pwact 0.1.27__py3-none-any.whl → 0.2.0__py3-none-any.whl

pwact/utils/constant.py

@@ -66,7 +66,9 @@ author: wuxingxing
 class TRAIN_INPUT_PARAM:
     save_p_matrix = "save_p_matrix" # for kpu
     raw_files = "raw_files"
-    datasets_path = "datasets_path"
+    valid_data = "valid_data"
+    train_data = "train_data"
+    format = "format"
     test_mvm_files = "test_movement_file"
     reserve_feature = "reserve_feature" #False
     reserve_work_dir = "reserve_work_dir" #False
@@ -357,7 +359,15 @@ class INIT_BULK:
 
     collection = "collection"
     npy_format_save_dir = "PWdata"
-    npy_format_name = "pwdata"
+    npy_format_name = "datapath.txt"
+
+    def get_save_format(save_format:str):
+        if save_format == PWDATA.pwmlff_npy:
+            return INIT_BULK.npy_format_save_dir
+        elif save_format==PWDATA.extxyz:
+            return "train.xyz"
+        else:
+            raise Exception("Error! The data_format only support ")
 
 class MODEL_TYPE:
     dp = "DP"
@@ -397,7 +407,7 @@ class TRAIN_FILE_STRUCTUR:
 
     # nep model
     nep_model_name ="nep_model.ckpt"
-    nep_model_lmps = "nep_to_lmps.txt"
+    nep_model_lmps = "nep5.txt"
 
 class EXPLORE_FILE_STRUCTURE:
     kpu= "kpu"
@@ -418,6 +428,7 @@ class EXPLORE_FILE_STRUCTURE:
     
     # for committee and kpu method 
     model_devi = "model_devi.out"
+    md_traj_error_record="error_traj.log"
     kpu_model_devi = "kpu_model_devi.out"
     devi_columns = ["devi_force", "config_index", "file_path"]
 

pwact/utils/file_operation.py

@@ -6,6 +6,20 @@ import re
 import json
 import numpy as np
 import random
+import torch
+
+def check_model_type(model_load_path):
+    try:
+        _model_checkpoint = torch.load(model_load_path, map_location=torch.device("cpu"))
+        model_type = _model_checkpoint['json_file']['model_type']
+    except Exception as e:
+        with open(model_load_path, 'r') as rf:
+            line = rf.readline()
+        if "nep" not in line:
+            raise Exception("ERROR! The input model file cannot be parsed!")
+        else:
+            model_type  = "NEP"
+        return model_type
 
 '''
 description: 

pwact/utils/process_tool.py

@@ -1,15 +1,26 @@
 import os
 import signal
 import subprocess
+from subprocess import Popen, PIPE
+import time
+from pwact.active_learning.slurm.slurm import scancle_byjobid
+def kill_process(pid:str, job_id:str):
+    if job_id is None:
+        try:
+            # 发送终止信号 (SIGTERM) 给指定的进程
+            os.kill(pid, signal.SIGTERM)
+            print(f"process {pid} has been terminated.")
+        except ProcessLookupError:
+            print(f"process {pid} non-existent.")
+        except PermissionError:
+            print(f"No permission to terminate the process {pid}.")
+        except Exception as e:
+            print(f"Error terminating process {pid}: {e}")
+    else:
+        scancle_byjobid(job_id)
+
+def get_pid():
+    pid = os.getpid()
+    job_id = os.getenv('SLURM_JOB_ID')
+    return "pid {} job {}".format(pid, job_id) if job_id is not None else "pid {}".format(pid)
 
-def kill_process(pid:int):
-    try:
-        # 发送终止信号 (SIGTERM) 给指定的进程
-        os.kill(pid, signal.SIGTERM)
-        print(f"process {pid} has been terminated.")
-    except ProcessLookupError:
-        print(f"process {pid} non-existent.")
-    except PermissionError:
-        print(f"No permission to terminate the process {pid}.")
-    except Exception as e:
-        print(f"Error terminating process {pid}: {e}")

pwact/utils/slurm_script.py

@@ -1,4 +1,5 @@
 import glob
+import re
 import os
 from math import ceil
 from pwact.utils.constant import DFT_STYLE
@@ -8,7 +9,6 @@ GPU_SCRIPT_HEAD = \
 #SBATCH --nodes={}\n\
 #SBATCH --ntasks-per-node={}\n\
 #SBATCH --gres=gpu:{}\n\
-#SBATCH --gpus-per-task={}\n\
 #SBATCH --partition={}\n\
 \
 "
@@ -22,20 +22,6 @@ CPU_SCRIPT_HEAD = \
 \
 "
 
