lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

Introduced ellipsoid pointer in quaternion data access

This commit is contained in:
Oliver Henrich 2020-12-03 12:57:55 +00:00
parent 5ea9d97024
commit 90f00c01a4
10 changed files with 30 additions and 20 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
src/USER-CGDNA/bond_oxdna_fene.cpp
View File

@ -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;
@ -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

5
src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
View File

@ -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;
@ -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
@ -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

5
src/USER-CGDNA/pair_oxdna2_dh.cpp
View File

@ -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;
@ -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
@ -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

5
src/USER-CGDNA/pair_oxdna_coaxstk.cpp
View File

@ -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;
@ -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
@ -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

5
src/USER-CGDNA/pair_oxdna_excv.cpp
View File

@ -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;
@ -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
@ -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

5
src/USER-CGDNA/pair_oxdna_hbond.cpp
View File

@ -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;
@ -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];
@ -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];

5
src/USER-CGDNA/pair_oxdna_stk.cpp
View File

@ -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;
@ -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

5
src/USER-CGDNA/pair_oxdna_xstk.cpp
View File

@ -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;
@ -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];
@ -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];

5
src/USER-CGDNA/pair_oxrna2_stk.cpp
View File

@ -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;
@ -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

5
src/USER-CGDNA/pair_oxrna2_xstk.cpp
View File

@ -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;
@ -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];
@ -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];