pwact 0.2.0__py3-none-any.whl → 0.2.2.dev0__py3-none-any.whl

pwact/utils/app_lib/do_eqv2model.py

@@ -0,0 +1,41 @@
+from ase.io import read
+from fairchem.core import OCPCalculator
+import os
+output_file = 'train.xyz'
+traj = read("select.xyz", index=":")
+calc = OCPCalculator(
+    checkpoint_path="/share/public/PWMLFF_test_data/eqv2-models/eqV2_31M_omat.pt",
+    cpu=False,
+)
+
+def atoms2xyzstr(atoms):
+    num_atom = atoms.get_global_number_of_atoms()
+    vol = atoms.get_volume()
+    pos = atoms.positions
+    forces = atoms.get_forces()
+    energy = atoms.get_potential_energy()
+    cell = atoms.cell
+    virial = -atoms.get_stress(voigt=False) * vol
+    xyzstr = "%d\n" % num_atom
+    xyz_head = 'Lattice="%.3f %.3f %.3f %.3f %.3f %.3f %.3f %.3f %.3f" Properties=species:S:1:pos:R:3:forces:R:3 energy=%.8f' 
+    xyz_format = (cell[0,0],cell[0,1],cell[0,2],cell[1,0],cell[1,1],cell[1,2],cell[2,0],cell[2,1],cell[2,2],energy)
+    if virial is not None:
+        xyz_head += ' virial="%.8f %.8f %.8f %.8f %.8f %.8f %.8f %.8f %.8f"'
+        xyz_format += (
+            virial[0,0], virial[0,1], virial[0,2],
+            virial[1,0], virial[1,1], virial[1,2],
+            virial[2,0], virial[2,1], virial[2,2]
+            )
+    xyz_head += '\n'
+    xyzstr += xyz_head % xyz_format
+    for i in range(num_atom):
+        xyzstr += "%2s %14.8f %14.8f %14.8f %14.8f %14.8f %14.8f\n" %\
+        (atoms[i].symbol,pos[i,0],pos[i,1],pos[i,2],forces[i,0],forces[i,1],forces[i,2])
+    return xyzstr
+
+f = open(output_file, "w")
+for i in range(len(traj)):
+    atoms = traj[i]
+    atoms.calc = calc
+    f.write(atoms2xyzstr(atoms))
+f.close()

pwact/utils/constant.py

@@ -41,6 +41,7 @@ class SLURM_JOB_TYPE:
     vasp_scf = "vasp/scf"
     vasp_aimd = "vasp/aimd"
     lammps = "lammps"
+    direct = "direct"
 
 '''
 description: 
@@ -138,6 +139,7 @@ class DFT_STYLE:
     pwmat = "pwmat"
     cp2k = "cp2k"
     lammps = "lammps"
+    bigmodel="bigmodel"
 
     '''
     description: 
@@ -156,6 +158,8 @@ class DFT_STYLE:
                 return PWDATA.cp2k_scf
             else:
                 return PWDATA.vasp_poscar
+        if dft_style.lower() == DFT_STYLE.bigmodel.lower():
+            return PWDATA.extxyz
 
     @staticmethod
     def get_normal_config(dft_style:str): # the input config file name of pwmat vasp and cp2k
@@ -249,17 +253,6 @@ class DFT_STYLE:
         scf_list = [_.lower() for _ in scf_list]
         return scf_list
     
-    '''
-    description: 
-        the files in scf does not need reserve
-    return {*}
-    author: wuxingxing
-    '''    
-    @staticmethod
-    def get_scf_del_list():
-        del_list = ["final.config"]
-        return del_list
-    
     @staticmethod
     def get_aimd_config(dft_style:str):
         if dft_style == DFT_STYLE.pwmat:
@@ -357,6 +350,20 @@ class INIT_BULK:
     scf_tag = "tag.scf.success"
     scf_tag_failed ="tag.scf.failed"
 
+    bigmodel="bigmodel"
+    bigmodel_job = "bigmodel.job"
+    bigmodel_tag = "tag.bigmodel.success"
+    bigmodel_tag_failed ="tag.bigmodel.failed"
+    bigmodel_traj = "traj.xyz"
+    
+    direct="direct"
+    direct_job = "direct.job"
+    direct_tag = "tag.direct.success"
+    direct_tag_failed ="tag.direct.failed"
+    candidate_xyz="candidate.xyz"
+    candidate_idx="candidate.json"
+    direct_traj = "select.xyz"
+
     collection = "collection"
     npy_format_save_dir = "PWdata"
     npy_format_name = "datapath.txt"
@@ -413,11 +420,18 @@ class EXPLORE_FILE_STRUCTURE:
     kpu= "kpu"
     md = "md"
     select = "select"
+    direct = "direct"
     md_tag = "tag.md.success"
     md_tag_faild = "tag.md.error"
     md_job = "md.job"
+    direct_tag = "tag.direct.success"
+    direct_tag_faild = "tag.direct.error"
+    direct_job = "direct.job"
     # selected image info file names
     candidate = "candidate.csv"
+    candidate_xyz="candidate.xyz"
+    select_idx = "select_idx.dat"
+    select_xyz = "select.xyz"
     # candidate_random = "candidate_random.csv"
     candidate_delete = "candidate_delete.csv"
     failed = "fail.csv"
@@ -446,11 +460,17 @@ class EXPLORE_FILE_STRUCTURE:
 
