hpc-task 0.1.2__py3-none-any.whl → 0.2.0__py3-none-any.whl

hpc_task/hpc.py

@@ -79,7 +79,7 @@ class HPCTask:
             abs_workdir = stdout.read().decode('utf-8').strip().split()[-1]
             workdir = Path(abs_workdir).relative_to(Path(self._remote_parent_workdir))
             if self.workdir is None:
-                self.workdir = str(workdir)
+                self.workdir = workdir.as_posix()
         return self.workdir
 
     @property
@@ -292,7 +292,6 @@ class HPCTask:
                 print(f"Waiting for the queue 10 seconds...")
                 sleep(10)
                 status = self.status
-                need_sync = False
             elif status in ('SUSPENDED', 'DONE'):
                 output = ''
                 err = f"Job {self.jobid} status: {status}"
@@ -327,12 +326,12 @@ class HPCTask:
             rel_path = Path(root).relative_to(local_path)
             remote_dir = remote_path / rel_path
             if str(rel_path) != ".":
-                _ensure_remote_dir_exists(sftp_client, str(remote_dir))
+                _ensure_remote_dir_exists(sftp_client, remote_dir.as_posix())
             # 上传文件
             for file in files:
                 local_file = Path(root) / file
                 remote_file = remote_dir / file
-                sftp_client.put(str(local_file), str(remote_file), confirm=False)
+                sftp_client.put(local_file.as_posix(), remote_file.as_posix(), confirm=False)
 
         return None
 
@@ -365,13 +364,14 @@ def _ensure_remote_dir_exists(sftp, remote_dir):
     except FileNotFoundError:
         # 递归创建目录
         parts = Path(remote_dir).parts
-        current_path = parts[0]
+        current_path = Path(parts[0])
         for part in parts[1:]:  # 跳过根目录
-            current_path = os.path.join(current_path, part)
+            # current_path = os.path.join(current_path, part)
+            current_path = current_path / part
             try:
-                sftp.stat(current_path)
+                sftp.stat(current_path.as_posix())
             except FileNotFoundError:
-                sftp.mkdir(current_path)
+                sftp.mkdir(current_path.as_posix())
 
 def _download_dir(sftp, remote, local):
     os.makedirs(local, exist_ok=True)

hpc_task/hpc_calculator/vasp.py

@@ -1,6 +1,10 @@
+import os
 import subprocess
+from pathlib import Path
 
+from ase.calculators import calculator
 from ase.calculators.vasp import Vasp as ase_Vasp
+import ase.io
 from hpc_task.hpc import HPCTask
 
 
@@ -44,3 +48,41 @@ class Vasp(ase_Vasp):
         if out is not None:
             out.write(stdout)
         return returncode, stderr
+
+    def execute_only(self):
+        """
+        仅仅执行 command 命令，从文件夹中读取 INCAR、POTCAR、POSCAR、KPOINTS
+        """
+        self.read_potcar(filename=self._indir('POTCAR'))
+        self.read_incar(filename=self._indir('INCAR'))
+        self.read_kpoints(filename=self._indir('KPOINTS'))
+        atoms = ase.io.read(filename=self._indir('POSCAR'))
+        # 需要读进去ase-sort.dat，否则结果会报错
+        sortfile = self._indir('ase-sort.dat')
+        if os.path.isfile(sortfile):
+            self.sort = []
+            self.resort = []
+            with open(sortfile) as fd:
+                for line in fd:
+                    sort, resort = line.split()
+                    self.sort.append(int(sort))
+                    self.resort.append(int(resort))
+        else:
+            # Redo the sorting
+            self.initialize(atoms)
+
+        command = self.make_command(self.command)
+        with self._txt_outstream() as out:
+            errorcode, stderr = self._run(command=command,
+                                          out=out,
+                                          directory=self.directory)
+
+        if errorcode:
+            raise calculator.CalculationFailed(
+                '{} in {} returned an error: {:d} stderr {}'.format(
+                    self.name, Path(self.directory).resolve(), errorcode,
+                    stderr))
+
+        # Read results from calculation
+        self.update_atoms(atoms)
+        self.read_results()

