[WIP] Implementation of 2D crystal former

.gitignore

@@ -2,3 +2,4 @@
 job*
 *.out
 __pycache__/
+./mp_20/*.csv

Makefile

@@ -0,0 +1,20 @@
+default: test
+
+.PHONY: test test-% train sample
+
+TESTS = $(shell find ./tests -name "test_*.py")
+
+test-%: 
+	python ./tests/test_$*.py
+
+test:
+	@for TEST in $(TESTS); do \
+		echo "run $$TEST"; \
+		python $$TEST; \
+	done
+
+train:
+	python ./main.py --folder ./data/ --train_path ./mp_20/train_layer_test.csv --valid_path ./mp_20/val_layer_test.csv --epochs 200
+
+sample:
+	python ./main.py --optimizer none --test_path ./mp_20/test_layer_test.csv --restore_path ./data/adam_bs_100_lr_0.0001_decay_0_clip_1_A_119_W_28_N_21_a_1_w_1_l_1_Nf_5_Kx_16_Kl_4_h0_256_l_16_H_16_k_64_m_64_e_32_drop_0.5/epoch_000100.pkl --spacegroup 65 --num_samples 10  --batchsize 200 --temperature 1.0 --elements C

c2db/A/2C/1/data.json

@@ -0,0 +1,44 @@
+{
+  "folder": "/home/niflheim2/cmr/C2DB-ASR/tree/A/C/C2-a6735a4a3797",
+  "uid": "2C-1",
+  "olduid": "C2-a6735a4a3797",
+  "international": "P6/mmm",
+  "number": 191,
+  "pointgroup": "6/mmm",
+  "has_inversion_symmetry": true,
+  "lgnum": 80,
+  "layergroup": "p6/mmm",
+  "bravais_type": "Hexagonal (hp)",
+  "thickness": 3.224913225352566e-08,
+  "label": "original03-18",
+  "gap": 0.0003000685114302737,
+  "gap_dir": 0.0003000685114309398,
+  "gap_dir_nosoc": 0.000308946496943463,
+  "evac": 2.3363375983102452,
+  "efermi": -4.248481577688634,
+  "vbm": -4.248631611944349,
+  "cbm": -4.2483315434329185,
+  "minhessianeig": -7.00605419619458e-12,
+  "dyn_stab": "Yes",
+  "gap_hse": 0.0002564957267392476,
+  "gap_dir_hse": 0.0002564957267392476,
+  "efermi_hse": -4.213085568171573,
+  "vbm_hse": -4.213213816034942,
+  "cbm_hse": -4.212957320308203,
+  "alphax_el": 6.574592003348396,
+  "alphay_el": 6.574592003348392,
+  "alphaz_el": 0.1533681498711251,
+  "plasmafrequency_x": 0.0,
+  "plasmafrequency_y": 0.0,
+  "energy": -18.453766945888727,
+  "icsd_id": 96620,
+  "cod_id": 9012705,
+  "doi": "10.1126/science.1102896",
+  "is_magnetic": false,
+  "spin_axis": "z",
+  "dE_zx": 0.0,
+  "dE_zy": 0.0,
+  "topology": "Z2=1,C_M=1",
+  "ehull": 0.0,
+  "hform": -0.007391614814171277
+}

c2db/A/2C/1/magmoms.json

@@ -0,0 +1,4 @@
+{
+"folder": "/home/niflheim2/cmr/C2DB-ASR/tree/A/C/C2-a6735a4a3797",
+"uid": "2C-1"
+}

c2db/A/2C/1/read.py

@@ -0,0 +1,7 @@
+import re
+
+def lattice_from_file(file_path):
+    f = open(file_path, "r")
+    lines = f.readlines()
+    lattice_str = re.search(r'Lattice="([^"]+)"', lines[1]).group(1)
+    lattice_list = [eval(v) for v in lattice_str]