 
 class LABEL_FILE_STRUCTURE:
+    bigmodel="bigmodel"
     scf = "scf"
     result = "result"
     scf_tag = "tag.scf.success"
     scf_tag_failed = "tag.scf.failed"
     scf_job = "scf.job"
+    bigmodel_job="bigmodel.job"
+    bigmodel_tag = "tag.bigmodel.success"
+    bigmodel_tag_failed = "tag.bigmodel.failed"
+    train_xyz = "train.xyz"
+
 
 class LAMMPS:
     input_lammps="in.lammps"

pwact/utils/file_operation.py

@@ -318,8 +318,15 @@ def get_file_extension(file_name:str, split_char = "."):
 @Author       :wuxingxing
 """
 
-def get_random_nums(start, end, n):
-    numsArray = set()
-    while len(numsArray) < n:
-        numsArray.add(random.randint(start, end-1))
-    return list(numsArray)
+def get_random_nums(start, end, n, seed=None):
+    if seed is not None:
+        local_random = random.Random(seed)  # 独立的随机实例
+        numsArray = set()
+        while len(numsArray) < n:
+            numsArray.add(local_random.randint(start, end-1))
+        return list(numsArray)
+    else:
+        numsArray = set()
+        while len(numsArray) < n:
+            numsArray.add(random.randint(start, end-1))
+        return list(numsArray)        

{pwact-0.2.0.dist-info → pwact-0.2.2.dev0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pwact
-Version: 0.2.0
+Version: 0.2.2.dev0
 Summary: PWACT is an open-source automated active learning platform based on PWMLFF for efficient data sampling.
 Home-page: https://github.com/LonxunQuantum/PWact
 Author: LonxunQuantum

