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Merge pull request #2507 from ohenrich/user-cgdna
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USER-CGDNA: Introduced ellipsoid pointer in quaternion data access
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@akohlmey
akohlmey committed Dec 7, 2020
2 parents 9feb741 + 90f00c0 commit 33888ec
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Showing 10 changed files with 30 additions and 20 deletions.
5 changes: 3 additions & 2 deletions src/USER-CGDNA/bond_oxdna_fene.cpp
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Expand Up @@ -173,6 +173,7 @@ void BondOxdnaFene::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
Expand All @@ -190,9 +191,9 @@ void BondOxdnaFene::compute(int eflag, int vflag)
b = bondlist[in][0];
type = bondlist[in][2];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);
qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

// vector COM-backbone site a and b
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5 changes: 3 additions & 2 deletions src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
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Expand Up @@ -133,6 +133,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int a,b,ia,ib,anum,bnum,atype,btype;

Expand All @@ -154,7 +155,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
a = alist[ia];
atype = type[a];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);

// vector COM a - stacking site a
Expand All @@ -178,7 +179,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)

btype = type[b];

qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

// vector COM b - stacking site b
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5 changes: 3 additions & 2 deletions src/USER-CGDNA/pair_oxdna2_dh.cpp
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Expand Up @@ -102,6 +102,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int a,b,ia,ib,anum,bnum,atype,btype;

Expand All @@ -120,7 +121,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
a = alist[ia];
atype = type[a];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);

// vector COM-backbone site a
Expand All @@ -140,7 +141,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
b &= NEIGHMASK;
btype = type[b];

qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

// vector COM-backbone site b
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5 changes: 3 additions & 2 deletions src/USER-CGDNA/pair_oxdna_coaxstk.cpp
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Expand Up @@ -145,6 +145,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int a,b,ia,ib,anum,bnum,atype,btype;

Expand All @@ -166,7 +167,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
a = alist[ia];
atype = type[a];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);

// vector COM a - stacking site a
Expand All @@ -190,7 +191,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)

btype = type[b];

qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

// vector COM b - stacking site b
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5 changes: 3 additions & 2 deletions src/USER-CGDNA/pair_oxdna_excv.cpp
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Expand Up @@ -134,6 +134,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int a,b,ia,ib,anum,bnum,atype,btype;

Expand All @@ -152,7 +153,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
a = alist[ia];
atype = type[a];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);

// vector COM - backbone and base site a
Expand All @@ -177,7 +178,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)

btype = type[b];

qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

// vector COM - backbone and base site b
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5 changes: 3 additions & 2 deletions src/USER-CGDNA/pair_oxdna_hbond.cpp
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Expand Up @@ -164,6 +164,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int a,b,ia,ib,anum,bnum,atype,btype;

Expand All @@ -185,7 +186,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
a = alist[ia];
atype = type[a];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);

ra_chb[0] = d_chb*ax[0];
Expand All @@ -203,7 +204,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)

btype = type[b];

qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

rb_chb[0] = d_chb*bx[0];
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5 changes: 3 additions & 2 deletions src/USER-CGDNA/pair_oxdna_stk.cpp
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Expand Up @@ -245,6 +245,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int a,b,in,atype,btype;

Expand All @@ -262,9 +263,9 @@ void PairOxdnaStk::compute(int eflag, int vflag)
a = bondlist[in][1];
b = bondlist[in][0];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);
qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

// vector COM a - stacking site a
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5 changes: 3 additions & 2 deletions src/USER-CGDNA/pair_oxdna_xstk.cpp
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Expand Up @@ -142,6 +142,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int a,b,ia,ib,anum,bnum,atype,btype;

Expand All @@ -163,7 +164,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
a = alist[ia];
atype = type[a];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);

ra_chb[0] = d_chb*ax[0];
Expand All @@ -181,7 +182,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)

btype = type[b];

qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

rb_chb[0] = d_chb*bx[0];
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5 changes: 3 additions & 2 deletions src/USER-CGDNA/pair_oxrna2_stk.cpp
View file
Expand Up @@ -262,6 +262,7 @@ void PairOxrna2Stk::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int a,b,in,atype,btype;

Expand All @@ -279,9 +280,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
a = bondlist[in][1];
b = bondlist[in][0];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);
qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

// vector COM a - 3'-stacking site a
Expand Down
5 changes: 3 additions & 2 deletions src/USER-CGDNA/pair_oxrna2_xstk.cpp
View file
Expand Up @@ -135,6 +135,7 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)

AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;

int a,b,ia,ib,anum,bnum,atype,btype;

Expand All @@ -156,7 +157,7 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
a = alist[ia];
atype = type[a];

qa=bonus[a].quat;
qa=bonus[ellipsoid[a]].quat;
MathExtra::q_to_exyz(qa,ax,ay,az);

ra_chb[0] = d_chb*ax[0];
Expand All @@ -174,7 +175,7 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)

btype = type[b];

qb=bonus[b].quat;
qb=bonus[ellipsoid[b]].quat;
MathExtra::q_to_exyz(qb,bx,by,bz);

rb_chb[0] = d_chb*bx[0];
Expand Down

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