 = sqrt(rsq2); @@ -2012,22 +2012,22 @@ int FixBondReact::check_constraints() vb1x = x1[0] - x2[0]; vb1y = x1[1] - x2[1]; vb1z = x1[2] - x2[2]; - domain->minimum_image(vb1x,vb1y,vb1z); + domain->minimum_image(FLERR, vb1x,vb1y,vb1z); vb2x = x3[0] - x2[0]; vb2y = x3[1] - x2[1]; vb2z = x3[2] - x2[2]; - domain->minimum_image(vb2x,vb2y,vb2z); + domain->minimum_image(FLERR, vb2x,vb2y,vb2z); vb2xm = -vb2x; vb2ym = -vb2y; vb2zm = -vb2z; - domain->minimum_image(vb2xm,vb2ym,vb2zm); + domain->minimum_image(FLERR, vb2xm,vb2ym,vb2zm); vb3x = x4[0] - x3[0]; vb3y = x4[1] - x3[1]; vb3z = x4[2] - x3[2]; - domain->minimum_image(vb3x,vb3y,vb3z); + domain->minimum_image(FLERR, vb3x,vb3y,vb3z); ax = vb1y*vb2zm - vb1z*vb2ym; ay = vb1z*vb2xm - vb1x*vb2zm; @@ -3908,7 +3908,7 @@ int FixBondReact::insert_atoms_setup(tagint **my_update_mega_glove, int iupdate) delx = coords[m][0] - x[i][0]; dely = coords[m][1] - x[i][1]; delz = coords[m][2] - x[i][2]; - domain->minimum_image(delx,dely,delz); + domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; if (rsq < overlapsq[rxnID]) { abortflag = 1; @@ -3926,7 +3926,7 @@ int FixBondReact::insert_atoms_setup(tagint **my_update_mega_glove, int iupdate) delx = coords[m][0] - myaddatom.x[0]; dely = coords[m][1] - myaddatom.x[1]; delz = coords[m][2] - myaddatom.x[2]; - domain->minimum_image(delx,dely,delz); + domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; if (rsq < overlapsq[rxnID]) { abortflag = 1; diff --git a/src/REPLICA/bosonic_exchange.cpp b/src/REPLICA/bosonic_exchange.cpp index 6ffbeb8eb7..261ba9d185 100644 --- a/src/REPLICA/bosonic_exchange.cpp +++ b/src/REPLICA/bosonic_exchange.cpp @@ -87,7 +87,7 @@ void BosonicExchange::diff_two_beads(const double *x1, int l1, const double *x2, double delx2 = x2[3 * l2 + 0] - x1[3 * l1 + 0]; double dely2 = x2[3 * l2 + 1] - x1[3 * l1 + 1]; double delz2 = x2[3 * l2 + 2] - x1[3 * l1 + 2]; - if (apply_minimum_image) { domain->minimum_image(delx2, dely2, delz2); } + if (apply_minimum_image) { domain->minimum_image(FLERR, delx2, dely2, delz2); } diff[0] = delx2; diff[1] = dely2; diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index 409c108628..181100b11b 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -348,7 +348,7 @@ void FixNEB::min_post_force(int /*vflag*/) delxp = x[i][0] - xprev[i][0]; delyp = x[i][1] - xprev[i][1]; delzp = x[i][2] - xprev[i][2]; - domain->minimum_image(delxp, delyp, delzp); + domain->minimum_image(FLERR, delxp, delyp, delzp); plen += delxp * delxp + delyp * delyp + delzp * delzp; dottangrad += delxp * f[i][0] + delyp * f[i][1] + delzp * f[i][2]; gradlen += f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2]; @@ -368,7 +368,7 @@ void FixNEB::min_post_force(int /*vflag*/) delxn = xnext[i][0] - x[i][0]; delyn = xnext[i][1] - x[i][1]; delzn = xnext[i][2] - x[i][2]; - domain->minimum_image(delxn, delyn, delzn); + domain->minimum_image(FLERR, delxn, delyn, delzn); nlen += delxn * delxn + delyn * delyn + delzn * delzn; gradnextlen += fnext[i][0] * fnext[i][0] + fnext[i][1] * fnext[i][1] + fnext[i][2] * fnext[i][2]; @@ -396,13 +396,13 @@ void FixNEB::min_post_force(int /*vflag*/) delxp = x[i][0] - xprev[i][0]; delyp = x[i][1] - xprev[i][1]; delzp = x[i][2] - xprev[i][2]; - domain->minimum_image(delxp, delyp, delzp); + domain->minimum_image(FLERR, delxp, delyp, delzp); plen += delxp * delxp + delyp * delyp + delzp * delzp; delxn = xnext[i][0] - x[i][0]; delyn = xnext[i][1] - x[i][1]; delzn = xnext[i][2] - x[i][2]; - domain->minimum_image(delxn, delyn, delzn); + domain->minimum_image(FLERR, delxn, delyn, delzn); if (vnext > veng && veng > vprev) { tangent[i][0] = delxn; diff --git a/src/REPLICA/fix_pimd_nvt.cpp b/src/REPLICA/fix_pimd_nvt.cpp