{pwact-0.2.0.dist-info → pwact-0.2.2.dev0.dist-info}/RECORD

@@ -1,18 +1,20 @@
 pwact/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pwact/main.py,sha256=gsWBnVrBXLbclzonbYhZKPgVOQxb3_FVfKCezlJZz9Y,15100
+pwact/main.py,sha256=FubLfN4QaqPEe7aYGzZhqvT2T2GEvMyU3hy07jvXEWU,15379
 pwact/active_learning/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/active_learning/environment.py,sha256=1vzOWnCNR2OXMFKz4DjQF2wb0aw1Xkjnz7cy1YGQrus,512
 pwact/active_learning/explore/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pwact/active_learning/explore/run_model_md.py,sha256=hrE-vMJBlvgxTiG0WFG86RX2Gi7ImtutF0PoT2RTTN0,21312
-pwact/active_learning/explore/select_image.py,sha256=bDhDbdu6aoFfAdq_z3ha6qnxDGrQjfoHPVOKH7_u1VQ,14470
+pwact/active_learning/explore/run_model_md.py,sha256=n3f6aSMr1Cpw_cSUrlH28JwoWW7VLwUMcF1XB0ao2sw,27448
+pwact/active_learning/explore/select_image.py,sha256=Qbdk4zhEfkvefY4MPtu7ErDL0XVfgfrBFPZUGDyiGF8,14468
 pwact/active_learning/init_bulk/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/active_learning/init_bulk/aimd.py,sha256=XzDlX2vylaljQKoUnv6nrI2NfiOdHZpq8qr3DenA1F4,10465
-pwact/active_learning/init_bulk/duplicate_scale.py,sha256=Z9mYBASy9gNLTV_db8lqfXpcahHbrQq6emae169P2wM,9468
-pwact/active_learning/init_bulk/init_bulk_run.py,sha256=B6miVKjY9ClxYW-SyhsY63OHdJRDeL6zc0BMW75SBg8,9151
-pwact/active_learning/init_bulk/relabel.py,sha256=DJR90gnC_AIWkcbWGcf2FYVCwPU40iP1uB48cTgGn7k,10447
+pwact/active_learning/init_bulk/direct.py,sha256=TBB7f13wbbURDgn4_IkgRZ-rwQ3p4gviNVYIAldi97U,9680
+pwact/active_learning/init_bulk/duplicate_scale.py,sha256=hlGAr27YJhOElMz5GMyN0wWoChia4Jj_tvENsJ3wSBs,9481
+pwact/active_learning/init_bulk/explore.py,sha256=ef1KA4Sii7sXSGncvomsLXTBtFM89H8Q5lYWGoAbN2U,15935
+pwact/active_learning/init_bulk/init_bulk_run.py,sha256=t-lCiraAtHEUtW-rdhfRuXYoWpP4eJndX3F3E6IxWt8,10871
+pwact/active_learning/init_bulk/relabel.py,sha256=I5vSmyDaCJtcJCWS6aAtlb72kAQSva4vCx4mn1BYXjg,11846
 pwact/active_learning/init_bulk/relax.py,sha256=edyCZLEylUckIwOLBa55agUMo-aedj0dvoyG165YpuE,10450
 pwact/active_learning/label/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pwact/active_learning/label/labeling.py,sha256=qtJdAGI_TyO0PtfexqCOITnHOnbTwVZCcaAH7BPGLCk,15102
+pwact/active_learning/label/labeling.py,sha256=JUdyaSvpspUwbMnhi65i6Cna0vWgMOAMNS1XTtqlygc,21740
 pwact/active_learning/slurm/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/active_learning/slurm/slurm.py,sha256=-Dmc2B9y4_27THCR2tZFXnwJvMmifivJeZ2FX8iy2Tw,16881
 pwact/active_learning/slurm/slurm_tool.py,sha256=-4tc5dkpAUP0vmEdmqM8oYLcsUwixa4Z8h5_E9Gevdg,1249
@@ -23,24 +25,24 @@ pwact/active_learning/train/dp_kpu.py,sha256=GkGKEGhLmOvPERqgTkf_0_vD9zOEPlBX2N7
 pwact/active_learning/train/train_model.py,sha256=F6DUOuTsYGvinv-qz2iqa2j7DPy3hnCySVUkx8DpR_U,11605
 pwact/active_learning/user_input/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/active_learning/user_input/cmd_infos.py,sha256=g1QW5Wi3JvmC5xEY4F-7AO1xBuJSjHG8IhZjom8haxQ,3728
-pwact/active_learning/user_input/init_bulk_input.py,sha256=7Suhxtgu84bn0ziL1RFF-7eSJUcLKJ2HF132RZmpNxw,6982
-pwact/active_learning/user_input/iter_input.py,sha256=ffGNq8Qm2mALEviVHpZ0nFuKrqy1FuWriI2hg8F54X0,12131
-pwact/active_learning/user_input/resource.py,sha256=bg1rkdjIzuj7pDUvp6h1yMWFT0PqYzH4BfX5tJ7MZzc,6812
-pwact/active_learning/user_input/scf_param.py,sha256=tHmGnWrWiZ1dD-EZHfvWtzKGnT6BjIhXKMXNhPmWSQc,10376
+pwact/active_learning/user_input/init_bulk_input.py,sha256=M8IlT4ABJUEwomb6eQGq8d3h1darMHtDlws1fcq077k,9422
+pwact/active_learning/user_input/iter_input.py,sha256=7k0M3BaP1dMWK2Bglvb2WXQ2Ugrfy0v7yMqPqWqNCdE,12744
+pwact/active_learning/user_input/resource.py,sha256=28rbsJ9qtkToeuXst7Q1Z189KpDd8YZ8bBK7cuDp7RU,7358
