diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index e9f1c528ef..040cbe7530 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -276,17 +276,17 @@ 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); - double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); + 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(delx2,dely2,delz2); - double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); + domain->minimum_image(delx2, dely2, delz2); + double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2); - double c = delx1*delx2 + dely1*dely2 + delz1*delz2; - c /= r1*r2; + double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2; + c /= r1 * r2; if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; double theta = acos(c); diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index 8e6685cac9..2d1e16b9e4 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -326,8 +326,8 @@ void DihedralMultiHarmonic::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -void DihedralMultiHarmonic::born_matrix(int nd, int i1, int i2, int i3, int i4, - double &du, double &du2) +void DihedralMultiHarmonic::born_matrix(int nd, int i1, int i2, int i3, int i4, double &du, + double &du2) { double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm; double sb1, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2; diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index eced454d68..e99d83f631 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -336,8 +336,7 @@ void DihedralOPLS::write_data(FILE *fp) /* ----------------------------------------------------------------------*/ -void DihedralOPLS::born_matrix(int nd, int i1, int i2, int i3, int i4, - double &du, double &du2) +void DihedralOPLS::born_matrix(int nd, int i1, int i2, int i3, int i4, double &du, double &du2) { double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm; double sb1, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2; @@ -425,9 +424,10 @@ void DihedralOPLS::born_matrix(int nd, int i1, int i2, int i3, int i4, si = sin(phi); if (fabs(si) < SMALLER) si = SMALLER; - du = k1[type] - 2.0 * k2[type] * sin(2.0 * phi) / si + 3.0 * k3[type] * sin(3.0 * phi) / si - - 4.0 * k4[type] * sin(4.0 * phi) / si; - du2 = (4.0 * k2[type] * si * cos(2.0 * phi) - 2.0 * k2[type] * sin(2.0 * phi) - - 9.0 * k3[type] * si * cos(3.0 * phi) + 3.0 * k3[type] * sin(3.0 * phi) - + 16.0 * k4[type] * si * cos(4.0 * phi) - 4.0 * k4[type] * sin(4.0 * phi)) / (si * si * si); + du = k1[type] - 2.0 * k2[type] * sin(2.0 * phi) / si + 3.0 * k3[type] * sin(3.0 * phi) / si - + 4.0 * k4[type] * sin(4.0 * phi) / si; + du2 = (4.0 * k2[type] * si * cos(2.0 * phi) - 2.0 * k2[type] * sin(2.0 * phi) - + 9.0 * k3[type] * si * cos(3.0 * phi) + 3.0 * k3[type] * sin(3.0 * phi) + + 16.0 * k4[type] * si * cos(4.0 * phi) - 4.0 * k4[type] * sin(4.0 * phi)) / + (si * si * si); } diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index ee94c2d9a7..40bb206bd2 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -214,8 +214,10 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : iarg += 2; } else if (strcmp(arg[iarg], "inputs") == 0) { if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, mycmd + " inputs", error); - if (strcmp(arg[iarg+1], "peratom") == 0) input_mode = PERATOM; - else if (strcmp(arg[iarg+1], "local") == 0) input_mode = LOCAL; + if (strcmp(arg[iarg + 1], "peratom") == 0) + input_mode = PERATOM; + else if (strcmp(arg[iarg + 1], "local") == 0) + input_mode = LOCAL; iarg += 2; } else error->all(FLERR, "Unknown compute {} keyword: {}", style, arg[iarg]); @@ -242,7 +244,7 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : for (auto &val : values) { if (val.which == ArgInfo::X || val.which == ArgInfo::V || val.which == ArgInfo::F) { - if (input_mode == LOCAL) error->all(FLERR,"Compute {} inputs must be all