ion-CSP 2.1.3__py3-none-any.whl → 2.1.5__py3-none-any.whl

ion_CSP/param/g16_sub.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+BASE_DIR="./"
+
+# 遍历所有.gjf文件
+for gjf in "$BASE_DIR"/*.gjf; do
+    # 安全校验文件存在性
+    [ -f "$gjf" ] || { echo "Skipping invalid file: $gjf"; continue; }
+    
+    # 提取带路径的文件名
+    full_name=$(basename "$gjf")
+    
+    # 安全提取基名（严格去除最后一个.gjf后缀）
+    base_name="${full_name%.*}"
+    
+    # 执行命令（示例）
+    g16 "$gjf" && formchk "${base_name}.chk"
+    if [ $? -ne 0 ] ; then 
+        touch "${base_name}.fchk"
+    fi
+done

ion_CSP/param/sub_final.sh

@@ -0,0 +1,91 @@
+#!/bin/bash
+
+# 设置变量
+BASE_DIR="./"
+INCAR_1="INCAR_1"
+INCAR_2="INCAR_2"
+INCAR_3="INCAR_3"
+POTCAR_H="POTCAR_H"
+POTCAR_C="POTCAR_C"
+POTCAR_N="POTCAR_N"
+POTCAR_O="POTCAR_O"
+
+# 检查必要文件是否存在
+if [[ ! -f "$INCAR_1" || ! -f "$INCAR_2" || ! -f "$INCAR_3" || ! -f "$POTCAR_H" || ! -f "$POTCAR_C" || ! -f "$POTCAR_N" || ! -f "$POTCAR_O" ]]; then
+    echo "Necessary files are missing, please check the path."
+    exit 1
+fi
+
+# 创建 POTCAR 文件
+create_potcar_from_poscar() {
+    poscar_file="$1"
+    output_file="POTCAR"
+    > "$output_file"  # 清空文件
+
+    # 读取 POSCAR 文件的第六行（元素行）
+    read -r element_line < <(sed -n '6p' "$poscar_file")
+
+    # 将元素转换为数组
+    IFS=' ' read -r -a elements <<< "$element_line"
+
+    # 根据元素拼接 POTCAR
+    for element in "${elements[@]}"; do
+        case $element in
+            H) cat "$POTCAR_H" >> "$output_file" ;;
+            C) cat "$POTCAR_C" >> "$output_file" ;;
+            N) cat "$POTCAR_N" >> "$output_file" ;;
+            O) cat "$POTCAR_O" >> "$output_file" ;;
+            *) echo "Warning: POTCAR for element $element not found." ;;
+        esac
+    done
+}
+
+# 提交第一步优化任务
+for contcar in ${BASE_DIR}/CONTCAR_*; do
+    if [[ $contcar =~ CONTCAR_(.*) ]]; then
+        sample=${BASH_REMATCH[1]}
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "$sample_dir"
+        cp "$contcar" "${sample_dir}/POSCAR"
+        cp "$INCAR_1" "${sample_dir}/INCAR"
+        create_potcar_from_poscar "${sample_dir}/POSCAR"  # 根据 POSCAR 创建 POTCAR
+        mv "POTCAR" "${sample_dir}/"  # 使用自动生成的 POTCAR
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All first step tasks have been submitted."
+
+# 提交第二步优化任务
+for sample in $(ls ${BASE_DIR}); do
+    if [ -f "${BASE_DIR}/${sample}/CONTCAR" ]; then
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "${sample_dir}/fine"
+        cp "${sample_dir}/CONTCAR" "${sample_dir}/fine/POSCAR"
+        cp "$INCAR_2" "${sample_dir}/fine/INCAR"
+        cp "${sample_dir}/POTCAR" "${sample_dir}/fine/POTCAR"
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}/fine" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All second step tasks have been submitted."
+
+# 提交第三步优化任务
+for sample in $(ls ${BASE_DIR}); do
+    if [ -f "${BASE_DIR}/${sample}/fine/CONTCAR" ]; then
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "${sample_dir}/fine/final"
+        cp "${sample_dir}/fine/CONTCAR" "${sample_dir}/fine/final/POSCAR"
+        cp "$INCAR_3" "${sample_dir}/fine/final/INCAR"
+        cp "${sample_dir}/fine/POTCAR" "${sample_dir}/fine/final/POTCAR"
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}/fine/final" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All third step tasks have been submitted."

