ion-CSP 2.0.8__py3-none-any.whl → 2.1.3__py3-none-any.whl

run/run_upload_download.py

@@ -0,0 +1,66 @@
+import os
+import yaml
+import logging
+import argparse
+from ion_CSP.log_and_time import log_and_time, StatusLogger
+from ion_CSP.upload_download import SSHBatchJob
+
+
+@log_and_time
+def main(work_dir, config):
+    task_name_3_1 = '3_upload_vasp'
+    task_3_1 = StatusLogger(work_dir=work_dir, task_name=task_name_3_1)
+    
+    batch_config = {"upload_prefixes": ["CONTCAR_", "OUTCAR_"]}
+    folder_name = os.path.normpath(os.path.abspath(work_dir)).split(os.sep)[-1]
+    job = SSHBatchJob(
+        work_dir=work_dir,
+        machine_json=config["upload_download"]["machine_json"],
+        machine_type="ssh_direct",
+    )
+    if not task_3_1.is_successful():
+        try:
+            task_3_1.set_running()
+            script = "steps_opt_monitor.sh"
+            command = f"./steps_opt_monitor.sh {folder_name}"
+            job.prepare_and_submit(
+                command=command, forward_common_files=[script], batch_config=batch_config
+            )
+            # 关闭 SFTP 和 SSH 客户端
+            job.close_connection()
+            task_3_1.set_success()
+        except Exception:
+            task_3_1.set_failure()
+            raise
+
+    if task_3_1.is_successful():
+        task_name_3_2 = '3_download_vasp'
+        task_3_2 = StatusLogger(work_dir=work_dir, task_name=task_name_3_2)
+        if not task_3_2.is_successful():
+            try:
+                task_3_2.set_running()
+                job.download_entire_folder()
+                job.client.exec_command(f"rm -r {job.remote_dir}/{folder_name}")
+                print(f"Deleted remote folder {folder_name}")
+                logging.info(f"Deleted remote folder {folder_name}")
+                # 关闭 SFTP 和 SSH 客户端
+                job.close_connection()
+                task_3_2.set_success()
+            except Exception:
+                task_3_2.set_failure()
+                raise
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Process files in a specified working directory")
+    parser.add_argument("work_dir", type=str, help="The working directory to run the script in")
+    args = parser.parse_args()
+    # 尝试读取配置文件
+    try:
+        with open(os.path.join(args.work_dir, "config.yaml"), "r") as file:
+            config = yaml.safe_load(file)
+    except FileNotFoundError:
+        print(f"config.yaml not found in {args.work_dir}.")
+        raise
+    # 调用主函数
+    main(args.work_dir, config)

run/run_vasp_processing.py

@@ -0,0 +1,42 @@
+from ion_CSP.vasp_processing import VaspProcessing
+from ion_CSP.log_and_time import StatusLogger
+from ion_CSP.log_and_time import log_and_time, merge_config, get_work_dir_and_config
+
+# 默认配置
+DEFAULT_CONFIG = {
+    "vasp_processing": {
+        "nodes": 2,  # VASP 分步优化占用 CPU 节点数
+        "molecules_prior": True,  # 是否检查离子晶体结构中所有离子的结构
+    },
+}
+
+@log_and_time
+def main(work_dir, config):
+    task_name = "4_vasp_processing"
+    task = StatusLogger(work_dir=work_dir, task_name=task_name)
+    try:
+        task.set_running()
+        result = VaspProcessing(work_dir=work_dir)
+        # 基于 dpdispatcher 模块，在远程CPU服务器上批量准备并提交VASP分步优化任务
+        # result.dpdisp_vasp_tasks(
+        #     machine=config["vasp_processing"]["machine"],
+        #     resources=config["vasp_processing"]["resources"],
+        #     nodes=config["vasp_processing"]["nodes"],
+        # )
+        # 批量读取 VASP 分步优化的输出文件，并将能量和密度等结果保存到目录中的相应CSV文件
+        result.read_vaspout_save_csv(config["vasp_processing"]["molecules_prior"])
+        task.set_success()
+    except Exception:
+        task.set_failure()
+        raise
+
+
+if __name__ == "__main__":
+    # 获取工作目录和配置
+    work_dir, config = get_work_dir_and_config()
+    # 合并配置（假设有merge_config函数）
+    config["vasp_processing"] = merge_config(
+        default_config=DEFAULT_CONFIG, user_config=config, key="vasp_processing"
+    )
+    # 调用主函数
+    main(work_dir, config)

