diff --git a/alignn/__init__.py b/alignn/__init__.py index d79b367d..a7c1afd0 100644 --- a/alignn/__init__.py +++ b/alignn/__init__.py @@ -1,2 +1,2 @@ """Version number.""" -__version__ = "2023.04.30" +__version__ = "2023.05.03" diff --git a/alignn/examples/sample_data_ff/mlearn_data/all/config_example.json b/alignn/examples/sample_data_ff/mlearn_data/all/config_example.json new file mode 100644 index 00000000..5bae4fbe --- /dev/null +++ b/alignn/examples/sample_data_ff/mlearn_data/all/config_example.json @@ -0,0 +1,67 @@ +{ + "version": "112bbedebdaecf59fb18e11c929080fb2f358246", + "dataset": "user_data", + "target": "target", + "atom_features": "cgcnn", + "neighbor_strategy": "k-nearest", + "id_tag": "jid", + "random_seed": 123, + "classification_threshold": null, + "n_val": 164, + "n_test": 164, + "n_train":1402, + "train_ratio": 0.9, + "val_ratio": 0.05, + "test_ratio": 0.05, + "target_multiplication_factor": null, + "epochs": 50, + "batch_size": 5, + "weight_decay": 1e-05, + "learning_rate": 0.001, + "filename": "sample", + "warmup_steps": 2000, + "criterion": "l1", + "optimizer": "adamw", + "scheduler": "onecycle", + "pin_memory": false, + "save_dataloader": false, + "write_checkpoint": true, + "write_predictions": true, + "store_outputs": false, + "progress": true, + "log_tensorboard": false, + "standard_scalar_and_pca": false, + "use_canonize": false, + "num_workers": 0, + "cutoff": 8.0, + "max_neighbors": 12, + "keep_data_order": false, + "normalize_graph_level_loss": false, + "distributed": false, + "n_early_stopping": null, + "output_dir": "out_continue", + "model": { + "name": "alignn_atomwise", + "alignn_layers": 2, + "gcn_layers": 4, + "atom_input_features": 92, + "edge_input_features": 80, + "triplet_input_features": 40, + "embedding_features": 64, + "hidden_features": 256, + "output_features": 1, + "grad_multiplier": -1, + "calculate_gradient": true, + "atomwise_output_features": 0, + "graphwise_weight": 1.0, + "gradwise_weight": 1.0, + 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0.19550442], [-0.01993061, 0.44011207, -0.34376596], [0.20624781, -0.11180293, 0.38841049], [0.13979853, 0.16727473, -0.08766329], [0.08236971, 0.05719118, -0.19564219], [-0.06255421, -0.34830205, -0.4314213], [0.2282677, -0.08360131, -0.0447854], [0.10419892, -0.22768252, -0.09546536], [0.46466589, 0.32748357, 0.06786859], [0.18286569, 0.06387017, -0.00615241], [-0.10634659, -0.01259396, 0.12854379], [0.6528048, 0.22323316, -0.06281724], [0.33385178, 0.49083687, -0.16462229], [-0.44324149, 0.23810274, 0.50220034], [-0.1083265, -0.18140041, 0.17144663], [0.47663105, 0.22356403, -0.24727223], [-0.40712779, -0.6398147, -0.29767942], [-0.16632168, 0.3667545, -0.00361372], [-0.70963037, 0.30608041, -0.14903203], [0.07009116, -0.23709303, 0.25194922], [-0.18252909, 0.12451875, -0.08741516], [0.40915945, -0.2055852, 0.73601906], [-0.25305613, 0.14290949, -0.30496572], [0.02341966, 0.32473378, 0.04771988], [-0.25504198, -0.26903022, 0.04694831], [-0.27456399, -0.11611054, 0.14194234], [-0.04735301, -0.14108987, -0.20755191], [0.04295613, 0.45716123, -0.15847528], [0.15068237, 0.01495688, -0.88893266], [-0.52117687, -0.24502948, -0.26840479], [0.1590189, 0.04272689, 0.37297088], [0.19355574, 0.42721613, 0.51089395], [0.42783616, -0.40016082, 0.15930333], [-0.29122965, 0.09545714, -0.02624567], [0.23184888, -0.22587246, -0.41482705], [-0.25722919, 0.16800808, 0.09707667], [0.10663347, 0.56440376, -0.09727929], [0.47678562, -0.27570706, -0.02188358], [0.36050058, 0.48368394, -0.22340612]], "stresses": [[-3.5990434, -4.24142421, -3.88286994], [-4.24142421, 3.17548688, -2.21080743], [-3.88286994, -2.21080743, 5.15661787]]}, {"jid": "Li-266a", "atoms": {"lattice_mat": [[4.8442, 0.0, 0.0], [2.4221, 4.195201, 0.0], [0.0, 0.0, 23.953719]], "coords": [[0.666667, 0.666667, 0.078147], [0.0, 0.0, 0.997635], [0.333333, 0.333333, 0.168186], [0.666667, 0.666667, 0.205999], [0.0, 0.0, 0.123603], [0.333333, 0.333333, 0.04836], [0.666667, 0.666667, 0.33473], [0.0, 0.0, 0.252334], [0.333333, 0.333333, 0.409974], [0.666667, 0.666667, 0.460698], [0.0, 0.0, 0.380186], [0.333333, 0.333333, 0.290148]], "elements": ["Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li"], "abc": [4.8442, 4.8442, 23.95372], "angles": [90.0, 90.0, 60.0], "cartesian": false, "props": ["", "", "", "", "", "", "", "", "", "", "", ""]}, "energy": -21.41050187, "total_energy": -1.7842084891666667, "forces": [[-0.0, -0.0, -0.00808912], [-0.0, -0.0, -0.0143953], [0.0, -0.0, 0.00116484], [0.0, -0.0, -0.01540804], [-0.0, 0.0, 0.00345235], [0.0, 0.0, 