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enable and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-03-18 00:06:28 -04:00
parent 6d38ce5284
commit 32612d3f5b
7 changed files with 631 additions and 647 deletions
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215
src/angle.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
@ -14,20 +13,20 @@
#include "angle.h"
#include "atom.h"
#include "atom_masks.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "suffix.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
Angle::Angle(LAMMPS *lmp) : Pointers(lmp)
Angle::Angle(LAMMPS *_lmp) : Pointers(_lmp)
{
energy = 0.0;
virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0;
@ -67,10 +66,9 @@ Angle::~Angle()
void Angle::init()
{
if (!allocated && atom->nangletypes)
error->all(FLERR,"Angle coeffs are not set");
if (!allocated && atom->nangletypes) error->all(FLERR, "Angle coeffs are not set");
for (int i = 1; i <= atom->nangletypes; i++)
if (setflag[i] == 0) error->all(FLERR,"All angle coeffs are not set");
if (setflag[i] == 0) error->all(FLERR, "All angle coeffs are not set");
init_style();
}
@ -94,7 +92,7 @@ void Angle::init()
void Angle::ev_setup(int eflag, int vflag, int alloc)
{
int i,n;
int i, n;
evflag = 1;
@ -104,11 +102,9 @@ void Angle::ev_setup(int eflag, int vflag, int alloc)
vflag_global = vflag & (VIRIAL_PAIR | VIRIAL_FDOTR);
vflag_atom = vflag & VIRIAL_ATOM;
if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL)
vflag_atom = 1;
if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL) vflag_atom = 1;
cvflag_atom = 0;
if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL)
cvflag_atom = 1;
if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL) cvflag_atom = 1;
vflag_either = vflag_global || vflag_atom || cvflag_atom;
// reallocate per-atom arrays if necessary
@ -117,28 +113,29 @@ void Angle::ev_setup(int eflag, int vflag, int alloc)
maxeatom = atom->nmax;
if (alloc) {
memory->destroy(eatom);
memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom");
memory->create(eatom, comm->nthreads * maxeatom, "angle:eatom");
}
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
if (alloc) {
memory->destroy(vatom);
memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom");
memory->create(vatom, comm->nthreads * maxvatom, 6, "angle:vatom");
}
}
if (cvflag_atom && atom->nmax > maxcvatom) {
maxcvatom = atom->nmax;
if (alloc) {
memory->destroy(cvatom);
memory->create(cvatom,comm->nthreads*maxcvatom,9,"angle:cvatom");
memory->create(cvatom, comm->nthreads * maxcvatom, 9, "angle:cvatom");
}
}
// zero accumulators
if (eflag_global) energy = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (vflag_global)
for (i = 0; i < 6; i++) virial[i] = 0.0;
if (eflag_atom && alloc) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
@ -179,25 +176,25 @@ void Angle::ev_setup(int eflag, int vflag, int alloc)
virial = r1F1 + r2F2 + r3F3 = (r1-r2) F1 + (r3-r2) F3 = del1*f1 + del2*f3
------------------------------------------------------------------------- */
void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
double eangle, double *f1, double *f3,
double delx1, double dely1, double delz1,
double delx2, double dely2, double delz2)
void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond, double eangle, double *f1,
