diff --git a/src/CG-DNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp index 317b6b3c9b..a8cd52e651 100644 --- a/src/CG-DNA/bond_oxdna_fene.cpp +++ b/src/CG-DNA/bond_oxdna_fene.cpp @@ -146,14 +146,13 @@ void BondOxdnaFene::ev_tally_xyz(int i, int j, int nlocal, int newton_bond, doub ------------------------------------------------------------------------- */ void BondOxdnaFene::compute(int eflag, int vflag) { - - int a, b, in, type; - double delf[3], delta[3], deltb[3]; // force, torque increment;; - double delr[3], ebond, fbond; - double rsq, Deltasq, rlogarg; - double r, rr0, rr0sq; + int a,b,in,type; + double delf[3],delta[3],deltb[3]; // force, torque increment;; + double delr[3],ebond,fbond; + double rsq,Deltasq,rlogarg; + double r,rr0,rr0sq; // vectors COM-backbone site in lab frame - double ra_cs[3], rb_cs[3]; + double ra_cs[3],rb_cs[3]; // Cartesian unit vectors in lab frame double ax[3],ay[3],az[3]; double bx[3],by[3],bz[3]; @@ -188,13 +187,13 @@ void BondOxdnaFene::compute(int eflag, int vflag) b = bondlist[in][0]; type = bondlist[in][2]; - ax[0] = nx_xtrct[a][0]; - ax[1] = nx_xtrct[a][1]; - ax[2] = nx_xtrct[a][2]; - bx[0] = nx_xtrct[b][0]; - bx[1] = nx_xtrct[b][1]; - bx[2] = nx_xtrct[b][2]; - // (a/b)y/z not needed here as oxDNA(1) co-linear + ax[0] = nx_xtrct[a][0]; + ax[1] = nx_xtrct[a][1]; + ax[2] = nx_xtrct[a][2]; + bx[0] = nx_xtrct[b][0]; + bx[1] = nx_xtrct[b][1]; + bx[2] = nx_xtrct[b][2]; + // (a/b)y/z not needed here as oxDNA(1) co-linear // vector COM-backbone site a and b compute_interaction_sites(ax, ay, az, ra_cs); @@ -266,7 +265,7 @@ void BondOxdnaFene::compute(int eflag, int vflag) if (evflag) ev_tally_xyz(a, b, nlocal, newton_bond, ebond, delf[0], delf[1], delf[2], x[a][0] - x[b][0], x[a][1] - x[b][1], x[a][2] - x[b][2]); - } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/CG-DNA/pair_oxdna_coaxstk.cpp b/src/CG-DNA/pair_oxdna_coaxstk.cpp index a5b94403da..e03de69f57 100644 --- a/src/CG-DNA/pair_oxdna_coaxstk.cpp +++ b/src/CG-DNA/pair_oxdna_coaxstk.cpp @@ -405,7 +405,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag) gamma = d_cs - d_cst; gammacub = gamma * gamma * gamma; rinv_ss_cub = rinv_ss * rinv_ss * rinv_ss; - aybx = MathExtra::dot3(ay,bx); azbx = MathExtra::dot3(az,bx); rax = MathExtra::dot3(delr_st_norm,ax); @@ -545,7 +544,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag) gamma = d_cs - d_cst; gammacub = gamma * gamma * gamma; rinv_ss_cub = rinv_ss * rinv_ss * rinv_ss; - aybx = MathExtra::dot3(ay,bx); azbx = MathExtra::dot3(az,bx); rax = MathExtra::dot3(delr_st_norm,ax); diff --git a/src/CG-DNA/pair_oxdna_excv.cpp b/src/CG-DNA/pair_oxdna_excv.cpp index 096d9b5171..2ae5995ebb 100644 --- a/src/CG-DNA/pair_oxdna_excv.cpp +++ b/src/CG-DNA/pair_oxdna_excv.cpp @@ -115,9 +115,6 @@ void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3], void PairOxdnaExcv::compute(int eflag, int vflag) { - - //printf("\n ExcVol HERE, proc = %d \n", comm->me); - double delf[3],delta[3],deltb[3]; // force, torque increment; double evdwl,fpair,factor_lj; double rtmp_s[3],rtmp_b[3]; diff --git a/src/CG-DNA/pair_oxdna_hbond.cpp b/src/CG-DNA/pair_oxdna_hbond.cpp index 07a1ce332b..eb04d74f2e 100644 --- a/src/CG-DNA/pair_oxdna_hbond.cpp +++ b/src/CG-DNA/pair_oxdna_hbond.cpp @@ -218,7 +218,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag) rb_chb[0] = d_chb*bx[0]; rb_chb[1] = d_chb*bx[1]; rb_chb[2] = d_chb*bx[2]; - + // vector h-bonding site b to a delr_hb[0] = x[a][0] + ra_chb[0] - x[b][0] - rb_chb[0]; delr_hb[1] = x[a][1] + ra_chb[1] - x[b][1] - rb_chb[1];