git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13601 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MANYBODY/pair_bop.cpp

@@ -1258,26 +1258,8 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
   i_tag=tag[i];
   itype = map[type[i]]+1;
 
+  memset(bt_sg,0,sizeof(struct B_SG)*nb_sg);
   for(m=0;m<nb_sg;m++) {
-    for(pp=0;pp<3;pp++) {
-      bt_sg[m].dAA[pp]=0.0;
-      bt_sg[m].dBB[pp]=0.0;
-      bt_sg[m].dCC[pp]=0.0;
-      bt_sg[m].dDD[pp]=0.0;
-      bt_sg[m].dEE[pp]=0.0;
-      bt_sg[m].dEE1[pp]=0.0;
-      bt_sg[m].dFF[pp]=0.0;
-      bt_sg[m].dAAC[pp]=0.0;
-      bt_sg[m].dBBC[pp]=0.0;
-      bt_sg[m].dCCC[pp]=0.0;
-      bt_sg[m].dDDC[pp]=0.0;
-      bt_sg[m].dEEC[pp]=0.0;
-      bt_sg[m].dFFC[pp]=0.0;
-      bt_sg[m].dGGC[pp]=0.0;
-      bt_sg[m].dUT[pp]=0.0;
-      bt_sg[m].dSigB1[pp]=0.0;
-      bt_sg[m].dSigB[pp]=0.0;
-    }
     bt_sg[m].i=-1;
     bt_sg[m].j=-1;
     bt_sg[m].temp=-1;
@@ -3821,7 +3803,6 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
     }
   }
   return(sigB);
-  destroy_sigma();
 }
 
 /* ---------------------------------------------------------------------- */

src/MANYBODY/pair_comb.cpp

@@ -1419,10 +1419,15 @@ void PairComb::sm_table()
   // direct 1/r energy with Slater 1S orbital overlap
 
   for (i = 0; i < n; i++) {
+    if (map[i+1] < 0) continue;
     r = drin;
-    itype = params[i].ielement;
+    itype = params[map[i+1]].ielement;
     iparam_i = elem2param[itype][itype][itype];
     z = params[iparam_i].esm1;
+
+    if (comm->me == 0 && screen)
+      fprintf(screen,"  element[%d] = %-2s, z = %g\n",i+1,elements[map[i+1]],z);
+
     for (j = 0; j < ncoul; j++) {
       exp2er = exp(-2.0 * z * r);
       phin[j][i] = 1.0 - exp2er * (1.0 + 2.0 * z * r * (1.0 + z * r));
@@ -1432,10 +1437,12 @@ void PairComb::sm_table()
   }
 
   for (i = 0; i < n; i ++) {
+    if (map[i+1] < 0) continue;
     for (j = 0; j < n; j ++) {
+      if (map[j+1] < 0) continue;
       r = drin;
       if (j == i) {
-        itype = params[i].ielement;
+        itype = params[map[i+1]].ielement;
         inty = intype[itype][itype];
         iparam_i = elem2param[itype][itype][itype];
         z = params[iparam_i].esm1;
@@ -1460,8 +1467,8 @@ void PairComb::sm_table()
           r += dra;
         }
       } else if (j != i) {
-        itype = params[i].ielement;
+        itype = params[map[i+1]].ielement;
-        jtype = params[j].ielement;
+        jtype = params[map[j+1]].ielement;
         inty = intype[itype][jtype];
         iparam_ij = elem2param[itype][jtype][jtype];
         ea = params[iparam_ij].esm1;

src/MANYBODY/pair_comb3.cpp

@@ -2441,14 +2441,18 @@ void PairComb3::tables()
   // direct 1/r energy with Slater 1S orbital overlap
   
   for (i = 0; i < n; i++) {
+    if (map[i+1] < 0) continue;
     r = drin - dra; 
-    itype = i;
+    itype = map[i+1];
     iparam_i = elem2param[itype][itype][itype];
     z = params[iparam_i].esm;
     exp2ershift = exp(-2.0*z*rc);
     afbshift = -exp2ershift*(z+1.0/rc);
     dafbshift = exp2ershift*(2.0*z*z+2.0*z/rc+1.0/(rc*rc));
 
