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  1. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-0.pt +3 -0
  2. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-10.pt +3 -0
  3. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-12.pt +3 -0
  4. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-16.pt +3 -0
  5. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-18.pt +3 -0
  6. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-2.pt +3 -0
  7. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-22.pt +3 -0
  8. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-30.pt +3 -0
  9. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-4.pt +3 -0
  10. maceoff_spice_v2_dft_charges/checkpoints/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_epoch-6.pt +3 -0
  11. maceoff_spice_v2_dft_charges/logs/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123.log +0 -0
  12. maceoff_spice_v2_dft_charges/results/mace_scf_spice_2_low_force_filter_r6_128ch_charges_only_run-123_train.txt +0 -0
  13. maceoff_spice_v2_dft_charges/train.sh +39 -0
  14. model_fitting/analysis_md.ipynb +0 -0
  15. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-632.pt +3 -0
  16. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-634.pt +3 -0
  17. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-642.pt +3 -0
  18. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-644.pt +3 -0
  19. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-646.pt +3 -0
  20. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-660.pt +3 -0
  21. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-674.pt +3 -0
  22. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-680.pt +3 -0
  23. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-682.pt +3 -0
  24. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-688.pt +3 -0
  25. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-696.pt +3 -0
  26. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-710.pt +3 -0
  27. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-780.pt +3 -0
  28. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-798.pt +3 -0
  29. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-802_swa.pt +3 -0
  30. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-826_swa.pt +3 -0
  31. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-834_swa.pt +3 -0
  32. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-850_swa.pt +3 -0
  33. model_fitting/checkpoints/mace_pol_spice_v1_run-123_epoch-956_swa.pt +3 -0
  34. model_fitting/chgnolin_md_snapshot_25_scf_steps.xyz +140 -0
  35. model_fitting/chignolin.xyz +0 -0
  36. model_fitting/chignolin_formatted.xyz +140 -0
  37. model_fitting/chignolin_md.xyz +0 -0
  38. model_fitting/chignolin_md_scf.xyz +0 -0
  39. model_fitting/chignolin_md_scf_10_steps.xyz +0 -0
  40. model_fitting/chignolin_md_scf_25_steps copy.xyz +0 -0
  41. model_fitting/chignolin_md_scf_25_steps.xyz +0 -0
  42. model_fitting/logs/mace_pol_spice_v1_run-123.log +0 -0
  43. model_fitting/mace_md_pol_test/mace_md.log +20 -0
  44. model_fitting/mace_md_pol_test/prepared_system.pdb +142 -0
  45. model_fitting/mace_pol_spice_v1.model +3 -0
  46. model_fitting/mace_pol_spice_v1_stage_2_5step.model +3 -0
  47. model_fitting/mace_pol_spice_v1_stage_2_5step_swa.model +3 -0
  48. model_fitting/mace_pol_spice_v1_swa.model +3 -0
  49. model_fitting/results/mace_pol_spice_v1_run-123_train.txt +0 -0
  50. model_fitting/run_md.py +28 -0
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+ source ~/.bashrc
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+ conda activate mace-scf
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+
