Unverified Commit 8212dca6 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1447 from ohenrich/user-cgdna 

Homogenised label of relative hbond and stk strength to conform with oxDNA literature
parents 97ce76e7 d7dd7812

src/USER-CGDNA/pair_oxdna2_coaxstk.cpp

+1 −1
Original line number Diff line number Diff line
@@ -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);

src/USER-CGDNA/pair_oxdna_coaxstk.cpp

+1 −1
Original line number Diff line number Diff line
@@ -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);

src/USER-CGDNA/pair_oxdna_hbond.cpp

+6 −6
Original line number Diff line number Diff line
@@ -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];

src/USER-CGDNA/pair_oxdna_stk.cpp

+6 −6
Original line number Diff line number Diff line
@@ -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];

src/USER-CGDNA/pair_oxdna_xstk.cpp

+1 −1
Original line number Diff line number Diff line
@@ -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);

src/USER-CGDNA/pair_oxdna2_dh.cpp

+2 −2

File changed.

Contains only whitespace changes.

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