Hi, all, I have some questions about the bonding issue.
First, the original number of bonding type is 8. I add one more type bonding, so right now I have 9 types of bonding.
The procedure to do that is: I disconnect some of the original bondings ( change type to be 0). For example: 1 2 3 4 -> 1 0 3 4. I read the manual of Lammps and it also state the method in this way.
After that, I add one more bonding at the end of the list, like 1000 9 10 11.
However, while I run the datafile, there still exist errors:
LAMMPS (15 May 2015)
Reading data file ...
orthogonal box = (9.47114 9.69814 0.137311) to (108.096 104.901 39.4727)
4 by 4 by 2 MPI processor grid
reading atoms ...
31905 atoms
reading velocities ...
31905 velocities
scanning bonds ...
ERROR on proc 25: Invalid bond type in Bonds section of data file (atom.cpp:922)
ERROR on proc 16: Invalid bond type in Bonds section of data file (atom.cpp:922)
ERROR on proc 8: Invalid bond type in Bonds section of data file (atom.cpp:922)
ERROR on proc 1: Invalid bond type in Bonds section of data file (atom.cpp:922)
ERROR on proc 6: Invalid bond type in Bonds section of data file (atom.cpp:922)
ERROR on proc 4: Invalid bond type in Bonds section of data file (atom.cpp:922)
ERROR on proc 13: Invalid bond type in Bonds section of data file (atom.cpp:922)
ERROR on proc 11: Invalid bond type in Bonds section of data file (atom.cpp:922)
ERROR on proc 28: Invalid bond type in Bonds section of data file (atom.cpp:922)
ERROR on proc 17: Invalid bond type in Bonds section of data file (atom.cpp:922)
Thanks.
Haoxiang Huang
Hi, all, I have some questions about the bonding issue.
First, the original number of bonding type is 8. I add one more type bonding, so right now I have 9 types of bonding.
The procedure to do that is: I disconnect some of the original bondings ( change type to be 0). For example: 1 2 3 4 -> 1 0 3 4. I read the manual of Lammps and it also state the method in this way.
After that, I add one more bonding at the end of the list, like 1000 9 10 11.
However, while I run the datafile, there still exist errors:
have a look at the header section of the data file. it specifies the
total number of (bond) types that can be used in the data file. you
need to change that to match the rest of the data file. note, that you
can "reserve" space for more types than what are actually used in the
data file, but once this number is set, you cannot change it, i.e. add
a new type to the system.
axel.
Hi, I already changed the header to be
31905 atoms
34424 bonds
54481 angles
81486 dihedrals
17534 impropers
8 atom types
9 bond types
13 angle types
18 dihedral types
7 improper types
but the error still exists. Do I need to change 9 to 10 to include type 0? Thanks.
Hi, I already changed the header to be
31905 atoms
34424 bonds
54481 angles
81486 dihedrals
17534 impropers
8 atom types
9 bond types
13 angle types
18 dihedral types
7 improper types
but the error still exists. Do I need to change 9 to 10 to include type 0? Thanks.
from the read_data documentation:
Bonds section:
one line per bond
line syntax: ID type atom1 atom2
ID = bond number (1-Nbonds)
type = bond type (1-Nbondtype)
atom1,atom2 = IDs of 1st,2nd atoms in bond
example:
12 3 17 29
The Bonds section must appear after the Atoms section. All values in
this section must be integers (1, not 1.0).
thus cannot specify a bond with type 0 in a data file. i don't
understand this anyway, you wrote that you wanted those bonds to be of
type 9 not 0.
axel.
So, if I want to delete the bonds, I just need to delete the lines of bonds and update the ID in bond section & header. I try like 12 3 17 29 -> 12 0 17 29 to delete the bond, but it did not work.
So, if I want to delete the bonds, I just need to delete the lines of bonds and update the ID in bond section & header. I try like 12 3 17 29 -> 12 0 17 29 to delete the bond, but it did not work.
yes, that is what i just wrote that you cannot do. please read the
documentation and don't guess.
thanks,
axel.