tx258/lammps-gran-kokkos
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simplify and use fmtlib

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This commit is contained in:
Axel Kohlmeyer
2021-07-29 14:09:49 -04:00
parent 3a968b81ad
commit 9cf790a2fe
2 changed files with 23 additions and 40 deletions
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60
src/CG-DNA/bond_oxdna_fene.cpp
View File

@ -17,25 +17,30 @@
#include "bond_oxdna_fene.h"
#include <cmath>
#include "atom.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 "comm.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "neighbor.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondOxdnaFene::BondOxdnaFene(LAMMPS *lmp) : Bond(lmp)
/* ----------------------------------------------------------------------
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];
}
/* ---------------------------------------------------------------------- */
@ -43,30 +48,14 @@ BondOxdnaFene::BondOxdnaFene(LAMMPS *lmp) : Bond(lmp)
BondOxdnaFene::~BondOxdnaFene()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(Delta);
memory->destroy(r0);
}
}
/* ----------------------------------------------------------------------
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])
{
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
------------------------------------------------------------------------- */
@ -198,8 +187,8 @@ 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,ay,az,ra_cs);
compute_interaction_sites(bx,by,bz,rb_cs);
compute_interaction_sites(ax,ra_cs);
compute_interaction_sites(bx,rb_cs);
// vector backbone site b to a
delr[0] = x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0];
@ -218,11 +207,8 @@ void BondOxdnaFene::compute(int eflag, int vflag)
// if r > 2*Delta something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " %g",
update->ntimestep,atom->tag[a],atom->tag[b],r);
error->warning(FLERR,str);
error->warning(FLERR,"FENE bond too long: {} {} {} {}",
update->ntimestep,atom->tag[a],atom->tag[b],r);
rlogarg = 0.1;
}
@ -398,10 +384,8 @@ double BondOxdnaFene::single(int type, double rsq, int /*i*/, int /*j*/,
// if r > 2*Delta something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g",
update->ntimestep,sqrt(rsq));
error->warning(FLERR,str);
error->warning(FLERR,"FENE bond too long: {} {:.8}",
update->ntimestep,sqrt(rsq));
rlogarg = 0.1;
}

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

@ -26,9 +26,8 @@ namespace LAMMPS_NS {
class BondOxdnaFene : public Bond {
public:
BondOxdnaFene(class LAMMPS *);
BondOxdnaFene(class LAMMPS *lmp) : Bond(lmp) {}
virtual ~BondOxdnaFene();
virtual void compute_interaction_sites(double *, double *, double *, double *);
virtual void compute(int, int);
void coeff(int, char **);
void init_style();