git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@638 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/atom_vec_ellipsoid.cpp

@@ -44,6 +44,8 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp, int narg, char **arg) :
   size_data_atom = 9;
   size_data_vel = 7;
   xcol_data = 3;
+
+  atom->angmom_flag = atom->torque_flag = atom->quat_flag = 1;
 }
 
 /* ---------------------------------------------------------------------- */

src/ASPHERE/compute_temp_asphere.cpp

@@ -35,7 +35,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all("Illegal compute temp command");
 
-  if (atom->quat == NULL || atom->angmom == NULL)
+  if (!atom->quat_flag || !atom->angmom_flag)
     error->all("Compute temp/asphere requires atom attributes quat, angmom");
 
   scalar_flag = vector_flag = 1;

src/ASPHERE/fix_npt_asphere.cpp

@@ -34,7 +34,7 @@ using namespace LAMMPS_NS;
 FixNPTASphere::FixNPTASphere(LAMMPS *lmp, int narg, char **arg) :
   FixNPT(lmp, narg, arg)
 {
-  if (atom->quat == NULL || atom->angmom == NULL || atom->torque == NULL)
+  if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag)
     error->all("Fix npt/asphere requires atom attributes "
 	       "quat, angmom, torque");
 }

src/ASPHERE/fix_nve_asphere.cpp

@@ -37,7 +37,7 @@ FixNVEASphere::FixNVEASphere(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
   if (narg < 3) error->all("Illegal fix nve/asphere command");
-  if (atom->quat == NULL || atom->angmom == NULL || atom->torque == NULL)
+  if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag)
     error->all("Fix nve/asphere requires atom attributes "
 	       "quat, angmom, torque");
   inertia = 

src/ASPHERE/fix_nvt_asphere.cpp

@@ -36,7 +36,7 @@ using namespace LAMMPS_NS;
 FixNVTASphere::FixNVTASphere(LAMMPS *lmp, int narg, char **arg) :
   FixNVT(lmp, narg, arg)
 {
-  if (atom->quat == NULL || atom->angmom == NULL || atom->torque == NULL)
+  if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag)
     error->all("Fix nvt/asphere requires atom attributes "
 	       "quat, angmom, torque");
 }

src/ASPHERE/pair_gayberne.cpp

@@ -375,7 +375,7 @@ double PairGayBerne::init_one(int i, int j)
 
 void PairGayBerne::init_style()
 {
-  if (atom->quat == NULL || atom->torque == NULL)
+  if (!atom->quat_flag || !atom->torque_flag)
     error->all("Pair gayberne requires atom attributes quat, torque");
 
   // per-type shape precalculations

src/CLASS2/pair_lj_class2_coul_cut.cpp

@@ -327,7 +327,7 @@ double PairLJClass2CoulCut::init_one(int i, int j)
 
 void PairLJClass2CoulCut::init_style()
 {
-  if (atom->q == NULL)
+  if (!atom->q_flag)
     error->all("Pair style lj/class2/coul/cut requires atom attribute q");
 }
 

src/CLASS2/pair_lj_class2_coul_long.cpp

@@ -333,7 +333,7 @@ double PairLJClass2CoulLong::init_one(int i, int j)
 
 void PairLJClass2CoulLong::init_style()
 {
-  if (atom->q == NULL)
+  if (!atom->q_flag)
     error->all("Pair style lj/class2/coul/long requires atom attribute q");
 
   cut_coulsq = cut_coul * cut_coul;

src/DIPOLE/atom_vec_dipole.cpp

@@ -39,6 +39,8 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp, int narg, char **arg) :
   size_data_atom = 9;
   size_data_vel = 7;
   xcol_data = 4;
+
+  atom->q_flag = atom->mu_flag = atom->omega_flag = atom->torque_flag = 1;
 }
 
 /* ----------------------------------------------------------------------

src/DIPOLE/compute_temp_dipole.cpp

@@ -33,7 +33,7 @@ ComputeTempDipole::ComputeTempDipole(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all("Illegal compute temp/dipole command");
 