ion_CSP/param/sub_ori.sh

@@ -0,0 +1,74 @@
+#!/bin/bash
+
+# 设置变量
+BASE_DIR="./"
+INCAR_1="INCAR_1"
+INCAR_2="INCAR_2"
+POTCAR_H="POTCAR_H"
+POTCAR_C="POTCAR_C"
+POTCAR_N="POTCAR_N"
+POTCAR_O="POTCAR_O"
+
+# 检查必要文件是否存在
+if [[ ! -f "$INCAR_1" || ! -f "$INCAR_2" || ! -f "$POTCAR_H" || ! -f "$POTCAR_C" || ! -f "$POTCAR_N" || ! -f "$POTCAR_O" ]]; then
+    echo "Necessary files are missing, please check the path."
+    exit 1
+fi
+
+# 创建 POTCAR 文件
+create_potcar_from_poscar() {
+    poscar_file="$1"
+    output_file="POTCAR"
+    > "$output_file"  # 清空文件
+
+    # 读取 POSCAR 文件的第六行（元素行）
+    read -r element_line < <(sed -n '6p' "$poscar_file")
+
+    # 将元素转换为数组
+    IFS=' ' read -r -a elements <<< "$element_line"
+
+    # 根据元素拼接 POTCAR
+    for element in "${elements[@]}"; do
+        case $element in
+            H) cat "$POTCAR_H" >> "$output_file" ;;
+            C) cat "$POTCAR_C" >> "$output_file" ;;
+            N) cat "$POTCAR_N" >> "$output_file" ;;
+            O) cat "$POTCAR_O" >> "$output_file" ;;
+            *) echo "Warning: POTCAR for element $element not found." ;;
+        esac
+    done
+}
+
+# 提交第一步优化任务
+for contcar in ${BASE_DIR}/CONTCAR_*; do
+    if [[ $contcar =~ CONTCAR_(.*) ]]; then
+        sample=${BASH_REMATCH[1]}
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "$sample_dir"
+        cp "$contcar" "${sample_dir}/POSCAR"
+        cp "$INCAR_1" "${sample_dir}/INCAR"
+        create_potcar_from_poscar "${sample_dir}/POSCAR"  # 根据 POSCAR 创建 POTCAR
+        mv "POTCAR" "${sample_dir}/"  # 使用自动生成的 POTCAR
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All first step tasks have been submitted."
+
+# 提交第二步优化任务
+for sample in $(ls ${BASE_DIR}); do
+    if [ -f "${BASE_DIR}/${sample}/CONTCAR" ]; then
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "${sample_dir}/fine"
+        cp "${sample_dir}/CONTCAR" "${sample_dir}/fine/POSCAR"
+        cp "$INCAR_2" "${sample_dir}/fine/INCAR"
+        cp "${sample_dir}/POTCAR" "${sample_dir}/fine/"
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}/fine" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All second step tasks have been submitted."

ion_CSP/param/sub_supple.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+
+# 设置变量
+BASE_DIR="./"
+INCAR_3="INCAR_3"
+POTCAR_H="POTCAR_H"
+POTCAR_C="POTCAR_C"
+POTCAR_N="POTCAR_N"
+POTCAR_O="POTCAR_O"
+
+# 检查必要文件是否存在
+if [[ ! -f "$INCAR_3" || ! -f "$POTCAR_H" || ! -f "$POTCAR_C" || ! -f "$POTCAR_N" || ! -f "$POTCAR_O" ]]; then
+    echo "Necessary files are missing, please check the path."
+    exit 1
+fi
+
+# 创建 POTCAR 文件
+create_potcar_from_poscar() {
+    poscar_file="$1"
+    output_file="POTCAR"
+    > "$output_file"  # 清空文件
+
+    # 读取 POSCAR 文件的第六行（元素行）
+    read -r element_line < <(sed -n '6p' "$poscar_file")
+
+    # 将元素转换为数组
+    IFS=' ' read -r -a elements <<< "$element_line"
+
+    # 根据元素拼接 POTCAR
+    for element in "${elements[@]}"; do
+        case $element in
+            H) cat "$POTCAR_H" >> "$output_file" ;;
+            C) cat "$POTCAR_C" >> "$output_file" ;;
+            N) cat "$POTCAR_N" >> "$output_file" ;;
+            O) cat "$POTCAR_O" >> "$output_file" ;;
+            *) echo "Warning: POTCAR for element $element not found." ;;
+        esac
+    done
+}
+
+# 提交第三步优化任务
+for sample in $(ls ${BASE_DIR}); do
+    if [ -f "${BASE_DIR}/${sample}/fine/CONTCAR" ]; then
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "${sample_dir}/fine/final"
+        cp "${sample_dir}/fine/CONTCAR" "${sample_dir}/fine/final/POSCAR"
+        cp "$INCAR_3" "${sample_dir}/fine/final/INCAR"
+        create_potcar_from_poscar "${sample_dir}/fine/final/POSCAR"  # 根据 POSCAR 创建 POTCAR
+        mv "POTCAR" "${sample_dir}/fine/final/"  # 使用自动生成的 POTCAR
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}/fine/final" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All third step tasks have been submitted."