+    if (comm->me == 0 && screen)
+      fprintf(screen,"  element[%d] = %-2s, z = %g\n",i+1,elements[map[i+1]],z);
+    
     for (j = 0; j < ncoul; j++) {
       exp2er = exp(-2.0 * z * r);
       phin[j][i] = 1.0 - exp2er * (1.0 + 2.0 * z * r * (1.0 + z * r));
@@ -2460,10 +2464,12 @@ void PairComb3::tables()
   }
 
   for (i = 0; i < n; i ++) {
+    if (map[i+1] < 0) continue;
     for (j = 0; j < n; j ++) {
+      if (map[j+1] < 0) continue;
       r = drin - dra; 
       if (j == i) {
-        itype = i;
+        itype = map[i+1];
         inty = intype[itype][itype];
         iparam_i = elem2param[itype][itype][itype];
         z = params[iparam_i].esm;
@@ -2488,8 +2494,8 @@ void PairComb3::tables()
                   r += dra; 
         }
       } else if (j != i) {
-        itype = i;
+        itype = map[i+1];
-        jtype = j;
+        jtype = map[j+1];
         inty = intype[itype][jtype];
         iparam_ij = elem2param[itype][jtype][jtype];
         ea = params[iparam_ij].esm;

src/MOLECULE/bond_table.cpp

@@ -304,7 +304,7 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
   while (1) {
     if (fgets(line,MAXLINE,fp) == NULL)
       error->one(FLERR,"Did not find keyword in table file");
-    if (strspn(line," \t\n") == strlen(line)) continue;    // blank line
+    if (strspn(line," \t\n\r") == strlen(line)) continue;    // blank line
     if (line[0] == '#') continue;                          // comment
     char *word = strtok(line," \t\n\r");
     if (strcmp(word,keyword) == 0) break;           // matching keyword

src/RIGID/fix_rigid.cpp

@@ -250,6 +250,9 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
     if (domain->dimension == 2) fflag[i][2] = tflag[i][0] = tflag[i][1] = 0.0;
   }
 
+  // number of linear rigid bodies is counted later
+  nlinear = 0; 
+
   // parse optional args
 
   int seed;
@@ -687,6 +690,7 @@ void FixRigid::init()
     ndof += fflag[ibody][0] + fflag[ibody][1] + fflag[ibody][2];
     ndof += tflag[ibody][0] + tflag[ibody][1] + tflag[ibody][2];
   }
+  ndof -= nlinear;
   if (ndof > 0.0) tfactor = force->mvv2e / (ndof * force->boltz);
   else tfactor = 0.0;
 }
@@ -1140,12 +1144,16 @@ int FixRigid::dof(int tgroup)
   // 2d body with any finite-size M should have 3 dof, remove (2N+3M) - 3
 
   int n = 0;
+  nlinear = 0;
   if (domain->dimension == 3) {
     for (int ibody = 0; ibody < nbody; ibody++)
       if (nall[ibody]+mall[ibody] == nrigid[ibody]) {
         n += 3*nall[ibody] + 6*mall[ibody] - 6;
         if (inertia[ibody][0] == 0.0 || inertia[ibody][1] == 0.0 ||
-            inertia[ibody][2] == 0.0) n++;
+            inertia[ibody][2] == 0.0) {
+          n++;
+          nlinear++;
+        }
       }
   } else if (domain->dimension == 2) {
     for (int ibody = 0; ibody < nbody; ibody++)

src/RIGID/fix_rigid.h

@@ -72,6 +72,7 @@ class FixRigid : public Fix {
 
   int dimension;            // # of dimensions
   int nbody;                // # of rigid bodies
+  int nlinear;              // # of linear rigid bodies
   int *nrigid;              // # of atoms in each rigid body
   int *mol2body;            // convert mol-ID to rigid body index
   int *body2mol;            // convert rigid body index to mol-ID

src/RIGID/fix_rigid_nh_small.cpp

@@ -59,17 +59,19 @@ FixRigidNHSmall::FixRigidNHSmall(LAMMPS *lmp, int narg, char **arg) :
       (p_flag[2] == 1 && p_period[2] <= 0.0)) 
     error->all(FLERR,"Fix rigid/small npt/nph period must be > 0.0");
 