-  if (atom->omega == NULL || atom->shape == NULL)
+  if (!atom->omega_flag || atom->shape == NULL)
     error->all("Compute temp/dipole requires atom attributes omega, shape");
 
   scalar_flag = vector_flag = 1;

src/DIPOLE/fix_nve_dipole.cpp

@@ -32,8 +32,8 @@ FixNVEDipole::FixNVEDipole(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
   if (narg != 3) error->all("Illegal fix nve/dipole command");
-  if (atom->mu == NULL || atom->omega == NULL || 
-      atom->torque == NULL || atom->shape == NULL)
+  if (!atom->mu_flag || !atom->omega_flag || 
+      !atom->torque_flag || atom->shape == NULL)
     error->all("Fix nve/dipole requires atom attributes "
 	       "mu, omega, torque, shape");
   inertia = new double[atom->ntypes+1];

src/DIPOLE/pair_dipole_cut.cpp

@@ -406,8 +406,8 @@ double PairDipoleCut::init_one(int i, int j)
 
 void PairDipoleCut::init_style()
 {
-  if (atom->q == NULL || atom->mu == NULL || 
-      atom->torque == NULL || atom->dipole == NULL)
+  if (!atom->q_flag || !atom->mu_flag || 
+      !atom->torque_flag || atom->dipole == NULL)
     error->all("Pair dipole/cut requires atom attributes "
 	       "q, mu, torque, dipole");
 }

src/GRANULAR/atom_vec_granular.cpp

@@ -39,6 +39,9 @@ AtomVecGranular::AtomVecGranular(LAMMPS *lmp, int narg, char **arg) :
   size_data_vel = 7;
   xcol_data = 5;
 
+  atom->radius_flag = atom->density_flag = atom->rmass_flag = 1;
+  atom->xphi_flag = atom->omega_flag = atom->torque_flag = 1;
+
   PI = 4.0*atan(1.0);
 }
 

src/GRANULAR/fix_freeze.cpp

@@ -27,7 +27,7 @@ FixFreeze::FixFreeze(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all("Illegal fix freeze command");
 
-  if (atom->torque == NULL)
+  if (!atom->torque_flag)
     error->all("Fix freeze requires atom attribute torque");
 }
 

src/GRANULAR/fix_gran_diag.cpp

@@ -46,7 +46,7 @@ FixGranDiag::FixGranDiag(LAMMPS *lmp, int narg, char **arg) :
   if (nevery <= 0) error->all("Illegal fix gran/diag command");
   first = 1;
 
-  if (atom->radius == NULL || atom->rmass == NULL || atom->omega == NULL)
+  if (!atom->radius_flag || !atom->rmass_flag || !atom->omega_flag)
     error->all("Fix gran/diag requires atom attributes radius, rmass, omega");
 
   MPI_Comm_rank(world,&me);

src/GRANULAR/fix_nve_gran.cpp

@@ -33,7 +33,7 @@ FixNVEGran::FixNVEGran(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all("Illegal fix nve/gran command");
 
-  if (atom->xphi == NULL || atom->omega == NULL || atom->torque == NULL)
+  if (!atom->xphi_flag || !atom->omega_flag || !atom->torque_flag)
     error->all("Fix nve/gran requires atom attributes "
 	       "xphi, omega, torque");
 }

src/GRANULAR/fix_pour.cpp

@@ -42,10 +42,8 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg < 6) error->all("Illegal fix pour command");
 
-  /*
-  if (atom->radius == NULL || atom->rmass == NULL)
+  if (!atom->radius_flag || !atom->rmass_flag)
     error->all("Fix pour requires atom attributes radius, rmass");
-  */
 
   if (domain->triclinic) error->all("Cannot use fix pour with triclinic box");
 

src/GRANULAR/fix_wall_gran.cpp

@@ -45,7 +45,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg < 4) error->all("Illegal fix wall/gran command");
 
-  if (atom->radius == NULL || atom->omega == NULL || atom->torque == NULL)
+  if (!atom->radius_flag || !atom->omega_flag || !atom->torque_flag)
     error->all("Fix wall/gran requires atom attributes radius, omega, torque");
 
   restart_peratom = 1;

src/GRANULAR/pair_gran_history.cpp

@@ -325,7 +325,7 @@ void PairGranHistory::init_style()
 {
   int i;
 
-  if (atom->radius == NULL || atom->omega == NULL || atom->torque == NULL)
+  if (!atom->radius_flag || !atom->omega_flag || !atom->torque_flag)
     error->all("Pair granular requires atom attributes radius, omega, torque");
 
   xkkt = xkk * 2.0/7.0;

src/KSPACE/ewald.cpp

@@ -83,8 +83,7 @@ void Ewald::init()
   if (domain->triclinic) error->all("Cannot use Ewald with triclinic box");
   if (force->dimension == 2) error->all("Cannot use Ewald with 2d simulation");
 
