Format fix. More options in readme

basic_function/packaged_function.py

-from basic_function import format_parser
-from basic_function import CSP_generator_normal
-import os
-import concurrent.futures
-import sys
-
-
-
-def process_crystal(seed, sg, molecules,output_path,add_name):
-    aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=sg)
-    molecules_number = sum(len(molecule.atoms) for molecule in molecules)
-    new_crystal = aaa.generate(seed=seed)
-    sys.stdout.flush()
-    if new_crystal is not None:
-        cif_out = format_parser.write_cif_file(new_crystal)
-        with open(f"{output_path}/structures/{add_name}_{sg}_{seed}_z{len(molecules)}_{molecules_number}.cif", 'w') as target:
-            target.writelines(cif_out)
-        return True
-    return False
-
-def CSP_generater_parallel(molecules,output_path,need_structure = 100, space_group_list=[1],max_workers=8,add_name='',start_seed=1):
-    space_groups = space_group_list
-    accept_count = need_structure
-
-    try:
-        os.makedirs("{}/structures".format(output_path))
-    except:
-        print("Warning, these is already an structures folder in this path, skip mkdir")
-    for sg in space_groups:
-        accept = 0
-        seed = start_seed
-
-        with concurrent.futures.ProcessPoolExecutor(max_workers=max_workers) as executor:
-            futures = {}
-            while accept < accept_count:
-                # submit new task
-                while len(futures) < max_workers and accept + len(futures) < accept_count:
-                    future = executor.submit(process_crystal, seed, sg, molecules, output_path,add_name)
-                    futures[future] = seed
-                    seed += 1
-
-                # check the finished task
-                done, _ = concurrent.futures.wait(futures, return_when=concurrent.futures.FIRST_COMPLETED)
-                for future in done:
-                    if future.result():
-                        accept += 1
-                    # remove it from list, no matter what result it is
-                    del futures[future]
-
-                # cancel all task if the number need is arrived.
-                if accept >= accept_count:
-                    for future in futures:
-                        future.cancel()
-                    break
-
-
-def CSP_generater_serial(molecules,output_path,need_structure = 100, densely_pack_method=False, space_group_list=[1]):
-    """
-    :param molecules: a list [molecule1, molecule2, ...]
-    :param output_path: a str indicate the path of output folder
-    :param need_structure: int
-    :param space_group_list:a list indicate the space group need to search
-    """
-    try:
-        os.makedirs("{}\\structures".format(output_path))
-    except:
-        print("Warning, these is already an structures folder in this path, skip mkdir")
-    for sg in space_group_list:
-        aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=sg)
-        accept=0
-        i=1
-        while accept<need_structure:
-            new_crystal = aaa.generate(seed=i,densely_pack_method=densely_pack_method)
-            if new_crystal==None:
-                i += 1
-                continue
-            cif_out = format_parser.write_cif_file(new_crystal)
-            target = open("{}\\structures\\{}_{}.cif".format(output_path,sg,i), 'w')
-            target.writelines(cif_out)
-            target.close()
-            accept+=1
-            i += 1
-
-
-def CSP_generater_one_test(molecules,output_path,space_group=1,seed=1):
-    """
-    used to test the generator for a given space group and seed
-    :param molecules: a list [molecule1, molecule2, ...]
-    :param output_path: a str indicate the path of output folder
-    :param space_group: a list indicate the space group need to search
-    :param seed: int
-    :return: write out a cif
-    """
-    aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=space_group)
-    new_crystal = aaa.generate(seed=seed, test=True)
-    if new_crystal==None:
-        print("Return failed generate")
-    else:
-        cif_out = format_parser.write_cif_file(new_crystal,sym=True)
-        target = open("{}\\{}_{}.cif".format(output_path,space_group,seed), 'w')
-        target.writelines(cif_out)
-        target.close()
+from basic_function import format_parser
+from basic_function import CSP_generator_normal
+import os
+import concurrent.futures
+import sys
+
+
+
+def process_crystal(seed, sg, molecules,output_path,add_name):
+    aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=sg)
+    molecules_number = sum(len(molecule.atoms) for molecule in molecules)