ion_CSP/task_manager.py

@@ -29,18 +29,15 @@ class TaskManager:
     def _get_version(self):
         """版本获取"""
         try:
-            # 使用 importlib 动态加载
-            spec = importlib.util.spec_from_file_location(
-                "ion_CSP", 
-                os.path.join(self.project_root, "src/ion_CSP/__init__.py")
-            )
-            module = importlib.util.module_from_spec(spec)
-            spec.loader.exec_module(module)
-            return module.__version__
+            return importlib.metadata.version("ion_CSP")
+        except importlib.metadata.PackageNotFoundError:
+            logging.error("Version detection failed")
+            return "unknown"
         except Exception as e:
             logging.error(f"Version detection failed: {e}")
             return "unknown"
 
+
     def _detect_env(self):
         """检测运行环境 - Detect execution environment"""
         if Path("/.dockerenv").exists() or "DOCKER" in os.environ:
@@ -367,7 +364,7 @@ class TaskManager:
         """主菜单循环 - Main menu loop"""
         while True:
             os.system("clear" if os.name == "posix" else "cls")
-            print("========== Task Execution Sys1tem ==========")
+            print("========== Task Execution System ==========")
             print(f"Current Version: {self.version}")
             print(f"Current Environment: {self.envs}")
             print(f"Current Directory: {self.workspace}")

{ion_csp-2.1.3.dist-info → ion_csp-2.1.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.1.3
+Version: 2.1.5
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang
@@ -13,6 +13,7 @@ Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ase==3.23.0
+Requires-Dist: scipy==1.15.2
 Requires-Dist: deepmd-kit==3.0.1
 Requires-Dist: torch==2.5.0
 Requires-Dist: dpdispatcher==0.6.7
@@ -132,8 +133,8 @@ graph TD
 本项目采用MIT许可证，详见LICENSE文件。
 
 ## 技术支持
-- **文档更新**：2025年5月
-- **最新版本**：v2.1.0
+- **文档更新**：2025年6月
+- **最新版本**：v2.1.5
 - **问题追踪**：https://github.com/bagabaga007/ion_CSP/issues
 
 ---
@@ -239,6 +240,6 @@ graph TD
 MIT License, see LICENSE file.
 
 ## Support
-- Documentation last updated: May 2025
-- Latest version: v2.1.0
+- Documentation last updated: June 2025
+- Latest version: v2.1.5
 - Issue tracker: https://github.com/bagabaga007/ion_CSP/issues

