How to set axis_rule?

[hewg2008]

In your guide，you provide the following description:
"axis_rule": [0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0],

"_comment":	" default rule: []",
"_comment":	" user defined rule: for each type provides two axes, ",
"_comment":	"                    for each axis: (a_or_r, type, idx)",
"_comment":	"                    if type < 0, exclude type -(type+1)",
"_comment":        "                    for water (O:0, H:1) it can be",
"_comment":        "                    [0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0]",

My system is CH(C:0, H:1), and I made exactly the same setting as your example, when I ran train.py, it came out with below traceback:

Traceback (most recent call last):
File "/opt/deepmd/bin/dp_train", line 128, in
_main()
File "/opt/deepmd/bin/dp_train", line 98, in _main
_do_work(jdata, run_opt)
File "/opt/deepmd/bin/dp_train", line 113, in _do_work
data = DataSystem(systems, set_pfx, batch_size, test_size, rcut, run_opt)
File "/opt/deepmd/bin/../lib/deepmd/DataSystem.py", line 31, in init
self.data_systems.append(DataSets(ii, set_prefix))
File "/opt/deepmd/lib/deepmd/Data.py", line 30, in init
self.load_batch_set (self.train_dirs[self.set_count % self.get_numb_set()])
File "/opt/deepmd/lib/deepmd/Data.py", line 166, in load_batch_set
self.atom_ener_batch = self.atom_ener_batch[:, self.idx_map]
IndexError: index 1 is out of bounds for axis 1 with size 1.

Please kindly help.

Thanks.

[jameswind]

Does your system only contain two atoms? One C and one H?

…

On Mon, Jul 1, 2019 at 10:40 PM Wengan He ***@***.***> wrote: In your guide，you provide the following description: "axis_rule": [0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0], "_comment": " default rule: []", "_comment": " user defined rule: for each type provides two axes, ", "_comment": " for each axis: (a_or_r, type, idx)", "_comment": " if type < 0, exclude type -(type+1)", "_comment": " for water (O:0, H:1) it can be", "_comment": " [0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0]", My system is CH(C:0, H:1), and I made exactly the same setting as your example, when I ran train.py, it came out with below traceback: Traceback (most recent call last): File "/opt/deepmd/bin/dp_train", line 128, in _main() File "/opt/deepmd/bin/dp_train", line 98, in _main _do_work(jdata, run_opt) File "/opt/deepmd/bin/dp_train", line 113, in _do_work data = DataSystem(systems, set_pfx, batch_size, test_size, rcut, run_opt) File "/opt/deepmd/bin/../lib/deepmd/DataSystem.py", line 31, in *init* self.data_systems.append(DataSets(ii, set_prefix)) File "/opt/deepmd/lib/deepmd/Data.py", line 30, in *init* self.load_batch_set (self.train_dirs[self.set_count % self.get_numb_set()]) File "/opt/deepmd/lib/deepmd/Data.py", line 166, in load_batch_set self.atom_ener_batch = self.atom_ener_batch[:, self.idx_map] IndexError: index 1 is out of bounds for axis 1 with size 1. Please kindly help. Thanks. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/deepmodeling/deepmd-kit/issues/38?email_source=notifications&email_token=AEJ6DCYNGG3K6DCZ3M2U2HDP5IJPPA5CNFSM4H4TDGS2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G4VBZSQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEJ6DC7I555CVTCVBZUMBCDP5IJPPANCNFSM4H4TDGSQ> .

[hewg2008]

Yes, only two atom types with 24 atoms, one type is C, the other type is H.

[jameswind]

Then you cannot use the non-smooth version, which requires at least 3 atoms to define the local frame. Please try the smooth one.

…

On Tue, Jul 2, 2019 at 11:00 AM Wengan He ***@***.***> wrote: Yes, only two atom types with 24 atoms, one type is C, the other type is H. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/deepmodeling/deepmd-kit/issues/38?email_source=notifications&email_token=AEJ6DC52PT4G5DNEMM6PLTTP5LAFXA5CNFSM4H4TDGS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODY75CRA#issuecomment-507498820>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEJ6DC4LSTABN5MQRNI463DP5LAFXANCNFSM4H4TDGSQ> .

[hewg2008]

Thanks, but a little confused, my system has actually 24 atoms, much more than 3 atoms. Or do you mean the system should be with at least 3 atom types?

[hewg2008]

Already worked. Thanks for the kind help.