-  if (domain->dimension == 2 && p_flag[2])
+  dimension = domain->dimension;
+  
+  if (dimension == 2 && p_flag[2])
     error->all(FLERR,"Invalid fix rigid/small npt/nph command "
                "for a 2d simulation");
-  if (domain->dimension == 2 && (pcouple == YZ || pcouple == XZ))
+  if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
     error->all(FLERR,"Invalid fix rigid/small npt/nph command "
                "for a 2d simulation");
 
   if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
     error->all(FLERR,"Invalid fix rigid/small npt/nph command "
                "pressure settings");
-  if (pcouple == XYZ && domain->dimension == 3 && p_flag[2] == 0)
+  if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
     error->all(FLERR,"Invalid fix rigid/small npt/nph command "
                "pressure settings");
   if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
@@ -97,12 +99,12 @@ FixRigidNHSmall::FixRigidNHSmall(LAMMPS *lmp, int narg, char **arg) :
                "Cannot use fix rigid/small npt/nph on a "
                "non-periodic dimension");
   
-  if (pcouple == XYZ && domain->dimension == 3 &&
+  if (pcouple == XYZ && dimension == 3 &&
       (p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
        p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
        p_period[0] != p_period[1] || p_period[0] != p_period[2]))
     error->all(FLERR,"Invalid fix rigid/small npt/nph command pressure settings");
-  if (pcouple == XYZ && domain->dimension == 2 &&
+  if (pcouple == XYZ && dimension == 2 &&
       (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
        p_period[0] != p_period[1]))
     error->all(FLERR,"Invalid fix rigid/small npt/nph command pressure settings");
@@ -224,7 +226,6 @@ void FixRigidNHSmall::init()
   boltz = force->boltz;
   nktv2p = force->nktv2p;
   mvv2e = force->mvv2e;
-  dimension = domain->dimension;
 
   if (force->kspace) kspace_flag = 1;
   else kspace_flag = 0;
@@ -322,7 +323,7 @@ void FixRigidNHSmall::setup(int vflag)
     nf_r = dimension * nlocal_body;
     for (int ibody = 0; ibody < nlocal_body; ibody++) {
       Body *b = &body[ibody];
-      for (int k = 0; k < domain->dimension; k++) 
+      for (int k = 0; k < dimension; k++) 
         if (fabs(b->inertia[k]) < EPSILON) nf_r--;
     }
   } else if (dimension == 2) {

src/RIGID/fix_rigid_small.cpp

@@ -123,6 +123,9 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
   MPI_Allreduce(&maxmol,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
   maxmol = itmp;
 
+  // number of linear molecules is counted later
+  nlinear = 0;
+
   // parse optional args
 
   int seed;
@@ -1028,12 +1031,16 @@ int FixRigidSmall::dof(int tgroup)
   double *inertia;
 
   int n = 0;
+  nlinear = 0;
   if (domain->dimension == 3) {
     for (int ibody = 0; ibody < nlocal_body; ibody++) {
       if (counts[ibody][0]+counts[ibody][1] == counts[ibody][2]) {
         n += 3*counts[ibody][0] + 6*counts[ibody][1] - 6;
         inertia = body[ibody].inertia;
-        if (inertia[0] == 0.0 || inertia[1] == 0.0 || inertia[2] == 0.0) n++;
+        if (inertia[0] == 0.0 || inertia[1] == 0.0 || inertia[2] == 0.0) {
+          n++;
+          nlinear++;
+        }
       }
     }
   } else if (domain->dimension == 2) {
@@ -3404,7 +3411,7 @@ double FixRigidSmall::compute_scalar()
   double tall;
   MPI_Allreduce(&t,&tall,1,MPI_DOUBLE,MPI_SUM,world);
 