ion_csp-2.1.5.dist-info/RECORD

@@ -0,0 +1,44 @@
+ion_CSP/__init__.py,sha256=L5DyCHC4xoiu_KnOW1rVheNbNVooNtuyr75m1z6YbkU,374
+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=e_B0OIRb7nnrNGKuM8PttuRdwOkOH1YtZwBkP7GIZv8,19660
+ion_CSP/identify_molecules.py,sha256=hFKXS0Jjd7LyMsYGc9RmnoRPu1ibXF9fYO_9lR3wTfo,4634
+ion_CSP/log_and_time.py,sha256=-RCycW1VB7sa3bjQZiF7c8i73iam8S41qgJxlHRqJaw,9406
+ion_CSP/mlp_opt.py,sha256=ox4Qxg4D6WzrB8dxVnUWmAngnOA_wdcInP5UhBWsH4c,5535
+ion_CSP/read_mlp_density.py,sha256=3N7kgM2RCe1gbP8QxpgtwYRaj77w4niNglWA5VDoQsk,11209
+ion_CSP/steps_opt_monitor.sh,sha256=1klPjnK0gqkDbvI9PtjdK5qidJ5G0Mo8q1SfrlLW5xM,3330
+ion_CSP/task_manager.py,sha256=pz9xPkCFBpKmeZFgylfUV5iSs4tgbasTZkX0m3lIlWE,16568
+ion_CSP/upload_download.py,sha256=Hiz5jKOy9x26hJJdcpt-owQdVUbzzGuGOelro6JozY8,23801
+ion_CSP/vasp_processing.py,sha256=TshMNs7fA0zABvk4sKlVjofJFwGH9DVYcCGbcUpoH1s,31542
+ion_CSP/model/model.pt,sha256=5D9HTP5b7jUOv3kHltT71ORzhgt5p96awjbqC4oZVjQ,24649402
+ion_CSP/model/options/README.md,sha256=ifoeNXF2CfwqUjt3Xmh5qUl-e4hfP4eMV4EkqV7GU30,182
+ion_CSP/model/options/model.ckpt-4000000.pt,sha256=5D9HTP5b7jUOv3kHltT71ORzhgt5p96awjbqC4oZVjQ,24649402
+ion_CSP/param/INCAR_0,sha256=qh0cOez9-Lv0wVyf6bCrQ92kWiioOsx-tXthcx2GXtE,295
+ion_CSP/param/INCAR_1,sha256=GhWmKUcG01XYISIBOoPRSEEtTgbLeZd7-VeZE5WvXnY,351
+ion_CSP/param/INCAR_2,sha256=951-1SxWO3pZjXmTWcOeDAnaSpUuepyn2FzOXegwRIU,319
+ion_CSP/param/INCAR_3,sha256=zX6W-oX2xTYc8OEkbfzJiyapI2-uBrMpAJcyyypRJ1E,319
+ion_CSP/param/POTCAR_C,sha256=BygEoI0xTgy87Xvqko948Rfj5Nw-qAkwhfd5CvJQ5yA,209530
+ion_CSP/param/POTCAR_H,sha256=ypnE6_RSPVdygq79elXWiZ7gIj6rGVP2VeRXbzY6c74,142686
+ion_CSP/param/POTCAR_N,sha256=n9-vHqk9sJ6A3C3e1yTw9r9SZKDJc1mArgcfdJ0APA4,213434
+ion_CSP/param/POTCAR_O,sha256=S5LYsbk2ZWoDj6hLxRucM48wNHgf7BQcCylgwGdL4hA,222698
+ion_CSP/param/g16_sub.sh,sha256=WOxXhBiPjpZ8eJwdLdLtCfVsWPWh0USxrBbX9u3cunk,519
+ion_CSP/param/sub_final.sh,sha256=jQSEgNThM8UJT4Vd6AzBFeccn-xoqG-fpSTiXmwzZhM,3222
+ion_CSP/param/sub_ori.sh,sha256=JBERlc-VOVCNaKGwiJR8oq7Nyf0KV4JpHEVT5sE5s8E,2497
+ion_CSP/param/sub_supple.sh,sha256=23cam7WyW7-80J8O-Bs45qYkabk3mxZDgiHZvf48KBM,1887
+ion_csp-2.1.5.dist-info/licenses/LICENSE,sha256=2J6A8GT2iIf2LhuWO1_0ilgx7ijzzpQ2BXU7rHKe8Cc,1068
+run/__init__.py,sha256=_9EAXp4cv41ARbxahCkihwqY4F00Y18tBeTauWeD9mw,186
+run/main_CSP.py,sha256=UaYHlh7BSxar4uGppPi-V0cFDpB14212Oy6gta59LfA,5898
+run/main_EE.py,sha256=4L0VbbgUaYaDJM-6EjffphxMoWAHaZchEaSCVJxsdls,6345
+run/run_convert_SMILES.py,sha256=85a8-UXPxPo3Yw_iYED_QF47yNTvYRnJHm3PC1d-d_Q,2056
+run/run_empirical_estimate.py,sha256=U_yvQ5gMiBkDEabHXLJSAEm0EzGHhSKs6xmWoEC_gjc,2831
+run/run_gen_opt.py,sha256=_Zcsu0FkuZTfiGKSWNaK17LiyQ3qrP30F66UN5QemCo,2727
+run/run_read_mlp_density.py,sha256=aSJjWS1jH-D7qzx7RnpMPSTH7KEZp2b35dg1b2OQSCM,1864
+run/run_upload_download.py,sha256=wuTAdy4bgdduD7TJtgHwo_fTpHKlkAwmgRknClDLYDo,2436
+run/run_vasp_processing.py,sha256=hziE4cZwmIWvVaZtwHn9Dl35apYSLlMvSVIbCyd5mFg,1612
+run/update_changelog.py,sha256=ShnVG7v3qSQAzWUA90bFbWGwI3lwfbA_ugov6avS3jU,2121
+ion_csp-2.1.5.dist-info/METADATA,sha256=YmomKcyGXzBZ-e9GWVpM2txQjPBlF6sAORk3sZ7Fw-0,6554
+ion_csp-2.1.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+ion_csp-2.1.5.dist-info/entry_points.txt,sha256=NexQJDs9f69kJA2DgoU6tsA3V8a66nadJRem1U_c_6g,54
+ion_csp-2.1.5.dist-info/top_level.txt,sha256=Vp0RHefYscYU7uQ4Fu6bOKhC_ASrdGOzZxYfN5r0f2M,12
+ion_csp-2.1.5.dist-info/RECORD,,

