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Fixed whitespace issues

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This commit is contained in:
Oliver Henrich
2021-11-03 10:59:04 +00:00
parent cf968ef286
commit b8970366e0
12 changed files with 103 additions and 112 deletions
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4
src/CG-DNA/bond_oxdna_fene.cpp
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@ -174,7 +174,7 @@ void BondOxdnaFene::compute(int eflag, int vflag)
ebond = 0.0;
ev_init(eflag, vflag);
// n(x/y/z)_xtrct = extracted q_to_exyz from oxdna_excv
// n(x/y/z)_xtrct = extracted local unit vectors in lab frame from oxdna_excv
int dim;
nx_xtrct = (double **) force->pair->extract("nx",dim);
ny_xtrct = (double **) force->pair->extract("ny",dim);
@ -194,7 +194,7 @@ void BondOxdnaFene::compute(int eflag, int vflag)
bx[0] = nx_xtrct[b][0];
bx[1] = nx_xtrct[b][1];
bx[2] = nx_xtrct[b][2];
//(a/b)y/z not needed here as oxDNA(1) co-linear
// (a/b)y/z not needed here as oxDNA(1) co-linear
// vector COM-backbone site a and b
compute_interaction_sites(ax, ay, az, ra_cs);

2
src/CG-DNA/bond_oxdna_fene.h
View File

@ -40,7 +40,7 @@ class BondOxdnaFene : public Bond {
protected:
double *k, *Delta, *r0; // FENE
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for q_to_exyz storage
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
void allocate();
void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double);

37
src/CG-DNA/pair_oxdna_coaxstk.cpp
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@ -106,9 +106,6 @@ PairOxdnaCoaxstk::~PairOxdnaCoaxstk()
void PairOxdnaCoaxstk::compute(int eflag, int vflag)
{
//printf("\n Coaxstk HERE, proc = %d \n", comm->me);
double delf[3],delt[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair,factor_lj;
double v1tmp[3],v2tmp[3],v3tmp[3];
@ -162,7 +159,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// n(x/y/z)_xtrct = extracted q_to_exyz from oxdna_excv
// n(x/y/z)_xtrct = extracted local unit vectors in lab frame from oxdna_excv
int dim;
nx_xtrct = (double **) force->pair->extract("nx",dim);
ny_xtrct = (double **) force->pair->extract("ny",dim);
@ -176,9 +173,9 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
atype = type[a];
ax[0] = nx_xtrct[a][0];
ax[1] = nx_xtrct[a][1];
ax[2] = nx_xtrct[a][2];
//a(y/z) not needed here as oxDNA(1) co-linear
ax[1] = nx_xtrct[a][1];
ax[2] = nx_xtrct[a][2];
// a(y/z) not needed here as oxDNA(1) co-linear
// vector COM a - stacking site a
ra_cst[0] = d_cst*ax[0];
@ -202,9 +199,9 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
btype = type[b];
bx[0] = nx_xtrct[b][0];
bx[1] = nx_xtrct[b][1];
bx[2] = nx_xtrct[b][2];
//b(y/z) not needed here as oxDNA(1) co-linear
bx[1] = nx_xtrct[b][1];
bx[2] = nx_xtrct[b][2];
// b(y/z) not needed here as oxDNA(1) co-linear
// vector COM b - stacking site b
rb_cst[0] = d_cst*bx[0];
@ -256,12 +253,12 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
// early rejection criterium
if (f4t1) {
az[0] = nz_xtrct[a][0];
az[1] = nz_xtrct[a][1];
az[2] = nz_xtrct[a][2];
bz[0] = nz_xtrct[b][0];
bz[1] = nz_xtrct[b][1];
bz[2] = nz_xtrct[b][2];
az[0] = nz_xtrct[a][0];
az[1] = nz_xtrct[a][1];
az[2] = nz_xtrct[a][2];
bz[0] = nz_xtrct[b][0];
bz[1] = nz_xtrct[b][1];
bz[2] = nz_xtrct[b][2];
cost4 = MathExtra::dot3(az,bz);
if (cost4 > 1.0) cost4 = 1.0;
@ -398,9 +395,9 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
// cosphi3 and cosphi4 (=cosphi3) force and virial
if (cosphi3) {
ay[0] = ny_xtrct[a][0];
ay[1] = ny_xtrct[a][1];
ay[2] = ny_xtrct[a][2];
ay[0] = ny_xtrct[a][0];
ay[1] = ny_xtrct[a][1];
ay[2] = ny_xtrct[a][2];
finc = -f2 * f4t1* f4t4 * f4t5 * f4t6 * 2.0 * f5c3 * df5c3 * factor_lj;
fpair += finc;
@ -408,6 +405,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
gamma = d_cs - d_cst;
gammacub = gamma * gamma * gamma;
rinv_ss_cub = rinv_ss * rinv_ss * rinv_ss;
aybx = MathExtra::dot3(ay,bx);
azbx = MathExtra::dot3(az,bx);
rax = MathExtra::dot3(delr_st_norm,ax);
@ -547,6 +545,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
gamma = d_cs - d_cst;
gammacub = gamma * gamma * gamma;
rinv_ss_cub = rinv_ss * rinv_ss * rinv_ss;
aybx = MathExtra::dot3(ay,bx);
azbx = MathExtra::dot3(az,bx);
rax = MathExtra::dot3(delr_st_norm,ax);