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+ mpirun -np 16 python /home/jhm/software/mace-tools/scripts/will_train.py \
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+ --name="mace_scf_spice_2_low_force_filter_r6_128ch_charges_only" \
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+ --train_file="../processed_maceoff_scf_spice_2/train" \
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+ --test_file "../processed_maceoff_scf_spice_2/test" \
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+ --valid_file="../processed_maceoff_scf_spice_2/val" \
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+ --statistics_file="../processed_maceoff_scf_spice_2/statistics.json" \
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+ --config_type_weights='{"Default":1.0}' \
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+ --model="Polarizable" \
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+ --hidden_irreps='128x0e + 128x1o' \
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+ --loss="energy_forces_atomic_multipoles" \
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+ --distributed \
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+ --num_workers=4\
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+ --num_interactions=2 \
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+ --eval_interval=2 \
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+ --batch_size=32 \
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+ --valid_batch_size=32 \
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+ --max_num_epochs=200\
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+ --error_table="DensityEnergyRMSE" \
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+ --swa\
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+ --lr=5e-2 \
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+ --swa_lr=5e-3 \
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+ --start_swa=100\
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+ --device="cuda"\
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+ --kspace_cutoff_factor=1.0 \
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+ --field_dependence_type="biased_local_linear" \
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+ --energy_key="energy" \
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+ --forces_key="forces" \
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+ --atomic_multipoles_weight=10 \
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+ --swa_atomic_multipoles_weight=1000 \
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+ --atomic_multipoles_max_l=0 \
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+ --atomic_multipoles_smearing_width=1.5 \
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+ --keep_checkpoints \
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+ --atomic_multipoles_key="mbis_multipoles" \
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+ --default_dtype="float64" \
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+ --restart_latest \
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+ --scf_training_options='{"num_scf_steps":0, "constant_charge":True, "mixing_parameter": 1.0, "use_autograd_forces": True}'
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model_fitting/chignolin_md.xyz ADDED
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model_fitting/chignolin_md_scf.xyz ADDED
The diff for this file is too large to render. See raw diff
 
model_fitting/chignolin_md_scf_10_steps.xyz ADDED
The diff for this file is too large to render. See raw diff
 
model_fitting/chignolin_md_scf_25_steps copy.xyz ADDED
