run LAMMPS problem

[KK33999]

Hello everyone, I have a question to discuss. I trained the potential function using the DeePMD-kit v3.0.2 version DPA2 descriptor, and the energy and force accuracy were also in good agreement during the dp test process. However, when I used this potential function to run LAMMPS molecular dynamics, I found that it would scatter the structure after 20 ps. The specific details of my training are: 1. Select the temperature range of 50K-500K and use VASP to run AIMD. Check that the structure of the last step is not scattered and select 80% of all data for training. 2. Use the LAMMPS template as follows.

variable			t equal 50

log				log_$t.lammps  
units           		metal                                                  
boundary        		p p p           
atom_style     		atomic # full  # charge  dipole     
read_data	  		stru.data  
mass			1  A      
mass 			2  B

group			A  type 1
group			B  type 2     

pair_style	deepmd 	./graph.pth        
pair_coeff  		* *	                                 
velocity        		all create $t 23456789 dist gaussian

timestep        		0.001
fix             		1 all nvt temp $t $t 0.1 
                                               
thermo_style    	custom step temp pe ke etotal press density lx ly lz vol         
thermo          		100                                                                                         

dump			1 all custom 10 $t.dump id type x y z 

thermo			10                       

run             		500000

My guess is whether AIMD data needs to be cleaned? I don't know, I hope someone can give some suggestions or similar experiences.

[njzjz]

Do you know the active learning? It may be just because the data is not enough.

[KK33999]

Finally, I expanded the dataset with dpgen and achieved good results. Thank you for your answer. Best wishes.

[pillowill]

May I ask how you successfully ran LAMMPS? I am using version 3.1.1 of DeepMD-kit. The tutorial I am following is at https://deepmodeling.com/articles/detail/972da94c-bc35-43b2-af20-6ca943727015/DeePMD-PyTorch. The contents of in.lammps are as follows：

bulk water

units metal
boundary p p p
atom_style atomic

neighbor 2.0 bin
neigh_modify every 10 delay 0 check no

read_data water.lmp
mass 1 16
mass 2 2

See https://deepmd.rtfd.io/lammps/ for usage

pair_style deepmd frozen_model.pth

If atom names (O H in this example) are not set in the pair_coeff command, the type_map defined by the training parameter will be used by default.

pair_coeff * * O H

velocity all create 330.0 23456789

fix 1 all nvt temp 330.0 330.0 0.5
timestep 0.0005
thermo_style custom step pe ke etotal temp press vol
thermo 100
dump 1 all custom 100 water.dump id type x y z

run 1000
The runtime error is displayed as follows:
(deepmd-pt) HeYu@uubntu:~/deepmd/deepmd-kit/examples/water/lmp$ lmp -in in.lammps
LAMMPS (2 Aug 2023 - Development - 27347ce4a1)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
triclinic box = (0 0 0) to (12.4447 12.4447 12.4447) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
192 atoms
read_data CPU = 0.002 seconds
Exception:
Unknown builtin op: deepmd::border_op.
Could not find any similar ops to deepmd::border_op. This op may not exist or may not be currently supported in TorchScript.
:
File "code/torch/deepmd/pt/model/descriptor/repformers.py", line 238
_34 = torch.tensor(real_nloc, dtype=3, device=torch.device("cpu"))
_35 = torch.tensor(torch.sub(real_nall, real_nloc), dtype=3, device=torch.device("cpu"))
ret = ops.deepmd.border_op(_27, _28, _29, _31, _32, g10, _33, _34, _35)
~~~~~~~~~~~~~~~~~~~~ <--- HERE
g1_ext0 = torch.unsqueeze(ret[0], 0)
if has_spin:

---

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

[iProzd]

Hi @pillowill , it appears that DeePMD-kit or LAMMPS may not be installed correctly. I recommend using the offline packages (refer to the installation guide and v3.1.1 release) to ensure both are set up properly. Once installed, please ensure you freeze your checkpoint (*.pt) into a model file (*.pth) using this specific version before running the LAMMPS script. You may also find the DPA2 tutorial and our newest DPA3 model helpful.