Merge pull request #45 from usnistgov/develop

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usnistgov · Nov 15, 2021 · b5e8f50 · b5e8f50
2 parents 7c2bd37 + 484b755
commit b5e8f50
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Showing 9 changed files with 154 additions and 64 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -38,4 +38,8 @@ jobs:
         coverage report -m
         codecov
         codecov --token="85bd9c5d-9e55-4f6d-bd69-350ee5e3bb41"
-        # alignn_train_folder.py --root_dir "alignn/examples/sample_data" --config "alignn/examples/sample_data/config_example.json" --output_dir=temp
+        echo 'Train folder'
+        train_folder.py -h 
+        echo 'Pre-trained models'
+        pretrained.py -h
+        #train_folder.py --root_dir "alignn/examples/sample_data" --config "alignn/examples/sample_data/config_example.json" --output_dir=temp
diff --git a/alignn/__init__.py b/alignn/__init__.py
@@ -1,2 +1,2 @@
 """Version number."""
-__version__ = "2021.11.13"
+__version__ = "2021.11.14"
diff --git a/alignn/config.py b/alignn/config.py
@@ -19,9 +19,13 @@
 
 # from typing import List
 
-VERSION = (
-    subprocess.check_output(["git", "rev-parse", "HEAD"]).decode().strip()
-)
+try:
+    VERSION = (
+        subprocess.check_output(["git", "rev-parse", "HEAD"]).decode().strip()
+    )
+except Exception as exp:
+    VERSION = "NA"
+    pass
 
 
 FEATURESET_SIZE = {"basic": 11, "atomic_number": 1, "cfid": 438, "cgcnn": 92}

diff --git a/alignn/pretrained.py b/alignn/pretrained.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 """Module to download and load pre-trained ALIGNN models."""
 import requests
 import os
@@ -12,11 +14,119 @@
 from jarvis.core.atoms import Atoms
 from jarvis.core.graphs import Graph
 
-all_models = loadjson(
-    str(os.path.join(os.path.dirname(__file__), "pretrained_models.json"))
-)
-
-
+# Name of the model, figshare link, number of outouts
+all_models = {
+    "jv_formation_energy_peratom_alignn": [
+        "https://figshare.com/ndownloader/files/31458679",
+        1,
+    ],
+    "jv_optb88vdw_total_energy_alignn": [
+        "https://figshare.com/ndownloader/files/31459642",
+        1,
+    ],
+    "jv_optb88vdw_bandgap_alignn": [
+        "https://figshare.com/ndownloader/files/31459636",
+        1,
+    ],
+    "jv_mbj_bandgap_alignn": [
+        "https://figshare.com/ndownloader/files/31458694",
+        1,
+    ],
+    "jv_spillage_alignn": [
+        "https://figshare.com/ndownloader/files/31458736",
+        1,
+    ],
+    "jv_slme_alignn": ["https://figshare.com/ndownloader/files/31458727", 1],
+    "jv_bulk_modulus_kv_alignn": [
+        "https://figshare.com/ndownloader/files/31458649",
+        1,
+    ],
+    "jv_shear_modulus_gv_alignn": [
+        "https://figshare.com/ndownloader/files/31458724",
+        1,
+    ],
+    "jv_n-Seebeck_alignn": [
+        "https://figshare.com/ndownloader/files/31458718",
+        1,
+    ],
+    "jv_n-powerfact_alignn": [
+        "https://figshare.com/ndownloader/files/31458712",
+        1,
+    ],
+    "jv_magmom_oszicar_alignn": [
+        "https://figshare.com/ndownloader/files/31458685",
+        1,
+    ],
+    "jv_kpoint_length_unit_alignn": [
+        "https://figshare.com/ndownloader/files/31458682",
+        1,
+    ],
+    "jv_avg_elec_mass_alignn": [
+        "https://figshare.com/ndownloader/files/31458643",
+        1,
+    ],
+    "jv_avg_hole_mass_alignn": [
+        "https://figshare.com/ndownloader/files/31458646",
+        1,
+    ],
+    "jv_epsx_alignn": ["https://figshare.com/ndownloader/files/31458667", 1],
+    "jv_mepsx_alignn": ["https://figshare.com/ndownloader/files/31458703", 1],
+    "jv_max_efg_alignn": [
+        "https://figshare.com/ndownloader/files/31458691",
+        1,
+    ],
+    "jv_ehull_alignn": ["https://figshare.com/ndownloader/files/31458658", 1],
+    "jv_dfpt_piezo_max_dielectric_alignn": [
+        "https://figshare.com/ndownloader/files/31458652",
+        1,
+    ],
+    "jv_dfpt_piezo_max_dij_alignn": [
+        "https://figshare.com/ndownloader/files/31458655",
+        1,
+    ],
+    "jv_exfoliation_energy_alignn": [
+        "https://figshare.com/ndownloader/files/31458676",
+        1,
+    ],
+    "mp_e_form_alignnn": [
+        "https://figshare.com/ndownloader/files/31458811",
+        1,
+    ],
+    "mp_gappbe_alignnn": [
+        "https://figshare.com/ndownloader/files/31458814",
+        1,
+    ],
+    "qm9_U0_alignn": ["https://figshare.com/ndownloader/files/31459054", 1],
+    "qm9_U_alignn": ["https://figshare.com/ndownloader/files/31459051", 1],
+    "qm9_alpha_alignn": ["https://figshare.com/ndownloader/files/31459027", 1],
+    "qm9_gap_alignn": ["https://figshare.com/ndownloader/files/31459036", 1],
+    "qm9_G_alignn": ["https://figshare.com/ndownloader/files/31459033", 1],
+    "qm9_HOMO_alignn": ["https://figshare.com/ndownloader/files/31459042", 1],
+    "qm9_LUMO_alignn": ["https://figshare.com/ndownloader/files/31459045", 1],
+    "qm9_ZPVE_alignn": ["https://figshare.com/ndownloader/files/31459057", 1],
+    "hmof_co2_absp_alignnn": [
+        "https://figshare.com/ndownloader/files/31459198",
+        5,
+    ],
+    "hmof_max_co2_adsp_alignnn": [
+        "https://figshare.com/ndownloader/files/31459207",
+        1,
+    ],
+    "hmof_surface_area_m2g_alignnn": [
+        "https://figshare.com/ndownloader/files/31459222",
+        1,
+    ],
+    "hmof_surface_area_m2cm3_alignnn": [
+        "https://figshare.com/ndownloader/files/31459219",
+        1,
+    ],
+    "hmof_pld_alignnn": ["https://figshare.com/ndownloader/files/31459216", 1],
+    "hmof_lcd_alignnn": ["https://figshare.com/ndownloader/files/31459201", 1],
+    "hmof_void_fraction_alignnn": [
+        "https://figshare.com/ndownloader/files/31459228",
+        1,
+    ],
+}
 parser = argparse.ArgumentParser(
     description="Atomistic Line Graph Neural Network Pretrained Models"
 )