-CONDA_ENV = '__conda_setup="$(\'/data/home/wuxingxing/anaconda3/bin/conda\' \'shell.bash\' \'hook\' 2> /dev/null)"\n' \
-       'if [ $? -eq 0 ]; then\n' \
-       '    eval "$__conda_setup"\n' \
-       'else\n' \
-       '    if [ -f "/data/home/wuxingxing/anaconda3/etc/profile.d/conda.sh" ]; then\n' \
-       '        . "/data/home/wuxingxing/anaconda3/etc/profile.d/conda.sh"\n' \
-       '    else\n' \
-       '        export PATH="/data/home/wuxingxing/anaconda3/bin:$PATH"\n' \
-       '    fi\n' \
-       'fi\n' \
-       'unset __conda_setup\n' \
-       '# <<< conda initialize <<<\n' \
-       'conda activate torch2_feat\n\n'
-
 '''
 Description: 
 Obtain the execution status of the slurm jobs under the 'dir'
@@ -71,6 +57,24 @@ def get_slurm_job_run_info(dir:str, job_patten:str="*.job", tag_patten:str="tag.
             
     return slurm_failed, slurm_success
 
+def recheck_slurm_by_jobtag(slurm_files:list[str], tag):
+    remain_job = []
+    for slurm_file in slurm_files:
+        with open(slurm_file, 'r') as f:
+            content = f.read()
+        cd_pattern = r'cd\s+([^\n]+)'
+        directories = re.findall(cd_pattern, content)        
+        if not directories:
+            raise Exception("Error! There is no task in the slurm.job file {}".format(slurm_file))
+        for directory in directories:
+            directory = directory.strip()
+            success_file = os.path.join(directory, tag)
+            if os.path.exists(success_file):
+                continue
+            else:
+                remain_job.append(slurm_file)
+                break
+    return remain_job
 
 '''
 description: 
@@ -146,14 +150,13 @@ def set_slurm_script_content(
             script += CPU_SCRIPT_HEAD.format(job_name, number_node, cpu_per_node, queue_name)
             script += "export CUDA_VISIBLE_DEVICES=''\n"
         else:
-            script += GPU_SCRIPT_HEAD.format(job_name, number_node, cpu_per_node, gpu_per_node, 1, queue_name)
+            script += GPU_SCRIPT_HEAD.format(job_name, number_node, cpu_per_node, gpu_per_node, queue_name)
         
         for custom_flag in custom_flags:
             script += custom_flag + "\n"
         
         # set conda env
         script += "\n"
-        # script += CONDA_ENV
         # script += "\n"
 
         script += "echo \"SLURM_SUBMIT_DIR is $SLURM_SUBMIT_DIR\"\n\n"

{pwact-0.1.27.dist-info → pwact-0.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pwact
-Version: 0.1.27
+Version: 0.2.0
 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-0.1.27.dist-info → pwact-0.2.0.dist-info}/RECORD