local"); + if (input_mode == LOCAL) error->all(FLERR, "Compute {} inputs must be all local"); } else if (val.which == ArgInfo::COMPUTE) { val.val.c = modify->get_compute_by_id(val.id); @@ -251,11 +253,14 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : if (input_mode == PERATOM) { if (!val.val.c->peratom_flag) - error->all(FLERR, "Compute {} compute {} does not calculate per-atom values", style, val.id); + error->all(FLERR, "Compute {} compute {} does not calculate per-atom values", style, + val.id); if (val.argindex == 0 && val.val.c->size_peratom_cols != 0) - error->all(FLERR, "Compute {} compute {} does not calculate a per-atom vector", style, val.id); + error->all(FLERR, "Compute {} compute {} does not calculate a per-atom vector", style, + val.id); if (val.argindex && val.val.c->size_peratom_cols == 0) - error->all(FLERR, "Compute {} compute {} does not calculate a per-atom array", style, val.id); + error->all(FLERR, "Compute {} compute {} does not calculate a per-atom array", style, + val.id); if (val.argindex && val.argindex > val.val.c->size_peratom_cols) error->all(FLERR, "Compute {} compute {} array is accessed out-of-range", style, val.id); @@ -263,9 +268,11 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : if (!val.val.c->local_flag) error->all(FLERR, "Compute {} compute {} does not calculate local values", style, val.id); if (val.argindex == 0 && val.val.c->size_local_cols != 0) - error->all(FLERR, "Compute {} compute {} does not calculate a local vector", style, val.id); + error->all(FLERR, "Compute {} compute {} does not calculate a local vector", style, + val.id); if (val.argindex && val.val.c->size_local_cols == 0) - error->all(FLERR, "Compute {} compute {} does not calculate a local array", style, val.id); + error->all(FLERR, "Compute {} compute {} does not calculate a local array", style, + val.id); if (val.argindex && val.argindex > val.val.c->size_local_cols) error->all(FLERR, "Compute {} compute {} array is accessed out-of-range", style, val.id); } @@ -278,7 +285,8 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : if (!val.val.f->peratom_flag) error->all(FLERR, "Compute {} fix {} does not calculate per-atom values", style, val.id); if (val.argindex == 0 && (val.val.f->size_peratom_cols != 0)) - error->all(FLERR, "Compute {} fix {} does not calculate a per-atom vector", style, val.id); + error->all(FLERR, "Compute {} fix {} does not calculate a per-atom vector", style, + val.id); if (val.argindex && (val.val.f->size_peratom_cols == 0)) error->all(FLERR, "Compute {} fix {} does not calculate a per-atom array", style, val.id); if (val.argindex && (val.argindex > val.val.f->size_peratom_cols)) @@ -296,7 +304,7 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : } } else if (val.which == ArgInfo::VARIABLE) { - if (input_mode == LOCAL) error->all(FLERR,"Compute {} inputs must be all local"); + if (input_mode == LOCAL) error->all(FLERR, "Compute {} inputs must be all local"); val.val.v = input->variable->find(val.id.c_str()); if (val.val.v < 0) error->all(FLERR, "Variable name {} for compute {} does not exist", val.id, style); @@ -417,7 +425,8 @@ void ComputeReduce::compute_vector() } else if (mode == MINN) { if (!replace) { for (int m = 0; m < nvalues; m++) - MPI_Allreduce(&onevec[m], &vector[m], 1, MPI_DOUBLE, this->scalar_reduction_operation, world); + MPI_Allreduce(&onevec[m], &vector[m], 1, MPI_DOUBLE, this->scalar_reduction_operation, + world); } else { for (int m = 0; m < nvalues; m++) @@ -437,7 +446,8 @@ void ComputeReduce::compute_vector() } else if (mode == MAXX) { if (!replace) { for (int m = 0; m < nvalues; m++) - MPI_Allreduce(&onevec[m], &vector[m], 1, MPI_DOUBLE, this->scalar_reduction_operation, world); + MPI_Allreduce(&onevec[m], &vector[m], 1, MPI_DOUBLE, this->scalar_reduction_operation, + world); } else { for (int m = 0; m < nvalues; m++) diff --git a/src/create_box.cpp b/src/create_box.cpp index 8a74ffd7bd..93e699e06b 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -49,11 +49,13 @@ void CreateBox::command(int narg, char **arg) Region *region = nullptr; int triclinic_general = 0; - if (strcmp(arg[1],"NULL") == 0) triclinic_general = 1; + if (strcmp(arg[1], "NULL") == 0) + triclinic_general = 1; else { region = domain->get_region_by_id(arg[1]); if (!region) error->all(FLERR, "Create_box region {} does not exist", arg[1]); - if (region->bboxflag == 0) error->all(FLERR, "Create_box region does not support a bounding box"); + if (region->bboxflag == 0) + error->all(FLERR, "Create_box region does not support a bounding box"); region->init(); } @@ -77,9 +79,9 @@ void CreateBox::command(int narg, char **arg) domain->boxlo[2] = region->extent_zlo; domain->boxhi[2] = region->extent_zhi; - // region is prism - // seutp restricted triclinic box - // set simulation domain from prism params + // region is prism + // seutp restricted triclinic box + // set simulation domain from prism params } else { domain->triclinic = 1; @@ -97,17 +99,17 @@ void CreateBox::command(int narg, char **arg) if (domain->dimension == 2) { if (domain->boxlo[2] >= 0.0 || domain->boxhi[2] <= 0.0) - error->all(FLERR,"Create_box region zlo/zhi for 2d simulation must straddle 0.0"); + error->all(FLERR, "Create_box region zlo/zhi for 2d simulation must straddle 0.0"); } - // setup general triclinic box (with no region) - // read next box extent arguments to create ABC edge vectors + origin - // define_general_triclinic() converts - // ABC edge vectors + origin to restricted triclinic + // setup general triclinic box (with no region) + // read next box extent arguments to create ABC edge vectors + origin + // define_general_triclinic() converts + // ABC edge vectors + origin to restricted triclinic } else if (triclinic_general) { if (!domain->lattice->is_general_triclinic()) - error->all(FLERR,"Create_box for general triclinic requires triclnic/general lattice"); + error->all(FLERR, "Create_box for general triclinic requires triclnic/general lattice"); if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "create_box general triclinic", error); @@ -121,42 +123,50 @@ void CreateBox::command(int narg, char **arg) if (domain->dimension == 2) if (clo != -0.5 || chi != 0.5) - error->all(FLERR,"Create_box for general triclinic requires clo = -0.5 and chi = 0.5"); + error->all(FLERR, "Create_box for general triclinic requires clo = -0.5 and chi = 0.5"); // use lattice2box() to generate origin and ABC vectors // origin = abc lo // ABC vectors = hi in one dim - origin - double avec[3],bvec[3],cvec[3],origin[3]; - double px,py,pz; + double avec[3], bvec[3], cvec[3], origin[3]; + double px, py, pz; - px = alo; py = blo; pz = clo; - domain->lattice->lattice2box(px,py,pz); + px = alo; + py = blo; + pz = clo; + domain->lattice->lattice2box(px, py, pz); origin[0] = px; origin[1] = py; origin[2] = pz; - px = ahi; py = blo; pz = clo; - domain->lattice->lattice2box(px,py,pz); + px = ahi; + py = blo; + pz = clo; + domain->lattice->lattice2box(px, py, pz); avec[0] = px - origin[0]; avec[1] = py - origin[1]; avec[2] = pz - origin[2]; - px = alo; py = bhi; pz = clo; - domain->lattice->lattice2box(px,py,pz); + px = alo; + py = bhi; + pz = clo; + domain->lattice->lattice2box(px, py, pz); bvec[0] = px - origin[0]; bvec[1] = py - origin[1]; bvec[2] = pz - origin[2]; - px = alo; py = blo; pz = chi; - domain->lattice->lattice2box(px,py,pz); + px = alo; + py = blo; + pz = chi; + domain->lattice->lattice2box(px, py, pz); cvec[0] = px - origin[0]; cvec[1] = py - origin[1]; cvec[2] = pz - origin[2]; // define general triclinic box within Domain class - domain->define_general_triclinic(avec,bvec,cvec,origin); + domain->define_general_triclinic(avec, bvec, cvec, origin); } // if