Add option to export structure in LAMMPS format in abistruct.py export

abipy/core/structure.py

@@ -1806,6 +1806,13 @@ def convert(self, fmt: str = "cif", **kwargs) -> str:
                 return Poscar(self).get_str(significant_figures=12)
             except AttributeError:
                 return Poscar(self).get_string(significant_figures=12)
+
+        elif fmt.lower() == "lammps":
+            from pymatgen.io.lammps.data import LammpsData
+            # Convert the structure to a LAMMPS data file
+            lammps_data = LammpsData.from_structure(self)
+            return lammps_data.get_str()
+
         else:
             return super().to(fmt=fmt, **kwargs)
 

abipy/eph/gstore.py

@@ -15,7 +15,7 @@
 from monty.functools import lazy_property
 #from monty.termcolor import cprint
 from abipy.core.structure import Structure
-from abipy.core.mixins import AbinitNcFile, Has_Structure, Has_ElectronBands, Has_Header, NotebookWriter
+from abipy.core.mixins import AbinitNcFile, Has_Structure, Has_ElectronBands, Has_Header #, NotebookWriter
 from abipy.tools.typing import PathLike
 #from abipy.tools.plotting import (add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt, set_axlims, set_visible,
 #    rotate_ticklabels, ax_append_title, set_ax_xylabels, linestyles)
@@ -26,7 +26,6 @@
 from abipy.eph.common import BaseEphReader
 
 
-
 class GstoreFile(AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands): # , NotebookWriter):
     """
     This file stores the e-ph matrix elements and provides methods to analyze and plot results.
@@ -178,15 +177,15 @@ def from_gstore(cls, gstore: GstoreFile, spin: int):
 
         vk_cart_ibz, vkmat_cart_ibz = None, None
         if ncr.with_vk == 1:
-           # NCF_CHECK(nctk_def_arrays(spin_ncid, nctkarr_t("vk_cart_ibz", "dp", "three, nb, gstore_nkibz")))
-           vk_cart_ibz = ncr.read_value("vk_cart_ibz", path=path)
+            # NCF_CHECK(nctk_def_arrays(spin_ncid, nctkarr_t("vk_cart_ibz", "dp", "three, nb, gstore_nkibz")))
+            vk_cart_ibz = ncr.read_value("vk_cart_ibz", path=path)
 
         if ncr.with_vk == 2:
-           # Full (nb x nb) matrix.
-           # Have to transpose (nb_kq, nb_k) submatrix written by Fortran.
-           # NCF_CHECK(nctk_def_arrays(spin_ncid, nctkarr_t("vkmat_cart_ibz", "dp", "two, three, nb, nb, gstore_nkibz")))
-           vkmat_cart_ibz = ncr.read_value("vkmat_cart_ibz", path=path).transpose(0, 1, 3, 2, 4).copy()
-           vkmat_cart_ibz = vkmat_cart_ibz[...,0] + 1j*vkmat_cart_ibz[...,1]
+            # Full (nb x nb) matrix.
+            # Have to transpose (nb_kq, nb_k) submatrix written by Fortran.
+            # NCF_CHECK(nctk_def_arrays(spin_ncid, nctkarr_t("vkmat_cart_ibz", "dp", "two, three, nb, nb, gstore_nkibz")))
+            vkmat_cart_ibz = ncr.read_value("vkmat_cart_ibz", path=path).transpose(0, 1, 3, 2, 4).copy()
+            vkmat_cart_ibz = vkmat_cart_ibz[...,0] + 1j*vkmat_cart_ibz[...,1]
 
         # Note conversion between Fortran and python convention.
         bstart = ncr.read_value("bstart", path=path) - 1
@@ -382,7 +381,6 @@ def path2group(self) -> dict:
         return self.rootgrp.groups
 
 
-
 class GstoreRobot(Robot, RobotWithEbands):
     """
     This robot analyzes the results contained in multiple GSTORE.nc files.
@@ -413,38 +411,38 @@ def compare(self) -> None:
 
     @staticmethod
     def compare_two_gstores(gstore1: GstoreFile, gstore2: GstoreFile):
-       """
-       Helper function to compare two GSTORE files.
-       """
-       aname_list = ["structure", "nsppol", "cplex", "nkbz", "nkibz",
-                     "nqbz", "nqibz", "completed", "kzone", "qzone", "kfilter", "gmode",
-                     "brange_spin", "erange_spin", "glob_spin_nq", "glob_nk_spin",
-                    ]
-
-       for aname in aname_list:
-           # Get attributes in gstore first, then in gstore.r, else raise.
-           if hasattr(gstore1, aname):
-               val1, val2 = getattr(gstore1, aname), getattr(gstore2, aname)
-           elif hasattr(gstore1.r, aname):
-               val1, val2 = getattr(gstore1.r, aname), getattr(gstore2.r, aname)
-           else:
-               raise AttributeError(f"Cannot find attribute `{aname=}` neither in gstore not in gstore.r")
+        """
+        Helper function to compare two GSTORE files.
+        """
+        aname_list = ["structure", "nsppol", "cplex", "nkbz", "nkibz",
+                      "nqbz", "nqibz", "completed", "kzone", "qzone", "kfilter", "gmode",
+                      "brange_spin", "erange_spin", "glob_spin_nq", "glob_nk_spin",
+                     ]
+
+        for aname in aname_list:
+            # Get attributes in gstore first, then in gstore.r, else raise.
+            if hasattr(gstore1, aname):
+                val1, val2 = getattr(gstore1, aname), getattr(gstore2, aname)
+            elif hasattr(gstore1.r, aname):
+                val1, val2 = getattr(gstore1.r, aname), getattr(gstore2.r, aname)
+            else:
+                raise AttributeError(f"Cannot find attribute `{aname=}` neither in gstore not in gstore.r")
 