-  double tfactor = force->mvv2e / (6.0*nbody * force->boltz);
+  double tfactor = force->mvv2e / ((6.0*nbody - nlinear) * force->boltz);
   tall *= tfactor;
   return tall;
 }

src/RIGID/fix_rigid_small.h

@@ -81,6 +81,7 @@ class FixRigidSmall : public Fix {
   int setupflag;            // 1 if body properties are setup, else 0
   int commflag;             // various modes of forward/reverse comm
   int nbody;                // total # of rigid bodies
+  int nlinear;              // total # of linear rigid bodies
   tagint maxmol;            // max mol-ID
   double maxextent;         // furthest distance from body owner to body atom
 

src/USER-MISC/compute_ackland_atom.cpp

@@ -232,47 +232,50 @@ void ComputeAcklandAtom::compute_peratom()
         }
       }
 
+      if (chi[7] > 0 || n0 < 11) structure[i] = UNKNOWN;
+      else if (chi[0] == 7) structure[i] = BCC;
+      else if (chi[0] == 6) structure[i] = FCC;
+      else if (chi[0] == 3) structure[i] = HCP;
+      else {
         // Deviations from the different lattice structures
 
-      double delta_bcc = 0.35*chi[4]/(double)(chi[5]+chi[6]-chi[4]);
         double delta_cp = fabs(1.-(double)chi[6]/24.);
-      double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6.))+
+
-                               (double)chi[2])/6.0;
+        // ensure we do not get divide by zero
-      double delta_hcp = (fabs((double)chi[0]-3.)+
+        // and if we will, make delta_bcc irrelevant
-                          fabs((double)chi[0]+(double)chi[1]+
+        double delta_bcc = delta_cp + 1.0;
-                               (double)chi[2]+(double)chi[3]-9.0))/12.0;
+        int chi56m4 = chi[5]+chi[6]-chi[4];
+
+        // note that chi[7] presumed zero 
+        if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4;
+
+        double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
+                                 +(double)chi[2])/6.0;
+
+        double delta_hcp = (fabs((double)chi[0]-3.)+fabs((double)chi[0]
+                            +(double)chi[1]+(double)chi[2]+(double)chi[3]
+                            -9.0))/12.0;
 
 	 // Identification of the local structure according to the reference
 
-      if (chi[0] == 7)       { delta_bcc = 0.; }
+        if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1 
-      else if (chi[0] == 6)  { delta_fcc = 0.; }
+            && delta_hcp >= 0.1) structure[i] = UNKNOWN;
-      else if (chi[0] <= 3)  { delta_hcp = 0.; }
 
-      if (chi[7] > 0.)
+	// not part of Ackland-Jones 2006; included for backward compatibility
-         structure[i] = UNKNOWN;
+        if (chi[4] < 3. && n1 == 12) structure[i] = ICO;
-      else
+
-      if (chi[4] < 3.)
+        else {
-      {
+	  if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
-         if (n1 > 13 || n1 < 11)
+	  else {
-            structure[i] = UNKNOWN;
+	    if (n0 > 12) structure[i] = UNKNOWN;
-         else
+	    else {
-            structure[i] = ICO;
+	      if (delta_fcc < delta_hcp) structure[i] = FCC;
-      } else
-      if (delta_bcc <= delta_cp)
-      {
-         if (n1 < 11)
-            structure[i] = UNKNOWN;
-         else
-            structure[i] = BCC;
-      } else
-      if (n1 > 12 || n1 < 11)
-         structure[i] = UNKNOWN;
-      else
-      if (delta_fcc < delta_hcp)
-         structure[i] = FCC;
 	      else
 	      structure[i] = HCP;
-
+	    }
+	  }
+	}
+      }
     } else structure[i] = 0.0;
   }
 }

src/fix_wall.cpp

@@ -67,7 +67,7 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
       else if (strcmp(arg[iarg],"zlo") == 0) newwall = ZLO;
       else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI;
 
