diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/USER-CGDNA/pair_oxdna2_dh.h index 2a41524126..da72060927 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.h +++ b/src/USER-CGDNA/pair_oxdna2_dh.h @@ -28,7 +28,7 @@ class PairOxdna2Dh : public Pair { public: PairOxdna2Dh(class LAMMPS *); virtual ~PairOxdna2Dh(); - virtual void compute_interaction_sites(double *, double *, double *, + virtual void compute_interaction_sites(double *, double *, double *, double *); virtual void compute(int, int); void settings(int, char **); diff --git a/src/USER-CGDNA/pair_oxrna2_dh.cpp b/src/USER-CGDNA/pair_oxrna2_dh.cpp index 045a6aa6bc..7cc785ad39 100644 --- a/src/USER-CGDNA/pair_oxrna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxrna2_dh.cpp @@ -35,7 +35,7 @@ PairOxrna2Dh::~PairOxrna2Dh() /* ---------------------------------------------------------------------- compute vector COM-sugar-phosphate backbone interaction site in oxRNA2 ------------------------------------------------------------------------- */ -void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], +void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3], double r[3]) { double d_cs_x=-0.4, d_cs_z=+0.2; diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.cpp b/src/USER-CGDNA/pair_oxrna2_hbond.cpp index 65f266ba36..08e1b1d737 100644 --- a/src/USER-CGDNA/pair_oxrna2_hbond.cpp +++ b/src/USER-CGDNA/pair_oxrna2_hbond.cpp @@ -27,7 +27,7 @@ PairOxrna2Hbond::PairOxrna2Hbond(LAMMPS *lmp) : PairOxdnaHbond(lmp) // sequence-specific base-pairing strength // A:0 C:1 G:2 U:3, 5'- [i][j] -3' - + alpha_hb[0][0] = 1.00000; alpha_hb[0][1] = 1.00000; alpha_hb[0][2] = 1.00000; diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp index 5fd32099f3..de2cd63799 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp @@ -49,7 +49,7 @@ PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp) // sequence-specific stacking strength // A:0 C:1 G:2 U:3, 5'- [i][j] -3' - eta_st[0][0] = 0.93851; + eta_st[0][0] = 0.93851; eta_st[0][1] = 1.12901; eta_st[0][2] = 1.15626; eta_st[0][3] = 0.88850; @@ -133,7 +133,7 @@ PairOxrna2Stk::~PairOxrna2Stk() tally energy and virial into global and per-atom accumulators NOTE: Although this is a pair style interaction, the algorithm below - follows the virial incrementation of the bond style. This is because + follows the virial incrementation of the bond style. This is because the bond topology is used in the main compute loop. ------------------------------------------------------------------------- */ @@ -391,13 +391,13 @@ void PairOxrna2Stk::compute(int eflag, int vflag) if (cost6p < -1.0) cost6p = -1.0; theta6p = acos(cost6p); - aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0]; - aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1]; - aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2]; + aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0]; + aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1]; + aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2]; - aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0]; - aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1]; - aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2]; + aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0]; + aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1]; + aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2]; cost9 = MathExtra::dot3(delr_ss_norm,aux3p); if (cost9 > 1.0) cost9 = 1.0;