Enabled unique base-pairing (7cf9ef42) · Commits · 郑智淋 / lammps

src/USER-CGDNA/pair_oxdna_hbond.cpp

+16 −5

Original line number	Diff line number	Diff line
		@@ -616,7 +616,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
		if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond");
		if (!allocated) allocate();

		int ilo,ihi,jlo,jhi;
		int ilo,ihi,jlo,jhi,imod4,jmod4;
		force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
		force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);

		@@ -729,8 +729,13 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
		for (int i = ilo; i <= ihi; i++) {
		for (int j = MAX(jlo,i); j <= jhi; j++) {

		imod4 = i%4;
		if (imod4 == 0) imod4 = 4;
		jmod4 = j%4;
		if (jmod4 == 0) jmod4 = 4;

		epsilon_hb[i][j] = epsilon_hb_one;
		if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[i-1][j-1];
		if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[imod4-1][jmod4-1];
		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;
		@@ -741,7 +746,7 @@ 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_hb[i-1][j-1];
		if (seqdepflag) shift_hb[i][j] *= alpha_hb[imod4-1][jmod4-1];

		a_hb1[i][j] = a_hb1_one;
		theta_hb1_0[i][j] = theta_hb1_0_one;
		@@ -820,6 +825,7 @@ void PairOxdnaHbond::init_list(int id, NeighList *ptr)

		double PairOxdnaHbond::init_one(int i, int j)
		{
		int imod4,jmod4;

		if (setflag[i][j] == 0) {
		error->all(FLERR,"Coefficient mixing not defined in oxDNA");
		@@ -828,8 +834,13 @@ double PairOxdnaHbond::init_one(int i, int j)
		error->all(FLERR,"Offset not supported in oxDNA");
		}

		imod4 = i%4;
		if (imod4 == 0) imod4 = 4;
		jmod4 = j%4;
		if (jmod4 == 0) jmod4 = 4;

		if (seqdepflag) {
		epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1];
		epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[imod4-1][jmod4-1] * alpha_hb[jmod4-1][imod4-1];
		}
		else {
		epsilon_hb[j][i] = epsilon_hb[i][j];
		@@ -844,7 +855,7 @@ 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_hb[i-1][j-1] * alpha_hb[j-1][i-1];
		shift_hb[j][i] = shift_hb[i][j] / alpha_hb[imod4-1][jmod4-1] * alpha_hb[jmod4-1][imod4-1];
		}
		else {
		shift_hb[j][i] = shift_hb[i][j];

src/USER-CGDNA/pair_oxdna_stk.cpp

+19 −7

Original line number	Diff line number	Diff line
		@@ -761,7 +761,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
		if (narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
		if (!allocated) allocate();

		int ilo,ihi,jlo,jhi;
		int ilo,ihi,jlo,jhi,imod4,jmod4;
		force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
		force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);

		@@ -860,8 +860,13 @@ void PairOxdnaStk::coeff(int narg, char **arg)
		for (int i = ilo; i <= ihi; i++) {
		for (int j = MAX(jlo,i); j <= jhi; j++) {

		imod4 = i%4;
		if (imod4 == 0) imod4 = 4;
		jmod4 = j%4;
		if (jmod4 == 0) jmod4 = 4;

		epsilon_st[i][j] = epsilon_st_one;
		if (seqdepflag) epsilon_st[i][j] *= eta_st[i-1][j-1];
		if (seqdepflag) epsilon_st[i][j] *= eta_st[imod4-1][jmod4-1];
		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;
		@@ -872,7 +877,7 @@ 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] *= eta_st[i-1][j-1];
		if (seqdepflag) shift_st[i][j] *= eta_st[imod4-1][jmod4-1];

		a_st4[i][j] = a_st4_one;
		theta_st4_0[i][j] = theta_st4_0_one;
		@@ -944,6 +949,8 @@ void PairOxdnaStk::init_list(int id, NeighList *ptr)
		double PairOxdnaStk::init_one(int i, int j)
		{

		int imod4,jmod4;

		if (setflag[i][j] == 0) {
		error->all(FLERR,"Coefficient mixing not defined in oxDNA");
		}
		@@ -951,8 +958,13 @@ double PairOxdnaStk::init_one(int i, int j)
		error->all(FLERR,"Offset not supported in oxDNA");
		}

		imod4 = i%4;
		if (imod4 == 0) imod4 = 4;
		jmod4 = j%4;
		if (jmod4 == 0) jmod4 = 4;

		if (seqdepflag) {
		epsilon_st[j][i] = epsilon_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1];
		epsilon_st[j][i] = epsilon_st[i][j] / eta_st[imod4-1][jmod4-1] * eta_st[jmod4-1][imod4-1];
		}
		else {
		epsilon_st[j][i] = epsilon_st[i][j];
		@@ -967,7 +979,7 @@ 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] / eta_st[i-1][j-1] * eta_st[j-1][i-1];
		shift_st[j][i] = shift_st[i][j] / eta_st[imod4-1][jmod4-1] * eta_st[jmod4-1][imod4-1];
		}
		else {
		shift_st[j][i] = shift_st[i][j];

Admin message