Add FlashMD

run/compile.txt

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+cmake ../cmake/ -DPKG_ML-METATOMIC=ON -DCMAKE_PREFIX_PATH=../../libtorch/share/cmake/

run/error.log

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+Traceback (most recent call last):
+  File "/home/filippo/code/virtualenvs/base/lib/python3.12/site-packages/metatrain/utils/io.py", line 186, in model_from_checkpoint
+    return architecture.__model__.load_checkpoint(checkpoint, context=context)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/filippo/code/virtualenvs/base/lib/python3.12/site-packages/metatrain/pet/model.py", line 708, in load_checkpoint
+    model.to(dtype).load_state_dict(model_state_dict)
+  File "/home/filippo/code/virtualenvs/base/lib/python3.12/site-packages/torch/nn/modules/module.py", line 2581, in load_state_dict
+    raise RuntimeError(
+RuntimeError: Error(s) in loading state_dict for PET:
+	Missing key(s) in state_dict: "additive_models.0.model.dummy_buffer", "additive_models.0.model.energy_composition_buffer". 
+
+The above exception was the direct cause of the following exception:
+
+Traceback (most recent call last):
+  File "/home/filippo/code/virtualenvs/base/lib/python3.12/site-packages/metatrain/__main__.py", line 110, in main
+    export_model(**args.__dict__)
+  File "/home/filippo/code/virtualenvs/base/lib/python3.12/site-packages/metatrain/cli/export.py", line 151, in export_model
+    model = load_model(path=path, hf_token=hf_token)
+            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/filippo/code/virtualenvs/base/lib/python3.12/site-packages/metatrain/utils/io.py", line 163, in load_model
+    return model_from_checkpoint(path, context="export")
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/filippo/code/virtualenvs/base/lib/python3.12/site-packages/metatrain/utils/io.py", line 188, in model_from_checkpoint
+    raise ValueError(
+ValueError: path '/tmp/tmpj6hmq_wy' is not a valid checkpoint for the pet architecture

run/flashmd.in

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+units metal
+
+atom_style atomic
+
+lattice fcc 3.615
+region box block 0 8 0 8 0 8
+create_box 1 box
+create_atoms 1 box
+mass 1 63.546
+
+pair_style metatomic pet-mad-latest.pt device cuda non_conservative on
+pair_coeff * * 14
+
+run_style verlet
+
+neighbor 2.0 bin
+timestep 0.001
+
+thermo 5
+
+velocity all create 300 87287 mom yes rot yes
+
+fix 1 all flashmd flashmd_model.pt types 14 energy energy_model.pt device cuda rescale_energy on
+# fix 2 all langevin 300.0 300.0 0.1 12345
+
+run 10

run/lammps.in

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+units metal
+
+atom_style atomic
+
+lattice fcc 3.615
+region box block 0 8 0 8 0 8
+create_box 1 box
+create_atoms 1 box
+mass 1 63.546
+
+pair_style metatomic pet-mad-latest.pt device cuda non_conservative on
+pair_coeff * * 14
+
+run_style verlet
+
+neighbor 2.0 bin
+timestep 0.001
+
+thermo 10
+
+velocity all create 300 87287 mom yes rot yes
+
+fix 1 all nve
+# fix 2 all langevin 300.0 300.0 0.1 12345
+
+run 100

run/lammps_respa.in

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+units metal
+
+atom_style atomic
+
+lattice fcc 3.615
+region box block 0 4 0 4 0 4
+create_box 1 box
+create_atoms 1 box
+mass 1 63.546
+
+pair_style hybrid/overlay metatomic_1 pet-mad-latest.pt device cuda non_conservative on scale 1.0 metatomic_2 pet-mad-latest.pt device cuda non_conservative on scale -1.0 metatomic pet-mad-latest.pt device cuda non_conservative off scale 1.0
+pair_coeff * * metatomic 14
+pair_coeff * * metatomic_1 14
+pair_coeff * * metatomic_2 14
+
+# pair_style hybrid/overlay metatomic_1 pet-mad-latest.pt device cuda non_conservative off scale 0.5 metatomic pet-mad-latest.pt device cuda non_conservative off scale 0.5
+# pair_coeff * * metatomic 14
+# pair_coeff * * metatomic_1 14
+
+# pair_style hybrid/overlay morse 6.0 lj/cut 7.5
+# pair_coeff * * morse 0.3429 1.444 2.491 6.0
+# pair_coeff * * lj/cut 0.01 2.5 7.5
+
+# pair_style lj/cut 7.5
+# pair_coeff * * 0.01 2.5 7.5
+
+run_style respa 2 8 hybrid 1 2 2
+
+# pair_style metatomic pet-mad-latest.pt device cuda
+# pair_coeff * * 14
+
+# pair_style hybrid/overlay metatomic_1 pet-mad-latest.pt device cuda scale 0.5 metatomic_2 pet-mad-latest.pt device cuda scale 0.5
+# pair_coeff * * metatomic_1 14
+# pair_coeff * * metatomic_2 14
+
+# pair_style hybrid/overlay metatomic_1 nickel-lj.pt device cuda scale 0.5 metatomic_2 nickel-lj.pt device cuda scale 0.5
+# pair_coeff * * metatomic_1 28
+# pair_coeff * * metatomic_2 28
+
+timestep 0.004
+
+thermo 10
+# thermo_modify format float %.6f
+
+velocity all create 300 87287 mom yes rot yes
+
+fix 1 all nve
+# fix 2 all langevin 300.0 300.0 0.1 12345
+
+run 125

