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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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232
src/fix_addforce.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
@ -31,16 +30,15 @@
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NONE,CONSTANT,EQUAL,ATOM};
enum { NONE, CONSTANT, EQUAL, ATOM };
/* ---------------------------------------------------------------------- */
FixAddForce::FixAddForce(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
xstr(nullptr), ystr(nullptr), zstr(nullptr), estr(nullptr),
idregion(nullptr), sforce(nullptr)
Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), estr(nullptr),
idregion(nullptr), region(nullptr), sforce(nullptr)
{
if (narg < 6) error->all(FLERR,"Illegal fix addforce command");
if (narg < 6) error->all(FLERR, "Illegal fix addforce command");
dynamic_group_allow = 1;
scalar_flag = 1;
@ -54,71 +52,68 @@ FixAddForce::FixAddForce(LAMMPS *lmp, int narg, char **arg) :
respa_level_support = 1;
ilevel_respa = 0;
xstr = ystr = zstr = nullptr;
if (utils::strmatch(arg[3],"^v_")) {
xstr = utils::strdup(arg[3]+2);
if (utils::strmatch(arg[3], "^v_")) {
xstr = utils::strdup(arg[3] + 2);
} 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);
if (utils::strmatch(arg[4], "^v_")) {
ystr = utils::strdup(arg[4] + 2);
} 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);
if (utils::strmatch(arg[5], "^v_")) {
zstr = utils::strdup(arg[5] + 2);
} else {
zvalue = utils::numeric(FLERR,arg[5],false,lmp);
zvalue = utils::numeric(FLERR, arg[5], false, lmp);
zstyle = CONSTANT;
}
// optional args
nevery = 1;
iregion = -1;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix addforce command");
nevery = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix addforce command");
if (strcmp(arg[iarg], "every") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix addforce command");
nevery = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (nevery <= 0) error->all(FLERR, "Illegal fix addforce command");
iarg += 2;
} else if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix addforce command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix addforce does not exist");
idregion = utils::strdup(arg[iarg+1]);
} else if (strcmp(arg[iarg], "region") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix addforce command");
region = domain->get_region_by_id(arg[iarg + 1]);
if (!region) error->all(FLERR, "Region {} for fix addforce does not exist", arg[iarg + 1]);
idregion = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg],"energy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix addforce command");
if (utils::strmatch(arg[iarg+1],"^v_")) {
estr = utils::strdup(arg[iarg+1]+2);
} else error->all(FLERR,"Illegal fix addforce command");
} else if (strcmp(arg[iarg], "energy") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix addforce command");
if (utils::strmatch(arg[iarg + 1], "^v_")) {
estr = utils::strdup(arg[iarg + 1] + 2);
} else
error->all(FLERR, "Illegal fix addforce command");
iarg += 2;
} else error->all(FLERR,"Illegal fix addforce command");
} else
error->all(FLERR, "Illegal fix addforce command");
}
force_flag = 0;
foriginal[0] = foriginal[1] = foriginal[2] = foriginal[3] = 0.0;
maxatom = 1;
memory->create(sforce,maxatom,4,"addforce:sforce");
memory->create(sforce, maxatom, 4, "addforce:sforce");
}
/* ---------------------------------------------------------------------- */
FixAddForce::~FixAddForce()
{
delete [] xstr;
delete [] ystr;
delete [] zstr;
delete [] estr;
delete [] idregion;
delete[] xstr;
delete[] ystr;
delete[] zstr;
delete[] estr;
delete[] idregion;
memory->destroy(sforce);
}
@ -143,60 +138,66 @@ void FixAddForce::init()
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0)
error->all(FLERR,"Variable name for fix addforce does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
else error->all(FLERR,"Variable for fix addforce is invalid style");
if (xvar < 0) error->all(FLERR, "Variable {} for fix addforce does not exist", xstr);
if (input->variable->equalstyle(xvar))
xstyle = EQUAL;
else if (input->variable->atomstyle(xvar))
xstyle = ATOM;
else
error->all(FLERR, "Variable {} for fix addforce is invalid style", xstr);
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0)
