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refactor group access, enable and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-04-14 22:01:48 -04:00
parent 4b400fb4a6
commit 69d9c5187e
187 changed files with 3016 additions and 2927 deletions
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165
src/fix_aveforce.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
@ -29,15 +28,15 @@
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NONE,CONSTANT,EQUAL};
enum { NONE, CONSTANT, EQUAL };
/* ---------------------------------------------------------------------- */
FixAveForce::FixAveForce(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
xstr(nullptr), ystr(nullptr), zstr(nullptr), idregion(nullptr)
Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), idregion(nullptr),
region(nullptr)
{
if (narg < 6) error->all(FLERR,"Illegal fix aveforce command");
if (narg < 6) error->all(FLERR, "Illegal fix aveforce command");
dynamic_group_allow = 1;
vector_flag = 1;
@ -49,61 +48,56 @@ FixAveForce::FixAveForce(LAMMPS *lmp, int narg, char **arg) :
xstr = ystr = zstr = nullptr;
if (utils::strmatch(arg[3],"^v_")) {
xstr = utils::strdup(arg[3]+2);
} else if (strcmp(arg[3],"NULL") == 0) {
if (utils::strmatch(arg[3], "^v_")) {
xstr = utils::strdup(arg[3] + 2);
} else if (strcmp(arg[3], "NULL") == 0) {
xstyle = NONE;
} else {
xvalue = utils::numeric(FLERR,arg[3],false,lmp);
xvalue = utils::numeric(FLERR, arg[3], false, lmp);
xstyle = CONSTANT;
}
if (utils::strmatch(arg[4],"^v_")) {
ystr = utils::strdup(arg[4]+2);
} else if (strcmp(arg[4],"NULL") == 0) {
if (utils::strmatch(arg[4], "^v_")) {
ystr = utils::strdup(arg[4] + 2);
} else if (strcmp(arg[4], "NULL") == 0) {
ystyle = NONE;
} else {
yvalue = utils::numeric(FLERR,arg[4],false,lmp);
yvalue = utils::numeric(FLERR, arg[4], false, lmp);
ystyle = CONSTANT;
}
if (utils::strmatch(arg[5],"^v_")) {
zstr = utils::strdup(arg[5]+2);
} else if (strcmp(arg[5],"NULL") == 0) {
if (utils::strmatch(arg[5], "^v_")) {
zstr = utils::strdup(arg[5] + 2);
} else if (strcmp(arg[5], "NULL") == 0) {
zstyle = NONE;
} else {
zvalue = utils::numeric(FLERR,arg[5],false,lmp);
zvalue = utils::numeric(FLERR, arg[5], false, lmp);
zstyle = CONSTANT;
}
// optional args
iregion = -1;
idregion = nullptr;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix aveforce command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix aveforce does not exist");
idregion = utils::strdup(arg[iarg+1]);
if (strcmp(arg[iarg], "region") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix aveforce command");
region = domain->get_region_by_id(arg[iarg + 1]);
if (!region) error->all(FLERR, "Region {} for fix aveforce does not exist", arg[iarg + 1]);
idregion = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix aveforce command");
} else
error->all(FLERR, "Illegal fix aveforce command");
}
foriginal_all[0] = foriginal_all[1] =
foriginal_all[2] = foriginal_all[3] = 0.0;
foriginal_all[0] = foriginal_all[1] = foriginal_all[2] = foriginal_all[3] = 0.0;
}
/* ---------------------------------------------------------------------- */
FixAveForce::~FixAveForce()
{
delete [] xstr;
delete [] ystr;
delete [] zstr;
delete [] idregion;
delete[] xstr;
delete[] ystr;
delete[] zstr;
delete[] idregion;
}
/* ---------------------------------------------------------------------- */
@ -125,41 +119,47 @@ void FixAveForce::init()
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0)
error->all(FLERR,"Variable name for fix aveforce does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else error->all(FLERR,"Variable for fix aveforce is invalid style");
if (xvar < 0) error->all(FLERR, "Variable name for fix aveforce does not exist");
if (input->variable->equalstyle(xvar))
xstyle = EQUAL;
else
error->all(FLERR, "Variable for fix aveforce is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0)
error->all(FLERR,"Variable name for fix aveforce does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else error->all(FLERR,"Variable for fix aveforce is invalid style");
if (yvar < 0) error->all(FLERR, "Variable name for fix aveforce does not exist");
if (input->variable->equalstyle(yvar))
ystyle = EQUAL;
else
error->all(FLERR, "Variable for fix aveforce is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0)
error->all(FLERR,"Variable name for fix aveforce does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else error->all(FLERR,"Variable for fix aveforce is invalid style");
if (zvar < 0) error->all(FLERR, "Variable name for fix aveforce does not exist");