2
src/CG-DNA/pair_oxdna_coaxstk.h
View File

@ -63,7 +63,7 @@ class PairOxdnaCoaxstk : public Pair {
double **a_cxst3p, **cosphi_cxst3p_ast, **b_cxst3p, **cosphi_cxst3p_c;
double **a_cxst4p, **cosphi_cxst4p_ast, **b_cxst4p, **cosphi_cxst4p_c;
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for q_to_exyz storage
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
virtual void allocate();
};

61
src/CG-DNA/pair_oxdna_excv.cpp
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@ -50,7 +50,7 @@ PairOxdnaExcv::~PairOxdnaExcv()
{
if (allocated) {
memory->destroy(nx);
memory->destroy(nx);
memory->destroy(ny);
memory->destroy(nz);
@ -156,24 +156,23 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over all local atoms, handle calculation of local reference frame
// loop over all local atoms, calculation of local reference frame
for (in = 0; in < atom->nlocal; in++) {
int n = alist[in];
double *qn,nx_temp[3],ny_temp[3],nz_temp[3]; // quaternion and Cartesian unit vectors in lab frame
qn=bonus[ellipsoid[n]].quat;
MathExtra::q_to_exyz(qn,nx_temp,ny_temp,nz_temp);
nx[n][0] = nx_temp[0];
nx[n][1] = nx_temp[1];
nx[n][2] = nx_temp[2];
ny[n][0] = ny_temp[0];
ny[n][1] = ny_temp[1];
ny[n][2] = ny_temp[2];
nz[n][0] = nz_temp[0];
nz[n][1] = nz_temp[1];
qn=bonus[ellipsoid[n]].quat;
MathExtra::q_to_exyz(qn,nx_temp,ny_temp,nz_temp);
nx[n][0] = nx_temp[0];
nx[n][1] = nx_temp[1];
nx[n][2] = nx_temp[2];
ny[n][0] = ny_temp[0];
ny[n][1] = ny_temp[1];
ny[n][2] = ny_temp[2];
nz[n][0] = nz_temp[0];
nz[n][1] = nz_temp[1];
nz[n][2] = nz_temp[2];
}
@ -188,14 +187,14 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
atype = type[a];
ax[0] = nx[a][0];
ax[1] = nx[a][1];
ax[2] = nx[a][2];
ay[0] = ny[a][0];
ay[1] = ny[a][1];
ay[2] = ny[a][2];
az[0] = nz[a][0];
az[1] = nz[a][1];
az[2] = nz[a][2];
ax[1] = nx[a][1];
ax[2] = nx[a][2];
ay[0] = ny[a][0];
ay[1] = ny[a][1];
ay[2] = ny[a][2];
az[0] = nz[a][0];
az[1] = nz[a][1];
az[2] = nz[a][2];
// vector COM - backbone and base site a
compute_interaction_sites(ax,ay,az,ra_cs,ra_cb);
@ -220,14 +219,14 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
btype = type[b];
bx[0] = nx[b][0];
bx[1] = nx[b][1];
bx[2] = nx[b][2];
by[0] = ny[b][0];
by[1] = ny[b][1];
by[2] = ny[b][2];
bz[0] = nz[b][0];
bz[1] = nz[b][1];
bz[2] = nz[b][2];
bx[1] = nx[b][1];
bx[2] = nx[b][2];
by[0] = ny[b][0];
by[1] = ny[b][1];
by[2] = ny[b][2];
bz[0] = nz[b][0];
bz[1] = nz[b][1];
bz[2] = nz[b][2];
// vector COM - backbone and base site b
compute_interaction_sites(bx,by,bz,rb_cs,rb_cb);

3
src/CG-DNA/pair_oxdna_excv.h
View File

@ -56,8 +56,7 @@ class PairOxdnaExcv : public Pair {
double **epsilon_bb, **sigma_bb, **cut_bb_ast, **cutsq_bb_ast;
double **lj1_bb, **lj2_bb, **b_bb, **cut_bb_c, **cutsq_bb_c;
// per-atom arrays for q_to_exyz storage
double **nx, **ny, **nz;
double **nx, **ny, **nz; // per-atom arrays for local unit vectors
virtual void allocate();
};