run/update_changelog.py

@@ -0,0 +1,68 @@
+import subprocess
+
+
+def get_commit_details():
+    # 获取提交信息，包括哈希、日期和消息
+    result = subprocess.run(
+        ["git", "log", "--pretty=format:%h %ad %s", "--date=short"],
+        capture_output=True,
+        text=True,
+    )
+    return result.stdout.splitlines()
+
+
+def get_commit_tags():
+    # 获取每个提交的标签信息
+    tags = {}
+    commits = get_commit_details()
+    for commit in commits:
+        hash_value = commit.split(" ")[0]
+        result = subprocess.run(
+            ["git", "tag", "--points-at", hash_value], capture_output=True, text=True
+        )
+        tag_list = result.stdout.strip().splitlines()
+        tags[hash_value] = tag_list
+    return tags
+
+
+def generate_changelog(commit_details, tags):
+    changelog_path = "CHANGELOG.md"
+
+    # 生成变更日志内容
+    new_changelog_content = []
+
+    # 添加标题
+    new_changelog_content.append("# Changelog\n\n")
+
+    # 添加每个提交的详细信息
+    for detail in commit_details:
+        hash_value, date, *message = detail.split(" ")
+        message = " ".join(message)  # 重新组合提交信息
+
+        # 检查是否有标签
+        if tags.get(hash_value):
+            # 添加标签信息
+            for tag in tags[hash_value]:
+                new_changelog_content.append(f"## {tag}\n")
+
+            # 添加提交信息
+            new_changelog_content.append(f"### {hash_value} ({date})\n")
+            new_changelog_content.append(f"{message}\n\n")
+        else:
+            # 如果没有标签，直接添加提交信息
+            new_changelog_content.append(f"### {hash_value} ({date})\n")
+            new_changelog_content.append(f"{message}\n\n")
+
+    # 写入 CHANGELOG.md
+    with open(changelog_path, "w") as file:
+        file.writelines(new_changelog_content)
+
+
+if __name__ == "__main__":
+    commit_details = get_commit_details()
+    tags = get_commit_tags()  # 获取每个提交的标签信息
+    if commit_details:
+        generate_changelog(commit_details, tags)
+        print("CHANGELOG.md has been updated.")
+    else:
+        print("No new commits found.")

ion_csp-2.1.3.dist-info/RECORD

@@ -1,28 +0,0 @@
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-ion_CSP/__main__.py,sha256=XlNCx5eMSrL7yld9ddSYXhjXvg2ZYGD_uk9LdqNabvs,74
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