index d11bc34337..53a4b779ae 100644 --- a/src/REPLICA/fix_pimd_nvt.cpp +++ b/src/REPLICA/fix_pimd_nvt.cpp @@ -579,13 +579,13 @@ void FixPIMDNVT::spring_force() double dely1 = xlast[1] - x[i][1]; double delz1 = xlast[2] - x[i][2]; xlast += 3; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); double delx2 = xnext[0] - x[i][0]; double dely2 = xnext[1] - x[i][1]; double delz2 = xnext[2] - x[i][2]; xnext += 3; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); double ff = fbond * _mass[type[i]]; diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index a65fc9a58f..0226755778 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -83,7 +83,7 @@ NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in, int n2step delx = buf_final[ii] - buf_init[ii]; dely = buf_final[ii + 1] - buf_init[ii + 1]; delz = buf_final[ii + 2] - buf_init[ii + 2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); x[i][0] = buf_init[ii] + fraction * delx; x[i][1] = buf_init[ii + 1] + fraction * dely; x[i][2] = buf_init[ii + 2] + fraction * delz; @@ -529,7 +529,7 @@ void NEB::readfile(char *file, int flag) dely = values.next_double() - x[m][1]; delz = values.next_double() - x[m][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); if (flag == 0) { x[m][0] += fraction * delx; diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 313bd3b59a..ceca4e8a47 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -434,7 +434,7 @@ bool FixEHEX::check_cluster(tagint *shake_atom, int n, Region *region) // take into account pbc - domain->minimum_image_big(xtemp); + domain->minimum_image_big(FLERR, xtemp); for (int k = 0; k < 3; k++) xcom[k] += mi * (x[lid[0]][k] + xtemp[k]); } diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index 5a85902609..f7673194a9 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -248,9 +248,9 @@ void FixRattle::vrattle3angle(int m) // take into account periodicity - domain->minimum_image(r01); - domain->minimum_image(r02); - domain->minimum_image(r12); + domain->minimum_image(FLERR, r01); + domain->minimum_image(FLERR, r02); + domain->minimum_image(FLERR, r12); // v01,v02,v12 = velocity differences @@ -323,7 +323,7 @@ void FixRattle::vrattle2(int m) // r01 = distance vec between atoms, with PBC MathExtra::sub3(x[i1],x[i0],r01); - domain->minimum_image(r01); + domain->minimum_image(FLERR, r01); // v01 = distance vectors for velocities @@ -375,8 +375,8 @@ void FixRattle::vrattle3(int m) MathExtra::sub3(x[i1],x[i0],r01); MathExtra::sub3(x[i2],x[i0],r02); - domain->minimum_image(r01); - domain->minimum_image(r02); + domain->minimum_image(FLERR, r01); + domain->minimum_image(FLERR, r02); // vp01,vp02 = distance vectors between velocities @@ -446,9 +446,9 @@ void FixRattle::vrattle4(int m) MathExtra::sub3(x[i2],x[i0],r02); MathExtra::sub3(x[i3],x[i0],r03); - domain->minimum_image(r01); - domain->minimum_image(r02); - domain->minimum_image(r03); + domain->minimum_image(FLERR, r01); + domain->minimum_image(FLERR, r02); + domain->minimum_image(FLERR, r03); // vp01,vp02,vp03 = distance vectors between velocities @@ -828,7 +828,7 @@ bool FixRattle::check2(double **v, int m, bool checkr, bool checkv) tagint i1 = atom->map(shake_atom[m][1]); MathExtra::sub3(x[i1],x[i0],r01); - domain->minimum_image(r01); + domain->minimum_image(FLERR, r01); MathExtra::sub3(v[i1],v[i0],v01); stat = !checkr || (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) <= tol); @@ -857,8 +857,8 @@ bool FixRattle::check3(double **v, int m, bool checkr, bool checkv) MathExtra::sub3(x[i1],x[i0],r01); MathExtra::sub3(x[i2],x[i0],r02); - domain->minimum_image(r01); - domain->minimum_image(r02); + domain->minimum_image(FLERR, r01); + domain->minimum_image(FLERR, r02); MathExtra::sub3(v[i1],v[i0],v01); MathExtra::sub3(v[i2],v[i0],v02); @@ -893,9 +893,9 @@ bool FixRattle::check4(double **v, int m, bool checkr, bool checkv) MathExtra::sub3(x[i2],x[i0],r02); MathExtra::sub3(x[i3],x[i0],r03); - domain->minimum_image(r01); - domain->minimum_image(r02); - domain->minimum_image(r03); + domain->minimum_image(FLERR, r01); + domain->minimum_image(FLERR, r02); + domain->minimum_image(FLERR, r03); MathExtra::sub3(v[i1],v[i0],v01); MathExtra::sub3(v[i2],v[i0],v02); @@ -932,9 +932,9 @@ bool FixRattle::check3angle(double **v, int m, bool checkr, bool checkv) MathExtra::sub3(x[i2],x[i0],r02); MathExtra::sub3(x[i2],x[i1],r12); - domain->minimum_image(r01); - domain->minimum_image(r02); - domain->minimum_image(r12); + domain->minimum_image(FLERR, r01); + domain->minimum_image(FLERR, r02); + domain->minimum_image(FLERR, r12); MathExtra::sub3(v[i1],v[i0],v01); MathExtra::sub3(v[i2],v[i0],v02); diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index d55b1fadd9..e6abda2dcf 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -2180,7 +2180,7 @@ void FixRigidSmall::setup_bodies_static() xgc = body[ibody].xgc; double delta[3]; MathExtra::sub3(xgc,xcm,delta); - domain->minimum_image_big(delta); + domain->minimum_image_big(FLERR, delta); MathExtra::transpose_matvec(ex,ey,ez,delta,body[ibody].xgc_body); MathExtra::add3(xcm,delta,xgc); } diff --git a/src/YAFF/angle_cross.cpp b/src/YAFF/angle_cross.cpp index 0ff3580715..3013885b3f 100644 --- a/src/YAFF/angle_cross.cpp +++ b/src/YAFF/angle_cross.cpp @@ -318,13 +318,13 @@ double AngleCross::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/YAFF/angle_mm3.cpp b/src/YAFF/angle_mm3.cpp index 9cc53e21de..bce4607caa 100644 --- a/src/YAFF/angle_mm3.cpp +++ b/src/YAFF/angle_mm3.cpp @@ -260,13 +260,13 @@ double AngleMM3::single(int type, int i1, int i2, int i3) double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; @@ -297,13 +297,13 @@ void AngleMM3::born_matrix(int type, int i1, int i2, int i3, double &du, double double delx1 = x[i1][0] - x[i2][0]; double dely1 = x[i1][1] - x[i2][1]; double delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); double delx2 = x[i3][0] - x[i2][0]; double dely2 = x[i3][1] - x[i2][1]; double delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); double c = delx1*delx2 + dely1*dely2 + delz1*delz2; diff --git a/src/YAFF/improper_distharm.cpp b/src/YAFF/improper_distharm.cpp index 69d14cc997..0230ae54e0 100644 --- a/src/YAFF/improper_distharm.cpp +++ b/src/YAFF/improper_distharm.cpp @@ -94,37 +94,37 @@ void ImproperDistHarm::compute(int eflag, int vflag) xab = x[i2][0] - x[i1][0]; yab = x[i2][1] - x[i1][1]; zab = x[i2][2] - x[i1][2]; - domain->minimum_image(xab,yab,zab); + domain->minimum_image(FLERR, xab,yab,zab); // bond 1->3 xac = x[i3][0] - x[i1][0]; yac = x[i3][1] - x[i1][1]; zac = x[i3][2] - x[i1][2]; - domain->minimum_image(xac,yac,zac); + domain->minimum_image(FLERR, xac,yac,zac); // bond 1->4 xad = x[i4][0] - x[i1][0]; yad = x[i4][1] - x[i1][1]; zad = x[i4][2] - x[i1][2]; - domain->minimum_image(xad,yad,zad); + domain->minimum_image(FLERR, xad,yad,zad); // bond 2-3 xbc = x[i3][0] - x[i2][0]; ybc = x[i3][1] - x[i2][1]; zbc = x[i3][2] - x[i2][2]; - domain->minimum_image(xbc,ybc,zbc); + domain->minimum_image(FLERR, xbc,ybc,zbc); // bond 2-4 xbd = x[i4][0] - x[i2][0]; ybd = x[i4][1] - x[i2][1]; zbd = x[i4][2] - x[i2][2]; - domain->minimum_image(xbd,ybd,zbd); + domain->minimum_image(FLERR, xbd,ybd,zbd); // bond 3-4 xcd = x[i4][0] - x[i3][0]; ycd = x[i4][1] - x[i3][1]; zcd = x[i4][2] - x[i3][2]; - domain->minimum_image(xcd,ycd,zcd); + domain->minimum_image(FLERR, xcd,ycd,zcd); xna = ybc*zcd - zbc*ycd; yna = -(xbc*zcd - zbc*xcd); diff --git