update

cmake/CMakeLists.txt

@@ -429,8 +429,7 @@ if(PKG_USER-MESONT)
   add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
   list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
   target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
-  #include(Packages/USER-MESONT)
-  #list(APPEND DEFAULT_PACKAGES "USER-MESONT")
+
   set(USER-MESONT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-MESONT)
   file(GLOB USER-MESONT_SOURCES ${USER-MESONT_SOURCES_DIR}/[^.]*.cpp)
   file(GLOB USER-MESONT_HEADERS ${USER-MESONT_SOURCES_DIR}/[^.]*.h)
@@ -438,7 +437,6 @@ if(PKG_USER-MESONT)
   RegisterStyles(${USER-MESONT_SOURCES_DIR})
   list(APPEND LIB_SOURCES ${USER-MESONT_SOURCES})
   include_directories(${USER-MESONT_SOURCES_DIR})
-  
 endif()
 
 if(PKG_USER-AWPMD)

doc/utils/sphinx-config/false_positives.txt

@@ -840,6 +840,7 @@ Espanol
 Eshelby
 eshelby
 eskm
+esph
 estretch
 esu
 esub
@@ -2647,6 +2648,7 @@ Schulten
 Schunk
 Schuring
 Schwen
+screenshot
 screenshots
 Scripta
 sdk

lib/mesont/Makefile.gfortran

@@ -52,4 +52,4 @@ clean:
 	-rm *.o *.mod $(LIB)
 
 tar:
-	-tar -cvf ../MESONT.tar $(FILES)
+	-tar -cvf ../MESONT.tar $(FILES)

lib/mesont/Makefile.serial

@@ -52,4 +52,4 @@ clean:
 	-rm *.o *.mod $(LIB)
 
 tar:
-	-tar -cvf ../MESONT.tar $(FILES)
+	-tar -cvf ../MESONT.tar $(FILES)

src/USER-MESONT/pair_mesont_tpm.cpp

@@ -413,6 +413,19 @@ void PairMESONTTPM::compute(int eflag, int vflag){
      X1, X2, X3, R123, L123, BBF2);
   }
 
+  //share new values of buckling
+  if (BendingMode == 1){
+    for (int i = 0; i < nall; i++){
+      int idx = ntlist.get_idx(i);
+      buckling[idx] = b_sort[i];
+    }
+    comm->forward_comm_pair(this);
+    for (int i = 0; i < nall; i++){
+      int idx = ntlist.get_idx(i);
+      b_sort[i] = buckling[idx];
+    }
+  }
+
   //segment-segment and segment-tube interactions
   int n_segments = ntlist.get_segments().size();
   double Rmax = 0.0;

src/atom.cpp

@@ -93,6 +93,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   ellipsoid = line = tri = body = NULL;
 
   // molecular systems
+
+  molecule = NULL;
+  molindex = molatom = NULL;
+
   bond_per_atom =  extra_bond_per_atom = 0;
   num_bond = NULL;
   bond_type = NULL;
@@ -146,7 +150,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
 
   // USER-MESONT package
 
-  mesont_flag = 0;
   length = NULL;
   buckling = NULL;
   bond_nt = NULL;
@@ -299,6 +302,11 @@ Atom::~Atom()
   memory->destroy(cv);
   memory->destroy(vest);
 
+  // USER-MESONT package
+  memory->destroy(length);
+  memory->destroy(buckling);
+  memory->destroy(bond_nt);
+
   memory->destroy(contact_radius);
   memory->destroy(smd_data_9);
   memory->destroy(smd_stress);
@@ -373,12 +381,6 @@ Atom::~Atom()
   for (int i = 0; i < nmolecule; i++) delete molecules[i];
   memory->sfree(molecules);
 
-  // USER-MESONT package
-
-  memory->destroy(length);
-  memory->destroy(buckling);
-  memory->destroy(bond_nt);
-
   // delete per-type arrays
 
   delete [] mass;
@@ -554,6 +556,12 @@ void Atom::peratom_create()
   add_peratom("cc",&cc,DOUBLE,1);
   add_peratom("cc_flux",&cc_flux,DOUBLE,1,1);         // set per-thread flag
 
