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Homogenised label of relative hbond and stk strength to conform with oxDNA literature

This commit is contained in:
Oliver Henrich 2019-05-02 16:48:41 +01:00
parent 97ce76e759
commit d7dd78126c
6 changed files with 17 additions and 17 deletions
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2
src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
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@ -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);

4
src/USER-CGDNA/pair_oxdna2_dh.cpp
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@ -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]);
}
}

2
src/USER-CGDNA/pair_oxdna_coaxstk.cpp
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@ -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);

12
src/USER-CGDNA/pair_oxdna_hbond.cpp
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@ -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];

12
src/USER-CGDNA/pair_oxdna_stk.cpp
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@ -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];

2
src/USER-CGDNA/pair_oxdna_xstk.cpp
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@ -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);