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model_fitting/chignolin_md_scf_25_steps.xyz ADDED
The diff for this file is too large to render. See raw diff
 
model_fitting/logs/mace_pol_spice_v1_run-123.log ADDED
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model_fitting/mace_md_pol_test/mace_md.log ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 2024-08-16 13:35:23.243 INFO: Using SMFF openff_unconstrained-1.0.0.offxml
2
+ 2024-08-16 13:35:23.284 INFO: Using reduced periodic box vectors (Vec3(x=3.5, y=0.0, z=0.0), Vec3(x=0.0, y=3.5, z=0.0), Vec3(x=0.0, y=0.0, z=3.5)) nm
3
+ 2024-08-16 13:35:23.284 INFO: Initialized topology with 138 atoms
4
+ 2024-08-16 13:35:23.297 WARNING: Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
5
+ 2024-08-16 13:52:05.528 INFO: Using SMFF openff_unconstrained-1.0.0.offxml
6
+ 2024-08-16 13:52:05.546 INFO: Using reduced periodic box vectors (Vec3(x=3.5, y=0.0, z=0.0), Vec3(x=0.0, y=3.5, z=0.0), Vec3(x=0.0, y=0.0, z=3.5)) nm
7
+ 2024-08-16 13:52:05.547 INFO: Initialized topology with 138 atoms
8
+ 2024-08-16 13:52:05.553 WARNING: Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
9
+ 2024-08-16 13:55:19.042 INFO: Using SMFF openff_unconstrained-1.0.0.offxml
10
+ 2024-08-16 13:55:19.060 INFO: Using reduced periodic box vectors (Vec3(x=3.5, y=0.0, z=0.0), Vec3(x=0.0, y=3.5, z=0.0), Vec3(x=0.0, y=0.0, z=3.5)) nm
11
+ 2024-08-16 13:55:19.060 INFO: Initialized topology with 138 atoms
12
+ 2024-08-16 13:55:19.067 WARNING: Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
13
+ 2024-08-16 13:55:53.890 INFO: Using SMFF openff_unconstrained-1.0.0.offxml
14
+ 2024-08-16 13:55:53.909 INFO: Using reduced periodic box vectors (Vec3(x=3.5, y=0.0, z=0.0), Vec3(x=0.0, y=3.5, z=0.0), Vec3(x=0.0, y=0.0, z=3.5)) nm
15
+ 2024-08-16 13:55:53.910 INFO: Initialized topology with 138 atoms
16
+ 2024-08-16 13:55:53.917 WARNING: Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
17
+ 2024-08-16 13:57:20.357 INFO: Using SMFF openff_unconstrained-1.0.0.offxml
18
+ 2024-08-16 13:57:20.375 INFO: Using reduced periodic box vectors (Vec3(x=3.5, y=0.0, z=0.0), Vec3(x=0.0, y=3.5, z=0.0), Vec3(x=0.0, y=0.0, z=3.5)) nm
19
+ 2024-08-16 13:57:20.376 INFO: Initialized topology with 138 atoms
20
+ 2024-08-16 13:57:20.382 WARNING: Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
model_fitting/mace_md_pol_test/prepared_system.pdb ADDED
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+ HETATM 93 92 mac A 1 1.127 -1.719 -1.310 1.00 0.00 N
96
+ HETATM 94 93 mac A 1 0.411 -3.025 -1.274 1.00 0.00 C
97
+ HETATM 95 94 mac A 1 -0.641 -3.013 -0.162 1.00 0.00 C
98
+ HETATM 96 95 mac A 1 -0.633 -2.164 0.707 1.00 0.00 O
99
+ HETATM 97 96 mac A 1 1.418 -4.147 -1.011 1.00 0.00 C
100
+ HETATM 98 97 mac A 1 2.633 -3.587 -0.532 1.00 0.00 O
101
+ HETATM 99 98 mac A 1 1.682 -4.912 -2.308 1.00 0.00 C
102
+ HETATM 100 99 mac A 1 1.108 -1.125 -0.531 1.00 0.00 H
103
+ HETATM 101 100 mac A 1 -0.073 -3.195 -2.224 1.00 0.00 H
104
+ HETATM 102 101 mac A 1 1.018 -4.825 -0.273 1.00 0.00 H
105
+ HETATM 103 102 mac A 1 3.275 -4.296 -0.450 1.00 0.00 H
106
+ HETATM 104 103 mac A 1 0.813 -5.501 -2.562 1.00 0.00 H
107
+ HETATM 105 104 mac A 1 2.533 -5.563 -2.176 1.00 0.00 H
108
+ HETATM 106 105 mac A 1 1.885 -4.210 -3.104 1.00 0.00 H
109
+ HETATM 107 106 mac A 1 -1.545 -3.955 -0.184 1.00 0.00 N
110
+ HETATM 108 107 mac A 1 -2.598 -4.011 0.868 1.00 0.00 C
111
+ HETATM 109 108 mac A 1 -1.960 -4.395 2.205 1.00 0.00 C
112
+ HETATM 110 109 mac A 1 -1.576 -5.528 2.417 1.00 0.00 O
113
+ HETATM 111 110 mac A 1 -3.640 -5.067 0.487 1.00 0.00 C
114
+ HETATM 112 111 mac A 1 -3.848 -5.068 -0.996 1.00 0.00 C
