Merge pull request lammps#4054 from akohlmey/consolidate-sphere-omega…

…-flag

Remove sphere_flag and replace with radius_flag and omega_flag as needed

doc/utils/sphinx-config/false_positives.txt

@@ -125,6 +125,7 @@ antisymmetry
 anton
 Antonelli
 api
+apolar
 Apoorva
 Appl
 Appshaw
@@ -799,6 +800,7 @@ dlabel
 dlambda
 DLAMMPS
 dll
+dlm
 dlopen
 dm
 dmax
@@ -1016,6 +1018,7 @@ Ercolessi
 Erdmann
 erf
 erfc
+erforce
 Erhart
 erorate
 erose
@@ -2236,8 +2239,10 @@ Mohd
 Mohles
 mol
 Mol
+molatom
 molfile
 Molfile
+molindex
 MolPairStyle
 moltemplate
 momb
@@ -2570,6 +2575,7 @@ ns
 Ns
 Nsample
 Nskip
+nspecial
 Nspecies
 nsq
 Nstart
@@ -3878,6 +3884,7 @@ versa
 Verstraelen
 ves
 vflag
+vfrac
 vhi
 vibrational
 Vij

src/BPM/atom_vec_bpm_sphere.cpp

@@ -35,7 +35,6 @@ AtomVecBPMSphere::AtomVecBPMSphere(LAMMPS *_lmp) : AtomVec(_lmp)
   radvary = 0;
 
   atom->molecule_flag = 1;
-  atom->sphere_flag = 1;
   atom->radius_flag = atom->rmass_flag = atom->omega_flag = atom->torque_flag = atom->quat_flag = 1;
 
   // strings with peratom variables to include in each AtomVec method

src/BPM/bond_bpm_rotational.cpp

@@ -645,7 +645,7 @@ void BondBPMRotational::init_style()
 {
   BondBPM::init_style();
 
-  if (!atom->quat_flag || !atom->sphere_flag)
+  if (!atom->quat_flag || !atom->radius_flag || !atom->omega_flag)
     error->all(FLERR, "Bond bpm/rotational requires atom style bpm/sphere");
   if (comm->ghost_velocity == 0)
     error->all(FLERR, "Bond bpm/rotational requires ghost atoms store velocity");

src/BPM/fix_nve_bpm_sphere.cpp

@@ -52,7 +52,7 @@ FixNVEBPMSphere::FixNVEBPMSphere(LAMMPS *_lmp, int narg, char **arg) : FixNVE(_l
 
   // error checks
 
-  if (!atom->quat_flag || !atom->sphere_flag)
+  if (!atom->quat_flag || !atom->radius_flag || !atom->omega_flag)
     error->all(FLERR, "Fix nve/bpm/sphere requires atom style bpm/sphere");
 }
 

src/BROWNIAN/fix_brownian_sphere.cpp

@@ -41,7 +41,6 @@ FixBrownianSphere::FixBrownianSphere(LAMMPS *lmp, int narg, char **arg) :
 
   if (!gamma_t_flag || !gamma_r_flag) error->all(FLERR, "Illegal fix brownian/sphere command.");
   if (!atom->mu_flag) error->all(FLERR, "Fix brownian/sphere requires atom attribute mu");
-  if (!atom->sphere_flag) error->all(FLERR, "Fix brownian/sphere requires atom style sphere");
 }
 
 /* ---------------------------------------------------------------------- */

src/COLLOID/fix_wall_colloid.cpp

@@ -34,7 +34,7 @@ FixWallColloid::FixWallColloid(LAMMPS *lmp, int narg, char **arg) : FixWall(lmp,
 
 void FixWallColloid::init()
 {
-  if (!atom->sphere_flag) error->all(FLERR, "Fix wall/colloid requires atom style sphere");
+  if (!atom->radius_flag) error->all(FLERR, "Fix wall/colloid requires atom attribute radius");
 
   // ensure all particles in group are extended particles
 

src/COLLOID/pair_brownian.cpp

@@ -435,7 +435,7 @@ void PairBrownian::coeff(int narg, char **arg)
 
 void PairBrownian::init_style()
 {
-  if (!atom->sphere_flag) error->all(FLERR, "Pair brownian requires atom style sphere");
+  if (!atom->radius_flag) error->all(FLERR, "Pair brownian requires atom attribute radius");
 