+  // USER-MESONT package
+
+  add_peratom("length",&length,DOUBLE,0);
+  add_peratom("buckling",&buckling,INT,0);
+  add_peratom("bond_nt",&bond_nt,tagintsize,2);
+
   // USER-SPH package
 
   add_peratom("rho",&rho,DOUBLE,0);
@@ -679,6 +687,7 @@ void Atom::set_atomflag_defaults()
   sp_flag = 0;
   x0_flag = 0;
   smd_flag = damage_flag = 0;
+  mesont_flag = 0;
   contact_radius_flag = smd_data_9_flag = smd_stress_flag = 0;
   eff_plastic_strain_flag = eff_plastic_strain_rate_flag = 0;
 
@@ -1236,16 +1245,23 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
         error->all(FLERR,"Incorrect atom format in data file");
     }
 
-    if (imageflag)
-      imagedata = ((imageint) (atoi(values[iptr]) + IMGMAX) & IMGMASK) |
-        (((imageint) (atoi(values[iptr+1]) + IMGMAX) & IMGMASK) << IMGBITS) |
-        (((imageint) (atoi(values[iptr+2]) + IMGMAX) & IMGMASK) << IMG2BITS);
-    else imagedata = ((imageint) IMGMAX << IMG2BITS) |
-           ((imageint) IMGMAX << IMGBITS) | IMGMAX;
+    int imx = 0;
+    int imy = 0;
+    int imz = 0;
+    if (imageflag) {
+      imx = utils::inumeric(FLERR,values[iptr],false,lmp);
+      imy = utils::inumeric(FLERR,values[iptr+1],false,lmp);
+      imz = utils::inumeric(FLERR,values[iptr+2],false,lmp);
+      if ((domain->dimension == 2) && (imz != 0))
+        error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems");
+    }
+    imagedata = ((imageint) (imx + IMGMAX) & IMGMASK) |
+        (((imageint) (imy + IMGMAX) & IMGMASK) << IMGBITS) |
+        (((imageint) (imz + IMGMAX) & IMGMASK) << IMG2BITS);
 
-    xdata[0] = atof(values[xptr]);
-    xdata[1] = atof(values[xptr+1]);
-    xdata[2] = atof(values[xptr+2]);
+    xdata[0] = utils::numeric(FLERR,values[xptr],false,lmp);
+    xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp);
+    xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp);
     if (shiftflag) {
       xdata[0] += shift[0];
       xdata[1] += shift[1];
@@ -2539,6 +2555,11 @@ void *Atom::extract(char *name)
   if (strcmp(name,"cv") == 0) return (void *) cv;
   if (strcmp(name,"vest") == 0) return (void *) vest;
 
+  // USER-MESONT package
+  if (strcmp(name,"length") == 0) return (void *) length;
+  if (strcmp(name,"buckling") == 0) return (void *) buckling;
+  if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
+
   if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
   if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9;
   if (strcmp(name, "smd_stress") == 0) return (void *) smd_stress;
@@ -2551,10 +2572,8 @@ void *Atom::extract(char *name)
   if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
   if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
 
-  // USER-MESONT package
-  if (strcmp(name,"length") == 0) return (void *) length;
-  if (strcmp(name,"buckling") == 0) return (void *) buckling;
-  if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
+  // end of customization section
+  // --------------------------------------------------------------------
 
   return NULL;
 }

src/atom.h

@@ -127,12 +127,6 @@ class Atom : protected Pointers {
   double *vest_temp;
   double *edpd_cv;               // heat capacity
   int cc_species;
-  double *contact_radius;
-  double **smd_data_9;
-  double **smd_stress;
-  double *eff_plastic_strain;
-  double *eff_plastic_strain_rate;
-  double *damage;
 
   // USER-MESONT package
 
@@ -140,6 +134,15 @@ class Atom : protected Pointers {
   int *buckling;
   tagint **bond_nt;
 
+  // USER-SMD package
+
+  double *contact_radius;
+  double **smd_data_9;
+  double **smd_stress;
+  double *eff_plastic_strain;
+  double *eff_plastic_strain_rate;
+  double *damage;
+
   // USER-SPH package
 
   double *rho,*drho,*esph,*desph,*cv;

src/compute_property_atom.cpp

@@ -376,6 +376,7 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
                    "vector does not exist");
       pack_choice[i] = &ComputePropertyAtom::pack_dname;
     }
+
     else if (strcmp(arg[iarg],"buckling") == 0) {
       if (!atom->mesont_flag)
         error->all(FLERR,"Compute property/atom for "