double *f3, double delx1, double dely1, double delz1, double delx2,
double dely2, double delz2)
{
double eanglethird,v[6];
double eanglethird, v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_bond) energy += eangle;
if (newton_bond)
energy += eangle;
else {
eanglethird = THIRD*eangle;
eanglethird = THIRD * eangle;
if (i < nlocal) energy += eanglethird;
if (j < nlocal) energy += eanglethird;
if (k < nlocal) energy += eanglethird;
}
}
if (eflag_atom) {
eanglethird = THIRD*eangle;
eanglethird = THIRD * eangle;
if (newton_bond || i < nlocal) eatom[i] += eanglethird;
if (newton_bond || j < nlocal) eatom[j] += eanglethird;
if (newton_bond || k < nlocal) eatom[k] += eanglethird;
@ -205,12 +202,12 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
}
if (vflag_either) {
v[0] = delx1*f1[0] + delx2*f3[0];
v[1] = dely1*f1[1] + dely2*f3[1];
v[2] = delz1*f1[2] + delz2*f3[2];
v[3] = delx1*f1[1] + delx2*f3[1];
v[4] = delx1*f1[2] + delx2*f3[2];
v[5] = dely1*f1[2] + dely2*f3[2];
v[0] = delx1 * f1[0] + delx2 * f3[0];
v[1] = dely1 * f1[1] + dely2 * f3[1];
v[2] = delz1 * f1[2] + delz2 * f3[2];
v[3] = delx1 * f1[1] + delx2 * f3[1];
v[4] = delx1 * f1[2] + delx2 * f3[2];
v[5] = dely1 * f1[2] + dely2 * f3[2];
if (vflag_global) {
if (newton_bond) {
@ -222,56 +219,56 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
virial[5] += v[5];
} else {
if (i < nlocal) {
virial[0] += THIRD*v[0];
virial[1] += THIRD*v[1];
virial[2] += THIRD*v[2];
virial[3] += THIRD*v[3];
virial[4] += THIRD*v[4];
virial[5] += THIRD*v[5];
virial[0] += THIRD * v[0];
virial[1] += THIRD * v[1];
virial[2] += THIRD * v[2];
virial[3] += THIRD * v[3];
virial[4] += THIRD * v[4];
virial[5] += THIRD * v[5];
}
if (j < nlocal) {
virial[0] += THIRD*v[0];
virial[1] += THIRD*v[1];
virial[2] += THIRD*v[2];
virial[3] += THIRD*v[3];
virial[4] += THIRD*v[4];
virial[5] += THIRD*v[5];
virial[0] += THIRD * v[0];
virial[1] += THIRD * v[1];
virial[2] += THIRD * v[2];
virial[3] += THIRD * v[3];
virial[4] += THIRD * v[4];
virial[5] += THIRD * v[5];
}
if (k < nlocal) {
virial[0] += THIRD*v[0];
virial[1] += THIRD*v[1];
virial[2] += THIRD*v[2];
virial[3] += THIRD*v[3];
virial[4] += THIRD*v[4];
virial[5] += THIRD*v[5];
virial[0] += THIRD * v[0];
virial[1] += THIRD * v[1];
virial[2] += THIRD * v[2];
virial[3] += THIRD * v[3];
virial[4] += THIRD * v[4];
virial[5] += THIRD * v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i < nlocal) {
vatom[i][0] += THIRD*v[0];
vatom[i][1] += THIRD*v[1];
vatom[i][2] += THIRD*v[2];
vatom[i][3] += THIRD*v[3];
vatom[i][4] += THIRD*v[4];
vatom[i][5] += THIRD*v[5];
vatom[i][0] += THIRD * v[0];
vatom[i][1] += THIRD * v[1];
vatom[i][2] += THIRD * v[2];
vatom[i][3] += THIRD * v[3];
vatom[i][4] += THIRD * v[4];
vatom[i][5] += THIRD * v[5];
}
if (newton_bond || j < nlocal) {
vatom[j][0] += THIRD*v[0];
vatom[j][1] += THIRD*v[1];
vatom[j][2] += THIRD*v[2];
vatom[j][3] += THIRD*v[3];
vatom[j][4] += THIRD*v[4];
vatom[j][5] += THIRD*v[5];
vatom[j][0] += THIRD * v[0];
vatom[j][1] += THIRD * v[1];
vatom[j][2] += THIRD * v[2];
vatom[j][3] += THIRD * v[3];
vatom[j][4] += THIRD * v[4];
vatom[j][5] += THIRD * v[5];
}
if (newton_bond || k < nlocal) {
vatom[k][0] += THIRD*v[0];
vatom[k][1] += THIRD*v[1];
vatom[k][2] += THIRD*v[2];
vatom[k][3] += THIRD*v[3];
vatom[k][4] += THIRD*v[4];
vatom[k][5] += THIRD*v[5];
vatom[k][0] += THIRD * v[0];