ion_csp-2.0.8.dist-info/RECORD

@@ -1,19 +0,0 @@
-ion_CSP/__init__.py,sha256=M5RcbYDdt-UBVpsDKiJWJqLvSFfoBfU6aTUVccgK_BE,190
-ion_CSP/__main__.py,sha256=XlNCx5eMSrL7yld9ddSYXhjXvg2ZYGD_uk9LdqNabvs,74
-ion_CSP/convert_SMILES.py,sha256=4fndMcuIEypYtkXWBoS7W7uEXkZXVLeMDshdXEIk5kY,13864
-ion_CSP/empirical_estimate.py,sha256=_U5VRWSIAiJGcxnP3mnCHn8zKzviFEQhQwN7TjPTnCU,29089
-ion_CSP/gen_opt.py,sha256=aVZmf2RqePCwZShgpNvzqfntNAW0I0yctWHGXoe3mgw,19463
-ion_CSP/identify_molecules.py,sha256=hFKXS0Jjd7LyMsYGc9RmnoRPu1ibXF9fYO_9lR3wTfo,4634
-ion_CSP/log_and_time.py,sha256=6RKegXF8Gc1HqzAbE-PT9ejX3Ncyuz3v3FivujJt8to,9072
-ion_CSP/mlp_opt.py,sha256=ox4Qxg4D6WzrB8dxVnUWmAngnOA_wdcInP5UhBWsH4c,5535
-ion_CSP/read_mlp_density.py,sha256=TinsFGJPF0TPVZKMCzPyxuHBGrdeqw7yOnGh-78qbqo,11209
-ion_CSP/steps_opt_monitor.sh,sha256=1klPjnK0gqkDbvI9PtjdK5qidJ5G0Mo8q1SfrlLW5xM,3330
-ion_CSP/task_manager.py,sha256=S0QK7EJhKrQL1hzMqkR6a6y3Du027Ppyz-zHenWrFQ4,16241
-ion_CSP/upload_download.py,sha256=Hiz5jKOy9x26hJJdcpt-owQdVUbzzGuGOelro6JozY8,23801
-ion_CSP/vasp_processing.py,sha256=eQTMKIPBzi1X4HHTqWkHE1Lt8dvCCV-MXPCR3RtKYZ0,13977
-ion_csp-2.0.8.dist-info/licenses/LICENSE,sha256=2J6A8GT2iIf2LhuWO1_0ilgx7ijzzpQ2BXU7rHKe8Cc,1068
-ion_csp-2.0.8.dist-info/METADATA,sha256=pZg7XM0CD5Du6rQJvijc_VOyfvtFVlnmWAZiwBPmeIU,6380
-ion_csp-2.0.8.dist-info/WHEEL,sha256=QZxptf4Y1BKFRCEDxD4h2V0mBFQOVFLFEpvxHmIs52A,91
-ion_csp-2.0.8.dist-info/entry_points.txt,sha256=NexQJDs9f69kJA2DgoU6tsA3V8a66nadJRem1U_c_6g,54
-ion_csp-2.0.8.dist-info/top_level.txt,sha256=aYZa43dDebjLpWPN6bDIlBb6BVwA8gk4ajEjDDK9b9I,8
-ion_csp-2.0.8.dist-info/RECORD,,