   // if newton off, forces between atoms ij will be double computed
   // using different random numbers

src/COLLOID/pair_brownian_poly.cpp

@@ -318,8 +318,8 @@ void PairBrownianPoly::init_style()
 {
   if (force->newton_pair == 1)
     error->all(FLERR,"Pair brownian/poly requires newton pair off");
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Pair brownian/poly requires atom style sphere");
+  if (!atom->radius_flag)
+    error->all(FLERR,"Pair brownian/poly requires atom attribute radius");
 
   // ensure all particles are finite-size
   // for pair hybrid, should limit test to types using the pair style

src/COLLOID/pair_lubricate.cpp

@@ -527,8 +527,10 @@ void PairLubricate::coeff(int narg, char **arg)
 
 void PairLubricate::init_style()
 {
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Pair lubricate requires atom style sphere");
+  if (!atom->omega_flag)
+    error->all(FLERR,"Pair lubricate requires atom attribute omega");
+  if (!atom->radius_flag)
+    error->all(FLERR,"Pair lubricate requires atom attribute radius");
   if (comm->ghost_velocity == 0)
     error->all(FLERR,"Pair lubricate requires ghost atoms store velocity");
 

src/COLLOID/pair_lubricateU.cpp

@@ -1760,8 +1760,10 @@ void PairLubricateU::coeff(int narg, char **arg)
 
 void PairLubricateU::init_style()
 {
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Pair lubricateU requires atom style sphere");
+  if (!atom->omega_flag)
+    error->all(FLERR,"Pair lubricateU requires atom attribute omega");
+  if (!atom->radius_flag)
+    error->all(FLERR,"Pair lubricateU requires atom attribute radius");
   if (comm->ghost_velocity == 0)
     error->all(FLERR,"Pair lubricateU requires ghost atoms store velocity");
 

src/COLLOID/pair_lubricateU_poly.cpp

@@ -1121,12 +1121,13 @@ void PairLubricateUPoly::settings(int narg, char **arg)
 void PairLubricateUPoly::init_style()
 {
   if (force->newton_pair == 1)
-    error->all(FLERR,"Pair lubricateU/poly requires newton pair off");
+    error->all(FLERR, "Pair lubricateU/poly requires newton pair off");
   if (comm->ghost_velocity == 0)
-    error->all(FLERR,
-               "Pair lubricateU/poly requires ghost atoms store velocity");
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Pair lubricate/poly requires atom style sphere");
+    error->all(FLERR, "Pair lubricateU/poly requires ghost atoms store velocity");
+  if (!atom->omega_flag)
+    error->all(FLERR, "Pair lubricateU/poly requires atom attribute omega");
+  if (!atom->radius_flag)
+    error->all(FLERR, "Pair lubricateU/poly requires atom attribute radius");
 
   // ensure all particles are finite-size
   // for pair hybrid, should limit test to types using the pair style
@@ -1136,7 +1137,7 @@ void PairLubricateUPoly::init_style()
 
   for (int i = 0; i < nlocal; i++)
     if (radius[i] == 0.0)
-      error->one(FLERR,"Pair lubricate/poly requires extended particles");
+      error->one(FLERR,"Pair lubricateU/poly requires extended particles");
 
   // Set the isotropic constants depending on the volume fraction
 

src/COLLOID/pair_lubricate_poly.cpp

@@ -424,12 +424,13 @@ void PairLubricatePoly::compute(int eflag, int vflag)
 void PairLubricatePoly::init_style()
 {
   if (force->newton_pair == 1)
-    error->all(FLERR,"Pair lubricate/poly requires newton pair off");
+    error->all(FLERR, "Pair lubricate/poly requires newton pair off");
   if (comm->ghost_velocity == 0)
-    error->all(FLERR,
-               "Pair lubricate/poly requires ghost atoms store velocity");
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Pair lubricate/poly requires atom style sphere");
+    error->all(FLERR, "Pair lubricate/poly requires ghost atoms store velocity");
+  if (!atom->omega_flag)
+    error->all(FLERR, "Pair lubricate/poly requires atom attribute omega");
+  if (!atom->radius_flag)
+    error->all(FLERR, "Pair lubricate/poly requires atom attribute radius");
 
