From ad25a9529758d19a234af1c3be40d1516b708024 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 20 Sep 2017 11:13:13 -0400 Subject: [PATCH] whitespace cleanup --- examples/snap/Mo_Chen_PRM2017.snap | 2 +- potentials/Mo_Chen_PRM2017.snap | 2 +- potentials/Ta06A.snap | 2 +- potentials/W_2940_2017_2_He_JW2013.snap | 4 +- src/compute_centro_atom.cpp | 164 ++++++++++++------------ 5 files changed, 87 insertions(+), 87 deletions(-) diff --git a/examples/snap/Mo_Chen_PRM2017.snap b/examples/snap/Mo_Chen_PRM2017.snap index fefe32d0c7..e5e5f3e180 100644 --- a/examples/snap/Mo_Chen_PRM2017.snap +++ b/examples/snap/Mo_Chen_PRM2017.snap @@ -2,6 +2,6 @@ # DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) # Generated by Materials Virtual Lab # Definition of SNAP potential. -pair_style snap +pair_style snap pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo diff --git a/potentials/Mo_Chen_PRM2017.snap b/potentials/Mo_Chen_PRM2017.snap index 892bca6153..579315b3dd 100644 --- a/potentials/Mo_Chen_PRM2017.snap +++ b/potentials/Mo_Chen_PRM2017.snap @@ -1,6 +1,6 @@ # DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) # Generated by Materials Virtual Lab # Definition of SNAP potential. -pair_style snap +pair_style snap pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo diff --git a/potentials/Ta06A.snap b/potentials/Ta06A.snap index edcc002524..43ce31fdcc 100644 --- a/potentials/Ta06A.snap +++ b/potentials/Ta06A.snap @@ -2,7 +2,7 @@ # Definition of SNAP potential Ta_Cand06A # Assumes 1 LAMMPS atom type - + variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 73 diff --git a/potentials/W_2940_2017_2_He_JW2013.snap b/potentials/W_2940_2017_2_He_JW2013.snap index 45a31955b3..ff0827c138 100644 --- a/potentials/W_2940_2017_2_He_JW2013.snap +++ b/potentials/W_2940_2017_2_He_JW2013.snap @@ -8,8 +8,8 @@ variable zblz equal 74 # Specify hybrid with SNAP, ZBL, and long-range Coulomb pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 -pair_coeff 1 1 zbl ${zblz} ${zblz} -pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL +pair_coeff 1 1 zbl ${zblz} ${zblz} +pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL pair_coeff 2 2 table 1 He_He_JW2013.table HeHe pair_coeff 1 2 table 2 W_He_JW2013.table WHe #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index a22fb96f98..c76b569462 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -39,7 +39,7 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), distsq(NULL), nearest(NULL), centro(NULL) { - if (narg < 4 || narg > 6) + if (narg < 4 || narg > 6) error->all(FLERR,"Illegal compute centro/atom command"); if (strcmp(arg[3],"fcc") == 0) nnn = 12; @@ -49,13 +49,13 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) : // default values axes_flag = 0; - + // optional keywords - + int iarg = 4; while (iarg < narg) { if (strcmp(arg[iarg],"axes") == 0) { - if (iarg+2 > narg) + if (iarg+2 > narg) error->all(FLERR,"Illegal compute centro/atom command3"); if (strcmp(arg[iarg+1],"yes") == 0) axes_flag = 1; else if (strcmp(arg[iarg+1],"no") == 0) axes_flag = 0; @@ -70,7 +70,7 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) : peratom_flag = 1; if (!axes_flag) size_peratom_cols = 0; else size_peratom_cols = 10; - + nmax = 0; maxneigh = 0; } @@ -205,98 +205,98 @@ void ComputeCentroAtom::compute_peratom() } // check whether to include local crystal symmetry axes - + if (!axes_flag) { - - // if not nnn neighbors, centro = 0.0 + + // if not nnn neighbors, centro = 0.0 - if (n < nnn) { - centro[i] = 0.0; - continue; - } + if (n < nnn) { + centro[i] = 0.0; + continue; + } - // store nnn nearest neighs in 1st nnn locations of distsq and nearest + // store nnn nearest neighs in 1st nnn locations of distsq and nearest - select2(nnn,n,distsq,nearest); + select2(nnn,n,distsq,nearest); - // R = Ri + Rj for