diff --git a/alignn/pretrained_models.json b/alignn/pretrained_models.json
diff --git a/alignn/tests/test_prop.py b/alignn/tests/test_prop.py
@@ -36,14 +36,23 @@
 
 
 def test_runtime_training():
-    cmd1 = 'python alignn/scripts/train_folder.py --root_dir "alignn/examples/sample_data" --config "alignn/examples/sample_data/config_example.json"'
+    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/scripts/train_folder.py --root_dir "alignn/examples/sample_data" --classification_threshold 0.01 --config "alignn/examples/sample_data/config_example.json"'
+    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/scripts/train_folder.py --root_dir "alignn/examples/sample_data_multi_prop" --config "alignn/examples/sample_data/config_example.json"'
+    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():
+    tmp = config
+    # tmp["log_tensorboard"] = True
+    tmp["n_early_stopping"] = 2
+    tmp["model"]["name"] = "alignn"
+    config["write_predictions"] = True
+    result = train_dgl(tmp)
+
+
 def test_models():
     """Test CGCNN end to end training."""
     config["model"]["name"] = "dense_alignn"
@@ -57,6 +66,7 @@ def test_models():
     print()
     print()
 
+    config["write_predictions"] = True
     config["model"]["name"] = "alignn"
     t1 = time.time()
     result = train_dgl(config)
@@ -172,7 +182,7 @@ def test_models():
 
     config["model"]["name"] = "alignn_cgcnn"
     config["write_predictions"] = False
-    config["save_dataloader"] = False
+    config["save_dataloader"] = True
     config["classification_threshold"] = 0.0
     t1 = time.time()
     result = train_dgl(config)
@@ -226,6 +236,7 @@ def test_pretrained():
     os.system(cmd1)
 
 
+# test_minor_configs()
 # test_pretrained()
 # test_runtime_training()
 

diff --git a/alignn/train.py b/alignn/train.py
@@ -11,10 +11,15 @@
 from typing import Any, Dict, Union
 import ignite
 import torch
+
 from ignite.contrib.handlers import TensorboardLogger
-from ignite.handlers.stores import EpochOutputStore
+try:
+    from ignite.contrib.handlers.stores import EpochOutputStore
+    # For different version of pytorch-ignite
+except Exception as exp:
+    from ignite.handlers.stores import EpochOutputStore
 
-# from ignite.contrib.handlers.stores import EpochOutputStore
+    pass
 from ignite.handlers import EarlyStopping
 from ignite.contrib.handlers.tensorboard_logger import (
     global_step_from_engine,

diff --git a/alignn/scripts/train_folder.py → alignn/train_folder.py b/alignn/scripts/train_folder.py → alignn/train_folder.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 """Module to train for a folder with formatted dataset."""
 import csv
 import os

diff --git a/setup.py b/setup.py
@@ -10,7 +10,7 @@
 
 setuptools.setup(
     name="alignn",
-    version="2021.11.13",
+    version="2021.11.14",
     author="Kamal Choudhary, Brian DeCost",
     author_email="[email protected]",
     description="alignn",
@@ -33,12 +33,7 @@
         "pyparsing>=2.2.1,<3",
     ],
     # scripts=["alignn/alignn_train_folder.py"],
-    entry_points={
-        "console_scripts": [
-            "train_folder=alignn.script.train_folder"
-            "pretrained=alignn.pretrained"
-        ],
-    },
+    scripts=['alignn/pretrained.py','alignn/train_folder.py'],
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/usnistgov/alignn",