   // ensure all particles are finite-size
   // for pair hybrid, should limit test to types using the pair style
@@ -439,7 +440,7 @@ void PairLubricatePoly::init_style()
 
   for (int i = 0; i < nlocal; i++)
     if (radius[i] == 0.0)
-      error->one(FLERR,"Pair lubricate/poly requires extended particles");
+      error->one(FLERR,"Pair lubricate/poly requires only extended particles");
 
   neighbor->add_request(this, NeighConst::REQ_FULL);
 

src/COLLOID/pair_yukawa_colloid.cpp

@@ -121,8 +121,8 @@ void PairYukawaColloid::compute(int eflag, int vflag)
 
 void PairYukawaColloid::init_style()
 {
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Pair yukawa/colloid requires atom style sphere");
+  if (!atom->radius_flag)
+    error->all(FLERR,"Pair yukawa/colloid requires atom attribute radius");
 
   neighbor->add_request(this);
 

src/EXTRA-FIX/fix_viscous_sphere.cpp

@@ -38,7 +38,7 @@ FixViscousSphere::FixViscousSphere(LAMMPS *_lmp, int narg, char **arg) :
 {
   dynamic_group_allow = 1;
 
-  if (!atom->sphere_flag) error->all(FLERR, "Fix viscous/sphere requires atom style sphere");
+  if (!atom->omega_flag) error->all(FLERR, "Fix viscous/sphere requires atom attribute omega");
 
   if (narg < 4) error->all(FLERR, "Illegal fix viscous/sphere command");
 

src/GPU/pair_yukawa_colloid_gpu.cpp

@@ -123,7 +123,7 @@ void PairYukawaColloidGPU::compute(int eflag, int vflag)
 
 void PairYukawaColloidGPU::init_style()
 {
-  if (!atom->sphere_flag) error->all(FLERR, "Pair yukawa/colloid/gpu requires atom style sphere");
+  if (!atom->radius_flag) error->all(FLERR, "Pair style yukawa/colloid/gpu requires atom attribute radius");
 
   // Repeat cutsq calculation because done after call to init_style
   double maxcut = -1.0;

src/GRANULAR/compute_contact_atom.cpp

@@ -50,7 +50,7 @@ ComputeContactAtom::ComputeContactAtom(LAMMPS *lmp, int narg, char **arg) :
 
   // error checks
 
-  if (!atom->sphere_flag) error->all(FLERR, "Compute contact/atom requires atom style sphere");
+  if (!atom->radius_flag) error->all(FLERR, "Compute contact/atom requires atom attribute radius");
 }
 
 /* ---------------------------------------------------------------------- */

src/GRANULAR/fix_damping_cundall.cpp

@@ -40,7 +40,7 @@ FixDampingCundall::FixDampingCundall(LAMMPS *_lmp, int narg, char **arg) :
 {
   dynamic_group_allow = 1;
 
-  if (!atom->sphere_flag) error->all(FLERR, "Fix damping/cundall requires atom style sphere");
+  if (!atom->omega_flag) error->all(FLERR, "Fix damping/cundall requires atom attribute omega");
 
   if (narg < 5) utils::missing_cmd_args(FLERR, "fix damping/cundall", error);
 

src/GRANULAR/fix_wall_gran.cpp

@@ -57,8 +57,8 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg < 4) utils::missing_cmd_args(FLERR,"fix wall/gran", error);
 
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Fix wall/gran requires atom style sphere");
+  if (!atom->omega_flag) error->all(FLERR,"Fix wall/gran requires atom attribute omega");
+  if (!atom->radius_flag) error->all(FLERR,"Fix wall/gran requires atom attribute radius");
 
   create_attribute = 1;
 

src/GRANULAR/pair_gran_hooke_history.cpp

@@ -435,10 +435,10 @@ void PairGranHookeHistory::init_style()
 
   // error and warning checks
 
-  if (!atom->radius_flag || !atom->rmass_flag)
-    error->all(FLERR, "Pair granular requires atom attributes radius, rmass");
+  if (!atom->radius_flag || !atom->rmass_flag || !atom->omega_flag)
+    error->all(FLERR, "Pair gran/h* requires atom attributes radius, rmass, omega");
   if (comm->ghost_velocity == 0)
-    error->all(FLERR, "Pair granular requires ghost atoms store velocity");
+    error->all(FLERR, "Pair gran/h* requires ghost atoms store velocity");
 
   // need a granular neighbor list
 

src/GRANULAR/pair_granular.cpp

@@ -401,8 +401,8 @@ void PairGranular::init_style()
 {
   // error and warning checks
 
