jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix whitespace

This commit is contained in:
Richard Berger 2019-12-06 14:43:45 -05:00
parent 2d4d07521d
commit 00547d906b
4 changed files with 11 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
src/USER-CGDNA/pair_oxdna2_dh.h
View File

@ -28,7 +28,7 @@ class PairOxdna2Dh : public Pair {
public: public:
PairOxdna2Dh(class LAMMPS *); PairOxdna2Dh(class LAMMPS *);
virtual ~PairOxdna2Dh(); virtual ~PairOxdna2Dh();
virtual void compute_interaction_sites(double *, double *, double *, virtual void compute_interaction_sites(double *, double *, double *,
double *); double *);
virtual void compute(int, int); virtual void compute(int, int);
void settings(int, char **); void settings(int, char **);

2
src/USER-CGDNA/pair_oxrna2_dh.cpp
View File

@ -35,7 +35,7 @@ PairOxrna2Dh::~PairOxrna2Dh()
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
compute vector COM-sugar-phosphate backbone interaction site in oxRNA2 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 e3[3], double r[3])
{ {
double d_cs_x=-0.4, d_cs_z=+0.2; double d_cs_x=-0.4, d_cs_z=+0.2;

2
src/USER-CGDNA/pair_oxrna2_hbond.cpp
View File

@ -27,7 +27,7 @@ PairOxrna2Hbond::PairOxrna2Hbond(LAMMPS *lmp) : PairOxdnaHbond(lmp)
// sequence-specific base-pairing strength // sequence-specific base-pairing strength
// A:0 C:1 G:2 U:3, 5'- [i][j] -3' // A:0 C:1 G:2 U:3, 5'- [i][j] -3'
alpha_hb[0][0] = 1.00000; alpha_hb[0][0] = 1.00000;
alpha_hb[0][1] = 1.00000; alpha_hb[0][1] = 1.00000;
alpha_hb[0][2] = 1.00000; alpha_hb[0][2] = 1.00000;

16
src/USER-CGDNA/pair_oxrna2_stk.cpp
View File

@ -49,7 +49,7 @@ PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp)
// sequence-specific stacking strength // sequence-specific stacking strength
// A:0 C:1 G:2 U:3, 5'- [i][j] -3' // 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][1] = 1.12901;
eta_st[0][2] = 1.15626; eta_st[0][2] = 1.15626;
eta_st[0][3] = 0.88850; eta_st[0][3] = 0.88850;
@ -133,7 +133,7 @@ PairOxrna2Stk::~PairOxrna2Stk()
tally energy and virial into global and per-atom accumulators tally energy and virial into global and per-atom accumulators
NOTE: Although this is a pair style interaction, the algorithm below 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. 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; if (cost6p < -1.0) cost6p = -1.0;
theta6p = acos(cost6p); theta6p = acos(cost6p);
aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0]; 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[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[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[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[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[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2];
cost9 = MathExtra::dot3(delr_ss_norm,aux3p); cost9 = MathExtra::dot3(delr_ss_norm,aux3p);
if (cost9 > 1.0) cost9 = 1.0; if (cost9 > 1.0) cost9 = 1.0;