error->all(FLERR,"Variable name for fix addforce does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
else error->all(FLERR,"Variable for fix addforce is invalid style");
if (yvar < 0) error->all(FLERR, "Variable {} for fix addforce does not exist", ystr);
if (input->variable->equalstyle(yvar))
ystyle = EQUAL;
else if (input->variable->atomstyle(yvar))
ystyle = ATOM;
else
error->all(FLERR, "Variable {} for fix addforce is invalid style", ystr);
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0)
error->all(FLERR,"Variable name for fix addforce does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
else error->all(FLERR,"Variable for fix addforce is invalid style");
if (zvar < 0) error->all(FLERR, "Variable {} for fix addforce does not exist", zstr);
if (input->variable->equalstyle(zvar))
zstyle = EQUAL;
else if (input->variable->atomstyle(zvar))
zstyle = ATOM;
else
error->all(FLERR, "Variable {} for fix addforce is invalid style", zstr);
}
if (estr) {
evar = input->variable->find(estr);
if (evar < 0)
error->all(FLERR,"Variable name for fix addforce does not exist");
if (input->variable->atomstyle(evar)) estyle = ATOM;
else error->all(FLERR,"Variable for fix addforce is invalid style");
} else estyle = NONE;
if (evar < 0) error->all(FLERR, "Variable {} for fix addforce does not exist", estr);
if (input->variable->atomstyle(evar))
estyle = ATOM;
else
error->all(FLERR, "Variable {} for fix addforce is invalid style", estr);
} else
estyle = NONE;
// 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 addforce does not exist");
if (idregion) {
region = domain->get_region_by_id(idregion);
if (!region) error->all(FLERR, "Region {} for fix addforce does not exist", idregion);
}
if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
varflag = ATOM;
else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
varflag = EQUAL;
else varflag = CONSTANT;
else
varflag = CONSTANT;
if (varflag == CONSTANT && estyle != NONE)
error->all(FLERR,"Cannot use variable energy with "
"constant force in fix addforce");
if ((varflag == EQUAL || varflag == ATOM) &&
update->whichflag == 2 && estyle == NONE)
error->all(FLERR,"Must use variable energy with fix addforce");
error->all(FLERR, "Cannot use variable energy with constant force in fix addforce");
if ((varflag == EQUAL || varflag == ATOM) && update->whichflag == 2 && estyle == NONE)
error->all(FLERR, "Must use variable energy with fix addforce");
if (utils::strmatch(update->integrate_style,"^respa")) {
ilevel_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
if (utils::strmatch(update->integrate_style, "^respa")) {
ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels - 1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa);
}
}
@ -204,12 +205,12 @@ void FixAddForce::init()
void FixAddForce::setup(int vflag)
{
if (utils::strmatch(update->integrate_style,"^verlet"))
if (utils::strmatch(update->integrate_style, "^verlet"))
post_force(vflag);
else {
(dynamic_cast<Respa *>( update->integrate))->copy_flevel_f(ilevel_respa);
post_force_respa(vflag,ilevel_respa,0);
(dynamic_cast<Respa *>( update->integrate))->copy_f_flevel(ilevel_respa);
(dynamic_cast<Respa *>(update->integrate))->copy_flevel_f(ilevel_respa);
post_force_respa(vflag, ilevel_respa, 0);
(dynamic_cast<Respa *>(update->integrate))->copy_f_flevel(ilevel_respa);
}
}
@ -238,23 +239,18 @@ void FixAddForce::post_force(int vflag)
v_init(vflag);
if (lmp->kokkos)
atom->sync_modify(Host, (unsigned int) (F_MASK | MASK_MASK),
(unsigned int) F_MASK);
atom->sync_modify(Host, (unsigned int) (F_MASK | MASK_MASK), (unsigned int) F_MASK);
// update region if necessary
Region *region = nullptr;
if (iregion >= 0) {
region = domain->regions[iregion];
region->prematch();
}
if (region) region->prematch();
// reallocate sforce array if necessary
if ((varflag == ATOM || estyle == ATOM) && atom->nmax > maxatom) {
maxatom = atom->nmax;
memory->destroy(sforce);
memory->create(sforce,maxatom,4,"addforce:sforce");
memory->create(sforce, maxatom, 4, "addforce:sforce");
}
// foriginal[0] = "potential energy" for added force
@ -270,9 +266,9 @@ void FixAddForce::post_force(int vflag)
double unwrap[3];
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;
domain->unmap(x[i],image[i],unwrap);