0.00360479], [0.0, -0.0, -0.00345235], [-0.0, 0.0, 0.01540804], [-0.0, -0.0, -0.00360479], [0.0, 0.0, 0.0143953], [0.0, 0.0, 0.00808912], [0.0, 0.0, -0.00116484]], "stresses": [[-3.18097963, 0.0, -0.0], [0.0, -3.18098075, 0.0], [-0.0, 0.0, 0.56392251]]}, {"jid": "Li-266a", "atoms": {"lattice_mat": [[4.8442, 0.0, 0.0], [2.4221, 4.195201, 0.0], [0.0, 0.0, 23.953719]], "coords": [[0.666667, 0.666667, 0.078147], [0.0, 0.0, 0.997635], [0.333333, 0.333333, 0.168186], [0.666667, 0.666667, 0.205999], [0.0, 0.0, 0.123603], [0.333333, 0.333333, 0.04836], [0.666667, 0.666667, 0.33473], [0.0, 0.0, 0.252334], [0.333333, 0.333333, 0.409974], [0.666667, 0.666667, 0.460698], [0.0, 0.0, 0.380186], [0.333333, 0.333333, 0.290148]], "elements": ["Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li"], "abc": [4.8442, 4.8442, 23.95372], "angles": [90.0, 90.0, 60.0], "cartesian": false, "props": ["", "", "", "", "", "", "", "", "", "", "", ""]}, "energy": -21.41050187, "total_energy": -1.7842084891666667, "forces": [[-0.0, -0.0, -0.00808912], [-0.0, -0.0, -0.0143953], [0.0, -0.0, 0.00116484], [0.0, -0.0, -0.01540804], [-0.0, 0.0, 0.00345235], [0.0, 0.0, 0.00360479], [0.0, -0.0, -0.00345235], [-0.0, 0.0, 0.01540804], [-0.0, -0.0, -0.00360479], [0.0, 0.0, 0.0143953], [0.0, 0.0, 0.00808912], [0.0, 0.0, -0.00116484]], "stresses": [[-3.18097963, 0.0, -0.0], [0.0, -3.18098075, 0.0], [-0.0, 0.0, 0.56392251]]}, {"jid": "Li-267a", "atoms": {"lattice_mat": [[3.429887, 0.0, 0.0], [-1.714943, 5.426396, 0.0], [0.0, 0.0, 21.705585]], "coords": [[0.678583, 0.357166, 0.445654], [0.405679, 0.811357, 0.408195], [0.096137, 0.192274, 0.343508], [0.80722, 0.614439, 0.309547], [0.493003, 0.986007, 0.243203], [0.206997, 0.413993, 0.206797], [0.89278, 0.785561, 0.140453], [0.603863, 0.207726, 0.106492], [0.294321, 0.588643, 0.041805], [0.021417, 0.042834, 0.004346]], "elements": ["Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li"], "abc": [3.42989, 5.690943, 21.70558], "angles": [90.0, 90.0, 107.5384], "cartesian": false, "props": ["", "", "", "", "", "", "", "", "", ""]}, "energy": -17.84897876, "total_energy": -1.784897876, "forces": [[0.0, 0.00387929, 0.00568886], [0.0, 0.00283128, 0.0015246], [0.0, 0.00082862, -0.00432485], [-0.0, -0.00787343, -0.01381481], [0.0, 0.00490646, 0.00509929], [-0.0, -0.00490646, -0.00509929], [0.0, 0.00787343, 0.01381481], [-0.0, -0.00082862, 0.00432485], [-0.0, -0.00283128, -0.0015246], [-0.0, -0.00387929, -0.00568886]], "stresses": [[-4.79167146, 2e-08, 0.16699715], [2e-08, -1.2110241, -1.1e-07], [0.16699715, -1.1e-07, 0.0248045]]}, {"jid": "Li-267a", "atoms": {"lattice_mat": [[3.429887, 0.0, 0.0], [-1.714943, 5.426396, 0.0], [0.0, 0.0, 21.705585]], "coords": [[0.678583, 0.357166, 0.445654], [0.405679, 0.811357, 0.408195], [0.096137, 0.192274, 0.343508], [0.80722, 0.614439, 0.309547], [0.493003, 0.986007, 0.243203], [0.206997, 0.413993, 0.206797], [0.89278, 0.785561, 0.140453], [0.603863, 0.207726, 0.106492], [0.294321, 0.588643, 0.041805], [0.021417, 0.042834, 0.004346]], "elements": ["Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li", "Li"], "abc": [3.42989, 5.690943, 21.70558], "angles": [90.0, 90.0, 107.5384], "cartesian": false, "props": ["", "", "", "", "", "", "", "", "", ""]}, "energy": -17.84897876, "total_energy": -1.784897876, "forces": [[0.0, 0.00387929, 0.00568886], [0.0, 0.00283128, 0.0015246], [0.0, 0.00082862, -0.00432485], [-0.0, -0.00787343, -0.01381481], [0.0, 0.00490646, 0.00509929], [-0.0, -0.00490646, -0.00509929], [0.0, 0.00787343, 0.01381481], [-0.0, -0.00082862, 0.00432485], [-0.0, -0.00283128, -0.0015246], [-0.0, -0.00387929, -0.00568886]], "stresses": [[-4.79167146, 2e-08, 0.16699715], [2e-08, -1.2110241, -1.1e-07], [0.16699715, -1.1e-07, 0.0248045]]}, {"jid": "Li-268a", "atoms": {"lattice_mat": [[3.426817, 0.0, 0.0], [0.0, 3.426817, 0.0], [0.0, 0.068536, 3.426132]], "coords": [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], "elements": ["Li", "Li"], "abc": [3.42682, 3.42682, 3.426816], "angles": [88.8539, 90.0, 90.0], "cartesian": false, "props": ["", ""]}, "energy": -3.79728684, "total_energy": -1.89864342, "forces": [[-0.0, 0.0, 0.0], [0.0, -0.0, -0.0]], "stresses": [[1.57714994, 0.0, -0.39595669], [0.0, 1.59316895, 0.0], [-0.39595669, 0.0, 1.6090107]]}, {"jid": "Li-268a", "atoms": {"lattice_mat": [[3.426817, 0.0, 0.0], [0.0, 3.426817, 0.0], [0.0, 0.068536, 3.426132]], "coords": [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], "elements": ["Li", "Li"], "abc": [3.42682, 3.42682, 3.426816], "angles": [88.8539, 90.0, 