a/src/YAFF/improper_sqdistharm.cpp b/src/YAFF/improper_sqdistharm.cpp index 1981c61f38..b7b699059c 100644 --- a/src/YAFF/improper_sqdistharm.cpp +++ b/src/YAFF/improper_sqdistharm.cpp @@ -94,37 +94,37 @@ void ImproperSQDistHarm::compute(int eflag, int vflag) xab = x[i2][0] - x[i1][0]; yab = x[i2][1] - x[i1][1]; zab = x[i2][2] - x[i1][2]; - domain->minimum_image(xab,yab,zab); + domain->minimum_image(FLERR, xab,yab,zab); // bond 1->3 xac = x[i3][0] - x[i1][0]; yac = x[i3][1] - x[i1][1]; zac = x[i3][2] - x[i1][2]; - domain->minimum_image(xac,yac,zac); + domain->minimum_image(FLERR, xac,yac,zac); // bond 1->4 xad = x[i4][0] - x[i1][0]; yad = x[i4][1] - x[i1][1]; zad = x[i4][2] - x[i1][2]; - domain->minimum_image(xad,yad,zad); + domain->minimum_image(FLERR, xad,yad,zad); // bond 2-3 xbc = x[i3][0] - x[i2][0]; ybc = x[i3][1] - x[i2][1]; zbc = x[i3][2] - x[i2][2]; - domain->minimum_image(xbc,ybc,zbc); + domain->minimum_image(FLERR, xbc,ybc,zbc); // bond 2-4 xbd = x[i4][0] - x[i2][0]; ybd = x[i4][1] - x[i2][1]; zbd = x[i4][2] - x[i2][2]; - domain->minimum_image(xbd,ybd,zbd); + domain->minimum_image(FLERR, xbd,ybd,zbd); // bond 3-4 xcd = x[i4][0] - x[i3][0]; ycd = x[i4][1] - x[i3][1]; zcd = x[i4][2] - x[i3][2]; - domain->minimum_image(xcd,ycd,zcd); + domain->minimum_image(FLERR, xcd,ycd,zcd); xna = ybc*zcd - zbc*ycd; yna = -(xbc*zcd - zbc*xcd); diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index b4a9334416..426f25953d 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -263,7 +263,7 @@ int ComputeAngleLocal::compute_angles(int flag) delx1 = x[atom1][0] - x[atom2][0]; dely1 = x[atom1][1] - x[atom2][1]; delz1 = x[atom1][2] - x[atom2][2]; - domain->minimum_image(delx1, dely1, delz1); + domain->minimum_image(FLERR, delx1, dely1, delz1); rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1; r1 = sqrt(rsq1); @@ -271,7 +271,7 @@ int ComputeAngleLocal::compute_angles(int flag) delx2 = x[atom3][0] - x[atom2][0]; dely2 = x[atom3][1] - x[atom2][1]; delz2 = x[atom3][2] - x[atom2][2]; - domain->minimum_image(delx2, dely2, delz2); + domain->minimum_image(FLERR, delx2, dely2, delz2); rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2; r2 = sqrt(rsq2); diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index 6354c67638..54c8c734c7 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -344,7 +344,7 @@ int ComputeBondLocal::compute_bonds(int flag) dx = x[atom1][0] - x[atom2][0]; dy = x[atom1][1] - x[atom2][1]; dz = x[atom1][2] - x[atom2][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); rsq = dx * dx + dy * dy + dz * dz; if (btype == 0) { diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index bd1e389e85..56718aa201 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -252,22 +252,22 @@ int ComputeDihedralLocal::compute_dihedrals(int flag) vb1x = x[atom1][0] - x[atom2][0]; vb1y = x[atom1][1] - x[atom2][1]; vb1z = x[atom1][2] - x[atom2][2]; - domain->minimum_image(vb1x, vb1y, vb1z); + domain->minimum_image(FLERR, vb1x, vb1y, vb1z); vb2x = x[atom3][0] - x[atom2][0]; vb2y = x[atom3][1] - x[atom2][1]; vb2z = x[atom3][2] - x[atom2][2]; - domain->minimum_image(vb2x, vb2y, vb2z); + domain->minimum_image(FLERR, vb2x, vb2y, vb2z); vb2xm = -vb2x; vb2ym = -vb2y; vb2zm = -vb2z; - domain->minimum_image(vb2xm, vb2ym, vb2zm); + domain->minimum_image(FLERR, vb2xm, vb2ym, vb2zm); vb3x = x[atom4][0] - x[atom3][0]; vb3y = x[atom4][1] - x[atom3][1]; vb3z = x[atom4][2] - x[atom3][2]; - domain->minimum_image(vb3x, vb3y, vb3z); + domain->minimum_image(FLERR, vb3x, vb3y, vb3z); ax = vb1y * vb2zm - vb1z * vb2ym; ay = vb1z * vb2xm - vb1x * vb2zm; diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp index ff8f069a03..fe5e373789 100644 --- a/src/compute_improper_local.cpp +++ b/src/compute_improper_local.cpp @@ -183,17 +183,17 @@ int ComputeImproperLocal::compute_impropers(int flag) vb1x = x[atom1][0] - x[atom2][0]; vb1y = x[atom1][1] - x[atom2][1]; vb1z = x[atom1][2] - x[atom2][2]; - domain->minimum_image(vb1x, vb1y, vb1z); + domain->minimum_image(FLERR, vb1x, vb1y, vb1z); vb2x = x[atom3][0] - x[atom2][0]; vb2y = x[atom3][1] - x[atom2][1]; vb2z = x[atom3][2] - x[atom2][2]; - domain->minimum_image(vb2x, vb2y, vb2z); + domain->minimum_image(FLERR, vb2x, vb2y, vb2z); vb3x = x[atom4][0] - x[atom3][0]; vb3y = x[atom4][1] - x[atom3][1]; vb3z = x[atom4][2] - x[atom3][2]; - domain->minimum_image(vb3x, vb3y, vb3z); + domain->minimum_image(FLERR, vb3x, vb3y, vb3z); ss1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z); ss2 = 1.0 / (vb2x * vb2x + vb2y * vb2y + vb2z * vb2z); diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 93f4519d3c..68ab376692 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -875,7 +875,7 @@ void CreateAtoms::add_random() delx = xone[0] - x[i][0]; dely = xone[1] - x[i][1]; delz = xone[2] - x[i][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); distsq = delx * delx + dely * dely + delz * delz; if (distsq < odistsq) { reject = 1; @@ -891,7 +891,7 @@ void CreateAtoms::add_random() delx = xmol[j][0] - x[i][0]; dely = xmol[j][1] - x[i][1]; delz = xmol[j][2] - x[i][2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); distsq = delx * delx + dely * dely + delz * delz; if (distsq < odistsq) { reject = 1; diff --git a/src/domain.cpp b/src/domain.cpp index 31350482bd..33764d70cc 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1136,7 +1136,7 @@ void Domain::box_too_small_check() delx = x[i][0] - x[k][0]; dely = x[i][1] - x[k][1]; delz = x[i][2] - x[k][2]; - minimum_image(delx,dely,delz); + minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; maxbondme = MAX(maxbondme,rsq); } @@ -1205,6 +1205,7 @@ void Domain::subbox_too_small_check(double thresh) "could lead to lost atoms"); } +// clang-format on /* ---------------------------------------------------------------------- minimum image convention in periodic dimensions use 1/2 of box size as test @@ -1218,39 +1219,45 @@ void Domain::subbox_too_small_check(double thresh) ------------------------------------------------------------------------- */ static constexpr double MAXIMGCOUNT = 16; - -void Domain::minimum_image(double &dx, double &dy, double &dz) const +void Domain::minimum_image(const std::string &file, int line, double &dx, double &dy, + double &dz) const { if (triclinic == 0) { if (xperiodic) { if (fabs(dx) > (MAXIMGCOUNT * xprd)) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dx); while (fabs(dx) > xprd_half) { - if (dx < 0.0) dx += xprd; - else dx -= xprd; + if (dx < 0.0) + dx += xprd; + else + dx -= xprd; } } if (yperiodic) { if (fabs(dy) > (MAXIMGCOUNT * yprd)) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dy); while (fabs(dy) > yprd_half) { - if (dy < 0.0) dy += yprd; - else dy -= yprd; + if (dy < 0.0) + dy += yprd; + else + dy -= yprd; } } if (zperiodic) { if (fabs(dz) > (MAXIMGCOUNT * zprd)) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dz); while (fabs(dz) > zprd_half) { - if (dz < 0.0) dz += zprd; - else dz -= zprd; + if (dz < 0.0) + dz += zprd; + else + dz -= zprd; } } } else { if (zperiodic) { if (fabs(dz) > (MAXIMGCOUNT * zprd)) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dz); while (fabs(dz) > zprd_half) { if (dz < 0.0) { dz += zprd; @@ -1265,7 +1272,7 @@ void Domain::minimum_image(double &dx, double &dy, double &dz) const } if (yperiodic) { if (fabs(dy) > (MAXIMGCOUNT * yprd)) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dy); while (fabs(dy) > yprd_half) { if (dy < 0.0) { dy += yprd; @@ -1278,10 +1285,12 @@ void Domain::minimum_image(double &dx, double &dy, double &dz) const } if (xperiodic) { if (fabs(dx) > (MAXIMGCOUNT * xprd)) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dx); while (fabs(dx) > xprd_half) { - if (dx < 0.0) dx += xprd; - else dx -= xprd; + if (dx < 0.0) + dx += xprd; + else + dx -= xprd; } } } @@ -1298,61 +1307,63 @@ void Domain::minimum_image(double &dx, double &dy, double &dz) const this applies for example to fix rigid/small ------------------------------------------------------------------------- */ -void Domain::minimum_image_big(double &dx, double &dy, double &dz) const +void Domain::minimum_image_big(const std::string &file, int line, double &dx, double &dy, + double &dz) const { if (triclinic == 0) { if (xperiodic) { - double dfactor = dx/xprd + 0.5; + double dfactor = dx / xprd + 0.5; if (dx < 0) dfactor -= 1.0; if (dfactor > MAXSMALLINT) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dx); dx -= xprd * static_cast(dfactor); } if (yperiodic) { - double dfactor = dy/yprd + 0.5; + double dfactor = dy / yprd + 0.5; if (dy < 0) dfactor -= 1.0; if (dfactor > MAXSMALLINT) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dy); dy -= yprd * static_cast(dfactor); } if (zperiodic) { - double dfactor = dz/zprd + 0.5; + double dfactor = dz / zprd + 0.5; if (dz < 0) dfactor -= 1.0; if (dfactor > MAXSMALLINT) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dz); dz -= zprd * static_cast(dfactor); } } else { if (zperiodic) { - double dfactor = dz/zprd + 0.5; + double dfactor = dz / zprd + 0.5; if (dz < 0) dfactor -= 1.0; if (dfactor > MAXSMALLINT) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dz); int factor = static_cast(dfactor); dz -= zprd * factor; dy -= yz * factor; dx -= xz * factor; } if (yperiodic) { - double dfactor = dy/yprd + 0.5; + double dfactor = dy / yprd + 0.5; if (dy < 0) dfactor -= 1.0; if (dfactor > MAXSMALLINT) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dy); int factor = static_cast(dfactor); dy -= yprd * factor; dx -= xy * factor; } if (xperiodic) { - double dfactor = dx/xprd + 0.5; + double dfactor = dx / xprd + 0.5; if (dx < 0) dfactor -= 1.0; if (dfactor > MAXSMALLINT) - error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx); + error->one(file, line, "Atoms have moved too far apart ({}) for minimum image\n", dx); dx -= xprd * static_cast(dfactor); } } } +// clang-format off /* ---------------------------------------------------------------------- return local index of atom J or any of its images that is closest to atom I if J is not a valid index like -1, just return it diff --git a/src/domain.h b/src/domain.h index 9c745f05b8..f2e6c0632e 100644 --- a/src/domain.h +++ b/src/domain.h @@ -127,10 +127,16 @@ class Domain : protected Pointers { void image_check(); void box_too_small_check(); void subbox_too_small_check(double); - void minimum_image(double &, double &, double &) const; - void minimum_image(double *delta) const { minimum_image(delta[0], delta[1], delta[2]); } - void minimum_image_big(double &, double &, double &) const; - void minimum_image_big(double *delta) const { minimum_image_big(delta[0], delta[1], delta[2]); } + void minimum_image(const std::string &, int, double &, double &, double &) const; + void minimum_image(const std::string &file, int line, double *delta) const + { + minimum_image(file, line, delta[0], delta[1], delta[2]); + } + void minimum_image_big(const std::string &, int, double &, double &, double &) const; + void minimum_image_big(const std::string &file, int line, double *delta) const + { + minimum_image_big(file, line, delta[0], delta[1], delta[2]); + } int closest_image(int, int); int