hpc-task 0.1.3__tar.gz → 0.2.0__tar.gz

{hpc_task-0.1.3 → hpc_task-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hpc_task
-Version: 0.1.3
+Version: 0.2.0
 Summary: HPC Task python library.
 Home-page: https://gitee.com/pjren/hpc_task
 Author: Renpj

hpc_task-0.2.0/hpc_task/hpc_calculator/vasp.py

@@ -0,0 +1,88 @@
+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
+
+
+class Vasp(ase_Vasp):
+    def __init__(self,
+                 atoms=None,
+                 restart=None,
+                 directory='.',
+                 label='vasp',
+                 command=None,
+                 hpctask:HPCTask=None,
+                 **kwargs):
+        super().__init__(
+            atoms=atoms,
+            restart=restart,
+            directory=directory,
+            label=label,
+            command=command,
+            **kwargs
+        )
+        self.hpctask = hpctask
+
+    def _run(self, command=None, out=None, directory=None):
+        """Method to explicitly execute VASP"""
+        if command is None:
+            command = self.command
+
+        if self.hpctask is not None:
+            remote_cmd = f"gosh-remote -vv client run '{command}'"
+            returncode, stderr, stdout = self.hpctask.execute(remote_cmd)
+
+        else:
+            result = subprocess.run(command,
+                                    shell=True,
+                                    cwd=directory,
+                                    capture_output=True,
+                                    text=True)
+            stdout = result.stdout
+            returncode = result.returncode
+            stderr = result.stderr
+        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-0.1.3 → hpc_task-0.2.0}/hpc_task.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hpc_task
-Version: 0.1.3
+Version: 0.2.0
 Summary: HPC Task python library.
 Home-page: https://gitee.com/pjren/hpc_task
 Author: Renpj

{hpc_task-0.1.3 → hpc_task-0.2.0}/setup.py

@@ -10,7 +10,7 @@ install_requires = [
 
 setup(
     name='hpc_task',
-    version='0.1.3',
+    version='0.2.0',
     url='https://gitee.com/pjren/hpc_task',
     license='MIT',
     author='Renpj',

{hpc_task-0.1.3 → hpc_task-0.2.0}/tests/test_task.py

@@ -153,3 +153,31 @@ class TestHPCTask:
         # finish job
         hpc.postrun()
         hpc.close()
+
+    def test_hpc_vasp_execute_only(self):
+        workdir = 'test_hpc_vasp_execute_only'
+        Path(workdir).mkdir(parents=True, exist_ok=True)
+        shutil.copyfile('test_files/INCAR', Path(workdir)/'INCAR')
+        shutil.copyfile('test_files/POSCAR', Path(workdir)/'POSCAR')
+        shutil.copyfile('test_files/POTCAR', Path(workdir)/'POTCAR')
+        shutil.copyfile('test_files/KPOINTS', Path(workdir)/'KPOINTS')
+
+        # 队列占据
+        hpc = HPCTask(workdir=workdir)
+        hpc.scriptdir = '/data/bin/remote.job'
+        hpc.connect(target_host, jump_host)
+        hpc.prerun()
+        calc = hpc_Vasp(
+                    directory=workdir,
+                    command='mpirun -np 2 vasp_gam',
+                    hpctask=hpc,  # 这个非常关键
+                    )
+        # 计算
+        calc.execute_only()
+        atoms = calc.atoms
+        atoms.calc = calc
+        e = atoms.get_potential_energy()
+        print(f"Energy of N2 is {e} eV.")
+        # finish job
+        hpc.postrun()
+        hpc.close()

hpc_task-0.1.3/hpc_task/hpc_calculator/vasp.py

@@ -1,46 +0,0 @@
-import subprocess
-
-from ase.calculators.vasp import Vasp as ase_Vasp
-from hpc_task.hpc import HPCTask
-
-
-class Vasp(ase_Vasp):
-    def __init__(self,
-                 atoms=None,
-                 restart=None,
-                 directory='.',
-                 label='vasp',
-                 command=None,
-                 hpctask:HPCTask=None,
-                 **kwargs):
-        super().__init__(
-            atoms=atoms,
-            restart=restart,
-            directory=directory,
-            label=label,
-            command=command,
-            **kwargs
-        )
-        self.hpctask = hpctask
-
-    def _run(self, command=None, out=None, directory=None):
-        """Method to explicitly execute VASP"""
-        if command is None:
-            command = self.command
-
-        if self.hpctask is not None:
-            remote_cmd = f"gosh-remote -vv client run '{command}'"
-            returncode, stderr, stdout = self.hpctask.execute(remote_cmd)
-
-        else:
-            result = subprocess.run(command,
-                                    shell=True,
-                                    cwd=directory,
-                                    capture_output=True,
-                                    text=True)
-            stdout = result.stdout
-            returncode = result.returncode
-            stderr = result.stderr
-        if out is not None:
-            out.write(stdout)
-        return returncode, stderr