-  if (atom->q == NULL)
-    error->all("Must use charged atom style with kspace style");
+  if (!atom->q_flag) error->all("Kspace style requires atom attribute q");
 
   if (slabflag == 0 && domain->nonperiodic > 0)
     error->all("Cannot use nonperiodic boundaries with Ewald");

src/KSPACE/pair_buck_coul_long.cpp

@@ -300,7 +300,7 @@ double PairBuckCoulLong::init_one(int i, int j)
 
 void PairBuckCoulLong::init_style()
 {
-  if (atom->q == NULL)
+  if (!atom->q_flag)
     error->all("Pair style buck/coul/long requires atom attribute q");
 
   cut_coulsq = cut_coul * cut_coul;

src/KSPACE/pair_lj_charmm_coul_long.cpp

@@ -747,7 +747,7 @@ double PairLJCharmmCoulLong::init_one(int i, int j)
 
 void PairLJCharmmCoulLong::init_style()
 {
-  if (atom->q == NULL)
+  if (!atom->q_flag)
     error->all("Pair style lj/charmm/coul/long requires atom attribute q");
 
   // require cut_lj_inner < cut_lj

src/KSPACE/pair_lj_cut_coul_long.cpp

@@ -721,7 +721,7 @@ void PairLJCutCoulLong::init_style()
 {
   int i,j;
 
-  if (atom->q == NULL)
+  if (!atom->q_flag)
     error->all("Pair style lj/cut/coul/long requires atom attribute q");
 
   cut_coulsq = cut_coul * cut_coul;

src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp

@@ -410,7 +410,7 @@ void PairLJCutCoulLongTIP4P::init_style()
     error->all("Pair style lj/cut/coul/long/tip4p requires atom IDs");
   if (!force->newton_pair) 
     error->all("Pair style lj/cut/coul/long/tip4p requires newton pair on");
-  if (atom->q == NULL)
+  if (!atom->q_flag)
     error->all("Pair style lj/cut/coul/long/tip4p requires atom attribute q");
 
   cut_coulsq = cut_coul * cut_coul;

src/KSPACE/pppm.cpp

@@ -109,8 +109,7 @@ void PPPM::init()
     error->all("Cannot (yet) use PPPM with triclinic box");
   if (force->dimension == 2) error->all("Cannot use PPPM with 2d simulation");
 
-  if (atom->q == NULL)
-    error->all("Must use charged atom style with kspace style");
+  if (!atom->q_flag) error->all("Kspace style requires atom attribute q");
 
   if (slabflag == 0 && domain->nonperiodic > 0)
     error->all("Cannot use nonperiodic boundaries with PPPM");

src/MAKE/Makefile.g++_meam

@@ -1,4 +1,4 @@
-# g++_meam = RedHat Linux box, g++, MPICH, FFTW, MEAM
+# g++_meam = RedHat Linux box, g++, MPICH, FFTW, MEAM library
 
 SHELL = /bin/sh
 #.IGNORE:

src/MOLECULE/atom_vec_angle.cpp

@@ -42,6 +42,8 @@ AtomVecAngle::AtomVecAngle(LAMMPS *lmp, int narg, char **arg) :
   size_data_atom = 6;
   size_data_vel = 4;
   xcol_data = 4;
+
+  atom->molecule_flag = 1;
 }
 
 /* ----------------------------------------------------------------------

src/MOLECULE/atom_vec_bond.cpp

@@ -41,6 +41,8 @@ AtomVecBond::AtomVecBond(LAMMPS *lmp, int narg, char **arg) :
   size_data_atom = 6;
   size_data_vel = 4;
   xcol_data = 4;
+
+  atom->molecule_flag = 1;
 }
 
 /* ----------------------------------------------------------------------

src/MOLECULE/atom_vec_full.cpp

@@ -44,6 +44,8 @@ AtomVecFull::AtomVecFull(LAMMPS *lmp, int narg, char **arg) :
   size_data_atom = 7;
   size_data_vel = 4;
   xcol_data = 5;
+
+  atom->molecule_flag = atom->q_flag = 1;
 }
 