34
src/CG-DNA/pair_oxdna_hbond.cpp
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@ -179,7 +179,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// n(x/y/z)_xtrct = extracted q_to_exyz from oxdna_excv
// n(x/y/z)_xtrct = extracted local unit vectors from oxdna_excv
int dim;
nx_xtrct = (double **) force->pair->extract("nx",dim);
ny_xtrct = (double **) force->pair->extract("ny",dim);
@ -193,10 +193,10 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
atype = type[a];
ax[0] = nx_xtrct[a][0];
ax[1] = nx_xtrct[a][1];
ax[2] = nx_xtrct[a][2];
ra_chb[0] = d_chb*ax[0];
ax[1] = nx_xtrct[a][1];
ax[2] = nx_xtrct[a][2];
ra_chb[0] = d_chb*ax[0];
ra_chb[1] = d_chb*ax[1];
ra_chb[2] = d_chb*ax[2];
@ -211,11 +211,11 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
btype = type[b];
bx[0] = nx_xtrct[b][0];
bx[1] = nx_xtrct[b][1];
bx[2] = nx_xtrct[b][2];
rb_chb[0] = d_chb*bx[0];
bx[0] = nx_xtrct[b][0];
bx[1] = nx_xtrct[b][1];
bx[2] = nx_xtrct[b][2];
rb_chb[0] = d_chb*bx[0];
rb_chb[1] = d_chb*bx[1];
rb_chb[2] = d_chb*bx[2];
@ -272,12 +272,12 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
// early rejection criterium
if (f4t3) {
az[0] = nz_xtrct[a][0];
az[1] = nz_xtrct[a][1];
az[2] = nz_xtrct[a][2];
bz[0] = nz_xtrct[b][0];
bz[1] = nz_xtrct[b][1];
bz[2] = nz_xtrct[b][2];
az[0] = nz_xtrct[a][0];
az[1] = nz_xtrct[a][1];
az[2] = nz_xtrct[a][2];
bz[0] = nz_xtrct[b][0];
bz[1] = nz_xtrct[b][1];
bz[2] = nz_xtrct[b][2];
cost4 = MathExtra::dot3(az,bz);
if (cost4 > 1.0) cost4 = 1.0;
@ -1249,4 +1249,4 @@ void *PairOxdnaHbond::extract(const char *str, int &dim)
if (strcmp(str,"dtheta_hb8_c") == 0) return (void *) dtheta_hb8_c;
return nullptr;
}
}

2
src/CG-DNA/pair_oxdna_hbond.h
View File

@ -67,7 +67,7 @@ class PairOxdnaHbond : public Pair {
double **a_hb8, **theta_hb8_0, **dtheta_hb8_ast;
double **b_hb8, **dtheta_hb8_c;
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for q_to_exyz storage
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
int seqdepflag;

39
src/CG-DNA/pair_oxdna_stk.cpp
View File

@ -212,9 +212,6 @@ void PairOxdnaStk::ev_tally_xyz(int i, int j, int nlocal, int newton_bond,
void PairOxdnaStk::compute(int eflag, int vflag)
{
//printf("\n Stk HERE, proc = %d \n", comm->me);
double delf[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair;
double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
@ -258,7 +255,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
evdwl = 0.0;
ev_init(eflag,vflag);
// n(x/y/z)_xtrct = extracted q_to_exyz from oxdna_excv
// n(x/y/z)_xtrct = extracted local unit vectors from oxdna_excv
int dim;
nx_xtrct = (double **) force->pair->extract("nx",dim);
ny_xtrct = (double **) force->pair->extract("ny",dim);
@ -282,13 +279,13 @@ void PairOxdnaStk::compute(int eflag, int vflag)
// a now in 3' direction, b in 5' direction
ax[0] = nx_xtrct[a][0];
ax[1] = nx_xtrct[a][1];
ax[2] = nx_xtrct[a][2];
bx[0] = nx_xtrct[b][0];
bx[1] = nx_xtrct[b][1];
bx[2] = nx_xtrct[b][2];
//(a/b)y/z not needed here as oxDNA(1) co-linear
ax[0] = nx_xtrct[a][0];
ax[1] = nx_xtrct[a][1];
ax[2] = nx_xtrct[a][2];
bx[0] = nx_xtrct[b][0];
bx[1] = nx_xtrct[b][1];
bx[2] = nx_xtrct[b][2];
// (a/b)y/z not needed here as oxDNA(1) co-linear
// vector COM a - stacking site a
ra_cst[0] = d_cst*ax[0];
@ -346,12 +343,12 @@ void PairOxdnaStk::compute(int eflag, int vflag)
// early rejection criterium
if (f1) {
az[0] = nz_xtrct[a][0];
az[1] = nz_xtrct[a][1];
az[2] = nz_xtrct[a][2];
bz[0] = nz_xtrct[b][0];
bz[1] = nz_xtrct[b][1];
bz[2] = nz_xtrct[b][2];
az[0] = nz_xtrct[a][0];
az[1] = nz_xtrct[a][1];
az[2] = nz_xtrct[a][2];
bz[0] = nz_xtrct[b][0];
bz[1] = nz_xtrct[b][1];
bz[2] = nz_xtrct[b][2];
// theta4 angle and correction
cost4 = MathExtra::dot3(bz,az);
@ -377,12 +374,12 @@ void PairOxdnaStk::compute(int eflag, int vflag)
// early rejection criterium
if (f4t5) {
ay[0] = ny_xtrct[a][0];
ay[0] = ny_xtrct[a][0];
ay[1] = ny_xtrct[a][1];
ay[2] = ny_xtrct[a][2];
by[0] = ny_xtrct[b][0];
ay[2] = ny_xtrct[a][2];
by[0] = ny_xtrct[b][0];
by[1] = ny_xtrct[b][1];
by[2] = ny_xtrct[b][2];
by[2] = ny_xtrct[b][2];
cost6p = MathExtra::dot3(delr_st_norm,az);
if (cost6p > 1.0) cost6p = 1.0;

