change the handling of reading "extra XXX per atom", so that the final choice...

change the handling of reading "extra XXX per atom", so that the final choice is the larger of the value in the file and the keyword

src/read_data.cpp

@@ -968,6 +968,7 @@ void ReadData::header(int firstpass)
     // search line for header keyword and set corresponding variable
     // customize for new header lines
     // check for triangles before angles so "triangles" not matched as "angles"
+    int extra_flag_value = 0;
 
     if (strstr(line,"atoms")) {
       sscanf(line,BIGINT_FORMAT,&natoms);
@@ -1029,17 +1030,26 @@ void ReadData::header(int firstpass)
         atom->nimpropertypes = nimpropertypes + extra_improper_types;
 
     // these settings only used by first data file
+    // also, these are obsolescent. we parse them to maintain backward
+    // compatibility, but the recommended way is to set them via keywords
+    // in the LAMMPS input file. In case these flags are set in both,
+    // the input and the data file, we use the larger of the two.
 
     } else if (strstr(line,"extra bond per atom")) {
-      if (addflag == NONE) sscanf(line,"%d",&atom->extra_bond_per_atom);
+      if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
+      atom->extra_bond_per_atom = MAX(atom->extra_bond_per_atom,extra_flag_value);
     } else if (strstr(line,"extra angle per atom")) {
-      if (addflag == NONE) sscanf(line,"%d",&atom->extra_angle_per_atom);
+      if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
+      atom->extra_angle_per_atom = MAX(atom->extra_angle_per_atom,extra_flag_value);
     } else if (strstr(line,"extra dihedral per atom")) {
-      if (addflag == NONE) sscanf(line,"%d",&atom->extra_dihedral_per_atom);
+      if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
+      atom->extra_dihedral_per_atom = MAX(atom->extra_dihedral_per_atom,extra_flag_value);
     } else if (strstr(line,"extra improper per atom")) {
-      if (addflag == NONE) sscanf(line,"%d",&atom->extra_improper_per_atom);
+      if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
+      atom->extra_improper_per_atom = MAX(atom->extra_improper_per_atom,extra_flag_value);
     } else if (strstr(line,"extra special per atom")) {
-      if (addflag == NONE) sscanf(line,"%d",&force->special_extra);
+      if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
+      force->special_extra = MAX(force->special_extra,extra_flag_value);
 
     // local copy of box info
     // so can treat differently for first vs subsequent data files

src/read_data.h

@@ -472,8 +472,8 @@ outside a non-periodic simulation box.
 
 E: Subsequent read data induced too many bonds per atom
 
-See the create_box extra/bond/per/atom or read_data "extra bond per
-atom" header value to set this limit larger.
+See the create_box extra/bond/per/atom or the read_data
+extra/bond/per/atom keyword to set this limit larger.
 
 E: Bonds assigned incorrectly
 
@@ -482,8 +482,8 @@ This means there is something invalid about the topology definitions.
 
 E: Subsequent read data induced too many angles per atom
 
-See the create_box extra/angle/per/atom or read_data "extra angle per
-atom" header value to set this limit larger.
+See the create_box extra/angle/per/atom or the read_data
+extra/angle/per/atom keyword to set this limit larger.
 
 E: Angles assigned incorrectly
 
@@ -493,8 +493,8 @@ definitions.
 
 E: Subsequent read data induced too many dihedrals per atom
 
-See the create_box extra/dihedral/per/atom or read_data "extra
-dihedral per atom" header value to set this limit larger.
+See the create_box extra/dihedral/per/atom or the read_data
+extra/dihedral/per/atom keyword to set this limit larger.
 
 E: Dihedrals assigned incorrectly
 
@@ -504,8 +504,8 @@ definitions.
 
 E: Subsequent read data induced too many impropers per atom
 
-See the create_box extra/improper/per/atom or read_data "extra
-improper per atom" header value to set this limit larger.
+See the create_box extra/improper/per/atom or the read_data
+extra/improper/per/atom keyword to set this limit larger.
 
 E: Impropers assigned incorrectly