 /* ----------------------------------------------------------------------

src/MOLECULE/atom_vec_molecular.cpp

@@ -44,6 +44,8 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp, int narg, char **arg) :
   size_data_atom = 6;
   size_data_vel = 4;
   xcol_data = 4;
+
+  atom->molecule_flag = 1;
 }
 
 /* ----------------------------------------------------------------------

src/MOLECULE/pair_lj_charmm_coul_charmm.cpp

@@ -323,7 +323,7 @@ double PairLJCharmmCoulCharmm::init_one(int i, int j)
 
 void PairLJCharmmCoulCharmm::init_style()
 {
-  if (atom->q == NULL)
+  if (!atom->q_flag)
     error->all("Pair style lj/charmm/coul/charmm requires atom attribute q");
 
   // require cut_lj_inner < cut_lj, cut_coul_inner < cut_coul

src/POEMS/fix_poems.cpp

@@ -59,12 +59,6 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
   virial_flag = 1;
   MPI_Comm_rank(world,&me);
 
-  // can't use with pure granular style since mass arrays are different
-  // hybrid granular style would be OK if fix were on non-granular atoms
-
-  if (atom->check_style("granular"))
-    error->all("Cannot use fix poems with atom style granular");
-
   // perform initial allocation of atom-based arrays
   // register with atom class
 
@@ -337,7 +331,7 @@ void FixPOEMS::init()
   int count = 0;
   for (int i = 0; i < modify->nfix; i++)
     if (strcmp(modify->fix[i]->style,"poems") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning("More than one poems fix");
+  if (count > 1 && comm->me == 0) error->warning("More than one fix poems");
 
   // error if npt,nph fix comes before rigid fix
 

src/atom.cpp

@@ -52,7 +52,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   nbonds = nangles = ndihedrals = nimpropers = 0;
   bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
 
-  // atom arrays
+  // initialize atom arrays
   // customize by adding new array
 
   tag = type = mask = image = NULL;
@@ -82,6 +82,14 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   improper_type = improper_atom1 = improper_atom2 = NULL;
   improper_atom3 = improper_atom4 = NULL;
 
+  // initialize atom array existence flags
+  // customize by adding new flag
+
+  molecule_flag = 0;
+  q_flag = mu_flag = 0;
+  xphi_flag = quat_flag = omega_flag = angmom_flag = torque_flag = 0;
+  radius_flag = density_flag = rmass_flag = vfrac_flag = 0;
+
   // ntype-length arrays
 
   mass = NULL;

src/atom.h

@@ -65,6 +65,14 @@ class Atom : protected Pointers {
   int **improper_type;
   int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
 
+  // per-atom array existence flags
+  // customize by adding new flag
+
+  int molecule_flag;
+  int q_flag,mu_flag;
+  int xphi_flag,quat_flag,omega_flag,angmom_flag,torque_flag;
+  int radius_flag,density_flag,rmass_flag,vfrac_flag;
+
   // extra peratom info in restart file destined for fix & diag 
 
   double **extra;

src/atom_vec_charge.cpp

@@ -36,6 +36,8 @@ AtomVecCharge::AtomVecCharge(LAMMPS *lmp, int narg, char **arg) :
   size_data_atom = 6;
   size_data_vel = 4;
   xcol_data = 4;
+
+  atom->q_flag = 1;
 }
 
 /* ----------------------------------------------------------------------

src/compute_rotate_dipole.cpp

@@ -30,7 +30,7 @@ ComputeRotateDipole::ComputeRotateDipole(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all("Illegal compute rotate/dipole command");
 
-  if (atom->dipole == NULL || atom->omega == NULL)
+  if (atom->dipole == NULL || !atom->omega_flag)
     error->all("Compute rotate/dipole requires atom attributes dipole, omega");
 
   scalar_flag = 1;

src/compute_rotate_gran.cpp

@@ -30,7 +30,7 @@ ComputeRotateGran::ComputeRotateGran(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all("Illegal compute rotate/gran command");
 