2
src/CG-DNA/pair_oxdna_stk.h
View File

@ -60,7 +60,7 @@ class PairOxdnaStk : public Pair {
double **a_st1, **cosphi_st1_ast, **b_st1, **cosphi_st1_c;
double **a_st2, **cosphi_st2_ast, **b_st2, **cosphi_st2_c;
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for q_to_exyz storage
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
int seqdepflag;

27
src/CG-DNA/pair_oxdna_xstk.cpp
View File

@ -111,9 +111,6 @@ PairOxdnaXstk::~PairOxdnaXstk()
void PairOxdnaXstk::compute(int eflag, int vflag)
{
//printf("\n Xstk HERE, proc = %d \n", comm->me);
double delf[3],delta[3],deltb[3]; // force, torque increment;
double evdwl,fpair,finc,tpair,factor_lj;
double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb;
@ -159,7 +156,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// n(x/y/z)_xtrct = extracted q_to_exyz from oxdna_excv
// n(x/y/z)_xtrct = extracted local unit vectors from oxdna_excv
int dim;
nx_xtrct = (double **) force->pair->extract("nx",dim);
ny_xtrct = (double **) force->pair->extract("ny",dim);
@ -173,9 +170,9 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
atype = type[a];
ax[0] = nx_xtrct[a][0];
ax[1] = nx_xtrct[a][1];
ax[2] = nx_xtrct[a][2];
//a(y/z) not needed here as oxDNA(1) co-linear
ax[1] = nx_xtrct[a][1];
ax[2] = nx_xtrct[a][2];
// a(y/z) not needed here as oxDNA(1) co-linear
ra_chb[0] = d_chb*ax[0];
ra_chb[1] = d_chb*ax[1];
@ -193,9 +190,9 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
btype = type[b];
bx[0] = nx_xtrct[b][0];
bx[1] = nx_xtrct[b][1];
bx[2] = nx_xtrct[b][2];
//b(y/z) not needed here as oxDNA(1) co-linear
bx[1] = nx_xtrct[b][1];
bx[2] = nx_xtrct[b][2];
// b(y/z) not needed here as oxDNA(1) co-linear
rb_chb[0] = d_chb*bx[0];
rb_chb[1] = d_chb*bx[1];
@ -254,12 +251,12 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
// early rejection criterium
if (f4t3) {
az[0] = nz_xtrct[a][0];
az[0] = nz_xtrct[a][0];
az[1] = nz_xtrct[a][1];
az[2] = nz_xtrct[a][2];
bz[0] = nz_xtrct[b][0];
bz[1] = nz_xtrct[b][1];
bz[2] = nz_xtrct[b][2];
az[2] = nz_xtrct[a][2];
bz[0] = nz_xtrct[b][0];
bz[1] = nz_xtrct[b][1];
bz[2] = nz_xtrct[b][2];
cost4 = MathExtra::dot3(az,bz);
if (cost4 > 1.0) cost4 = 1.0;

2
src/CG-DNA/pair_oxdna_xstk.h
View File

@ -66,7 +66,7 @@ class PairOxdnaXstk : public Pair {
double **a_xst8, **theta_xst8_0, **dtheta_xst8_ast;
double **b_xst8, **dtheta_xst8_c;
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for q_to_exyz storage
double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
virtual void allocate();