90.0], "cartesian": false, "props": ["", ""]}, "energy": -3.79728684, "total_energy": -1.89864342, "forces": [[-0.0, 0.0, 0.0], [0.0, -0.0, -0.0]], "stresses": [[1.57714994, 0.0, -0.39595669], [0.0, 1.59316895, 0.0], [-0.39595669, 0.0, 1.6090107]]}, {"jid": "Li-269a", "atoms": {"lattice_mat": [[3.426817, 0.0, 0.0], [0.0, 3.40964, 0.0], [0.0, 0.0, 3.426817]], "coords": [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], "elements": ["Li", "Li"], "abc": [3.42682, 3.40964, 3.42682], "angles": [90.0, 90.0, 90.0], "cartesian": false, "props": ["", ""]}, "energy": -3.79758871, "total_energy": -1.898794355, "forces": [[0.0, -0.0, -0.0], [-0.0, 0.0, 0.0]], "stresses": [[2.25197257, 0.0, -0.0], [0.0, 2.37004078, 0.0], [-0.0, 0.0, 2.25197257]]}, {"jid": "Li-269a", "atoms": {"lattice_mat": [[3.426817, 0.0, 0.0], [0.0, 3.40964, 0.0], [0.0, 0.0, 3.426817]], "coords": [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], "elements": ["Li", "Li"], "abc": [3.42682, 3.40964, 3.42682], "angles": [90.0, 90.0, 90.0], "cartesian": false, "props": ["", ""]}, "energy": -3.79758871, "total_energy": -1.898794355, "forces": [[0.0, -0.0, -0.0], [-0.0, 0.0, 0.0]], "stresses": [[2.25197257, 0.0, -0.0], [0.0, 2.37004078, 0.0], [-0.0, 0.0, 2.25197257]]}, {"jid": "Li-270a", "atoms": {"lattice_mat": [[3.426817, 0.0, 0.0], [0.0, 3.426817, 0.0], [0.0, -0.034268, 3.426646]], "coords": [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], "elements": ["Li", "Li"], "abc": [3.42682, 3.42682, 3.426821], "angles": [90.573, 90.0, 90.0], "cartesian": false, "props": ["", ""]}, "energy": -3.79771335, "total_energy": -1.898856675, "forces": [[0.0, 0.0, 0.0], [0.0, -0.0, -0.0]], "stresses": [[1.51369181, 0.0, -0.94340362], [0.0, 1.53657934, 0.0], [-0.94340362, 0.0, 1.51771073]]}, {"jid": "Li-270a", "atoms": {"lattice_mat": [[3.426817, 0.0, 0.0], [0.0, 3.426817, 0.0], [0.0, -0.034268, 3.426646]], "coords": [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], "elements": ["Li", "Li"], "abc": [3.42682, 3.42682, 3.426821], "angles": [90.573, 90.0, 90.0], "cartesian": false, "props": ["", ""]}, "energy": -3.79771335, "total_energy": -1.898856675, "forces": [[0.0, 0.0, 0.0], [0.0, -0.0, -0.0]], "stresses": [[1.51369181, 0.0, -0.94340362], [0.0, 1.53657934, 0.0], [-0.94340362, 0.0, 1.51771073]]}] \ No newline at end of file diff --git a/alignn/examples/sample_data_ff/mlearn_data/all/prepare_mlearn.py b/alignn/examples/sample_data_ff/mlearn_data/all/prepare_mlearn.py new file mode 100644 index 00000000..c53a7800 --- /dev/null +++ b/alignn/examples/sample_data_ff/mlearn_data/all/prepare_mlearn.py @@ -0,0 +1,153 @@ +"""Module for generating mlearn dataset.""" +# for m in Ni Cu Mo Ge Si Li; +# do wget https://github.com/materialsvirtuallab +# /mlearn/raw/master/data/${m}/training.json +# ; mv training.json ${m}_train.json; done; +from jarvis.core.atoms import pmg_to_atoms +from jarvis.db.jsonutils import dumpjson +from jarvis.db.jsonutils import loadjson +from pymatgen.core.structure import Structure +from collections import defaultdict +import os +import numpy as np +from ase.stress import voigt_6_to_full_3x3_stress + +# Ref: https://github.com/materialsvirtuallab/mlearn + +url = "wget https://github.com/materialsvirtuallab/mlearn/raw/master/data/" +mlearn_dat = [] +els = ["Ni", "Cu", "Mo", "Ge", "Si", "Li"] +train_count = 0 +val_count = 0 +test_count = 0 +for ii in els: + print(ii) + name = ii + "_train.json" + if not os.path.exists(name): + cmd = url + ii + "/training.json -O " + ii + "_train.json" + os.system(cmd) + + data = loadjson(name) + cmd = "rm " + ii + "_train.json" + os.system(cmd) + train_structures = [d["structure"] for d in data] + train_energies = [d["outputs"]["energy"] for d in data] + train_forces = [d["outputs"]["forces"] for d in data] + train_stresses = np.array( + voigt_6_to_full_3x3_stress( + np.array([d["outputs"]["virial_stress"] for d in data]) + ) + ).tolist() + print("train_structures", train_energies) + name = ii + "_test.json" + if not os.path.exists(name): + cmd = url + ii + "/test.json -O " + ii + "_test.json" + os.system(cmd) + data = loadjson(name) + cmd = "rm " + ii + "_test.json" + os.system(cmd) + test_structures = [d["structure"] for d in data] + test_energies = [d["outputs"]["energy"] for d in data] + test_forces = [d["outputs"]["forces"] for d in data] + # test_stresses = [d["outputs"]["virial_stress"] for d in data] + test_stresses = np.array( + voigt_6_to_full_3x3_stress( + np.array([d["outputs"]["virial_stress"] for d in data]) + ) + ).tolist() + + # For ALIGNN-FF + mem = [] + count = 0 + train_e = defaultdict() + test_e = defaultdict() + train_f = defaultdict() + test_f = defaultdict() + train_s = defaultdict() + test_s = defaultdict() + + for i, j, k, z in zip( + train_structures, train_energies, train_forces, train_stresses + ): + k = np.array(k) + z = np.array(z) + info = {} + atoms = pmg_to_atoms(Structure.from_dict(i)) + count += 1 + jid = ii + "-" + str(count) + info["jid"] = jid + info["atoms"] = atoms.to_dict() + info["energy"] = j # / atoms.num_atoms + info["total_energy"] = j / atoms.num_atoms + info["forces"] = k.tolist() + info["stresses"] = z.tolist() + mem.append(info) + mlearn_dat.append(info) + # train[jid]=json.dumps(info) + train_e[jid] = j + train_f[jid] = ";".join(map(str, k.flatten())) + train_s[jid] = ";".join(map(str, z.flatten())) + train_count += 1 + for i, j, k, z in zip( + test_structures, test_energies, test_forces, test_stresses + ): + k = np.array(k) + z = np.array(z) + info = {} + count += 1 + jid = ii + "-" + str(count) + info["jid"] = ii + "-" + str(count) + # atoms = pmg_to_atoms(i) + atoms = pmg_to_atoms(Structure.from_dict(i)) + info["atoms"] = atoms.to_dict() + info["energy"] = j # / atoms.num_atoms + info["total_energy"] = j / atoms.num_atoms + info["forces"] = k.tolist() + info["stresses"] = z.tolist() + # val[jid]=json.dumps(info) + mem.append(info) + mlearn_dat.append(info) + info["jid"] = info["jid"] + "a" + mlearn_dat.append(info) # For val set + test_e[jid] = j + test_f[jid] = ";".join(map(str, k.flatten())) + test_s[jid] = ";".join(map(str, z.flatten())) + test_count += 1 + print(len(mem), len(train_structures), len(test_structures)) + dat = {} + dat["train"] = train_e + dat["test"] = test_e + fname = "mlearn_" + ii + "_energy.json" + dumpjson(data=dat, filename=fname) + cmd = "zip " + fname + ".zip " + fname + os.system(cmd) + cmd = "rm " + fname + os.system(cmd) + + dat = {} + dat["train"] = train_f + dat["test"] = test_f + fname = "mlearn_" + ii + "_forces.json" + dumpjson(data=dat, filename=fname) + cmd = "zip " + fname + ".zip " + fname + os.system(cmd) + cmd = "rm " + fname + os.system(cmd) + + dat = {} + dat["train"] = train_s + dat["test"] = test_s + fname = "mlearn_" + ii + "_stresses.json" + dumpjson(data=dat, filename=fname) + cmd = "zip " + fname + ".zip " + fname + os.system(cmd) + cmd = "rm " + fname + os.system(cmd) +# For Figshare +print("train", train_count) +print("test", test_count) +dumpjson(data=mlearn_dat, filename="mlearn.json") +cmd = "zip mlearn.json.zip mlearn.json" +os.system(cmd) +cmd = "rm mlearn.json" +# os.system(cmd) diff --git a/alignn/ff/ff.py b/alignn/ff/ff.py index 0fb4b6c2..e511ec41 100644 --- a/alignn/ff/ff.py +++ b/alignn/ff/ff.py @@ -67,6 +67,15 @@ def default_path(): return dpath +def revised_path(): + """Get defaukt model path.""" + dpath = os.path.abspath( + str(os.path.join(os.path.dirname(__file__), "revised")) + ) + print("model_path", dpath) + return dpath + + # print("default_model_path", default_model_path) @@ -178,14 +187,14 @@ def calculate(self, atoms, properties=None, system_changes=None): mult = num_atoms else: mult = 1 - + # print('result["stresses"]',result["stresses"],result["stresses"].shape) self.results = { "energy": result["out"].detach().cpu().numpy() * num_atoms, "forces": result["grad"].detach().cpu().numpy() * mult * self.force_multiplier, "stress": full_3x3_to_voigt_6_stress( - result["stress"].detach().cpu().numpy() + result["stresses"][:3].reshape(3, 3).detach().cpu().numpy() ) * self.stress_wt # * num_atoms, diff --git a/alignn/ff/revised/__init__.py b/alignn/ff/revised/__init__.py new file mode 100644 index 00000000..e0820a7b --- /dev/null +++ b/alignn/ff/revised/__init__.py @@ -0,0 +1 @@ +"""Provide revised force-field file.""" diff --git a/alignn/ff/revised/best_model.pt b/alignn/ff/revised/best_model.pt new file mode 100644 index 00000000..95716994 Binary files /dev/null and b/alignn/ff/revised/best_model.pt differ diff --git a/alignn/ff/revised/config.json b/alignn/ff/revised/config.json new file mode 100644 index 00000000..56ee8331 --- /dev/null +++ b/alignn/ff/revised/config.json @@ -0,0 +1,64 @@ +{ + "version": "112bbedebdaecf59fb18e11c929080fb2f358246", + "dataset": "user_data", + "target": "target", + "atom_features": "cgcnn", + "neighbor_strategy": "k-nearest", + "id_tag": "jid", + "random_seed": 123, + "classification_threshold": null, + "n_val": null, + "n_test": null, + "n_train": null, + "train_ratio": 0.9, + "val_ratio": 0.05, + "test_ratio": 0.05, + "target_multiplication_factor": null, + "epochs": 100, + "batch_size": 16, + "weight_decay": 1e-05, + "learning_rate": 0.001, + "filename": "sample", + "warmup_steps": 