Unlike other angle styles, the hybrid angle style does not store angle +coefficient info for individual sub-styles in a binary restart +files. Thus when retarting a simulation from a restart +file, you need to re-specify angle_coeff commands. +
Related commands:
angle_coeff diff -Naur lammps-10Oct08/doc/angle_hybrid.txt lammps-11Oct08/doc/angle_hybrid.txt --- lammps-10Oct08/doc/angle_hybrid.txt 2007-06-25 18:03:39.000000000 -0600 +++ lammps-11Oct08/doc/angle_hybrid.txt 2008-10-09 08:47:45.000000000 -0600 @@ -55,6 +55,11 @@ "molecular" package (which it is by default). See the "Making LAMMPS"_Section_start.html#2_3 section for more info on packages. +Unlike other angle styles, the hybrid angle style does not store angle +coefficient info for individual sub-styles in a "binary restart +files"_restart.html. Thus when retarting a simulation from a restart +file, you need to re-specify angle_coeff commands. + [Related commands:] "angle_coeff"_angle_coeff.html diff -Naur lammps-10Oct08/doc/bond_hybrid.html lammps-11Oct08/doc/bond_hybrid.html --- lammps-10Oct08/doc/bond_hybrid.html 2007-06-25 08:36:36.000000000 -0600 +++ lammps-11Oct08/doc/bond_hybrid.html 2008-10-09 08:47:45.000000000 -0600 @@ -51,6 +51,11 @@ "molecular" package (which it is by default). See the Making LAMMPS section for more info on packages.
+Unlike other bond styles, the hybrid bond style does not store bond +coefficient info for individual sub-styles in a binary restart +files. Thus when retarting a simulation from a restart +file, you need to re-specify bond_coeff commands. +
Related commands:
bond_coeff, delete_bonds diff -Naur lammps-10Oct08/doc/bond_hybrid.txt lammps-11Oct08/doc/bond_hybrid.txt --- lammps-10Oct08/doc/bond_hybrid.txt 2007-06-25 18:03:39.000000000 -0600 +++ lammps-11Oct08/doc/bond_hybrid.txt 2008-10-09 08:47:45.000000000 -0600 @@ -48,6 +48,11 @@ "molecular" package (which it is by default). See the "Making LAMMPS"_Section_start.html#2_3 section for more info on packages. +Unlike other bond styles, the hybrid bond style does not store bond +coefficient info for individual sub-styles in a "binary restart +files"_restart.html. Thus when retarting a simulation from a restart +file, you need to re-specify bond_coeff commands. + [Related commands:] "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html diff -Naur lammps-10Oct08/doc/dihedral_hybrid.html lammps-11Oct08/doc/dihedral_hybrid.html --- lammps-10Oct08/doc/dihedral_hybrid.html 2007-06-25 08:36:36.000000000 -0600 +++ lammps-11Oct08/doc/dihedral_hybrid.html 2008-10-09 08:47:45.000000000 -0600 @@ -60,6 +60,11 @@ "molecular" package (which it is by default). See the Making LAMMPS section for more info on packages.
+Unlike other dihedral styles, the hybrid dihedral style does not store +dihedral coefficient info for individual sub-styles in a binary +restart files. Thus when retarting a simulation from a +restart file, you need to re-specify dihedral_coeff commands. +
Related commands:
dihedral_coeff diff -Naur lammps-10Oct08/doc/dihedral_hybrid.txt lammps-11Oct08/doc/dihedral_hybrid.txt --- lammps-10Oct08/doc/dihedral_hybrid.txt 2007-06-25 18:03:39.000000000 -0600 +++ lammps-11Oct08/doc/dihedral_hybrid.txt 2008-10-09 08:47:45.000000000 -0600 @@ -57,6 +57,11 @@ "molecular" package (which it is by default). See the "Making LAMMPS"_Section_start.html#2_3 section for more info on packages. +Unlike other dihedral styles, the hybrid dihedral style does not store +dihedral coefficient info for individual sub-styles in a "binary +restart files"_restart.html. Thus when retarting a simulation from a +restart file, you need to re-specify dihedral_coeff commands. + [Related commands:] "dihedral_coeff"_dihedral_coeff.html diff -Naur lammps-10Oct08/doc/fix_rigid.html lammps-11Oct08/doc/fix_rigid.html --- lammps-10Oct08/doc/fix_rigid.html 2008-01-09 16:22:14.000000000 -0700 +++ lammps-11Oct08/doc/fix_rigid.html 2008-10-08 09:02:35.000000000 -0600 @@ -94,7 +94,10 @@ msd will not compute the expected mean-squared displacement for such atoms, and the image flag values written to a dump file will be different than they would be if the -atoms were not in a rigid body. +atoms were not in a rigid body. It also means that if you have bonds +between a pair of rigid bodies and the bond straddles a periodic +boundary, you cannot use the replicate command to increase +the system size.