if (input->variable->equalstyle(zvar))
zstyle = EQUAL;
else
error->all(FLERR, "Variable for fix aveforce is invalid style");
}
// set index and check validity of region
if (iregion >= 0) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for fix aveforce does not exist");
if (idregion) {
region = domain->get_region_by_id(idregion);
if (!region) error->all(FLERR, "Region {} for fix aveforce does not exist", idregion);
}
if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL) varflag = EQUAL;
else varflag = CONSTANT;
if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
varflag = EQUAL;
else
varflag = CONSTANT;
if (utils::strmatch(update->integrate_style,"^respa")) {
nlevels_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,nlevels_respa-1);
else ilevel_respa = nlevels_respa-1;
if (utils::strmatch(update->integrate_style, "^respa")) {
nlevels_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels;
if (respa_level >= 0)
ilevel_respa = MIN(respa_level, nlevels_respa - 1);
else
ilevel_respa = nlevels_respa - 1;
}
}
@ -167,13 +167,13 @@ void FixAveForce::init()
void FixAveForce::setup(int vflag)
{
if (utils::strmatch(update->integrate_style,"^verlet"))
if (utils::strmatch(update->integrate_style, "^verlet"))
post_force(vflag);
else
for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) {
(dynamic_cast<Respa *>( update->integrate))->copy_flevel_f(ilevel);
post_force_respa(vflag,ilevel,0);
(dynamic_cast<Respa *>( update->integrate))->copy_f_flevel(ilevel);
(dynamic_cast<Respa *>(update->integrate))->copy_flevel_f(ilevel);
post_force_respa(vflag, ilevel, 0);
(dynamic_cast<Respa *>(update->integrate))->copy_f_flevel(ilevel);
}
}
@ -190,11 +190,7 @@ void FixAveForce::post_force(int /*vflag*/)
{
// update region if necessary
Region *region = nullptr;
if (iregion >= 0) {
region = domain->regions[iregion];
region->prematch();
}
if (region) region->prematch();
// sum forces on participating atoms
@ -208,7 +204,7 @@ void FixAveForce::post_force(int /*vflag*/)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
foriginal[0] += f[i][0];
foriginal[1] += f[i][1];
foriginal[2] += f[i][2];
@ -219,9 +215,9 @@ void FixAveForce::post_force(int /*vflag*/)
// add in requested amount, computed via variable evaluation if necessary
// wrap variable evaluation with clear/add
MPI_Allreduce(foriginal,foriginal_all,4,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(foriginal, foriginal_all, 4, MPI_DOUBLE, MPI_SUM, world);
int ncount = static_cast<int> (foriginal_all[3]);
int ncount = static_cast<int>(foriginal_all[3]);
if (ncount == 0) return;
if (varflag == EQUAL) {
@ -233,16 +229,16 @@ void FixAveForce::post_force(int /*vflag*/)
}
double fave[3];
fave[0] = foriginal_all[0]/ncount + xvalue;
fave[1] = foriginal_all[1]/ncount + yvalue;
fave[2] = foriginal_all[2]/ncount + zvalue;
fave[0] = foriginal_all[0] / ncount + xvalue;
fave[1] = foriginal_all[1] / ncount + yvalue;
fave[2] = foriginal_all[2] / ncount + zvalue;
// set force of all participating atoms to same value
// only for active dimensions
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
if (xstyle) f[i][0] = fave[0];
if (ystyle) f[i][1] = fave[1];
if (zstyle) f[i][2] = fave[2];
@ -256,13 +252,10 @@ void FixAveForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
// ave + extra force on selected RESPA level
// just ave on all other levels
if (ilevel == ilevel_respa) post_force(vflag);
else {
Region *region = nullptr;
if (iregion >= 0) {
region = domain->regions[iregion];
region->prematch();
}
if (ilevel == ilevel_respa) {
post_force(vflag);
} else {
if (region) region->prematch();
double **x = atom->x;
double **f = atom->f;
@ -274,26 +267,26 @@ void FixAveForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
foriginal[0] += f[i][0];
foriginal[1] += f[i][1];
foriginal[2] += f[i][2];
foriginal[3] += 1.0;
}
MPI_Allreduce(foriginal,foriginal_all,4,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(foriginal, foriginal_all, 4, MPI_DOUBLE, MPI_SUM, world);
int ncount = static_cast<int> (foriginal_all[3]);
int ncount = static_cast<int>(foriginal_all[3]);
if (ncount == 0) return;
double fave[3];
fave[0] = foriginal_all[0]/ncount;
fave[1] = foriginal_all[1]/ncount;
fave[2] = foriginal_all[2]/ncount;
fave[0] = foriginal_all[0] / ncount;
fave[1] = foriginal_all[1] / ncount;
fave[2] = foriginal_all[2] / ncount;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
if (xstyle) f[i][0] = fave[0];
if (ystyle) f[i][1] = fave[1];
if (zstyle) f[i][2] = fave[2];