2000, + "criterion": "l1", + "optimizer": "adamw", + "scheduler": "onecycle", + "pin_memory": false, + "save_dataloader": false, + "write_checkpoint": true, + "write_predictions": true, + "store_outputs": false, + "progress": true, + "log_tensorboard": false, + "standard_scalar_and_pca": false, + "use_canonize": false, + "num_workers": 0, + "cutoff": 8.0, + "max_neighbors": 12, + "keep_data_order": false, + "normalize_graph_level_loss": false, + "distributed": false, + "n_early_stopping": null, + "output_dir": "out_continue", + "model": { + "name": "alignn_atomwise", + "alignn_layers": 4, + "gcn_layers": 4, + "atom_input_features": 92, + "edge_input_features": 80, + "triplet_input_features": 40, + "embedding_features": 64, + "hidden_features": 256, + "output_features": 1, + "grad_multiplier": -1, + "calculate_gradient": true, + "atomwise_output_features": 0, + "graphwise_weight": 1.0, + "gradwise_weight": 10.0, + "stresswise_weight": 0.0, + "atomwise_weight": 0.0, + "link": "identity", + "zero_inflated": false, + "classification": false + } +} diff --git a/alignn/graphs.py b/alignn/graphs.py index 83c924fb..1857027a 100644 --- a/alignn/graphs.py +++ b/alignn/graphs.py @@ -7,6 +7,7 @@ from collections import OrderedDict from jarvis.analysis.structure.neighbors import NeighborsAnalysis from jarvis.core.specie import chem_data, get_node_attributes +import math # from jarvis.core.atoms import Atoms from collections import defaultdict @@ -158,6 +159,68 @@ def build_undirected_edgedata( return u, v, r +### +def radius_graph( + atoms=None, + cutoff=5, + bond_tol=0.5, + id=None, + atol=1e-5, +): + """Construct edge list for radius graph.""" + cart_coords = torch.tensor(atoms.cart_coords).type( + torch.get_default_dtype() + ) + frac_coords = torch.tensor(atoms.frac_coords).type( + torch.get_default_dtype() + ) + lattice_mat = torch.tensor(atoms.lattice_mat).type( + torch.get_default_dtype() + ) + # elements = atoms.elements + X_src = cart_coords + num_atoms = X_src.shape[0] + # determine how many supercells are needed for the cutoff radius + recp = 2 * math.pi * torch.linalg.inv(lattice_mat).T + recp_len = torch.tensor( + [i for i in (torch.sqrt(torch.sum(recp**2, dim=1)))] + ) + maxr = torch.ceil((cutoff + bond_tol) * recp_len / (2 * math.pi)) + nmin = torch.floor(torch.min(frac_coords, dim=0)[0]) - maxr + nmax = torch.ceil(torch.max(frac_coords, dim=0)[0]) + maxr + # construct the supercell index list + + all_ranges = [ + torch.arange(x, y, dtype=torch.get_default_dtype()) + for x, y in zip(nmin, nmax) + ] + cell_images = torch.cartesian_prod(*all_ranges) + + # tile periodic images into X_dst + # index id_dst into X_dst maps to atom id as id_dest % num_atoms + X_dst = (cell_images @ lattice_mat)[:, None, :] + X_src + X_dst = X_dst.reshape(-1, 3) + + # pairwise distances between atoms in (0,0,0) cell + # and atoms in all periodic image + dist = torch.cdist(X_src, X_dst) + + neighbor_mask = torch.bitwise_and( + dist <= cutoff, + ~torch.isclose( + dist, torch.tensor([0]).type(torch.get_default_dtype()), atol=atol + ), + ) + # get node indices for edgelist from neighbor mask + u, v = torch.where(neighbor_mask) + + r = (X_dst[v] - X_src[u]).float() + return u, v % num_atoms, r + + +### + + class Graph(object): """Generate a graph object.""" @@ -212,12 +275,15 @@ def atom_dgl_multigraph( id=id, use_canonize=use_canonize, ) + u, v, r = build_undirected_edgedata(atoms, edges) + elif neighbor_strategy == "radius_graph": + u, v, r = radius_graph(atoms, cutoff=cutoff) else: raise ValueError("Not implemented yet", neighbor_strategy) # elif neighbor_strategy == "voronoi": # edges = voronoi_edges(structure) - u, v, r = build_undirected_edgedata(atoms, edges) + # u, v, r = build_undirected_edgedata(atoms, edges) # build up atom attribute tensor sps_features = [] diff --git a/alignn/models/alignn_atomwise.py b/alignn/models/alignn_atomwise.py index bc60c73d..a121b985 100644 --- a/alignn/models/alignn_atomwise.py +++ b/alignn/models/alignn_atomwise.py @@ -45,7 +45,11 @@ class ALIGNNAtomWiseConfig(BaseSettings): zero_inflated: bool = False classification: bool = False force_mult_natoms: bool = False + energy_mult_natoms: bool = False include_pos_deriv: bool = False + use_cutoff_function: bool = False + inner_cutoff: float = 4 # Ansgtrom + stress_multiplier: float = 1 # batch_stress: bool = False class Config: @@ -54,6 +58,23 @@ class Config: env_prefix = "jv_model" +def cutoff_function_based_edges(r, inner_cutoff=4): + """Apply smooth cutoff to pairwise interactions + + r: bond lengths + inner_cutoff: cutoff radius + + inside cutoff radius, apply smooth cutoff envelope + outside cutoff radius: hard zeros + """ + ratio = r / inner_cutoff + return torch.where( + ratio <= 1, + 1 - 6 * ratio**5 + 15 * ratio**4 - 10 * ratio**3, + torch.zeros_like(r), + ) + + class EdgeGatedGraphConv(nn.Module): """Edge gated graph convolution from arxiv:1711.07553. @@ -213,8 +234,8 @@ def __init__( self.config = config if self.config.gradwise_weight == 0: self.config.calculate_gradient = False - if self.config.atomwise_weight == 0: - self.config.atomwise_output_features = None + # if self.config.atomwise_weight == 0: + # self.config.atomwise_output_features = None self.atom_embedding = MLPLayer( config.atom_input_features, config.hidden_features ) @@ -257,7 +278,8 @@ def __init__( ) self.readout = AvgPooling() - if config.atomwise_output_features is not None: + if config.atomwise_output_features > 0: + # if config.atomwise_output_features is not None: self.fc_atomwise = nn.Linear( config.hidden_features, config.atomwise_output_features ) @@ -308,6 +330,10 @@ def forward( # r = g.edata["r"].clone().detach().requires_grad_(True) bondlength = torch.norm(r, dim=1) + if self.config.use_cutoff_function: + bondlength = cutoff_function_based_edges( + bondlength, inner_cutoff=self.config.inner_cutoff + ) y = self.edge_embedding(bondlength) # ALIGNN updates: update node, edge, triplet features @@ -325,7 +351,8 @@ def forward( out = torch.squeeze(out) atomwise_pred = torch.empty(1) if ( - self.config.atomwise_output_features is not None + self.config.atomwise_output_features > 0 + # self.config.atomwise_output_features is not None and self.config.atomwise_weight != 0 ): atomwise_pred = self.fc_atomwise(x) @@ -347,10 +374,14 @@ def forward( dx = [g.ndata["coords"], r] else: dx = r + if self.config.energy_mult_natoms: + en_out = out * g.num_nodes() + else: + en_out = out dy = ( self.config.grad_multiplier * grad( - out, + en_out, dx, grad_outputs=torch.ones_like(out), create_graph=create_graph, @@ -371,15 +402,15 @@ def forward( # print('dy',dy.shape) # print('r',r.shape) # print('g.edata["V"]',g.edata["V"].shape) - stress = ( - -1 - * 160.21766208 - * ( - torch.matmul(r.T, dy) - # / (2 * g.edata["V"]) - / (2 * g.ndata["V"][0]) - ) - ) + # stress = ( + # -1 + # * 160.21766208 + # * ( + # torch.matmul(r.T, dy) + # # / (2 * g.edata["V"]) + # / (2 * g.ndata["V"][0]) + # ) + # ) # print("stress1", stress, stress.shape) # print("g.batch_size", g.batch_size) stresses = [] @@ -400,11 +431,11 @@ def forward( count_edge = count_edge + num_edges num_nodes = g.batch_num_nodes()[graph_id] count_node = count_node + num_nodes - # print("stresses.append", stresses[-1]) + # print("stresses.append",stresses[-1],stresses[-1].shape) for n in range(num_nodes): stresses.append(st) # stress = (stresses) - stress = torch.cat(stresses) + stress = self.config.stress_multiplier * torch.cat(stresses) # print("stress2", stress, stress.shape) # virial = ( # 160.21766208 @@ -419,7 +450,7 @@ def forward( out = self.softmax(out) result["out"] = out result["grad"] = gradient - result["stress"] = stress + result["stresses"] = stress result["atomwise_pred"] = atomwise_pred # print(result) return result diff --git a/alignn/tests/test_alignn_ff.py b/alignn/tests/test_alignn_ff.py index 8b42b08b..bb2fbc81 100644 --- a/alignn/tests/test_alignn_ff.py +++ b/alignn/tests/test_alignn_ff.py @@ -8,20 +8,28 @@ ForceField, get_interface_energy, ) +from alignn.graphs import Graph def test_alignnff(): atoms = JAtoms.from_dict(get_jid_data()["atoms"]) + atoms = JAtoms.from_dict( + get_jid_data(dataset="dft_3d", jid="JVASP-32")["atoms"] + ) + old_g = Graph.from_atoms(atoms=atoms) + g, lg = Graph.atom_dgl_multigraph(atoms) + g, lg = Graph.atom_dgl_multigraph(atoms, neighbor_strategy="radius_graph") model_path = default_path() print("model_path", model_path) + print("atoms", atoms) # atoms = atoms.make_supercell_matrix([2, 2, 2]) # atoms=atoms.strain_atoms(.05) # print(atoms) ev = ev_curve(atoms=atoms, model_path=model_path) - surf = surface_energy(atoms=atoms, model_path=model_path) - print(surf) - vac = vacancy_formation(atoms=atoms, model_path=model_path) - print(vac) + # surf = surface_energy(atoms=atoms, model_path=model_path) + # print('surf',surf) + # vac = vacancy_formation(atoms=atoms, model_path=model_path) + # print('vac',vac) ff = ForceField( jarvis_atoms=atoms, @@ -50,3 +58,6 @@ def test_alignnff(): subs_thickness=10 # film_atoms=atoms_al, subs_atoms=atoms_al2o3, model_path=model_path ) + + +# test_alignnff() diff --git a/alignn/tests/test_prop.py b/alignn/tests/test_prop.py index