-      for (int m = 0; m < nwall; m++)
+      for (int m = 0; (m < nwall) && (m < 6); m++)
         if (newwall == wallwhich[m])
           error->all(FLERR,"Wall defined twice in fix wall command");
 

src/fix_wall_reflect.cpp

@@ -58,7 +58,7 @@ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
       else if (strcmp(arg[iarg],"zlo") == 0) newwall = ZLO;
       else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI;
 
-      for (int m = 0; m < nwall; m++)
+      for (int m = 0; (m < nwall) && (m < 6); m++)
         if (newwall == wallwhich[m])
           error->all(FLERR,"Wall defined twice in fix wall/reflect command");
 

src/force.cpp

@@ -106,6 +106,13 @@ Force::~Force()
   if (improper) delete improper;
   if (kspace) delete kspace;
 
+  pair = NULL;
+  bond = NULL;
+  angle = NULL;
+  dihedral = NULL;
+  improper = NULL;
+  kspace = NULL;
+
   delete pair_map;
 }
 

src/read_data.cpp

@@ -1557,6 +1557,7 @@ void ReadData::open(char *file)
 void ReadData::parse_keyword(int first)
 {
   int eof = 0;
+  int done = 0;
 
   // proc 0 reads upto non-blank line plus 1 following line
   // eof is set to 1 if any read hits end-of-file
@@ -1565,8 +1566,11 @@ void ReadData::parse_keyword(int first)
     if (!first) {
       if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
     }
-    while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
+    while (eof == 0 && done == 0) {
+      int blank = strspn(line," \t\n\r");
+      if ((blank == strlen(line)) || (line[blank] == '#')) {
         if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
+      } else done = 1;
     }
     if (fgets(buffer,MAXLINE,fp) == NULL) eof = 1;
   }

src/read_restart.cpp

@@ -60,7 +60,9 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
      SPECIAL_LJ,SPECIAL_COUL,
      MASS,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER,
      MULTIPROC,MPIIO,PROCSPERFILE,PERPROC,
-     IMAGEINT,BOUNDMIN};
+     IMAGEINT,BOUNDMIN,TIMESTEP,
+     ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
+     COMM_MODE,COMM_CUTOFF,COMM_VEL};
 
 #define LB_FACTOR 1.1
 
@@ -866,6 +868,27 @@ void ReadRestart::header(int incompatible)
       read_int();
       read_double_vec(3,&force->special_coul[1]);
 
+    } else if (flag == TIMESTEP) {
+      update->dt = read_double();
+
+    } else if (flag == ATOM_ID) {
+      atom->tag_enable = read_int();
+    } else if (flag == ATOM_MAP_STYLE) {
+      atom->map_style = read_int();
+    } else if (flag == ATOM_MAP_USER) {
+      atom->map_user  = read_int();
+    } else if (flag == ATOM_SORTFREQ) {
+      atom->sortfreq = read_int();
+    } else if (flag == ATOM_SORTBIN) {
+      atom->userbinsize = read_double();
+      
+    } else if (flag == COMM_MODE) {
+      comm->mode = read_int();
+    } else if (flag == COMM_CUTOFF) {
+      comm->cutghostuser = read_double();
+    } else if (flag == COMM_VEL) {
+      comm->ghost_velocity = read_int();
+
     } else error->all(FLERR,"Invalid flag in header section of restart file");
 
     flag = read_int();

src/thermo.cpp

@@ -306,7 +306,7 @@ void Thermo::compute(int flag)
   // check for lost atoms
   // turn off normflag if natoms = 0 to avoid divide by 0
 
-  natoms = lost_check();
+  natoms = atom->natoms = lost_check();
   if (natoms == 0) normflag = 0;
   else normflag = normvalue;
 
@@ -380,11 +380,8 @@ bigint Thermo::lost_check()
   if (ntotal == atom->natoms) return ntotal;
 
   // if not checking or already warned, just return
-  // reset total atom count
-
   if (lostflag == IGNORE) return ntotal;
   if (lostflag == WARN && lostbefore == 1) {
-    atom->natoms = ntotal;
     return ntotal;
   }
 
