Merge branch 'develop' into rheo

src/atom.cpp

@@ -125,6 +125,8 @@ Atom::Atom(LAMMPS *_lmp) : Pointers(_lmp)
   radius = rmass = nullptr;
   ellipsoid = line = tri = body = nullptr;
   quat = nullptr;
+  temperature = nullptr;
+  heatflow = nullptr;
 
   // molecular systems
 
@@ -425,6 +427,9 @@ void Atom::peratom_create()
   add_peratom("tri",&tri,INT,0);
   add_peratom("body",&body,INT,0);
 
+  add_peratom("temperature",&temperature,DOUBLE,0);
+  add_peratom("heatflow",&heatflow,DOUBLE,0);
+
   // BPM package
 
   add_peratom("quat",&quat,DOUBLE,4);
@@ -631,6 +636,7 @@ void Atom::set_atomflag_defaults()
   molecule_flag = molindex_flag = molatom_flag = 0;
   q_flag = mu_flag = 0;
   rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
+  temperature_flag = heatflow_flag = 0;
   vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
   cs_flag = csforce_flag = vforce_flag = ervelforce_flag = etag_flag = 0;
   status_flag = 0;
@@ -1923,11 +1929,15 @@ void Atom::set_mass(const char *file, int line, const char *str, int type_offset
 
 void Atom::set_mass(const char *file, int line, int itype, double value)
 {
-  if (mass == nullptr) error->all(file,line, "Cannot set mass for atom style {}", atom_style);
+  if (mass == nullptr)
+    error->all(file,line, "Cannot set per-type mass for atom style {}", atom_style);
   if (itype < 1 || itype > ntypes)
     error->all(file,line,"Invalid type {} for atom mass {}", itype, value);
-  if (value <= 0.0) error->all(file,line,"Invalid atom mass value {}", value);
-
+  if (value <= 0.0) {
+    if (comm->me == 0)
+      error->warning(file,line,"Ignoring invalid mass value {} for atom type {}", value, itype);
+    return;
+  }
   mass[itype] = value;
   mass_setflag[itype] = 1;
 }
@@ -2840,6 +2850,14 @@ length of the data area, and a short description.
      - double
      - 4
      - four quaternion components of the particles
+   * - temperature
+     - double
+     - 1
+     - temperature of the particles
+   * - heatflow
+     - double
+     - 1
+     - heatflow of the particles
    * - i_name
      - int
      - 1
@@ -2896,6 +2914,8 @@ void *Atom::extract(const char *name)
   if (strcmp(name,"tri") == 0) return (void *) tri;
   if (strcmp(name,"body") == 0) return (void *) body;
   if (strcmp(name,"quat") == 0) return (void *) quat;
+  if (strcmp(name,"temperature") == 0) return (void *) temperature;
+  if (strcmp(name,"heatflow") == 0) return (void *) heatflow;
 
   // PERI PACKAGE
 
@@ -3028,6 +3048,8 @@ int Atom::extract_datatype(const char *name)
   if (strcmp(name,"tri") == 0) return LAMMPS_INT;
   if (strcmp(name,"body") == 0) return LAMMPS_INT;
   if (strcmp(name,"quat") == 0) return LAMMPS_DOUBLE_2D;
+  if (strcmp(name,"temperature") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"heatflow") == 0) return LAMMPS_DOUBLE;
 
   if (strcmp(name,"vfrac") == 0) return LAMMPS_DOUBLE;
   if (strcmp(name,"s0") == 0) return LAMMPS_DOUBLE;