e4e5e77e..307897db 100644 --- a/alignn/tests/test_prop.py +++ b/alignn/tests/test_prop.py @@ -8,6 +8,10 @@ from sklearn.metrics import mean_absolute_error import os from jarvis.core.atoms import Atoms +from alignn.train_folder import train_for_folder +from alignn.train_folder_ff import train_for_folder as train_for_folder_ff +from jarvis.db.figshare import get_jid_data +from alignn.ff.ff import AlignnAtomwiseCalculator, default_path, revised_path plt.switch_backend("agg") @@ -30,17 +34,19 @@ "optimizer": "adamw", "scheduler": "onecycle", "num_workers": 4, - "model": {"name": "alignn",}, + "model": { + "name": "alignn", + }, } -def test_runtime_training(): - cmd1 = 'python alignn/train_folder.py --root_dir "alignn/examples/sample_data" --config "alignn/examples/sample_data/config_example.json"' - os.system(cmd1) - cmd2 = 'python alignn/train_folder.py --root_dir "alignn/examples/sample_data" --classification_threshold 0.01 --config "alignn/examples/sample_data/config_example.json"' - os.system(cmd2) - cmd3 = 'python alignn/train_folder.py --root_dir "alignn/examples/sample_data_multi_prop" --config "alignn/examples/sample_data/config_example.json"' - os.system(cmd3) +# def test_runtime_training(): +# cmd1 = 'python alignn/train_folder.py --root_dir "alignn/examples/sample_data" --config "alignn/examples/sample_data/config_example.json"' +# os.system(cmd1) +# cmd2 = 'python alignn/train_folder.py --root_dir "alignn/examples/sample_data" --classification_threshold 0.01 --config "alignn/examples/sample_data/config_example.json"' +# os.system(cmd2) +# cmd3 = 'python alignn/train_folder.py --root_dir "alignn/examples/sample_data_multi_prop" --config "alignn/examples/sample_data/config_example.json"' +# os.system(cmd3) def test_minor_configs(): @@ -236,8 +242,78 @@ def test_pretrained(): get_multiple_predictions(atoms_array=[Si, Si]) +def test_alignn_train(): + root_dir = os.path.abspath( + os.path.join(os.path.dirname(__file__), "../examples/sample_data/") + ) + config = os.path.abspath( + os.path.join( + os.path.dirname(__file__), + "../examples/sample_data/config_example.json", + ) + ) + train_for_folder(root_dir=root_dir, config_name=config) + + root_dir = os.path.abspath( + os.path.join( + os.path.dirname(__file__), "../examples/sample_data_multi_prop/" + ) + ) + config = os.path.abspath( + os.path.join( + os.path.dirname(__file__), + "../examples/sample_data/config_example.json", + ) + ) + train_for_folder(root_dir=root_dir, config_name=config) + + root_dir = os.path.abspath( + os.path.join(os.path.dirname(__file__), "../examples/sample_data/") + ) + config = os.path.abspath( + os.path.join( + os.path.dirname(__file__), + "../examples/sample_data/config_example.json", + ) + ) + train_for_folder( + root_dir=root_dir, config_name=config, classification_threshold=0.01 + ) + + root_dir = os.path.abspath( + os.path.join(os.path.dirname(__file__), "../examples/sample_data_ff/") + ) + config = os.path.abspath( + os.path.join( + os.path.dirname(__file__), + "../examples/sample_data_ff/config_example_atomwise.json", + ) + ) + train_for_folder_ff(root_dir=root_dir, config_name=config) + + +def test_calculator(): + atoms = Atoms.from_dict( + get_jid_data(dataset="dft_3d", jid="JVASP-32")["atoms"] + ) + model_path = default_path() + calc = AlignnAtomwiseCalculator(path=model_path) + ase_atoms = atoms.ase_converter() + ase_atoms.calc = calc + energy = ase_atoms.get_potential_energy() + forces = ase_atoms.get_forces() + stress = ase_atoms.get_stress() + print("round(energy,3)", round(energy, 3)) + print("max(forces.flatten()),3)", max(forces.flatten())) + print("max(stress.flatten()),3)", max(stress.flatten())) + # assert round(energy,3)==round(-60.954999923706055,3) + # assert round(max(forces.flatten()),2)==round(0.08332983,2) + # assert round(max(stress.flatten()),2)==round(0.002801671050217803,2) + + # test_minor_configs() # test_pretrained() # test_runtime_training() - +# test_alignn_train() # test_models() +# test_calculator() diff --git a/alignn/train.py b/alignn/train.py index c455b112..27598798 100644 --- a/alignn/train.py +++ b/alignn/train.py @@ -393,7 +393,12 @@ def get_batch_errors(dat=[]): # - result["out"].cpu().detach().numpy() # ) # ) - + # print("target_out", info["target_out"][0]) + # print("pred_out", info["pred_out"][0]) + # print( + # "config.model.atomwise_output_features", + # config.model.atomwise_output_features, + # ) if ( config.model.atomwise_output_features > 0 # config.model.atomwise_output_features is not None @@ -433,30 +438,38 @@ def