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enabled and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2024-10-19 11:02:53 -04:00
parent 34ab2f862a
commit 760d871b7a
4 changed files with 405 additions and 360 deletions
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89
src/compute_improper_local.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
@ -13,36 +12,35 @@
------------------------------------------------------------------------- */
#include "compute_improper_local.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "molecule.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
static constexpr int DELTA = 10000;
static constexpr double SMALL = 0.001;
static constexpr double SMALL = 0.001;
/* ---------------------------------------------------------------------- */
ComputeImproperLocal::ComputeImproperLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
vlocal(nullptr), alocal(nullptr)
Compute(lmp, narg, arg), vlocal(nullptr), alocal(nullptr)
{
if (narg < 4) error->all(FLERR,"Illegal compute improper/local command");
if (narg < 4) error->all(FLERR, "Illegal compute improper/local command");
if (atom->avec->impropers_allow == 0)
error->all(FLERR,
"Compute improper/local used when impropers are not allowed");
error->all(FLERR, "Compute improper/local used when impropers are not allowed");
local_flag = 1;
nvalues = narg - 3;
@ -50,12 +48,16 @@ ComputeImproperLocal::ComputeImproperLocal(LAMMPS *lmp, int narg, char **arg) :
nvalues = 0;
for (int iarg = 3; iarg < narg; iarg++) {
if (strcmp(arg[iarg],"chi") == 0) cflag = nvalues++;
else error->all(FLERR,"Invalid keyword in compute improper/local command");
if (strcmp(arg[iarg], "chi") == 0)
cflag = nvalues++;
else
error->all(FLERR, "Invalid keyword in compute improper/local command");
}
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
if (nvalues == 1)
size_local_cols = 0;
else
size_local_cols = nvalues;
nmax = 0;
vlocal = nullptr;
@ -75,7 +77,7 @@ ComputeImproperLocal::~ComputeImproperLocal()
void ComputeImproperLocal::init()
{
if (force->improper == nullptr)
error->all(FLERR,"No improper style is defined for compute improper/local");
error->all(FLERR, "No improper style is defined for compute improper/local");
// do initial memory allocation so that memory_usage() is correct
@ -108,11 +110,11 @@ void ComputeImproperLocal::compute_local()
int ComputeImproperLocal::compute_impropers(int flag)
{
int i,m,n,ni,atom1,atom2,atom3,atom4,imol,iatom;
int i, m, n, ni, atom1, atom2, atom3, atom4, imol, iatom;
tagint tagprev;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
double ss1,ss2,ss3,r1,r2,r3,c0,c1,c2,s1,s2;
double s12,c;
double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z;
double ss1, ss2, ss3, r1, r2, r3, c0, c1, c2, s1, s2;
double s12, c;
double *cbuf;
double **x = atom->x;
@ -135,8 +137,10 @@ int ComputeImproperLocal::compute_impropers(int flag)
if (nvalues == 1) {
if (cflag >= 0) cbuf = vlocal;
} else {
if (cflag >= 0 && alocal) cbuf = &alocal[0][cflag];
else cbuf = nullptr;
if (cflag >= 0 && alocal)
cbuf = &alocal[0][cflag];
else
cbuf = nullptr;
}
}
@ -144,7 +148,8 @@ int ComputeImproperLocal::compute_impropers(int flag)
for (atom2 = 0; atom2 < nlocal; atom2++) {
if (!(mask[atom2] & groupbit)) continue;
if (molecular == Atom::MOLECULAR) ni = num_improper[atom2];
if (molecular == Atom::MOLECULAR)
ni = num_improper[atom2];
else {
if (molindex[atom2] < 0) continue;
imol = molindex[atom2];
@ -161,9 +166,9 @@ int ComputeImproperLocal::compute_impropers(int flag)
} else {
if (tag[atom2] != onemols[imol]->improper_atom2[atom2][i]) continue;
tagprev = tag[atom2] - iatom - 1;
atom1 = atom->map(onemols[imol]->improper_atom1[atom2][i]+tagprev);
atom3 = atom->map(onemols[imol]->improper_atom3[atom2][i]+tagprev);
atom4 = atom->map(onemols[imol]->improper_atom4[atom2][i]+tagprev);
atom1 = atom->map(onemols[imol]->improper_atom1[atom2][i] + tagprev);
atom3 = atom->map(onemols[imol]->improper_atom3[atom2][i] + tagprev);
atom4 = atom->map(onemols[imol]->improper_atom4[atom2][i] + tagprev);
}
if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
@ -178,21 +183,21 @@ int ComputeImproperLocal::compute_impropers(int flag)
vb1x = x[atom1][0] - x[atom2][0];
vb1y = x[atom1][1] - x[atom2][1];
vb1z = x[atom1][2] - x[atom2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
domain->minimum_image(vb1x, vb1y, vb1z);
vb2x = x[atom3][0] - x[atom2][0];
vb2y = x[atom3][1] - x[atom2][1];
vb2z = x[atom3][2] - x[atom2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
domain->minimum_image(vb2x, vb2y, vb2z);
vb3x = x[atom4][0] - x[atom3][0];
vb3y = x[atom4][1] - x[atom3][1];
vb3z = x[atom4][2] - x[atom3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
domain->minimum_image(vb3x, vb3y, vb3z);
ss1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
ss2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
ss3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
ss1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z);
ss2 = 1.0 / (vb2x * vb2x + vb2y * vb2y + vb2z * vb2z);
ss3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z);
r1 = sqrt(ss1);
r2 = sqrt(ss2);
@ -202,20 +207,20 @@ int ComputeImproperLocal::compute_impropers(int flag)
c1 = (vb1x * vb2x + vb1y * vb2y + vb1z * vb2z) * r1 * r2;
c2 = -(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) * r3 * r2;
s1 = 1.0 - c1*c1;
s1 = 1.0 - c1 * c1;
if (s1 < SMALL) s1 = SMALL;
s1 = 1.0 / s1;
s2 = 1.0 - c2*c2;
s2 = 1.0 - c2 * c2;
if (s2 < SMALL) s2 = SMALL;
s2 = 1.0 / s2;
s12 = sqrt(s1*s2);
c = (c1*c2 + c0) * s12;
s12 = sqrt(s1 * s2);
c = (c1 * c2 + c0) * s12;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
cbuf[n] = 180.0*acos(c)/MY_PI;
cbuf[n] = 180.0 * acos(c) / MY_PI;
}
n += nvalues;
}
@ -237,11 +242,11 @@ void ComputeImproperLocal::reallocate(int n)
if (nvalues == 1) {
memory->destroy(vlocal);
memory->create(vlocal,nmax,"improper/local:vector_local");
memory->create(vlocal, nmax, "improper/local:vector_local");
vector_local = vlocal;
} else {
memory->destroy(alocal);
memory->create(alocal,nmax,nvalues,"improper/local:array_local");
memory->create(alocal, nmax, nvalues, "improper/local:array_local");
array_local = alocal;
}
}
@ -252,6 +257,6 @@ void ComputeImproperLocal::reallocate(int n)
double ComputeImproperLocal::memory_usage()
{
double bytes = (double)nmax*nvalues * sizeof(double);
double bytes = (double) nmax * nvalues * sizeof(double);
return bytes;
}