c2db/A/2C/1/results-asr.stiffness.json

@@ -0,0 +1,108 @@
+{
+ "object_id": "asr.stiffness::Result",
+ "constructor": "asr.stiffness::Result",
+ "args": [],
+ "kwargs": {
+  "data": {
+   "speed_of_sound_x": 21373.063352135574,
+   "speed_of_sound_y": 21370.856641622737,
+   "c_11": 345.6538905582198,
+   "c_12": 70.60779871921024,
+   "c_13": 0.0005778599312093563,
+   "c_14": null,
+   "c_15": null,
+   "c_16": null,
+   "c_21": 70.56537570227611,
+   "c_22": 345.58251859948973,
+   "c_23": 5.3339141915441094e-05,
+   "c_24": null,
+   "c_25": null,
+   "c_26": null,
+   "c_31": -1.48020629620793e-13,
+   "c_32": -3.171870634731279e-14,
+   "c_33": 275.09324474892543,
+   "c_34": null,
+   "c_35": null,
+   "c_36": null,
+   "c_41": null,
+   "c_42": null,
+   "c_43": null,
+   "c_44": null,
+   "c_45": null,
+   "c_46": null,
+   "c_51": null,
+   "c_52": null,
+   "c_53": null,
+   "c_54": null,
+   "c_55": null,
+   "c_56": null,
+   "c_61": null,
+   "c_62": null,
+   "c_63": null,
+   "c_64": null,
+   "c_65": null,
+   "c_66": null,
+   "__links__": {
+    "strains--1.0%-xx": "C2-b088c34acc1b",
+    "strains-+1.0%-xx": "C2-df0c254be7f9",
+    "strains--1.0%-yy": "C2-65c455263aaa",
+    "strains-+1.0%-yy": "C2-2fc059f556fa",
+    "strains--1.0%-xy": "C2-9ec52112fdfe",
+    "strains-+1.0%-xy": "C2-92a5b8f033fd"
+   },
+   "stiffness_tensor": {
+    "__ndarray__": [
+     [
+      3,
+      3
+     ],
+     "float64",
+     [
+      345.6538905582198,
+      70.60779871921024,
+      0.0005778599312093563,
+      70.56537570227611,
+      345.58251859948973,
+      5.3339141915441094e-05,
+      -1.48020629620793e-13,
+      -3.171870634731279e-14,
+      275.09324474892543
+     ]
+    ]
+   },
+   "eigenvalues": {
+    "__ndarray__": [
+     [
+      3
+     ],
+     "float64",
+     [
+      416.20479762329126,
+      275.03161153441835,
+      275.09324474892543
+     ]
+    ]
+   },
+   "dynamic_stability_stiffness": "high"
+  },
+  "metadata": {
+   "asr_name": "asr.stiffness",
+   "resources": {
+    "time": 0.05871438980102539,
+    "ncores": 1,
+    "tstart": 1605182101.3158286,
+    "tend": 1605182101.374543
+   },
+   "params": {
+    "strain_percent": 1.0
+   },
+   "code_versions": {
+    "asr": "0.4.1-fef8a0ce2ab711c3284f5dbfd158907b17f534e9",
+    "ase": "3.21.0b1-8a83b7f6a6fd68b95b9f542d7c054fa7204d764a",
+    "gpaw": "20.10.1b1-7ff8d570c9d25f2af1c40c00271000e3ab505f1c"
+   },
+   "creates": {}
+  },
+  "strict": true
+ }
+}

c2db/A/2C/1/structure.xyz

@@ -0,0 +1,4 @@
+2
+Lattice="2.4672312604313453 -1.7550685731635223e-20 0.0 -1.233615630215672 2.1366849485446453 0.0 1.118374734265682e-17 0.0 15.0" Properties=species:S:1:pos:R:3 energy=-18.453766945888727 dipole="0.8699688255098961 -0.5022767355947244 3.473501422988429e-08" free_energy=-18.45387516640614 pbc="T T F"
+C        0.00000000       0.00000000       7.49999997
+C        1.23361563       0.71222832       7.50000001