get_batch_errors(dat=[]): # - result["grad"].cpu().detach().numpy() # ) # ) + # print("target_grad", info["target_grad"][0]) + # print("pred_grad", info["pred_grad"][0]) if config.model.stresswise_weight != 0: - # print('result["stress"]',result["stress"],result["stress"].shape) - # print('dats[0].ndata["stresses"]') + # print( + # 'result["stress"]', + # result["stresses"], + # result["stresses"].shape, + # ) + # print( + # 'dats[0].ndata["stresses"]', + # torch.cat(tuple(dats[0].ndata["stresses"])), + # dats[0].ndata["stresses"].shape, + # ) # ,torch.cat(dats[0].ndata["stresses"]), + # torch.cat(dats[0].ndata["stresses"]).shape) + # print('result["stresses"]',result["stresses"],result["stresses"].shape) # print(dats[0].ndata["stresses"],dats[0].ndata["stresses"].shape) loss4 = config.model.stresswise_weight * criterion( - torch.flatten(result["stress"].to(device)), - # (dats[0].ndata["stresses"]).to(device), - torch.flatten(dats[0].ndata["stresses"]).to(device), - # torch.flatten(torch.cat(dats[0].ndata["stresses"])).to(device), - # dats[0].ndata["stresses"][0].to(device), + (result["stresses"]).to(device), + torch.cat(tuple(dats[0].ndata["stresses"])).to(device), ) info["target_stress"] = ( - dats[0] - .ndata["stresses"] + torch.cat(tuple(dats[0].ndata["stresses"])) .cpu() .numpy() .tolist() # dats[0].ndata["stresses"][0].cpu().numpy().tolist() ) info["pred_stress"] = ( - result["stress"].cpu().detach().numpy().tolist() + result["stresses"].cpu().detach().numpy().tolist() ) - # print ("target_stress",info["target_stress"]) - # print ("pred_stress",info["pred_stress"]) + # print("target_stress", info["target_stress"][0]) + # print("pred_stress", info["pred_stress"][0]) train_result.append(info) loss = loss1 + loss2 + loss3 + loss4 loss.backward() @@ -514,6 +527,7 @@ def get_batch_errors(dat=[]): info["pred_out"] = ( result["out"].cpu().detach().numpy().tolist() ) + if ( config.model.atomwise_output_features > 0 and config.model.atomwise_weight != 0 @@ -545,17 +559,23 @@ def get_batch_errors(dat=[]): # dats[0].ndata["stresses"][0].to(device), # ) loss4 = config.model.stresswise_weight * criterion( - torch.flatten(result["stress"].to(device)), + # torch.flatten(result["stress"].to(device)), # (dats[0].ndata["stresses"]).to(device), - torch.flatten(dats[0].ndata["stresses"]).to(device), + # torch.flatten(dats[0].ndata["stresses"]).to(device), # torch.flatten(torch.cat(dats[0].ndata["stresses"])).to(device), # dats[0].ndata["stresses"][0].to(device), + (result["stresses"]).to(device), + torch.cat(tuple(dats[0].ndata["stresses"])).to(device), ) info["target_stress"] = ( - dats[0].ndata["stresses"][0].cpu().numpy().tolist() + torch.cat(tuple(dats[0].ndata["stresses"])) + .cpu() + .numpy() + .tolist() + # dats[0].ndata["stresses"][0].cpu().numpy().tolist() ) info["pred_stress"] = ( - result["stress"].cpu().detach().numpy().tolist() + result["stresses"].cpu().detach().numpy().tolist() ) loss = loss1 + loss2 + loss3 + loss4 val_result.append(info) @@ -648,9 +668,11 @@ def get_batch_errors(dat=[]): ) if config.model.stresswise_weight != 0: loss4 = config.model.stresswise_weight * criterion( - torch.flatten(result["stress"].to(device)), + # torch.flatten(result["stress"].to(device)), # (dats[0].ndata["stresses"]).to(device), - torch.flatten(dats[0].ndata["stresses"]).to(device), + # torch.flatten(dats[0].ndata["stresses"]).to(device), + result["stresses"].to(device), + torch.cat(tuple(dats[0].ndata["stresses"])).to(device), # torch.flatten(torch.cat(dats[0].ndata["stresses"])).to(device), # dats[0].ndata["stresses"][0].to(device), ) @@ -659,10 +681,13 @@ def get_batch_errors(dat=[]): # dats[0].ndata["stresses"].to(device), # ) info["target_stress"] = ( - dats[0].ndata["stresses"][0].cpu().numpy().tolist() + torch.cat(tuple(dats[0].ndata["stresses"])) + .cpu() + .numpy() + .tolist() ) info["pred_stress"] = ( - result["stress"].cpu().detach().numpy().tolist() + result["stresses"].cpu().detach().numpy().tolist() ) test_result.append(info) loss = loss1 + loss2 + loss3 + loss4 diff --git a/setup.py b/setup.py index 152daf44..69cc5e54 100644 --- a/setup.py +++ b/setup.py @@ -10,7 +10,7 @@ setuptools.setup( name="alignn", - version="2023.04.30", + version="2023.05.03", author="Kamal Choudhary, Brian DeCost", author_email="kamal.choudhary@nist.gov", description="alignn", @@ -33,7 +33,10 @@ "ase", # "dgl-cu101>=0.6.0", ], - package_data={"alignn.ff": ["best_model.pt", "config.json"]}, + package_data={ + "alignn.ff": ["best_model.pt", "config.json"], + "alignn.ff.revised": ["best_model.pt", "config.json"], + }, scripts=[ "alignn/pretrained.py", "alignn/train_folder.py",