vatom[k][1] += THIRD * v[1];
vatom[k][2] += THIRD * v[2];
vatom[k][3] += THIRD * v[3];
vatom[k][4] += THIRD * v[4];
vatom[k][5] += THIRD * v[5];
}
}
}
@ -289,60 +286,60 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
double a1[3];
// a1 = r10 = (2*r12 - r32)/3
a1[0] = THIRD*(2*delx1-delx2);
a1[1] = THIRD*(2*dely1-dely2);
a1[2] = THIRD*(2*delz1-delz2);
a1[0] = THIRD * (2 * delx1 - delx2);
a1[1] = THIRD * (2 * dely1 - dely2);
a1[2] = THIRD * (2 * delz1 - delz2);
cvatom[i][0] += a1[0]*f1[0];
cvatom[i][1] += a1[1]*f1[1];
cvatom[i][2] += a1[2]*f1[2];
cvatom[i][3] += a1[0]*f1[1];
cvatom[i][4] += a1[0]*f1[2];
cvatom[i][5] += a1[1]*f1[2];
cvatom[i][6] += a1[1]*f1[0];
cvatom[i][7] += a1[2]*f1[0];
cvatom[i][8] += a1[2]*f1[1];
cvatom[i][0] += a1[0] * f1[0];
cvatom[i][1] += a1[1] * f1[1];
cvatom[i][2] += a1[2] * f1[2];
cvatom[i][3] += a1[0] * f1[1];
cvatom[i][4] += a1[0] * f1[2];
cvatom[i][5] += a1[1] * f1[2];
cvatom[i][6] += a1[1] * f1[0];
cvatom[i][7] += a1[2] * f1[0];
cvatom[i][8] += a1[2] * f1[1];
}
if (newton_bond || j < nlocal) {
double a2[3];
double f2[3];
// a2 = r20 = ( -r12 - r32)/3
a2[0] = THIRD*(-delx1-delx2);
a2[1] = THIRD*(-dely1-dely2);
a2[2] = THIRD*(-delz1-delz2);
a2[0] = THIRD * (-delx1 - delx2);
a2[1] = THIRD * (-dely1 - dely2);
a2[2] = THIRD * (-delz1 - delz2);
f2[0] = - f1[0] - f3[0];
f2[1] = - f1[1] - f3[1];
f2[2] = - f1[2] - f3[2];
f2[0] = -f1[0] - f3[0];
f2[1] = -f1[1] - f3[1];
f2[2] = -f1[2] - f3[2];
cvatom[j][0] += a2[0]*f2[0];
cvatom[j][1] += a2[1]*f2[1];
cvatom[j][2] += a2[2]*f2[2];
cvatom[j][3] += a2[0]*f2[1];
cvatom[j][4] += a2[0]*f2[2];
cvatom[j][5] += a2[1]*f2[2];
cvatom[j][6] += a2[1]*f2[0];
cvatom[j][7] += a2[2]*f2[0];
cvatom[j][8] += a2[2]*f2[1];
cvatom[j][0] += a2[0] * f2[0];
cvatom[j][1] += a2[1] * f2[1];
cvatom[j][2] += a2[2] * f2[2];
cvatom[j][3] += a2[0] * f2[1];
cvatom[j][4] += a2[0] * f2[2];
cvatom[j][5] += a2[1] * f2[2];
cvatom[j][6] += a2[1] * f2[0];
cvatom[j][7] += a2[2] * f2[0];
cvatom[j][8] += a2[2] * f2[1];
}
if (newton_bond || k < nlocal) {
double a3[3];
// a3 = r30 = ( -r12 + 2*r32)/3
a3[0] = THIRD*(-delx1+2*delx2);
a3[1] = THIRD*(-dely1+2*dely2);
a3[2] = THIRD*(-delz1+2*delz2);
a3[0] = THIRD * (-delx1 + 2 * delx2);
a3[1] = THIRD * (-dely1 + 2 * dely2);
a3[2] = THIRD * (-delz1 + 2 * delz2);
cvatom[k][0] += a3[0]*f3[0];
cvatom[k][1] += a3[1]*f3[1];
cvatom[k][2] += a3[2]*f3[2];
cvatom[k][3] += a3[0]*f3[1];
cvatom[k][4] += a3[0]*f3[2];
cvatom[k][5] += a3[1]*f3[2];
cvatom[k][6] += a3[1]*f3[0];
cvatom[k][7] += a3[2]*f3[0];
cvatom[k][8] += a3[2]*f3[1];
cvatom[k][0] += a3[0] * f3[0];
cvatom[k][1] += a3[1] * f3[1];
cvatom[k][2] += a3[2] * f3[2];
cvatom[k][3] += a3[0] * f3[1];
cvatom[k][4] += a3[0] * f3[2];
cvatom[k][5] += a3[1] * f3[2];
cvatom[k][6] += a3[1] * f3[0];
cvatom[k][7] += a3[2] * f3[0];
cvatom[k][8] += a3[2] * f3[1];
}
}
}
@ -351,8 +348,8 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
double Angle::memory_usage()
{
double bytes = (double)comm->nthreads*maxeatom * sizeof(double);
bytes += (double)comm->nthreads*maxvatom*6 * sizeof(double);
bytes += (double)comm->nthreads*maxcvatom*9 * sizeof(double);
double bytes = (double) comm->nthreads * maxeatom * sizeof(double);
bytes += (double) comm->nthreads * maxvatom * 6 * sizeof(double);
bytes += (double) comm->nthreads * maxcvatom * 9 * sizeof(double);
return bytes;
}