run/log.out

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+LAMMPS (2 Apr 2025)
+KOKKOS mode with Kokkos version 4.6.0 is enabled (src/KOKKOS/kokkos.cpp:72)
+  will use up to 1 GPU(s) per node
+  using 1 OpenMP thread(s) per MPI task
+Lattice spacing in x,y,z = 3.615 3.615 3.615
+Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
+  1 by 1 by 1 MPI processor grid
+Created 256 atoms
+  using lattice units in orthogonal box = (0 0 0) to (14.46 14.46 14.46)
+  create_atoms CPU = 0.002 seconds
+
+This is an unamed model
+=======================
+
+Model references
+----------------
+
+Please cite the following references when using this model:
+- about the architecture of this model:
+  * https://arxiv.org/abs/2305.19302v3
+
+Running simulation on cuda:0 device with float32 data
+
+This is an unamed model
+=======================
+
+Model references
+----------------
+
+Please cite the following references when using this model:
+- about the architecture of this model:
+  * https://arxiv.org/abs/2305.19302v3
+
+Running simulation on cuda:0 device with float32 data
+
+This is an unamed model
+=======================
+
+Model references
+----------------
+
+Please cite the following references when using this model:
+- about the architecture of this model:
+  * https://arxiv.org/abs/2305.19302v3
+
+Running simulation on cuda:0 device with float32 data
+Respa levels:
+  1 = bond angle dihedral improper hybrid-1
+  2 = hybrid-2 hybrid-3 kspace
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+- https://arxiv.org/abs/2305.19302v3
+The log file lists these citations in BibTeX format.
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11
+  ghost atom cutoff = 11
+  binsize = 11, bins = 2 2 2
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair metatomic_1, perpetual
+      attributes: full, newton on, ghost, kokkos_device
+      pair build: full/bin/ghost/kk/device
+      stencil: full/ghost/bin/3d
+      bin: kk/device
+  (2) pair metatomic_2, perpetual, copy from (1)
+      attributes: full, newton on, ghost, kokkos_device
+      pair build: copy/kk/device
+      stencil: none
+      bin: none
+  (3) pair metatomic, perpetual, copy from (1)
+      attributes: full, newton on, ghost, kokkos_device
+      pair build: copy/kk/device
+      stencil: none
+      bin: none
+Setting up r-RESPA run ...
+  Unit style    : metal
+  Current step  : 0
+  Time steps    : 1:0.0005 2:0.004
+  r-RESPA fixes :
+WARNING: Fix RESPA not compatible with sending data in Kokkos communication (src/KOKKOS/comm_kokkos.cpp:766)
+WARNING: Fix with atom-based arrays not compatible with sending data in Kokkos communication, switching to classic exchange/border communication (src/KOKKOS/comm_kokkos.cpp:779)
+WARNING: Fix RESPA not compatible with Kokkos sorting on device (src/KOKKOS/atom_kokkos.cpp:212)
+WARNING: Fix with atom-based arrays not compatible with Kokkos sorting on device, switching to classic host sorting (src/KOKKOS/atom_kokkos.cpp:218)
+Per MPI rank memory allocation (min/avg/max) = 5.002 | 5.002 | 5.002 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   300           -1335.9207      0             -1326.0323      144805.16    
+        10   76.484066     -1328.5359      0             -1326.0149      170127.28    
+        20   129.11323     -1330.2771      0             -1326.0214      167276.46    
+        30   166.90739     -1331.5227      0             -1326.0212      159896.11    
+        40   146.05235     -1330.8333      0             -1326.0192      161028.24    
+        50   160.36688     -1331.3071      0             -1326.0212      160333.22    
+        60   138.56125     -1330.5868      0             -1326.0196      163124.55    
+        70   150.7026      -1330.9877      0             -1326.0203      161852.1     
+        80   160.91314     -1331.3247      0             -1326.0208      160387.36    
+        90   142.18906     -1330.7065      0             -1326.0198      162289.83    
+       100   153.95673     -1331.0951      0             -1326.0205      160916.04    
+       110   144.51871     -1330.7836      0             -1326.02        162449.65    
+       120   144.34685     -1330.7783      0             -1326.0205      162959.63    
+       125   142.50892     -1330.7173      0             -1326.02        162950.24    
+Loop time of 40.4834 on 1 procs for 125 steps with 256 atoms
+
+Performance: 1.067 ns/day, 22.491 hours/ns, 3.088 timesteps/s, 790.448 atom-step/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 37.894     | 37.894     | 37.894     |   0.0 | 93.60
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.1415     | 1.1415     | 1.1415     |   0.0 |  2.82
+Output  | 0.0018303  | 0.0018303  | 0.0018303  |   0.0 |  0.00
+Modify  | 1.4299     | 1.4299     | 1.4299     |   0.0 |  3.53
+Other   |            | 0.01648    |            |       |  0.04
+
+Nlocal:            256 ave         256 max         256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4375 ave        4375 max        4375 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       117248 ave      117248 max      117248 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 117248
+Ave neighs/atom = 458
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:42