git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15240 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/CLASS2/dihedral_class2.cpp

@@ -662,7 +662,8 @@ void DihedralClass2::coeff(int narg, char **arg)
     }
 
   } else if (strcmp(arg[1],"ebt") == 0) {
-    if (narg != 10) error->all(FLERR,"Incorrect args for dihedral coefficients");
+    if (narg != 10) 
+      error->all(FLERR,"Incorrect args for dihedral coefficients");
 
     double f1_1_one = force->numeric(FLERR,arg[2]);
     double f2_1_one = force->numeric(FLERR,arg[3]);
@@ -687,7 +688,8 @@ void DihedralClass2::coeff(int narg, char **arg)
     }
 
   } else if (strcmp(arg[1],"at") == 0) {
-    if (narg != 10) error->all(FLERR,"Incorrect args for dihedral coefficients");
+    if (narg != 10) 
+      error->all(FLERR,"Incorrect args for dihedral coefficients");
 
     double f1_1_one = force->numeric(FLERR,arg[2]);
     double f2_1_one = force->numeric(FLERR,arg[3]);
@@ -924,8 +926,10 @@ void DihedralClass2::read_restart(FILE *fp)
 void DihedralClass2::write_data(FILE *fp)
 {
   for (int i = 1; i <= atom->ndihedraltypes; i++)
-    fprintf(fp,"%d %g %g %g %g %g %g\n",
+    fprintf(fp,"%d %g %g %g %g %g %g\n",i,
-            i,k1[i],phi1[i],k2[i],phi2[i],k3[i],phi3[i]);
+            k1[i],phi1[i]*180.0/MY_PI,
+            k2[i],phi2[i]*180.0/MY_PI,
+            k3[i],phi3[i]*180.0/MY_PI);
 
   fprintf(fp,"\nAngleAngleTorsion Coeffs\n\n");
   for (int i = 1; i <= atom->ndihedraltypes; i++)

src/atom_vec_line.cpp

@@ -178,7 +178,7 @@ void AtomVecLine::copy(int i, int j, int delflag)
 
 /* ----------------------------------------------------------------------
    copy bonus data from I to J, effectively deleting the J entry
-   also reset ine that points to I to now point to J
+   also reset line that points to I to now point to J
 ------------------------------------------------------------------------- */
 
 void AtomVecLine::copy_bonus(int i, int j)
@@ -195,6 +195,10 @@ void AtomVecLine::copy_bonus(int i, int j)
 void AtomVecLine::clear_bonus()
 {
   nghost_bonus = 0;
+
+  if (atom->nextra_grow)
+    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+      modify->fix[atom->extra_grow[iextra]]->clear_bonus();
 }
 
 /* ----------------------------------------------------------------------

src/atom_vec_tri.cpp

@@ -206,6 +206,10 @@ void AtomVecTri::copy_bonus(int i, int j)
 void AtomVecTri::clear_bonus()
 {
   nghost_bonus = 0;
+
+  if (atom->nextra_grow)
+    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+      modify->fix[atom->extra_grow[iextra]]->clear_bonus();
 }
 
 /* ----------------------------------------------------------------------

src/fix.h

@@ -136,6 +136,7 @@ class Fix : protected Pointers {
   virtual void set_arrays(int) {}
   virtual void update_arrays(int, int) {}
   virtual void set_molecule(int, tagint, int, double *, double *, double *) {}
+  virtual void clear_bonus() {}
 
   virtual int pack_border(int, int *, double *) {return 0;}
   virtual int unpack_border(int, int, double *) {return 0;}