+pwact/active_learning/user_input/scf_param.py,sha256=QX_Dd6c9Q2sjV4lIKjfV7t-DgIwDKZp7fh2KY5HyKOU,11262
 pwact/active_learning/user_input/workdir.py,sha256=64J3wBbYzy6ztYHs513YHfEIF5d8zwv_WpF-U9HOEkA,8245
 pwact/active_learning/user_input/train_param/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/active_learning/user_input/train_param/model_param.py,sha256=4-bJAGOJDTLT11lLqpEZAWMqgen7zghHESfHeb0UUb4,4574
 pwact/active_learning/user_input/train_param/nep_param.py,sha256=04GEKqT2miZYxgVtxTEGIWJW5mUZriPcvwfgdp7IL0g,21249
 pwact/active_learning/user_input/train_param/nn_feature_type.py,sha256=eGmqfsPTlIpftzvUqHV_VziGQuUZ_KKqek3SQKZl85o,15640
-pwact/active_learning/user_input/train_param/optimizer_param.py,sha256=1Vl_BulrLkJmOPSetyn2HJMcwjizkkjrhvz0x8DzLRU,13084
+pwact/active_learning/user_input/train_param/optimizer_param.py,sha256=8zG3l6DqEjmwNCqRwpcA1J1oY2tm-J-V4zl3sM0G_ek,13085
 pwact/active_learning/user_input/train_param/train_param.py,sha256=rpLmOncwqQ82Hudwwl-VzZKJv2jCtrsCsJN2UpuHqKg,16640
 pwact/active_learning/user_input/train_param/work_file_param.py,sha256=3sQiHcquQO9hw0JexiMXkuf01gy871yjYz9GEZ3Icoo,12239
 pwact/bin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/data_format/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/data_format/configop.py,sha256=6JA84cK7Ck-t1z3iLz3pPVJ-q4srhDiQQhs9-G-cxY0,11772
 pwact/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pwact/utils/constant.py,sha256=swLs-0Lulc22ZvJ_cwEYTO8r5cxB3y5YB2EnwxhfRNE,18757
-pwact/utils/file_operation.py,sha256=1W5kGzGAznbAs2vyUhh5sDim62qQOkTPgphSOe_oDvI,9536
+pwact/utils/constant.py,sha256=qKiASMwMpROa_w29NEyUG6Uov8di4UGprXBIa7tUGjc,19482
+pwact/utils/file_operation.py,sha256=bfLezgJHD3BRtZFm0HwSGTNBPukVNICZFpXYWMs68A4,9827
 pwact/utils/format_input_output.py,sha256=oYFydQy3-btXzieO2O2LbHFoeRyhPnLVE4c5TNgS-IQ,1798
 pwact/utils/json_operation.py,sha256=BqBsnIjk1URoMW_s2yu7Gk8IBxlir-oo6ivt8P3RIqg,1794
 pwact/utils/pre_al_data_util.py,sha256=QE-axnVYUIyORFiVs-WK9-UaJlMUFY816_rSyYOOJc8,2542
@@ -51,13 +53,15 @@ pwact/utils/app_lib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSu
 pwact/utils/app_lib/common.py,sha256=lQmI-9Qumq62MNjr-eVlLL88ISDHBOb6vAfYYFcDIgM,6040
 pwact/utils/app_lib/cp2k.py,sha256=txd-eMDUOsWPug395WJOQz3aqhwz7eU4hcEZIWTF1OY,15492
 pwact/utils/app_lib/cp2k_dp.py,sha256=VP4gyPGhLcMAqAjrqCQSUiiGlESNlyYz7Gs3Q4QoUHo,6912
+pwact/utils/app_lib/do_direct_sample.py,sha256=G8VZH23c2vBJwG9pp_H9EvRVaRJPsQVliDH-v6l2Gek,4947
+pwact/utils/app_lib/do_eqv2model.py,sha256=cRVzagozELK6kCZuX6dqg2gDHQPr7n3TQk6JghDjiy4,1509
 pwact/utils/app_lib/lammps.py,sha256=t3nkBqwkViO6UbnInGKAHiwVngHKayeat2pPEtaZZIU,8015
 pwact/utils/app_lib/pwmat.py,sha256=PTRPkG_d00ibGhpCe2-4M7MW3dx2ZuAyb9hT2jl_LAs,18047
 pwact/utils/draw/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/utils/draw/hist_model_devi.py,sha256=o1Try-ekith2A7S6u1mt3zuTqaQwyw5tdURReh8BeLY,4945
-pwact-0.2.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-pwact-0.2.0.dist-info/METADATA,sha256=wlqbUATqsi_RBbpLC_1SytmOIFiUtIKqTIXNLs2bV9U,3658
-pwact-0.2.0.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-pwact-0.2.0.dist-info/entry_points.txt,sha256=p61auAnpbn8E2WjvHNBA7rb9_NRAOCew4zdcCj33cGc,42
-pwact-0.2.0.dist-info/top_level.txt,sha256=fY1_7sH5Lke4dC9L8MbYM4fT5aat5eCkAmpkIzY1SlM,6
-pwact-0.2.0.dist-info/RECORD,,
+pwact-0.2.2.dev0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+pwact-0.2.2.dev0.dist-info/METADATA,sha256=RGt1qWZv8xFV4H4W3oFbtZGmMs_sPK73JRJFwm2ZJbQ,3663
+pwact-0.2.2.dev0.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+pwact-0.2.2.dev0.dist-info/entry_points.txt,sha256=p61auAnpbn8E2WjvHNBA7rb9_NRAOCew4zdcCj33cGc,42
+pwact-0.2.2.dev0.dist-info/top_level.txt,sha256=fY1_7sH5Lke4dC9L8MbYM4fT5aat5eCkAmpkIzY1SlM,6
+pwact-0.2.2.dev0.dist-info/RECORD,,