molecular, zero out topology info diff --git a/src/fix_efield.cpp b/src/fix_efield.cpp index 81be66b3e3..a5f02cc7c8 100644 --- a/src/fix_efield.cpp +++ b/src/fix_efield.cpp @@ -114,7 +114,8 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) : } if (estr && pstr) - error->all(FLERR, "Must not use energy and potential keywords at the same time with fix efield"); + error->all(FLERR, + "Must not use energy and potential keywords at the same time with fix efield"); force_flag = 0; fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0; @@ -171,7 +172,8 @@ void FixEfield::init() if (xstr) { xvar = input->variable->find(xstr); - if (xvar < 0) error->all(FLERR, "Variable {} for x-field in fix {} does not exist", xstr, style); + if (xvar < 0) + error->all(FLERR, "Variable {} for x-field in fix {} does not exist", xstr, style); if (input->variable->equalstyle(xvar)) xstyle = EQUAL; else if (input->variable->atomstyle(xvar)) @@ -182,7 +184,8 @@ void FixEfield::init() if (ystr) { yvar = input->variable->find(ystr); - if (yvar < 0) error->all(FLERR, "Variable {} for y-field in fix {} does not exist", ystr, style); + if (yvar < 0) + error->all(FLERR, "Variable {} for y-field in fix {} does not exist", ystr, style); if (input->variable->equalstyle(yvar)) ystyle = EQUAL; else if (input->variable->atomstyle(yvar)) @@ -193,7 +196,8 @@ void FixEfield::init() if (zstr) { zvar = input->variable->find(zstr); - if (zvar < 0) error->all(FLERR, "Variable {} for z-field in fix {} does not exist", zstr, style); + if (zvar < 0) + error->all(FLERR, "Variable {} for z-field in fix {} does not exist", zstr, style); if (input->variable->equalstyle(zvar)) zstyle = EQUAL; else if (input->variable->atomstyle(zvar)) @@ -213,7 +217,8 @@ void FixEfield::init() if (pstr) { pvar = input->variable->find(pstr); - if (pvar < 0) error->all(FLERR, "Variable {} for potential in fix {} does not exist", pstr, style); + if (pvar < 0) + error->all(FLERR, "Variable {} for potential in fix {} does not exist", pstr, style); if (input->variable->atomstyle(pvar)) pstyle = ATOM; else @@ -244,8 +249,10 @@ void FixEfield::init() error->all(FLERR, "Cannot use variable energy with constant efield in fix {}", style); if (varflag == CONSTANT && pstyle != NONE) error->all(FLERR, "Cannot use variable potential with constant efield in fix {}", style); - if ((varflag == EQUAL || varflag == ATOM) && update->whichflag == 2 && estyle == NONE && pstyle == NONE) - error->all(FLERR, "Must use variable energy or potential with fix {} during minimization", style); + if ((varflag == EQUAL || varflag == ATOM) && update->whichflag == 2 && estyle == NONE && + pstyle == NONE) + error->all(FLERR, "Must use variable energy or potential with fix {} during minimization", + style); if (utils::strmatch(update->integrate_style, "^respa")) { ilevel_respa = (dynamic_cast(update->integrate))->nlevels - 1; @@ -403,8 +410,10 @@ void FixEfield::post_force(int vflag) } f[i][2] += fz; fsum[3] += fz; - if (pstyle == ATOM) fsum[0] += qe2f * q[i] * efield[i][3]; - else if (estyle == ATOM) fsum[0] += efield[i][3]; + if (pstyle == ATOM) + fsum[0] += qe2f * q[i] * efield[i][3]; + else if (estyle == ATOM) + fsum[0] += efield[i][3]; } } @@ -504,8 +513,10 @@ void FixEfield::update_efield_variables() } else if (zstyle == ATOM) { input->variable->compute_atom(zvar, igroup, &efield[0][2], 4, 0); } - if (pstyle == ATOM) input->variable->compute_atom(pvar, igroup, &efield[0][3], 4, 0); - else if (estyle == ATOM) input->variable->compute_atom(evar, igroup, &efield[0][3], 4, 0); + if (pstyle == ATOM) + input->variable->compute_atom(pvar, igroup, &efield[0][3], 4, 0); + else if (estyle == ATOM) + input->variable->compute_atom(evar, igroup, &efield[0][3], 4, 0); modify->addstep_compute(update->ntimestep + 1); }