c2db_problem.ipynb

@@ -0,0 +1,72 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "C2DB dataset has two components: `data.json` and `structure.xyz`.\n",
+    "The `data.json` file stores properties of the material:\n",
+    "```\n",
+    "{\n",
+    "  \"folder\": \"/home/niflheim2/cmr/C2DB-ASR/tree/A/C/C2-a6735a4a3797\",\n",
+    "  \"uid\": \"2C-1\",\n",
+    "  \"olduid\": \"C2-a6735a4a3797\",\n",
+    "  \"international\": \"P6/mmm\",\n",
+    "  \"number\": 191,\n",
+    "  \"pointgroup\": \"6/mmm\",\n",
+    "  \"has_inversion_symmetry\": true,\n",
+    "  \"lgnum\": 80,\n",
+    "  \"layergroup\": \"p6/mmm\",\n",
+    "  \"bravais_type\": \"Hexagonal (hp)\",\n",
+    "  \"thickness\": 3.224913225352566e-08,\n",
+    "  \"label\": \"original03-18\",\n",
+    "  \"gap\": 0.0003000685114302737,\n",
+    "  \"gap_dir\": 0.0003000685114309398,\n",
+    "  \"gap_dir_nosoc\": 0.000308946496943463,\n",
+    "  \"evac\": 2.3363375983102452,\n",
+    "  \"efermi\": -4.248481577688634,\n",
+    "  \"vbm\": -4.248631611944349,\n",
+    "  \"cbm\": -4.2483315434329185,\n",
+    "  \"minhessianeig\": -7.00605419619458e-12,\n",
+    "  \"dyn_stab\": \"Yes\",\n",
+    "  \"gap_hse\": 0.0002564957267392476,\n",
+    "  \"gap_dir_hse\": 0.0002564957267392476,\n",
+    "  \"efermi_hse\": -4.213085568171573,\n",
+    "  \"vbm_hse\": -4.213213816034942,\n",
+    "  \"cbm_hse\": -4.212957320308203,\n",
+    "  \"alphax_el\": 6.574592003348396,\n",
+    "  \"alphay_el\": 6.574592003348392,\n",
+    "  \"alphaz_el\": 0.1533681498711251,\n",
+    "  \"plasmafrequency_x\": 0.0,\n",
+    "  \"plasmafrequency_y\": 0.0,\n",
+    "  \"energy\": -18.453766945888727,\n",
+    "  \"icsd_id\": 96620,\n",
+    "  \"cod_id\": 9012705,\n",
+    "  \"doi\": \"10.1126/science.1102896\",\n",
+    "  \"is_magnetic\": false,\n",
+    "  \"spin_axis\": \"z\",\n",
+    "  \"dE_zx\": 0.0,\n",
+    "  \"dE_zy\": 0.0,\n",
+    "  \"topology\": \"Z2=1,C_M=1\",\n",
+    "  \"ehull\": 0.0,\n",
+    "  \"hform\": -0.007391614814171277\n",
+    "}\n",
+    "```\n",
+    "And the `structure.xyz` file stores information about the cell and the lattice:\n",
+    "```\n",
+    "2\n",
+    "Lattice=\"2.4672312604313453 -1.7550685731635223e-20 0.0 -1.233615630215672 2.1366849485446453 0.0 1.118374734265682e-17 0.0 15.0\" Properties=species:S:1:pos:R:3 energy=-18.453766945888727 dipole=\"0.8699688255098961 -0.5022767355947244 3.473501422988429e-08\" free_energy=-18.45387516640614 pbc=\"T T F\"\n",
+    "C        0.00000000       0.00000000       7.49999997\n",
+    "C        1.23361563       0.71222832       7.50000001\n",
+    "```\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

c2db_try.py

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+import matplotlib.pyplot as plt
+from ase.db import connect
+
+db = connect('c2db.db')
+rows = db.select('layergroup')
+
+rows.layergroup

crystalformer.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: crystalformer
+Version: 0.3
+Summary: CrystalFormer is a transformer-based autoregressive model specifically designed for space group-controlled generation of crystalline materials.
+Home-page: https://github.com/deepmodeling/CrystalFormer
+Author: iopcompphys
+Author-email: zdcao@iphy.ac.cn, wanglei@iphy.ac.cn
+License: Apache License
+Keywords: Crystal Generation
+Platform: any
+License-File: LICENSE

crystalformer.egg-info/SOURCES.txt

@@ -0,0 +1,38 @@
+LICENSE
+README.md
+setup.py
+crystalformer/__init__.py
+crystalformer.egg-info/PKG-INFO
+crystalformer.egg-info/SOURCES.txt
+crystalformer.egg-info/dependency_links.txt
+crystalformer.egg-info/top_level.txt
+crystalformer/data/layer.csv
+crystalformer/data/wyckoff_list.csv
+crystalformer/data/wyckoff_symbols.csv
+crystalformer/extension/__init__.py
+crystalformer/extension/experimental.py
+crystalformer/extension/loss.py
+crystalformer/extension/mcmc.py
+crystalformer/extension/model.py
+crystalformer/extension/train.py
+crystalformer/extension/transformer.py
+crystalformer/src/__init__.py
+crystalformer/src/attention.py
+crystalformer/src/checkpoint.py
+crystalformer/src/elements.py
+crystalformer/src/lattice.py
+crystalformer/src/loss.py
+crystalformer/src/mcmc.py
+crystalformer/src/sample.py
+crystalformer/src/sym_group.py
+crystalformer/src/train.py
+crystalformer/src/transformer.py
+crystalformer/src/utils.py
+crystalformer/src/von_mises.py
+crystalformer/src/wyckoff.py
+tests/test_fc_mask.py
+tests/test_lattice.py
+tests/test_sampling.py
+tests/test_transformer.py
+tests/test_utils.py
+tests/test_wyckoff.py

crystalformer.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

crystalformer.egg-info/top_level.txt

@@ -0,0 +1 @@
+crystalformer