Restart, fix_modify, output, run start/stop, minimize info:
diff -Naur lammps-10Oct08/doc/fix_rigid.txt lammps-11Oct08/doc/fix_rigid.txt --- lammps-10Oct08/doc/fix_rigid.txt 2008-01-09 16:22:14.000000000 -0700 +++ lammps-11Oct08/doc/fix_rigid.txt 2008-10-08 09:02:35.000000000 -0600 @@ -87,7 +87,10 @@ msd"_fix_msd.html will not compute the expected mean-squared displacement for such atoms, and the image flag values written to a "dump file"_dump.html will be different than they would be if the -atoms were not in a rigid body. +atoms were not in a rigid body. It also means that if you have bonds +between a pair of rigid bodies and the bond straddles a periodic +boundary, you cannot use the "replicate"_replicate command to increase +the system size. [Restart, fix_modify, output, run start/stop, minimize info:] diff -Naur lammps-10Oct08/doc/improper_hybrid.html lammps-11Oct08/doc/improper_hybrid.html --- lammps-10Oct08/doc/improper_hybrid.html 2007-06-25 08:36:36.000000000 -0600 +++ lammps-11Oct08/doc/improper_hybrid.html 2008-10-09 08:47:45.000000000 -0600 @@ -59,6 +59,11 @@ "molecular" package (which it is by default). See the Making LAMMPS section for more info on packages. +Unlike other improper styles, the hybrid improper style does not store +improper coefficient info for individual sub-styles in a binary +restart files. Thus when retarting a simulation from a +restart file, you need to re-specify improper_coeff commands. +
Related commands:
improper_coeff diff -Naur lammps-10Oct08/doc/improper_hybrid.txt lammps-11Oct08/doc/improper_hybrid.txt --- lammps-10Oct08/doc/improper_hybrid.txt 2007-06-25 18:03:39.000000000 -0600 +++ lammps-11Oct08/doc/improper_hybrid.txt 2008-10-09 08:47:45.000000000 -0600 @@ -56,6 +56,11 @@ "molecular" package (which it is by default). See the "Making LAMMPS"_Section_start.html#2_3 section for more info on packages. +Unlike other improper styles, the hybrid improper style does not store +improper coefficient info for individual sub-styles in a "binary +restart files"_restart.html. Thus when retarting a simulation from a +restart file, you need to re-specify improper_coeff commands. + [Related commands:] "improper_coeff"_improper_coeff.html diff -Naur lammps-10Oct08/doc/pair_eam.html lammps-11Oct08/doc/pair_eam.html --- lammps-10Oct08/doc/pair_eam.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-11Oct08/doc/pair_eam.html 2008-10-09 08:47:45.000000000 -0600 @@ -333,9 +333,9 @@ shift, table, and tail options.
The eam pair styles do not write their information to binary restart -files, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. +files, since it is stored in tabulated potential files. +Thus, you need to re-specify the pair_style and pair_coeff commands in +an input script that reads a restart file.
The eam pair styles can only be used via the pair keyword of the run_style respa command. They do not support the diff -Naur lammps-10Oct08/doc/pair_eam.txt lammps-11Oct08/doc/pair_eam.txt --- lammps-10Oct08/doc/pair_eam.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-11Oct08/doc/pair_eam.txt 2008-10-09 08:47:45.000000000 -0600 @@ -325,9 +325,9 @@ shift, table, and tail options. The eam pair styles do not write their information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. +files"_restart.html, since it is stored in tabulated potential files. +Thus, you need to re-specify the pair_style and pair_coeff commands in +an input script that reads a restart file. The eam pair styles can only be used via the {pair} keyword of the "run_style respa"_run_style.html command. They do not support the diff -Naur lammps-10Oct08/doc/replicate.html lammps-11Oct08/doc/replicate.html --- lammps-10Oct08/doc/replicate.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-11Oct08/doc/replicate.html 2008-10-08 09:02:35.000000000 -0600 @@ -59,6 +59,16 @@ information to be stored. This is because the replicate command does not know how to replicate that information for new atoms it creates.