-  if (atom->radius == NULL || atom->rmass == NULL || atom->omega == NULL)
+  if (!atom->radius_flag || !atom->rmass_flag || !atom->omega_flag)
     error->all("Compute rotate/gran requires atom attributes "
 	       "radius, rmass, omega");
 

src/compute_temp_deform.cpp

@@ -69,13 +69,13 @@ void ComputeTempDeform::init()
 
   for (i = 0; i < modify->nfix; i++)
     if (strcmp(modify->fix[i]->style,"deform") == 0) {
-      if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP && 
+      if (((FixDeform *) modify->fix[i])->remapflag == X_REMAP && 
 	  comm->me == 0)
-	error->warning("Using fix nvt/sllod with inconsistent fix deform remapping");
+	error->warning("Using compute temp/deform with inconsistent fix deform remap option");
       break;
     }
   if (i == modify->nfix && comm->me == 0)
-    error->warning("Using fix nvt/sllod with no fix deform defined");
+    error->warning("Using compute temp/deform with no fix deform defined");
 }
 
 /* ---------------------------------------------------------------------- */

src/fix_deform.cpp

@@ -315,7 +315,7 @@ void FixDeform::init()
   int count = 0;
   for (int i = 0; i < modify->nfix; i++)
     if (strcmp(modify->fix[i]->style,"deform") == 0) count++;
-  if (count > 1) error->warning("More than one fix deform");
+  if (count > 1) error->all("More than one fix deform");
 
   // Kspace setting
 

src/fix_nvt_sllod.cpp

@@ -53,13 +53,13 @@ void FixNVTSlodd::init()
   int i;
   for (i = 0; i < modify->nfix; i++)
     if (strcmp(modify->fix[i]->style,"deform") == 0) {
-      if (((FixDeform *) modify->fix[i])->remapflag == X_REMAP && 
+      if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP && 
 	  comm->me == 0)
-	error->warning("Using compute temp/deform with fix deform remapping coords");
+	error->warning("Using fix nvt/sllod with inconsistent fix deform remap option");
       break;
     }
   if (i == modify->nfix && comm->me == 0)
-    error->warning("Using compute temp/deform with no fix deform defined");
+    error->warning("Using fix nvt/sllod with no fix deform defined");
 }
 
 /* ---------------------------------------------------------------------- */

src/fix_rigid.cpp

@@ -162,7 +162,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
 
   // error check on nbody
 
-  if (nbody == 0) error->all("No rigid bodies defined by fix rigid");
+  if (nbody == 0) error->all("No rigid bodies defined");
 
   // create all nbody-length arrays
 

src/pair_buck_coul_cut.cpp

@@ -297,7 +297,7 @@ double PairBuckCoulCut::init_one(int i, int j)
 
 void PairBuckCoulCut::init_style()
 {
-  if (atom->q == NULL)
+  if (!atom->q_flag)
     error->all("Pair style buck/coul/cut requires atom attribute q");
 }
 

src/pair_lj_cut_coul_cut.cpp

@@ -322,7 +322,7 @@ double PairLJCutCoulCut::init_one(int i, int j)
 
 void PairLJCutCoulCut::init_style()
 {
-  if (atom->q == NULL)
+  if (!atom->q_flag)
     error->all("Pair style lj/cut/coul/cut requires atom attribute q");
 }
 

src/variable.cpp

@@ -719,7 +719,7 @@ double Variable::evaluate(char *str, Tree *tree)
 
     } else if (tree) {
 
-      if (strlen(arg)) error->all("Invalid atom vector argument in variable");
+      if (strlen(arg)) error->all("Invalid atom vector in variable");
 
       // customize by adding atom vector to this list and to if statement
       // mass,x,y,z,vx,vy,vz,fx,fy,fz

src/verlet.cpp

@@ -96,7 +96,7 @@ void Verlet::init()
   // don't need to clear f_pair if atom_style is only granular (no virial)
 
   torqueflag = 0;
-  if (atom->torque) torqueflag = 1;
+  if (atom->torque_flag) torqueflag = 1;
   pairflag = 1;
   if (strcmp(atom->atom_style,"granular") == 0) pairflag = 0;
 

src/write_restart.cpp

@@ -219,9 +219,12 @@ void WriteRestart::write(char *file)
     sprintf(perproc,"%s%d%s",file,me,ptr+1);
     *ptr = '%';
     fp = fopen(perproc,"wb");
+    if (fp == NULL) {
+      char str[128];
+      sprintf(str,"Cannot open restart file %s",perproc);
+      error->one(str);
+    }
     delete [] perproc;
-    if (fp == NULL) error->one("Cannot open restart file");
-
     fwrite(&send_size,sizeof(int),1,fp);
     fwrite(buf,sizeof(double),send_size,fp);
     fclose(fp);