closest_image(const double *const, int); void closest_image(const double *const, const double *const, double *const); @@ -185,7 +191,7 @@ class Domain : protected Pointers { // but is a far-away image that should be treated as an unbonded neighbor // inline since called from neighbor build inner loop - inline int minimum_image_check(double dx, double dy, double dz) + inline int minimum_image_check(double dx, double dy, double dz) const { if (xperiodic && fabs(dx) > xprd_half) return 1; if (yperiodic && fabs(dy) > yprd_half) return 1; diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 609223a9ec..83f4999f43 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -1245,7 +1245,7 @@ void DumpImage::create_image() delz = x[atom2][2] - x[atom1][2]; if (bcolor == ATOM || domain->minimum_image_check(delx,dely,delz)) { - domain->minimum_image(delx,dely,delz); + domain->minimum_image(FLERR, delx,dely,delz); xmid[0] = x[atom1][0] + 0.5*delx; xmid[1] = x[atom1][1] + 0.5*dely; xmid[2] = x[atom1][2] + 0.5*delz; diff --git a/src/fix_deposit.cpp b/src/fix_deposit.cpp index c9d09fa8b7..46a8adad7b 100644 --- a/src/fix_deposit.cpp +++ b/src/fix_deposit.cpp @@ -401,7 +401,7 @@ void FixDeposit::pre_exchange() delx = coord[0] - x[i][0]; dely = coord[1] - x[i][1]; delz = 0.0; - domain->minimum_image(delx,dely,delz); + domain->minimum_image(FLERR, delx,dely,delz); if (dimension == 2) rsq = delx*delx; else rsq = delx*delx + dely*dely; if (rsq > deltasq) continue; @@ -476,7 +476,7 @@ void FixDeposit::pre_exchange() delx = coords[m][0] - x[i][0]; dely = coords[m][1] - x[i][1]; delz = coords[m][2] - x[i][2]; - domain->minimum_image(delx,dely,delz); + domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; if (rsq < nearsq) flag = 1; } diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index 05aaf321a7..608708ce6d 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -273,7 +273,7 @@ void FixIndent::post_force(int /*vflag*/) delx = x[i][0] - ctr[0]; dely = x[i][1] - ctr[1]; delz = x[i][2] - ctr[2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); r = sqrt(delx * delx + dely * dely + delz * delz); if (side == OUTSIDE) { dr = r - radius; @@ -313,7 +313,7 @@ void FixIndent::post_force(int /*vflag*/) if (mask[i] & groupbit) { double del[3] = {x[i][0] - ctr[0], x[i][1] - ctr[1], x[i][2] - ctr[2]}; del[cdim] = 0; - domain->minimum_image(del[0], del[1], del[2]); + domain->minimum_image(FLERR, del[0], del[1], del[2]); r = sqrt(del[0] * del[0] + del[1] * del[1] + del[2] * del[2]); if (side == OUTSIDE) { dr = r - radius; @@ -360,7 +360,7 @@ void FixIndent::post_force(int /*vflag*/) delx = x[i][0] - ctr[0]; dely = x[i][1] - ctr[1]; delz = x[i][2] - ctr[2]; - domain->minimum_image(delx, dely, delz); + domain->minimum_image(FLERR, delx, dely, delz); double x0[3] = {delx + ctr[0], dely + ctr[1], delz + ctr[2]}; r = sqrt(delx * delx + dely * dely + delz * delz); diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp index e011c79d9d..5b537303dd 100644 --- a/src/fix_minimize.cpp +++ b/src/fix_minimize.cpp @@ -119,7 +119,7 @@ void FixMinimize::reset_coords() dx = dx0 = x[i][0] - x0[n]; dy = dy0 = x[i][1] - x0[n+1]; dz = dz0 = x[i][2] - x0[n+2]; - domain->minimum_image(dx,dy,dz); + domain->minimum_image(FLERR, dx,dy,dz); if (dx != dx0) x0[n] = x[i][0] - dx; if (dy != dy0) x0[n+1] = x[i][1] - dy; if (dz != dz0) x0[n+2] = x[i][2] - dz; diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 9b157ee90f..8900d68a3c 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -284,7 +284,7 @@ void FixRestrain::restrain_bond(int m) delx = x[i1][0] - x[i2][0]; dely = x[i1][1] - x[i2][1]; delz = x[i1][2] - x[i2][2]; - domain->minimum_image(delx,dely,delz); + domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; r = sqrt(rsq); @@ -357,7 +357,7 @@ void FixRestrain::restrain_lbound(int m) delx = x[i1][0] - x[i2][0]; dely = x[i1][1] - x[i2][1]; delz = x[i1][2] - x[i2][2]; - domain->minimum_image(delx,dely,delz); + domain->minimum_image(FLERR, delx,dely,delz); rsq = delx*delx + dely*dely + delz*delz; r = sqrt(rsq); @@ -442,7 +442,7 @@ void FixRestrain::restrain_angle(int m) delx1 = x[i1][0] - x[i2][0]; dely1 = x[i1][1] - x[i2][1]; delz1 = x[i1][2] - x[i2][2]; - domain->minimum_image(delx1,dely1,delz1); + domain->minimum_image(FLERR, delx1,dely1,delz1); rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; r1 = sqrt(rsq1); @@ -452,7 +452,7 @@ void FixRestrain::restrain_angle(int m) delx2 = x[i3][0] - x[i2][0]; dely2 = x[i3][1] - x[i2][1]; delz2 = x[i3][2] - x[i2][2]; - domain->minimum_image(delx2,dely2,delz2); + domain->minimum_image(FLERR, delx2,dely2,delz2); rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; r2 = sqrt(rsq2); @@ -564,26 +564,26 @@ void FixRestrain::restrain_dihedral(int m) vb1x = x[i1][0] - x[i2][0]; vb1y = x[i1][1] - x[i2][1]; vb1z = x[i1][2] - x[i2][2]; - domain->minimum_image(vb1x,vb1y,vb1z); + domain->minimum_image(FLERR, vb1x,vb1y,vb1z); // 2nd bond vb2x = x[i3][0] - x[i2][0]; vb2y = x[i3][1] - x[i2][1]; vb2z = x[i3][2] - x[i2][2]; - domain->minimum_image(vb2x,vb2y,vb2z); + domain->minimum_image(FLERR, vb2x,vb2y,vb2z); vb2xm = -vb2x; vb2ym = -vb2y; vb2zm = -vb2z; - domain->minimum_image(vb2xm,vb2ym,vb2zm); + domain->minimum_image(FLERR, vb2xm,vb2ym,vb2zm); // 3rd bond vb3x = x[i4][0] - x[i3][0]; vb3y = x[i4][1] - x[i3][1]; vb3z = x[i4][2] - x[i3][2]; - domain->minimum_image(vb3x,vb3y,vb3z); + domain->minimum_image(FLERR, vb3x,vb3y,vb3z); ax = vb1y*vb2zm - vb1z*vb2ym; ay = vb1z*vb2xm - vb1x*vb2zm; diff --git a/src/ntopo.cpp b/src/ntopo.cpp index a6c7a199e2..7358e7d72f 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -109,7 +109,7 @@ void NTopo::bond_check() dxstart = dx = x[i][0] - x[j][0]; dystart = dy = x[i][1] - x[j][1]; dzstart = dz = x[i][2] - x[j][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; } @@ -138,17 +138,17 @@ void NTopo::angle_check() dxstart = dx = x[i][0] - x[j][0]; dystart = dy = x[i][1] - x[j][1]; dzstart = dz = x[i][2] - x[j][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; dxstart = dx = x[i][0] - x[k][0]; dystart = dy = x[i][1] - x[k][1]; dzstart = dz = x[i][2] - x[k][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; dxstart = dx = x[j][0] - x[k][0]; dystart = dy = x[j][1] - x[k][1]; dzstart = dz = x[j][2] - x[k][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; } @@ -178,32 +178,32 @@ void NTopo::dihedral_check(int nlist, int **list) dxstart = dx = x[i][0] - x[j][0]; dystart = dy = x[i][1] - x[j][1]; dzstart = dz = x[i][2] - x[j][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; dxstart = dx = x[i][0] - x[k][0]; dystart = dy = x[i][1] - x[k][1]; dzstart = dz = x[i][2] - x[k][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; dxstart = dx = x[i][0] - x[l][0]; dystart = dy = x[i][1] - x[l][1]; dzstart = dz = x[i][2] - x[l][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; dxstart = dx = x[j][0] - x[k][0]; dystart = dy = x[j][1] - x[k][1]; dzstart = dz = x[j][2] - x[k][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; dxstart = dx = x[j][0] - x[l][0]; dystart = dy = x[j][1] - x[l][1]; dzstart = dz = x[j][2] - x[l][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; dxstart = dx = x[k][0] - x[l][0]; dystart = dy = x[k][1] - x[l][1]; dzstart = dz = x[k][2] - x[l][2]; - domain->minimum_image(dx, dy, dz); + domain->minimum_image(FLERR, dx, dy, dz); if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1; }