foriginal[0] -= xvalue*unwrap[0] + yvalue*unwrap[1] + zvalue*unwrap[2];
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
domain->unmap(x[i], image[i], unwrap);
foriginal[0] -= xvalue * unwrap[0] + yvalue * unwrap[1] + zvalue * unwrap[2];
foriginal[1] += f[i][0];
foriginal[2] += f[i][1];
foriginal[3] += f[i][2];
@ -286,37 +282,39 @@ void FixAddForce::post_force(int vflag)
v[3] = xvalue * unwrap[1];
v[4] = xvalue * unwrap[2];
v[5] = yvalue * unwrap[2];
v_tally(i,v);
v_tally(i, v);
}
}
// variable force, wrap with clear/add
// potential energy = evar if defined, else 0.0
// wrap with clear/add
// variable force, wrap with clear/add
// potential energy = evar if defined, else 0.0
// wrap with clear/add
} else {
double unwrap[3];
modify->clearstep_compute();
if (xstyle == EQUAL) xvalue = input->variable->compute_equal(xvar);
if (xstyle == EQUAL)
xvalue = input->variable->compute_equal(xvar);
else if (xstyle == ATOM)
input->variable->compute_atom(xvar,igroup,&sforce[0][0],4,0);
if (ystyle == EQUAL) yvalue = input->variable->compute_equal(yvar);
input->variable->compute_atom(xvar, igroup, &sforce[0][0], 4, 0);
if (ystyle == EQUAL)
yvalue = input->variable->compute_equal(yvar);
else if (ystyle == ATOM)
input->variable->compute_atom(yvar,igroup,&sforce[0][1],4,0);
if (zstyle == EQUAL) zvalue = input->variable->compute_equal(zvar);
input->variable->compute_atom(yvar, igroup, &sforce[0][1], 4, 0);
if (zstyle == EQUAL)
zvalue = input->variable->compute_equal(zvar);
else if (zstyle == ATOM)
input->variable->compute_atom(zvar,igroup,&sforce[0][2],4,0);
if (estyle == ATOM)
input->variable->compute_atom(evar,igroup,&sforce[0][3],4,0);
input->variable->compute_atom(zvar, igroup, &sforce[0][2], 4, 0);
if (estyle == ATOM) input->variable->compute_atom(evar, igroup, &sforce[0][3], 4, 0);
modify->addstep_compute(update->ntimestep + 1);
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;
domain->unmap(x[i],image[i],unwrap);
if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
domain->unmap(x[i], image[i], unwrap);
if (xstyle == ATOM) xvalue = sforce[i][0];
if (ystyle == ATOM) yvalue = sforce[i][1];
if (zstyle == ATOM) zvalue = sforce[i][2];
@ -324,9 +322,9 @@ void FixAddForce::post_force(int vflag)
if (estyle == ATOM) {
foriginal[0] += sforce[i][3];
} else {
if (xstyle) foriginal[0] -= xvalue*unwrap[0];
if (ystyle) foriginal[0] -= yvalue*unwrap[1];
if (zstyle) foriginal[0] -= zvalue*unwrap[2];
if (xstyle) foriginal[0] -= xvalue * unwrap[0];
if (ystyle) foriginal[0] -= yvalue * unwrap[1];
if (zstyle) foriginal[0] -= zvalue * unwrap[2];
}
foriginal[1] += f[i][0];
foriginal[2] += f[i][1];
@ -336,13 +334,13 @@ void FixAddForce::post_force(int vflag)
if (ystyle) f[i][1] += yvalue;
if (zstyle) f[i][2] += zvalue;
if (evflag) {
v[0] = xstyle ? xvalue*unwrap[0] : 0.0;
v[1] = ystyle ? yvalue*unwrap[1] : 0.0;
v[2] = zstyle ? zvalue*unwrap[2] : 0.0;
v[3] = xstyle ? xvalue*unwrap[1] : 0.0;
v[4] = xstyle ? xvalue*unwrap[2] : 0.0;
v[5] = ystyle ? yvalue*unwrap[2] : 0.0;
v_tally(i,v);
v[0] = xstyle ? xvalue * unwrap[0] : 0.0;
v[1] = ystyle ? yvalue * unwrap[1] : 0.0;
v[2] = zstyle ? zvalue * unwrap[2] : 0.0;
v[3] = xstyle ? xvalue * unwrap[1] : 0.0;
v[4] = xstyle ? xvalue * unwrap[2] : 0.0;
v[5] = ystyle ? yvalue * unwrap[2] : 0.0;
v_tally(i, v);
}
}
}
@ -372,7 +370,7 @@ double FixAddForce::compute_scalar()
// only sum across procs one time
if (force_flag == 0) {
MPI_Allreduce(foriginal,foriginal_all,4,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(foriginal, foriginal_all, 4, MPI_DOUBLE, MPI_SUM, world);
force_flag = 1;
}
return foriginal_all[0];
@ -387,10 +385,10 @@ double FixAddForce::compute_vector(int n)
// only sum across procs one time
if (force_flag == 0) {
MPI_Allreduce(foriginal,foriginal_all,4,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(foriginal, foriginal_all, 4, MPI_DOUBLE, MPI_SUM, world);
force_flag = 1;
}
return foriginal_all[n+1];
return foriginal_all[n + 1];
}
/* ----------------------------------------------------------------------
@ -400,6 +398,6 @@ double FixAddForce::compute_vector(int n)
double FixAddForce::memory_usage()
{
double bytes = 0.0;
if (varflag == ATOM) bytes = maxatom*4 * sizeof(double);
if (varflag == ATOM) bytes = maxatom * 4 * sizeof(double);
return bytes;
}