added vasp asimmodule

asimtools/asimmodules/lammps/lammps.py

@@ -125,14 +125,14 @@ def lammps(
             command, check=False, capture_output=True, text=True,
         )
 
-    with open('lmp_stdout.txt', 'w', encoding='utf-8') as f:
+    with open('lmp_stdout.txt', 'a+', encoding='utf-8') as f:
         f.write(completed_process.stdout)
 
     if completed_process.returncode != 0:
         err_txt = f'Failed to run {lmp_inp_file}\n'
-        err_txt += 'See lmp.stderr.txt for details.'
+        err_txt += 'See lmp_stderr.txt for details.'
         logging.error(err_txt)
-        with open('lmp_stderr.txt', 'w', encoding='utf-8') as f:
+        with open('lmp_stderr.txt', 'a+', encoding='utf-8') as f:
             f.write(completed_process.stderr)
         completed_process.check_returncode()
         return {}

asimtools/asimmodules/vasp/vasp.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+'''
+Runs VASP based on input files and optionally MP settings. 
+Heavily uses pymatgen for IO and MP settings.
+VASP must be installed 
+
+Author: [email protected]
+'''
+from typing import Dict, Optional, Sequence
+import os
+import sys
+from pathlib import Path
+from numpy.random import randint
+import subprocess
+import logging
+from ase.io import read
+from pymatgen.io.ase import AseAtomsAdaptor
+from pymatgen.io.vasp import Poscar
+from pymatgen.io.vasp.sets import (
+    MPRelaxSet, MPStaticSet, MPNonSCFSet, MPScanRelaxSet
+)
+from asimtools.utils import (
+    get_atoms,
+)
+
+def vasp(
+    image: Optional[Dict],
+    vaspinput_args: Optional[Dict] = None,
+    command: str = 'vasp_std',
+    mpset: Optional[str] = None,
+    write_image_output: bool = False,
+) -> Dict:
+    """Run VASP with given input files and specified image
+
+    :param image: Initial image for VASP calculation. Image specification,
+        see :func:`asimtools.utils.get_atoms`
+    :type image: Dict
+    :param vaspinput_args: Dictionary of VASP input arguments. 
+        See :class:`pymatgen.io.vasp.inputs.VaspInput`
+    :type vaspinput_args: Dict
+    :param command: Command with which to run VASP, defaults to 'vasp_std'
+    :type command: str, optional
+    :param mpset: Material Project VASP set to use, defaults to None
+    :type mpset: str, optional
+    :param write_image_output: Whether to write output image in standard 
+        asimtools format to file, defaults to False
+    :type write_image_output: bool, optional
+    """
+
+    if vaspinput_args:
+        if image is not None:
+            atoms = get_atoms(**image)
+            struct = AseAtomsAdapter.get_structure(atoms)
+        vaspinput = VaspInput(
+            poscar=Poscar(struct),
+            **vaspinput_args
+        )
+    else:
+        atoms = get_atoms(**image)
+        struct = AseAtomsAdaptor.get_structure(atoms)
+        if mpset == 'MPRelaxSet':
+            vasp_input = MPRelaxSet(struct)
+        elif mpset == 'MPStaticSet':
+            vasp_input = MPStaticSet(struct)
+        elif mpset == 'MPNonSCFSet':
+            vasp_input = MPNonSCFSet(struct)
+        elif mpset == 'MPScanRelaxSet':
+            vasp_input = MPScanRelaxSet(struct)
+        else:
+            raise ValueError(f'Unknown MPSet: {mpset}')
+
+        vasp_input.write_input("./")
+
+    command = command.split(' ')
+    completed_process = subprocess.run(
+            command, check=False, capture_output=True, text=True,
+        )
+
+    with open('vasp_stdout.txt', 'a+', encoding='utf-8') as f:
+        f.write(completed_process.stdout)
+
+    if completed_process.returncode != 0:
+        err_txt = f'Failed to run VASP\n'
+        err_txt += 'See vasp_stderr.txt for details.'
+        logging.error(err_txt)
+        with open('vasp_stderr.txt', 'a+', encoding='utf-8') as f:
+            f.write(completed_process.stderr)
+        completed_process.check_returncode()
+        return {}
+
+    if write_image_output:
+        atoms_output = read('OUTCAR')
+        atoms_output.write(
+            'image_output.xyz',
+            format='extxyz',
+        )
+
+    return {}

asimtools/job.py

@@ -406,7 +406,6 @@ def gen_input_files(
         images = self.sim_input.get('args', {}).get('images', False)
         if images and write_image:
             if images.get('images', False) or images.get('image_file', False):
-                print(write_image, os.getcwd(), images)
                 images = get_images(**images)
                 input_images_file = 'images_input.xyz' # Relative to workdir
                 ase.io.write(
@@ -948,7 +947,6 @@ def submit(self, dependency: Union[List,None] = None, debug: bool = False) -> Li
                             descend=True
                         )
                     if not cur_step_complete:
-                        print(f'XXXX Step {step+i} not complete, submitting')
                         slurm_flags = curjob.env['slurm']['flags']
                         if isinstance(slurm_flags, list):
                             job_name = curjob.sim_input.get('job_name',False)

examples/external/VASP/vasp_mpset_sim_input.yaml

@@ -0,0 +1,9 @@
+asimmodule: vasp.vasp
+workdir: vasp_mpset_results
+env_id: inline
+args:
+  image:
+    name: Na
+    builder: bulk
+  mpset: MPStaticSet
+  command: vasp_std