@@ -1,63 +1,63 @@
 pwact/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pwact/main.py,sha256=EKFcwo_gk9BWhg3zU36RW7NXMLDfyhzrtjtvcv4h5dQ,17036
+pwact/main.py,sha256=gsWBnVrBXLbclzonbYhZKPgVOQxb3_FVfKCezlJZz9Y,15100
 pwact/active_learning/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pwact/active_learning/environment.py,sha256=KvyMaOXrM-HMMma4SnoOQFO6fZxDsk0Fsyyy7xqfGCo,684
+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=opflniIxbT8SSPNwkGXcd8j_GVpWvDexhFhxYXXO8Yk,21053
-pwact/active_learning/explore/select_image.py,sha256=dmsMoxFwQ7JDPHK2vRFzUfXeEovT86cmUnmEm-qrfwE,12665
+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/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=FG1EAXvuBJ1ERCg2htFVooif8mxcx4XyVgOoKF-1B_Q,8683
+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/relax.py,sha256=edyCZLEylUckIwOLBa55agUMo-aedj0dvoyG165YpuE,10450
 pwact/active_learning/label/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pwact/active_learning/label/labeling.py,sha256=tAFyTZjg64cNkG2_3p8qn5pc5F3je64UBgXnJT5PYtU,15687
+pwact/active_learning/label/labeling.py,sha256=qtJdAGI_TyO0PtfexqCOITnHOnbTwVZCcaAH7BPGLCk,15102
 pwact/active_learning/slurm/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pwact/active_learning/slurm/slurm.py,sha256=xIDePutt8Q00--61y-RemT4Ky6qL9258kykaxKhIw8w,15637
+pwact/active_learning/slurm/slurm.py,sha256=-Dmc2B9y4_27THCR2tZFXnwJvMmifivJeZ2FX8iy2Tw,16881
 pwact/active_learning/slurm/slurm_tool.py,sha256=-4tc5dkpAUP0vmEdmqM8oYLcsUwixa4Z8h5_E9Gevdg,1249
 pwact/active_learning/test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/active_learning/test/test.py,sha256=TXsk-gDDOHDLywVljpqA-zHK3-PrZbGAHnK1T7T6T-o,3587
 pwact/active_learning/train/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/active_learning/train/dp_kpu.py,sha256=GkGKEGhLmOvPERqgTkf_0_vD9zOEPlBX2N7vuSQG_-c,9317
-pwact/active_learning/train/train_model.py,sha256=NXqTKrl7Lb_UGt2-Lq_gLM9iZDAZFY09nxP_aGtBdrE,10525
+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=NCUAB1xpa67MXHRRWAkmWZjkQbTibE4EjmtlOmr0HdQ,6762
-pwact/active_learning/user_input/iter_input.py,sha256=zwFCI6dDFIEVWitEqBBZP7TtrSvxMbmSUEPiM0Z8ZOk,10732
+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=Cvwbab-SjMBSblBxA-5ETVlDpLQohP_xux2OjrPSCYU,10244
+pwact/active_learning/user_input/scf_param.py,sha256=tHmGnWrWiZ1dD-EZHfvWtzKGnT6BjIhXKMXNhPmWSQc,10376
 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=IoaQNwaXQFDXA7ET8NKptrkhvTE4lDknp23VccG6A1I,21251
+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/train_param.py,sha256=hsdVojgQZbQGSexZ_ckuxdqJpjJTN8sBOlRM6VHUYjA,15814
-pwact/active_learning/user_input/train_param/work_file_param.py,sha256=tmedoLodmkcSK6uRIXTML0BhXFkgE96zPX0_kAXmGoo,11631
+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=S2WaES4-9_FX_o6fLaBMw2uSIF1cUMLGj9APRRASy6Q,11984
+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=ZM43rI0JNHA_nVKdRW1YvPGCEkomRNgdmA3_L8hAVSY,18379
-pwact/utils/file_operation.py,sha256=LFQ247afF_nUhxagZTYqIYs9GrJCwsiI2EuDhoxWIKQ,9032
+pwact/utils/constant.py,sha256=swLs-0Lulc22ZvJ_cwEYTO8r5cxB3y5YB2EnwxhfRNE,18757
+pwact/utils/file_operation.py,sha256=1W5kGzGAznbAs2vyUhh5sDim62qQOkTPgphSOe_oDvI,9536
 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
-pwact/utils/process_tool.py,sha256=trzp6GbP_SYFiS_vheobV_FI4PSWVJvX3xHsFQ6DWME,478
-pwact/utils/slurm_script.py,sha256=mgueOrhYteg6XXvJitdjmbV4lzxMujuna9Jxr3wgC7Q,8237
+pwact/utils/process_tool.py,sha256=j4yp9DoPshTxTX3g7SS-yuEbBVhuoYNNZdAv2mq3efE,876
+pwact/utils/slurm_script.py,sha256=tbclNkYBVM-t8GeiLGNK2s5kxypjy8luf4ZrlHEGjjM,8278
 pwact/utils/tmp.py,sha256=en_GltoNwfA40vSHttMRi9cEg-8xnPZlvnnBq1_vHfw,2285
 pwact/utils/app_lib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pwact/utils/app_lib/common.py,sha256=lQmI-9Qumq62MNjr-eVlLL88ISDHBOb6vAfYYFcDIgM,6040
-pwact/utils/app_lib/cp2k.py,sha256=ljhCCHmZ2kfoXEXn5O7-D56EgTLn2a7H3y_TIkHiasY,13157
+pwact/utils/app_lib/cp2k.py,sha256=txd-eMDUOsWPug395WJOQz3aqhwz7eU4hcEZIWTF1OY,15492
 pwact/utils/app_lib/cp2k_dp.py,sha256=VP4gyPGhLcMAqAjrqCQSUiiGlESNlyYz7Gs3Q4QoUHo,6912
-pwact/utils/app_lib/lammps.py,sha256=2oxHJHdDxfDDWWmnjo0gMNwgGvxABwuDgDlb8kbhgfk,8037
+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-0.1.27.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-pwact-0.1.27.dist-info/METADATA,sha256=Kk2-JzZqYkUYiqFRbvXMFLiJBj5hV-jIITIG1U2G8q0,3659
-pwact-0.1.27.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-pwact-0.1.27.dist-info/entry_points.txt,sha256=p61auAnpbn8E2WjvHNBA7rb9_NRAOCew4zdcCj33cGc,42
-pwact-0.1.27.dist-info/top_level.txt,sha256=fY1_7sH5Lke4dC9L8MbYM4fT5aat5eCkAmpkIzY1SlM,6
-pwact-0.1.27.dist-info/RECORD,,
+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,,