{hpc_task-0.1.2.dist-info → hpc_task-0.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hpc_task
-Version: 0.1.2
+Version: 0.2.0
 Summary: HPC Task python library.
 Home-page: https://gitee.com/pjren/hpc_task
 Author: Renpj
@@ -61,13 +61,14 @@ hpc.close()  # 此时可以关闭 ssh 通道
 # 在运行时候再重新构造和连接 hpc
 hpc = HPCTask(jobid=jobid)  # workdir 会根据 jobid 提取得到
 hpc.connect(target_host)
-
+hpc.get_workdir()
 # 结构、计算参数设置
 atoms = ase.Atoms('N2', positions=[(0., 0., 0.), (1.4, 0., 0.)],
                   cell=[10, 10, 10], pbc=True)
 # calc 设置
 calc = hpc_Vasp(  
             xc='pbe',
+            directory=hpc.workdir,  # 必须设置, 会新建文件夹，并进入文件夹执行命令
             command='mpirun -np 8 vasp544_std',  # 必须设置，或者提供了 ASE vasp 的相关设置
             hpctask=hpc,  # 这个非常关键，必须提供
             gamma=True,

hpc_task-0.2.0.dist-info/RECORD

@@ -0,0 +1,11 @@
+hpc_task/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+hpc_task/hpc.py,sha256=nAf7dpoNh9gopk4GbYyPACvtZTCtwe8KfhR0h1pR0Nk,15219
+hpc_task/hpc_calculator/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+hpc_task/hpc_calculator/lasp.py,sha256=HD-DCyXoP0C3zuhgB8Da94QrADyZlrIa-ZlcFPvlpnQ,1059
+hpc_task/hpc_calculator/vasp.py,sha256=_hOfeD2_izj-sJ_QELsm4MItP3Ci07VSvj72g2TTReE,3001
+hpc_task/templates/__init__.py,sha256=qLeR7AflskortkH8K4eXnRvINl3otLLKHhTNO6Wnh8Q,695
+hpc_task-0.2.0.dist-info/licenses/LICENSE,sha256=iEk8UVtFW_L7ddFiCE_WFUjbOCaVc5fwNapeDmeY0WA,1063
+hpc_task-0.2.0.dist-info/METADATA,sha256=38lHbW5qoZq-aGIJmgZ1xiMWmB9XltR1Z20g4EDHPDg,2235
+hpc_task-0.2.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+hpc_task-0.2.0.dist-info/top_level.txt,sha256=6mflaHAkVGFi5mREsN5zh0KOO13pTNrTBRAAcwmHMVA,9
+hpc_task-0.2.0.dist-info/RECORD,,

hpc_task-0.1.2.dist-info/RECORD

@@ -1,11 +0,0 @@
-hpc_task/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-hpc_task/hpc.py,sha256=LKgxvHjymGzA287sZJJt4XrpnpjhgMMlBrMd55fpVBE,15152
-hpc_task/hpc_calculator/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-hpc_task/hpc_calculator/lasp.py,sha256=HD-DCyXoP0C3zuhgB8Da94QrADyZlrIa-ZlcFPvlpnQ,1059
-hpc_task/hpc_calculator/vasp.py,sha256=ipFqlFIDQNAa6DI51lwvY9hlacZ-Fdp2tZe16xDqjF0,1418
-hpc_task/templates/__init__.py,sha256=qLeR7AflskortkH8K4eXnRvINl3otLLKHhTNO6Wnh8Q,695
-hpc_task-0.1.2.dist-info/licenses/LICENSE,sha256=iEk8UVtFW_L7ddFiCE_WFUjbOCaVc5fwNapeDmeY0WA,1063
-hpc_task-0.1.2.dist-info/METADATA,sha256=_7d5ZpZnZ9rkJWzJwhSKxpZFuqOyRe3IK6azeFp9M-I,2114
-hpc_task-0.1.2.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-hpc_task-0.1.2.dist-info/top_level.txt,sha256=6mflaHAkVGFi5mREsN5zh0KOO13pTNrTBRAAcwmHMVA,9
-hpc_task-0.1.2.dist-info/RECORD,,