@@ -552,7 +549,7 @@ void Thermo::modify_params(int narg, char **arg)
         format_float_user = new char[n];
         strcpy(format_float_user,arg[iarg+2]);
       } else {
-        int i = atoi(arg[iarg+1]) - 1;
+        int i = force->inumeric(FLERR,arg[iarg+1]) - 1;
         if (i < 0 || i >= nfield_initial)
           error->all(FLERR,"Illegal thermo_modify command");
         if (format_user[i]) delete [] format_user[i];

src/write_data.cpp

@@ -73,6 +73,7 @@ void WriteData::command(int narg, char **arg)
   // noinit is a hidden arg, only used by -r command-line switch
 
   pairflag = II;
+  coeffflag = 1;
   int noinit = 0;
 
   int iarg = 1;
@@ -86,6 +87,9 @@ void WriteData::command(int narg, char **arg)
     } else if (strcmp(arg[iarg],"noinit") == 0) {
       noinit = 1;
       iarg++;
+    } else if (strcmp(arg[iarg],"nocoeff") == 0) {
+      coeffflag = 0;
+      iarg++;
     } else error->all(FLERR,"Illegal write_data command");
   }
 
@@ -176,7 +180,7 @@ void WriteData::write(char *file)
   if (me == 0) {
     header();
     type_arrays();
-    force_fields();
+    if (coeffflag) force_fields();
   }
 
   // per atom info

src/write_data.h

@@ -34,6 +34,7 @@ class WriteData : protected Pointers {
  private:
   int me,nprocs;
   int pairflag;
+  int coeffflag;
   FILE *fp;
   bigint nbonds_local,nbonds;
   bigint nangles_local,nangles;

src/write_dump.cpp

@@ -22,6 +22,8 @@
 #include "dump_image.h"
 #include "atom.h"
 #include "group.h"
+#include "input.h"
+#include "update.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -75,6 +77,9 @@ void WriteDump::command(int narg, char **arg)
   if (strcmp(arg[1],"cfg") == 0)
     ((DumpCFG *) dump)->multifile_override = 1;
 
+  if (update->first_update == 0)
+    error->warning(FLERR,"Calling write_dump before a full system init.");
+
   dump->init();
   dump->write();
 

src/write_dump.h

@@ -47,4 +47,12 @@ E: Unknown dump style
 
 The choice of dump style is unknown.
 
+W: Calling write_dump before a full system init.
+
+The write_dump command is used before the system has been fully
+initialized as part of a 'run' or 'minimize' command. Not all dump
+styles and features are fully supported at this point and thus the
+command may fail or produce incomplete or incorrect output. Insert
+a "run 0" command, if a full system init is required.
+
 */

src/write_restart.cpp

@@ -59,7 +59,9 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
      SPECIAL_LJ,SPECIAL_COUL,
      MASS,PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER,
      MULTIPROC,MPIIO,PROCSPERFILE,PERPROC,
-     IMAGEINT,BOUNDMIN};
+     IMAGEINT,BOUNDMIN,TIMESTEP,
+     ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
+     COMM_MODE,COMM_CUTOFF,COMM_VEL};
 
 enum{IGNORE,WARN,ERROR};                    // same as thermo.cpp
 
@@ -497,6 +499,18 @@ void WriteRestart::header()
   write_double_vec(SPECIAL_LJ,3,&force->special_lj[1]);
   write_double_vec(SPECIAL_COUL,3,&force->special_coul[1]);
 
+  write_double(TIMESTEP,update->dt);
+
+  write_int(ATOM_ID,atom->tag_enable);
+  write_int(ATOM_MAP_STYLE,atom->map_style);
+  write_int(ATOM_MAP_USER,atom->map_user);
+  write_int(ATOM_SORTFREQ,atom->sortfreq);
+  write_double(ATOM_SORTBIN,atom->userbinsize);
+
+  write_int(COMM_MODE,comm->mode);  
+  write_double(COMM_CUTOFF,comm->cutghostuser);
+  write_int(COMM_VEL,comm->ghost_velocity);
+
   // -1 flag signals end of header
 
   int flag = -1;