upload new medium with calibrated isolated atomic reference energies

.gitignore

@@ -6,4 +6,6 @@ dataset/
 training/
 benchmark/
 
+*.ipynb
+
 **.ipynb_checkpoints/

dataset/mptrj-gga-ggapu-statistics-isolated.json

@@ -1 +0,0 @@
-{"atomic_energies": "{1: -1.11723232, 2: -0.00045595, 3: -0.29734917, 4: -0.04262353, 5: -0.2911712, 6: -1.26281801, 7: -3.12555634, 8: -1.54690765, 9: -0.43794547, 10: -0.01216023, 11: -0.22858276, 12: -0.00994627, 13: -0.21672837, 14: -0.82583191, 15: -1.88719667, 16: -0.89091719, 17: -0.25828681, 18: -0.0235315, 19: -0.17827125, 20: -0.02596217, 21: -2.12966897, 22: -2.40532262, 23: -3.61232779, 24: -5.44620624, 25: -5.14592659, 26: -3.30583367, 27: -1.66614587, 28: -0.28412403, 29: -0.23745594, 30: -0.01098351, 31: -0.19854295, 32: -0.77924665, 33: -1.70136472, 34: -0.78345919, 35: -0.22687512, 36: -0.02265396, 37: -0.16194042, 38: -0.02823145, 39: -2.25679622, 40: -2.23742918, 41: -2.53481909, 42: -4.60213279, 43: -3.40289704, 44: -1.68884293, 45: -1.44016062, 46: -1.47521138, 47: -0.19840574, 48: -0.01374787, 49: -0.19672488, 50: -0.67963499, 51: -1.4302063, 52: -0.6573123, 53: -0.18858477, 54: -0.01267614, 55: -0.13452777, 56: -0.03157029, 57: -0.62794477, 58: -1.43642821, 59: -0.18584352, 60: -0.25876002, 61: -0.25695685, 62: -0.2542358, 63: -9.48606277, 64: -8.11540027, 65: -0.14584339, 66: -0.19488481, 67: -0.14569527, 68: -0.2516406, 69: -0.16381585, 70: -0.25265734, 71: -0.25255978, 72: -3.49292389, 73: -3.5659314, 74: -4.57101127, 75: -4.63436797, 76: -2.88280809, 77: -1.42793567, 78: -0.50244445, 79: -0.18479218, 80: -0.0105212, 81: -0.17939998, 82: -0.63069886, 83: -1.32462383, 89: -0.24210133, 90: -1.04419147, 91: -2.03239022, 92: -4.6443113, 93: -7.30273499, 94: -10.39244586}", "avg_num_neighbors": 61.964672446250916, "mean": 0.16409696359187365, "std": 0.8041538754478097, "atomic_numbers": "[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 89, 90, 91, 92, 93, 94]", "r_max": 6.0}

pretrained/2024-07-12-mace-128-L1_epoch-199.model

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fb3aa6eb8954755517d15c93aebe21a2060d781932cf1e63d7089f8d427dbb05
+size 44424713

pretrained/2024-07-12-mace-128-L1_epoch-199.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:23fa9c38b93008dbf2c0917ea84a49d91944143d80dd8fc1ca1197801ca0b6af
+size 156795562

tests/lammps/build-structure.py

@@ -6,5 +6,5 @@ Ni = bulk('Ni', cubic=True) * (2, 2, 2)
 H = Atom('H', position=Ni.cell.diagonal()/2)
 NiH = Ni + H
 
-write('initial.data', NiH, format='lammps-data', 
+write('initial_.data', NiH, format='lammps-data', 
       masses=True, atom_style='atomic')

tests/lammps/in.lammps

@@ -2,7 +2,7 @@
 # Global settings
 # ====================
 
-units           real
+units           metal
 atom_style      atomic
 atom_modify     map yes
 newton          on

tests/lammps/log.lammps

@@ -5,7 +5,7 @@ OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98
 # Global settings
 # ====================
 
-units           real
+units           metal
 atom_style      atomic
 atom_modify     map yes
 newton          on