each of npairs i,j pairs among nnn neighbors - // pairs = squared length of each R + // R = Ri + Rj for each of npairs i,j pairs among nnn neighbors + // pairs = squared length of each R - n = 0; - for (j = 0; j < nnn; j++) { - jj = nearest[j]; - for (k = j+1; k < nnn; k++) { - kk = nearest[k]; - delx = x[jj][0] + x[kk][0] - 2.0*xtmp; - dely = x[jj][1] + x[kk][1] - 2.0*ytmp; - delz = x[jj][2] + x[kk][2] - 2.0*ztmp; - pairs[n++] = delx*delx + dely*dely + delz*delz; + n = 0; + for (j = 0; j < nnn; j++) { + jj = nearest[j]; + for (k = j+1; k < nnn; k++) { + kk = nearest[k]; + delx = x[jj][0] + x[kk][0] - 2.0*xtmp; + dely = x[jj][1] + x[kk][1] - 2.0*ytmp; + delz = x[jj][2] + x[kk][2] - 2.0*ztmp; + pairs[n++] = delx*delx + dely*dely + delz*delz; - } - } - + } + } + } else { - - // calculate local crystal symmetry axes + + // calculate local crystal symmetry axes - // rsq1, rsq2 are two smallest values of R^2 - // R1, R2 are corresponding vectors Ri - Rj - // R3 is normal to R1, R2 + // rsq1, rsq2 are two smallest values of R^2 + // R1, R2 are corresponding vectors Ri - Rj + // R3 is normal to R1, R2 - double rsq1,rsq2; + double rsq1,rsq2; - double* r1 = &array_atom[i][1]; - double* r2 = &array_atom[i][4]; - double* r3 = &array_atom[i][7]; - - if (n < nnn) { - centro[i] = 0.0; - MathExtra::zero3(r1); - MathExtra::zero3(r2); - MathExtra::zero3(r3); - continue; - } + double* r1 = &array_atom[i][1]; + double* r2 = &array_atom[i][4]; + double* r3 = &array_atom[i][7]; + + if (n < nnn) { + centro[i] = 0.0; + MathExtra::zero3(r1); + MathExtra::zero3(r2); + MathExtra::zero3(r3); + continue; + } - // store nnn nearest neighs in 1st nnn locations of distsq and nearest + // store nnn nearest neighs in 1st nnn locations of distsq and nearest - select2(nnn,n,distsq,nearest); + select2(nnn,n,distsq,nearest); - n = 0; - rsq1 = rsq2 = cutsq; - for (j = 0; j < nnn; j++) { - jj = nearest[j]; - for (k = j+1; k < nnn; k++) { - kk = nearest[k]; - delx = x[jj][0] + x[kk][0] - 2.0*xtmp; - dely = x[jj][1] + x[kk][1] - 2.0*ytmp; - delz = x[jj][2] + x[kk][2] - 2.0*ztmp; - double rsq = delx*delx + dely*dely + delz*delz; - pairs[n++] = rsq; - - if (rsq < rsq2) { - if (rsq < rsq1) { - rsq2 = rsq1; - MathExtra::copy3(r1, r2); - rsq1 = rsq; - MathExtra::sub3(x[jj],x[kk],r1); - } else { - rsq2 = rsq; - MathExtra::sub3(x[jj],x[kk],r2); - } + n = 0; + rsq1 = rsq2 = cutsq; + for (j = 0; j < nnn; j++) { + jj = nearest[j]; + for (k = j+1; k < nnn; k++) { + kk = nearest[k]; + delx = x[jj][0] + x[kk][0] - 2.0*xtmp; + dely = x[jj][1] + x[kk][1] - 2.0*ytmp; + delz = x[jj][2] + x[kk][2] - 2.0*ztmp; + double rsq = delx*delx + dely*dely + delz*delz; + pairs[n++] = rsq; + + if (rsq < rsq2) { + if (rsq < rsq1) { + rsq2 = rsq1; + MathExtra::copy3(r1, r2); + rsq1 = rsq; + MathExtra::sub3(x[jj],x[kk],r1); + } else { + rsq2 = rsq; + MathExtra::sub3(x[jj],x[kk],r2); + } } - } - } + } + } - MathExtra::cross3(r1,r2,r3); - MathExtra::norm3(r1); - MathExtra::norm3(r2); - MathExtra::norm3(r3); + MathExtra::cross3(r1,r2,r3); + MathExtra::norm3(r1); + MathExtra::norm3(r2); + MathExtra::norm3(r3); } - + // store nhalf smallest pair distances in 1st nhalf locations of pairs - + select(nhalf,npairs,pairs); - + // centrosymmetry = sum of nhalf smallest squared values value = 0.0; @@ -306,9 +306,9 @@ void ComputeCentroAtom::compute_peratom() } else { centro[i] = 0.0; if (axes_flag) { - MathExtra::zero3(&array_atom[i][1]); - MathExtra::zero3(&array_atom[i][4]); - MathExtra::zero3(&array_atom[i][7]); + MathExtra::zero3(&array_atom[i][1]); + MathExtra::zero3(&array_atom[i][4]); + MathExtra::zero3(&array_atom[i][7]); } } } @@ -319,7 +319,7 @@ void ComputeCentroAtom::compute_peratom() for (ii = 0; ii < inum; ii++) { i = ilist[ii]; if (mask[i] & groupbit) - array_atom[i][0] = centro[i]; + array_atom[i][0] = centro[i]; } }