115
+ HETATM 113 112 mac A 1 -3.216 -5.882 -1.873 1.00 0.00 C
116
+ HETATM 114 113 mac A 1 -4.743 -4.236 -1.786 1.00 0.00 C
117
+ HETATM 115 114 mac A 1 -3.664 -5.596 -3.150 1.00 0.00 N
118
+ HETATM 116 115 mac A 1 -4.608 -4.591 -3.148 1.00 0.00 C
119
+ HETATM 117 116 mac A 1 -5.648 -3.218 -1.454 1.00 0.00 C
120
+ HETATM 118 117 mac A 1 -5.349 -3.958 -4.146 1.00 0.00 C
121
+ HETATM 119 118 mac A 1 -6.398 -2.577 -2.455 1.00 0.00 C
122
+ HETATM 120 119 mac A 1 -6.248 -2.947 -3.799 1.00 0.00 C
123
+ HETATM 121 120 mac A 1 -1.532 -4.627 -0.892 1.00 0.00 H
124
+ HETATM 122 121 mac A 1 -3.075 -3.047 0.957 1.00 0.00 H
125
+ HETATM 123 122 mac A 1 -3.295 -6.041 0.800 1.00 0.00 H
126
+ HETATM 124 123 mac A 1 -4.575 -4.843 0.980 1.00 0.00 H
127
+ HETATM 125 124 mac A 1 -2.478 -6.628 -1.618 1.00 0.00 H
128
+ HETATM 126 125 mac A 1 -3.364 -6.042 -3.968 1.00 0.00 H
129
+ HETATM 127 126 mac A 1 -5.766 -2.927 -0.422 1.00 0.00 H
130
+ HETATM 128 127 mac A 1 -5.228 -4.248 -5.180 1.00 0.00 H
131
+ HETATM 129 128 mac A 1 -7.093 -1.796 -2.187 1.00 0.00 H
132
+ HETATM 130 129 mac A 1 -6.827 -2.451 -4.564 1.00 0.00 H
133
+ HETATM 131 130 mac A 1 -1.844 -3.461 3.109 1.00 0.00 N
134
+ HETATM 132 131 mac A 1 -1.229 -3.774 4.431 1.00 0.00 C
135
+ HETATM 133 132 mac A 1 -1.877 -5.031 5.014 1.00 0.00 C
136
+ HETATM 134 133 mac A 1 -1.289 -6.092 4.882 1.00 0.00 O
137
+ HETATM 135 134 mac A 1 -2.949 -4.912 5.584 1.00 0.00 O
138
+ HETATM 136 135 mac A 1 -2.159 -2.553 2.918 1.00 0.00 H
139
+ HETATM 137 136 mac A 1 -0.169 -3.939 4.305 1.00 0.00 H
140
+ HETATM 138 137 mac A 1 -1.387 -2.946 5.106 1.00 0.00 H
141
+ TER 139 mac A 1
142
+ END
model_fitting/mace_pol_spice_v1.model ADDED
@@ -0,0 +1,3 @@
 
 
 
 
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:eece6f6258e8ff1f7bccd5fb3e837e5b998c5d38285d4305d299f52a7ebefd47
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+ size 14362770
model_fitting/mace_pol_spice_v1_stage_2_5step.model ADDED
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:07f62f251ecd98f463f29187944b68d4f66af81d6bc483e1d151300fb1a5c9bf
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+ size 14362770
model_fitting/mace_pol_spice_v1_stage_2_5step_swa.model ADDED
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:571fe0fab7b57af8fd2ec119cbdf89a805eed127eab8c846811bc24e84bac379
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+ size 14363326
model_fitting/mace_pol_spice_v1_swa.model ADDED
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:cff9619cddacf1d5c3c399a567ad7547c61945c188c426da2e8c6a323e63c7f0
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+ size 14363326
model_fitting/results/mace_pol_spice_v1_run-123_train.txt ADDED
The diff for this file is too large to render. See raw diff
 
model_fitting/run_md.py ADDED
@@ -0,0 +1,28 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ from ase import units
2
+ from ase.md.langevin import Langevin
3
+ from ase.io import read, write
4
+ import numpy as np
5
+ import time
6
+
7
+ from macetools.calculators.polarizable import MACEPolarizable
8
+
9
+ calculator = MACEPolarizable(
10
+ model_path="./mace_pol_spice_v1_swa.model",
11
+ device="cuda",
12
+ num_scf_steps=25,
13
+ total_charge_key="total_charge",
14
+ constant_charge=True,
15
+ )
16
+ init_conf = read("./chignolin_formatted.xyz", "0")
17
+ init_conf.set_calculator(calculator)
18
+
19
+ dyn = Langevin(init_conf, 1.0 * units.fs, temperature_K=300, friction=5e-3)
20
+
21
+
22
+ def write_frame():
23
+ dyn.atoms.write("chignolin_md_scf_25_steps_test.xyz", append=True)
24
+
25
+
26
+ dyn.attach(write_frame, interval=100)
27
+ dyn.run(100000)
28
+ print("MD finished!")