From d7dd78126c6423d6ecbdec7a93f505272fcbe0b3 Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Thu, 2 May 2019 16:48:41 +0100 Subject: [PATCH] Homogenised label of relative hbond and stk strength to conform with oxDNA literature --- src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 2 +- src/USER-CGDNA/pair_oxdna2_dh.cpp | 4 ++-- src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 2 +- src/USER-CGDNA/pair_oxdna_hbond.cpp | 12 ++++++------ src/USER-CGDNA/pair_oxdna_stk.cpp | 12 ++++++------ src/USER-CGDNA/pair_oxdna_xstk.cpp | 2 +- 6 files changed, 17 insertions(+), 17 deletions(-) diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index f54197aea7..dfea97f0bf 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -62,9 +62,9 @@ PairOxdna2Coaxstk::~PairOxdna2Coaxstk() memory->destroy(cut_cxst_hi); memory->destroy(cut_cxst_lc); memory->destroy(cut_cxst_hc); + memory->destroy(cutsq_cxst_hc); memory->destroy(b_cxst_lo); memory->destroy(b_cxst_hi); - memory->destroy(cutsq_cxst_hc); memory->destroy(a_cxst1); memory->destroy(theta_cxst1_0); diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 10e7121427..b4afad12db 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -225,8 +225,8 @@ void PairOxdna2Dh::compute(int eflag, int vflag) // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair, - evdwl,0.0,fpair,delr[0],delr[1],delr[2]); + if (evflag) ev_tally(a,b,nlocal,newton_pair, + evdwl,0.0,fpair,delr[0],delr[1],delr[2]); } } diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 6d3061620d..6f3fa4fa4e 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -62,9 +62,9 @@ PairOxdnaCoaxstk::~PairOxdnaCoaxstk() memory->destroy(cut_cxst_hi); memory->destroy(cut_cxst_lc); memory->destroy(cut_cxst_hc); + memory->destroy(cutsq_cxst_hc); memory->destroy(b_cxst_lo); memory->destroy(b_cxst_hi); - memory->destroy(cutsq_cxst_hc); memory->destroy(a_cxst1); memory->destroy(theta_cxst1_0); diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index d2aa236a05..8cd28f10c8 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -40,7 +40,7 @@ using namespace MFOxdna; // sequence-specific base-pairing strength // A:0 C:1 G:2 T:3, 5'- (i,j) -3' -static const double alpha[4][4] = +static const double alpha_hb[4][4] = {{1.00000,1.00000,1.00000,0.82915}, {1.00000,1.00000,1.15413,1.00000}, {1.00000,1.15413,1.00000,1.00000}, @@ -71,10 +71,10 @@ PairOxdnaHbond::~PairOxdnaHbond() memory->destroy(cut_hb_hi); memory->destroy(cut_hb_lc); memory->destroy(cut_hb_hc); + memory->destroy(cutsq_hb_hc); memory->destroy(b_hb_lo); memory->destroy(b_hb_hi); memory->destroy(shift_hb); - memory->destroy(cutsq_hb_hc); memory->destroy(a_hb1); memory->destroy(theta_hb1_0); @@ -732,7 +732,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) for (int j = MAX(jlo,i); j <= jhi; j++) { epsilon_hb[i][j] = epsilon_hb_one; - if (seqdepflag) epsilon_hb[i][j] *= alpha[i-1][j-1]; + if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[i-1][j-1]; a_hb[i][j] = a_hb_one; cut_hb_0[i][j] = cut_hb_0_one; cut_hb_c[i][j] = cut_hb_c_one; @@ -743,7 +743,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) b_hb_lo[i][j] = b_hb_lo_one; b_hb_hi[i][j] = b_hb_hi_one; shift_hb[i][j] = shift_hb_one; - if (seqdepflag) shift_hb[i][j] *= alpha[i-1][j-1]; + if (seqdepflag) shift_hb[i][j] *= alpha_hb[i-1][j-1]; a_hb1[i][j] = a_hb1_one; theta_hb1_0[i][j] = theta_hb1_0_one; @@ -831,7 +831,7 @@ double PairOxdnaHbond::init_one(int i, int j) } if (seqdepflag) { - epsilon_hb[j][i] = epsilon_hb[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1]; + epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1]; } else { epsilon_hb[j][i] = epsilon_hb[i][j]; @@ -846,7 +846,7 @@ double PairOxdnaHbond::init_one(int i, int j) cut_hb_lc[j][i] = cut_hb_lc[i][j]; cut_hb_hc[j][i] = cut_hb_hc[i][j]; if (seqdepflag) { - shift_hb[j][i] = shift_hb[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1]; + shift_hb[j][i] = shift_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1]; } else { shift_hb[j][i] = shift_hb[i][j]; diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 4cbc0317dd..93c65979ac 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -40,7 +40,7 @@ using namespace MFOxdna; // sequence-specific stacking strength // A:0 C:1 G:2 T:3, 5'- (i,j) -3' -static const double alpha[4][4] = +static const double eta_st[4][4] = {{1.11960,1.00852,0.96950,0.99632}, {1.01889,0.97804,1.02681,0.96950}, {0.98169,1.05913,0.97804,1.00852}, @@ -156,7 +156,7 @@ void PairOxdnaStk::compute(int eflag, int vflag) evdwl = 0.0; ev_init(eflag,vflag); - // loop over stacking interaction neighours using bond topology + // loop over stacking interaction neighbors using bond topology for (in = 0; in < nbondlist; in++) { @@ -774,7 +774,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) for (int j = MAX(jlo,i); j <= jhi; j++) { epsilon_st[i][j] = epsilon_st_one; - if (seqdepflag) epsilon_st[i][j] *= alpha[i-1][j-1]; + if (seqdepflag) epsilon_st[i][j] *= eta_st[i-1][j-1]; a_st[i][j] = a_st_one; cut_st_0[i][j] = cut_st_0_one; cut_st_c[i][j] = cut_st_c_one; @@ -785,7 +785,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) b_st_lo[i][j] = b_st_lo_one; b_st_hi[i][j] = b_st_hi_one; shift_st[i][j] = shift_st_one; - if (seqdepflag) shift_st[i][j] *= alpha[i-1][j-1]; + if (seqdepflag) shift_st[i][j] *= eta_st[i-1][j-1]; a_st4[i][j] = a_st4_one; theta_st4_0[i][j] = theta_st4_0_one; @@ -865,7 +865,7 @@ double PairOxdnaStk::init_one(int i, int j) } if (seqdepflag) { - epsilon_st[j][i] = epsilon_st[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1]; + epsilon_st[j][i] = epsilon_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1]; } else { epsilon_st[j][i] = epsilon_st[i][j]; @@ -880,7 +880,7 @@ double PairOxdnaStk::init_one(int i, int j) cut_st_lc[j][i] = cut_st_lc[i][j]; cut_st_hc[j][i] = cut_st_hc[i][j]; if (seqdepflag) { - shift_st[j][i] = shift_st[i][j] / alpha[i-1][j-1] * alpha[j-1][i-1]; + shift_st[j][i] = shift_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1]; } else { shift_st[j][i] = shift_st[i][j]; diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 071886556c..1365d0d2b2 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -62,9 +62,9 @@ PairOxdnaXstk::~PairOxdnaXstk() memory->destroy(cut_xst_hi); memory->destroy(cut_xst_lc); memory->destroy(cut_xst_hc); + memory->destroy(cutsq_xst_hc); memory->destroy(b_xst_lo); memory->destroy(b_xst_hi); - memory->destroy(cutsq_xst_hc); memory->destroy(a_xst1); memory->destroy(theta_xst1_0);