-  if (!atom->radius_flag || !atom->rmass_flag)
-    error->all(FLERR,"Pair granular requires atom attributes radius, rmass");
+  if (!atom->radius_flag || !atom->rmass_flag || !atom->omega_flag)
+    error->all(FLERR,"Pair granular requires atom attributes radius, rmass, omega");
   if (comm->ghost_velocity == 0)
     error->all(FLERR,"Pair granular requires ghost atoms store velocity");
 

src/KOKKOS/fix_wall_gran_old.cpp

@@ -68,8 +68,8 @@ FixWallGranOld::FixWallGranOld(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg < 4) error->all(FLERR,"Illegal fix wall/gran command");
 
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Fix wall/gran requires atom style sphere");
+  if (!atom->omega_flag) error->all(FLERR,"Fix {} requires atom attribute omega", style);
+  if (!atom->radius_flag) error->all(FLERR,"Fix {} requires atom attribute radius", style);
 
   create_attribute = 1;
   limit_damping = 0;

src/OPENMP/fix_nh_sphere_omp.cpp

@@ -37,8 +37,8 @@ typedef struct { double x,y,z; } dbl3_t;
 FixNHSphereOMP::FixNHSphereOMP(LAMMPS *lmp, int narg, char **arg) :
   FixNHOMP(lmp, narg, arg)
 {
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Fix nvt/nph/npt sphere requires atom style sphere");
+  if (!atom->omega_flag) error->all(FLERR,"Fix {} requires atom attribute omega", style);
+  if (!atom->radius_flag) error->all(FLERR,"Fix {} requires atom attribute radius", style);
 }
 
 /* ---------------------------------------------------------------------- */

src/atom.cpp

@@ -619,7 +619,7 @@ void Atom::set_atomflag_defaults()
   // identical list as 2nd customization in atom.h
 
   labelmapflag = 0;
-  sphere_flag = ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
+  ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
   quat_flag = 0;
   peri_flag = electron_flag = 0;
   wavepacket_flag = sph_flag = 0;

src/atom.h

@@ -180,7 +180,7 @@ class Atom : protected Pointers {
   // 1 if variable is used, 0 if not
 
   int labelmapflag, types_style;
-  int sphere_flag, ellipsoid_flag, line_flag, tri_flag, body_flag;
+  int ellipsoid_flag, line_flag, tri_flag, body_flag;
   int peri_flag, electron_flag;
   int wavepacket_flag, sph_flag;
 

src/atom_vec_line.cpp

@@ -44,7 +44,6 @@ AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
   atom->line_flag = 1;
   atom->molecule_flag = atom->rmass_flag = 1;
   atom->radius_flag = atom->omega_flag = atom->torque_flag = 1;
-  atom->sphere_flag = 1;
 
   nlocal_bonus = nghost_bonus = nmax_bonus = 0;
   bonus = nullptr;

src/atom_vec_sphere.cpp

@@ -32,7 +32,6 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
   molecular = Atom::ATOMIC;
   radvary = 0;
 
-  atom->sphere_flag = 1;
   atom->radius_flag = atom->rmass_flag = atom->omega_flag = atom->torque_flag = 1;
 
   // strings with peratom variables to include in each AtomVec method

src/atom_vec_tri.cpp

@@ -47,7 +47,6 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
   atom->molecule_flag = atom->rmass_flag = 1;
   atom->radius_flag = atom->omega_flag = atom->angmom_flag = 1;
   atom->torque_flag = 1;
-  atom->sphere_flag = 1;
 
   nlocal_bonus = nghost_bonus = nmax_bonus = 0;
   bonus = nullptr;

src/compute_erotate_sphere.cpp

@@ -34,7 +34,7 @@ ComputeERotateSphere::ComputeERotateSphere(LAMMPS *lmp, int narg, char **arg) :
 
   // error check
 
-  if (!atom->sphere_flag) error->all(FLERR, "Compute erotate/sphere requires atom style sphere");
+  if (!atom->omega_flag) error->all(FLERR, "Compute erotate/sphere requires atom attribute omega");
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_erotate_sphere_atom.cpp

@@ -40,8 +40,10 @@ ComputeErotateSphereAtom(LAMMPS *lmp, int narg, char **arg) :
 
   // error check
 
-  if (!atom->sphere_flag)
-    error->all(FLERR,"Compute erotate/sphere/atom requires atom style sphere");
+  if (!atom->omega_flag)
+    error->all(FLERR,"Compute erotate/sphere/atom requires atom attribute omega");
+  if (!atom->radius_flag)
+    error->all(FLERR,"Compute erotate/sphere/atom requires atom attribute radius");
 
   nmax = 0;
 }