+Replicating a system that has rigid bodies (defined via the fix +rigid command), either currently defined or that +created the restart file which was read in before replicating, can +cause problems if there is a bond between a pair of rigid bodies that +straddle a periodic boundary. This is because the periodic image +information for particles in the rigid bodies are set differently than +for a non-rigid system and can result in a new bond being created that +spans the periodic box. Thus you cannot use the replicate command in +this scenario. +
Related commands: none
Default: none diff -Naur lammps-10Oct08/doc/replicate.txt lammps-11Oct08/doc/replicate.txt --- lammps-10Oct08/doc/replicate.txt 2008-02-29 18:13:20.000000000 -0700 +++ lammps-11Oct08/doc/replicate.txt 2008-10-08 09:02:35.000000000 -0600 @@ -56,6 +56,16 @@ information to be stored. This is because the replicate command does not know how to replicate that information for new atoms it creates. +Replicating a system that has rigid bodies (defined via the "fix +rigid"_fix_rigid.html command), either currently defined or that +created the restart file which was read in before replicating, can +cause problems if there is a bond between a pair of rigid bodies that +straddle a periodic boundary. This is because the periodic image +information for particles in the rigid bodies are set differently than +for a non-rigid system and can result in a new bond being created that +spans the periodic box. Thus you cannot use the replicate command in +this scenario. + [Related commands:] none [Default:] none diff -Naur lammps-10Oct08/src/read_restart.cpp lammps-11Oct08/src/read_restart.cpp --- lammps-10Oct08/src/read_restart.cpp 2007-10-05 16:58:10.000000000 -0600 +++ lammps-11Oct08/src/read_restart.cpp 2008-10-09 09:12:12.000000000 -0600 @@ -637,12 +637,7 @@ if (me == 0) fread(style,sizeof(char),n,fp); MPI_Bcast(style,n,MPI_CHAR,0,world); - if (force->pair == NULL || strcmp(style,force->pair_style)) { - if (force->pair && me == 0) - error->warning("Resetting pair_style to restart file value"); - force->create_pair(style); - } - + force->create_pair(style); delete [] style; force->pair->read_restart(fp); @@ -653,12 +648,7 @@ if (me == 0) fread(style,sizeof(char),n,fp); MPI_Bcast(style,n,MPI_CHAR,0,world); - if (force->bond == NULL || strcmp(style,force->bond_style)) { - if (force->bond && me == 0) - error->warning("Resetting bond_style to restart file value"); - force->create_bond(style); - } - + force->create_bond(style); delete [] style; force->bond->read_restart(fp); @@ -669,12 +659,7 @@ if (me == 0) fread(style,sizeof(char),n,fp); MPI_Bcast(style,n,MPI_CHAR,0,world); - if (force->angle == NULL || strcmp(style,force->angle_style)) { - if (force->angle && me == 0) - error->warning("Resetting angle_style to restart file value"); - force->create_angle(style); - } - + force->create_angle(style); delete [] style; force->angle->read_restart(fp); @@ -685,12 +670,7 @@ if (me == 0) fread(style,sizeof(char),n,fp); MPI_Bcast(style,n,MPI_CHAR,0,world); - if (force->dihedral == NULL || strcmp(style,force->dihedral_style)) { - if (force->dihedral && me == 0) - error->warning("Resetting dihedral_style to restart file value"); - force->create_dihedral(style); - } - + force->create_dihedral(style); delete [] style; force->dihedral->read_restart(fp); @@ -701,12 +681,7 @@ if (me == 0) fread(style,sizeof(char),n,fp); MPI_Bcast(style,n,MPI_CHAR,0,world); - if (force->improper == NULL || strcmp(style,force->improper_style)) { - if (force->improper && me == 0) - error->warning("Resetting improper_style to restart file value"); - force->create_improper(style); - } - + force->create_improper(style); delete [] style; force->improper->read_restart(fp);