+    new_crystal = aaa.generate(seed=seed)
+    sys.stdout.flush()
+    if new_crystal is not None:
+        cif_out = format_parser.write_cif_file(new_crystal)
+        with open(f"{output_path}/structures/{add_name}_{sg}_{seed}_z{len(molecules)}_{molecules_number}.cif", 'w') as target:
+            target.writelines(cif_out)
+        return True
+    return False
+
+def CSP_generater_parallel(molecules,output_path,need_structure = 100, space_group_list=[1],max_workers=8,add_name='',start_seed=1):
+    space_groups = space_group_list
+    accept_count = need_structure
+
+    try:
+        os.makedirs("{}/structures".format(output_path))
+    except:
+        print("Warning, these is already an structures folder in this path, skip mkdir")
+    for sg in space_groups:
+        accept = 0
+        seed = start_seed
+
+        with concurrent.futures.ProcessPoolExecutor(max_workers=max_workers) as executor:
+            futures = {}
+            while accept < accept_count:
+                # submit new task
+                while len(futures) < max_workers and accept + len(futures) < accept_count:
+                    future = executor.submit(process_crystal, seed, sg, molecules, output_path,add_name)
+                    futures[future] = seed
+                    seed += 1
+
+                # check the finished task
+                done, _ = concurrent.futures.wait(futures, return_when=concurrent.futures.FIRST_COMPLETED)
+                for future in done:
+                    if future.result():
+                        accept += 1
+                    # remove it from list, no matter what result it is
+                    del futures[future]
+
+                # cancel all task if the number need is arrived.
+                if accept >= accept_count:
+                    for future in futures:
+                        future.cancel()
+                    break
+
+
+def CSP_generater_serial(molecules,output_path,need_structure = 100, densely_pack_method=False, space_group_list=[1]):
+    """
+    :param molecules: a list [molecule1, molecule2, ...]
+    :param output_path: a str indicate the path of output folder
+    :param need_structure: int
+    :param space_group_list:a list indicate the space group need to search
+    """
+    try:
+        os.makedirs("{}\\structures".format(output_path))
+    except:
+        print("Warning, these is already an structures folder in this path, skip mkdir")
+    for sg in space_group_list:
+        aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=sg)
+        accept=0
+        i=1
+        while accept<need_structure:
+            new_crystal = aaa.generate(seed=i,densely_pack_method=densely_pack_method)
+            if new_crystal==None:
+                i += 1
+                continue
+            cif_out = format_parser.write_cif_file(new_crystal)
+            target = open("{}\\structures\\{}_{}.cif".format(output_path,sg,i), 'w')
+            target.writelines(cif_out)
+            target.close()
+            accept+=1
+            i += 1
+
+
+def CSP_generater_one_test(molecules,output_path,space_group=1,seed=1):
+    """
+    used to test the generator for a given space group and seed
+    :param molecules: a list [molecule1, molecule2, ...]
+    :param output_path: a str indicate the path of output folder
+    :param space_group: a list indicate the space group need to search
+    :param seed: int
+    :return: write out a cif
+    """
+    aaa = CSP_generator_normal.CrystalGenerator(molecules, space_group=space_group)
+    new_crystal = aaa.generate(seed=seed, test=True)
+    if new_crystal==None:
+        print("Return failed generate")
+    else:
+        cif_out = format_parser.write_cif_file(new_crystal,sym=True)
+        target = open("{}\\{}_{}.cif".format(output_path,space_group,seed), 'w')
+        target.writelines(cif_out)
+        target.close()

mace-bench/3rdparty/SevenNet/sevenn/__init__.py

-from importlib.metadata import version
-
-from packaging.version import Version
-
-__version__ = version('sevenn')
-
-from e3nn import __version__ as e3nn_ver
-
-if Version(e3nn_ver) < Version('0.5.0'):
-    raise ValueError(
-        'The e3nn version MUST be 0.5.0 or later due to changes in CG coefficient '
-        'convention.'
-    )
+from importlib.metadata import version
+
+from packaging.version import Version
+
+__version__ = version('sevenn')
+
+from e3nn import __version__ as e3nn_ver
+
+if Version(e3nn_ver) < Version('0.5.0'):
+    raise ValueError(
+        'The e3nn version MUST be 0.5.0 or later due to changes in CG coefficient '
+        'convention.'
+    )