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correct bug in derived CG-DNA FENE bond classes and optimize code

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This commit is contained in:
Axel Kohlmeyer
2021-07-30 10:48:15 -04:00
parent 4710b7bc9e
commit 5f401da462
6 changed files with 45 additions and 71 deletions
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29
src/CG-DNA/bond_oxdna2_fene.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,30 +18,16 @@
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondOxdna2Fene::BondOxdna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp)
{
}
/* ---------------------------------------------------------------------- */
BondOxdna2Fene::~BondOxdna2Fene()
{
}
/* ----------------------------------------------------------------------
compute vector COM-sugar-phosphate backbone interaction site in oxDNA2
------------------------------------------------------------------------- */
void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3],
double /*e3*/[3], double r[3])
void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3],
double r[3]) const
{
double d_cs_x=-0.34, d_cs_y=+0.3408;
r[0] = d_cs_x*e1[0] + d_cs_y*e2[0];
r[1] = d_cs_x*e1[1] + d_cs_y*e2[1];
r[2] = d_cs_x*e1[2] + d_cs_y*e2[2];
constexpr double d_cs_x = -0.34;
constexpr double d_cs_y = +0.3408;
r[0] = d_cs_x * e1[0] + d_cs_y * e2[0];
r[1] = d_cs_x * e1[1] + d_cs_y * e2[1];
r[2] = d_cs_x * e1[2] + d_cs_y * e2[2];
}

6
src/CG-DNA/bond_oxdna2_fene.h
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@ -26,9 +26,9 @@ namespace LAMMPS_NS {
class BondOxdna2Fene : public BondOxdnaFene {
public:
BondOxdna2Fene(class LAMMPS *);
virtual ~BondOxdna2Fene();
virtual void compute_interaction_sites(double *, double *, double *, double *);
BondOxdna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
virtual ~BondOxdna2Fene() {}
virtual void compute_interaction_sites(double *, double *, double *, double *) const;
};
} // namespace LAMMPS_NS

43
src/CG-DNA/bond_oxdna_fene.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -18,31 +17,20 @@
#include "bond_oxdna_fene.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "neighbor.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "atom_vec_ellipsoid.h"
#include "math_extra.h"
#include <cmath>
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
compute vector COM-sugar-phosphate backbone interaction site in oxDNA
------------------------------------------------------------------------- */
static void compute_interaction_sites(const double e1[3], double r[3])
{
constexpr double d_cs=-0.4;
r[0] = d_cs*e1[0];
r[1] = d_cs*e1[1];
r[2] = d_cs*e1[2];
}
/* ---------------------------------------------------------------------- */
BondOxdnaFene::~BondOxdnaFene()
@ -56,6 +44,19 @@ BondOxdnaFene::~BondOxdnaFene()
}
/* ----------------------------------------------------------------------
compute vector COM-sugar-phosphate backbone interaction site in oxDNA
------------------------------------------------------------------------- */
void BondOxdnaFene::compute_interaction_sites(double e1[3], double /*e2*/[3],
double /*e3*/[3], double r[3]) const
{
constexpr double d_cs=-0.4;
r[0] = d_cs*e1[0];
r[1] = d_cs*e1[1];
r[2] = d_cs*e1[2];
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
------------------------------------------------------------------------- */
@ -187,8 +188,8 @@ void BondOxdnaFene::compute(int eflag, int vflag)
MathExtra::q_to_exyz(qb,bx,by,bz);
// vector COM-backbone site a and b
compute_interaction_sites(ax,ra_cs);
compute_interaction_sites(bx,rb_cs);
compute_interaction_sites(ax,ay,az,ra_cs);
compute_interaction_sites(bx,by,bz,rb_cs);
// vector backbone site b to a
delr[0] = x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0];

1
src/CG-DNA/bond_oxdna_fene.h
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@ -28,6 +28,7 @@ class BondOxdnaFene : public Bond {
public:
BondOxdnaFene(class LAMMPS *lmp) : Bond(lmp) {}
virtual ~BondOxdnaFene();
virtual void compute_interaction_sites(double *, double *, double *, double *) const;
virtual void compute(int, int);
void coeff(int, char **);
void init_style();

30
src/CG-DNA/bond_oxrna2_fene.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,30 +18,17 @@
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondOxrna2Fene::BondOxrna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp)
{
}
/* ---------------------------------------------------------------------- */
BondOxrna2Fene::~BondOxrna2Fene()
{
}
/* ----------------------------------------------------------------------
compute vector COM-sugar-phosphate backbone interaction site in oxRNA2
------------------------------------------------------------------------- */
void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3],
double e3[3], double r[3])
void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3],
double r[3]) const
{
double d_cs_x=-0.4, d_cs_z=+0.2;
r[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
r[1] = d_cs_x*e1[1] + d_cs_z*e3[1];
r[2] = d_cs_x*e1[2] + d_cs_z*e3[2];
constexpr double d_cs_x = -0.4;
constexpr double d_cs_z = +0.2;
r[0] = d_cs_x * e1[0] + d_cs_z * e3[0];
r[1] = d_cs_x * e1[1] + d_cs_z * e3[1];
r[2] = d_cs_x * e1[2] + d_cs_z * e3[2];
}

7
src/CG-DNA/bond_oxrna2_fene.h
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@ -26,9 +26,10 @@ namespace LAMMPS_NS {
class BondOxrna2Fene : public BondOxdnaFene {
public:
BondOxrna2Fene(class LAMMPS *);
virtual ~BondOxrna2Fene();
virtual void compute_interaction_sites(double *, double *, double *, double *);
BondOxrna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
virtual ~BondOxrna2Fene() {}
virtual void compute_interaction_sites(double *, double *, double *, double *) const;
};
} // namespace LAMMPS_NS