            # Now compare val1 and val2 taking into account the type.
-           if isinstance(val1, (str, int, float, Structure)):
-               eq = val1 == val2
-           elif isinstance(val1, np.ndarray):
-               eq = np.allclose(val1, val2)
-           else:
-               raise TypeError(f"Don't know how to handle comparison for type: {type(val1)}")
-
-           if not eq:
-               raise RuntimeError(f"Different values of {aname=}, {val1=}, {val2=}")
-
-           # Compare gkq objects for each spin.
-           for spin in range(gstore1.nsppol):
-               gqk1, gqk2 = gstore1.gqk_spin[spin], gstore2.gqk_spin[spin]
-               gqk1.compare(gqk2)
+            if isinstance(val1, (str, int, float, Structure)):
+                eq = val1 == val2
+            elif isinstance(val1, np.ndarray):
+                eq = np.allclose(val1, val2)
+            else:
+                raise TypeError(f"Don't know how to handle comparison for type: {type(val1)}")
+
+            if not eq:
+                raise RuntimeError(f"Different values of {aname=}, {val1=}, {val2=}")
+
+            # Compare gkq objects for each spin.
+            for spin in range(gstore1.nsppol):
+                gqk1, gqk2 = gstore1.gqk_spin[spin], gstore2.gqk_spin[spin]
+                gqk1.compare(gqk2)
 
     def yield_figs(self, **kwargs):  # pragma: no cover
         """

abipy/flowtk/qutils.py

@@ -308,11 +308,12 @@ def get_slurm_template(body) -> str:
     """
     return """\
 #!/bin/bash
-
-# Please customize this section using your settings.
+#
+# Please CUSTOMIZE this section according to your cluster and the type of calculation
+#
 #SBATCH --job-name=my_job
-#SBATCH --output=%j_%x.out
-#SBATCH --error=%j_%x.err
+#SBATCH --output=%j_%x.slurm.out
+#SBATCH --error=%j_%x.slurm.err
 #SBATCH --partition=debug
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=64
@@ -337,11 +338,10 @@ def get_slurm_template(body) -> str:
 echo "number of mpi tasks: $SLURM_NTASKS tasks"
 echo "OMP_NUM_THREADS    : $OMP_NUM_THREADS"
 echo "number of gpus     : $SLURM_GPUS_ON_NODE"
-
 echo "------------------- Node list ------------------"
 echo $SLURM_JOB_NODELIST
 
-echo "---------------- Checking limits ---------------"
+echo "---------------- Printing limits ---------------"
 ulimit -s unlimited
 ulimit -a
 
@@ -350,6 +350,7 @@ def get_slurm_template(body) -> str:
 # ------------------------------------------------------------------------------
 
 echo "----------------- Environment ------------------"
+
 source $HOME/vasp.6.2.1/modules.sh
 module list
 
@@ -359,6 +360,7 @@ def get_slurm_template(body) -> str:
 
 {body}
 
+echo -n "This run completed on: "
 date
 """
 

abipy/ml/extxyz_generator.py

@@ -3,14 +3,14 @@
 from __future__ import annotations
 
 import os
-import numpy as np
+#import numpy as np
 import abipy.core.abinit_units as abu
 #try:
 #    import ase
 #except ImportError as exc:
 #    raise ImportError("ase not installed. Try `pip install ase`.") from exc
 from pathlib import Path
-from ase.atoms import Atoms
+#from ase.atoms import Atoms
 from ase.calculators.singlepoint import SinglePointCalculator
 from monty.string import list_strings  # marquee,
 #from monty.functools import lazy_property
@@ -22,7 +22,6 @@
 #from ase.calculators.calculator import Calculator
 #from ase.io.vasp import write_vasp_xdatcar, write_vasp
 from ase.stress import full_3x3_to_voigt_6_stress
-from ase.calculators.singlepoint import SinglePointCalculator
 from ase.io import write
 from pymatgen.io.vasp.outputs import Vasprun, Outcar
 from abipy.core import Structure
@@ -64,9 +63,9 @@ class ExtxyzIOWriter:
 
     @classmethod
     def from_top(cls, top: PathLike, ext: str):
-         from monty.os.path import find_exts
-         filepaths = find_exts(str(top), ext)
-         return cls(filepaths)
+        from monty.os.path import find_exts
+        filepaths = find_exts(str(top), ext)
+        return cls(filepaths)
 
     def __init__(self, filepaths: list[PathLike]):
         self.filepaths = list_strings(filepaths)
@@ -90,7 +89,7 @@ def to_string(self, verbose=0) -> str:
     def __str__(self) -> str:
         return self.to_string()
 
-    def write(self, xyz_filepath: PathLike, overwrite: bool=False):
+    def write(self, xyz_filepath: PathLike, overwrite: bool = False):
         """
         """
         if not overwrite and os.path.isfile(xyz_filepath):
@@ -134,7 +133,7 @@ def yield_atoms(self):
             yield atoms
 
 
-def check_vasp_success(vasprun, outcar, verbose: int = 1) -> bool:
+def check_vasp_success(vasprun: Vasprun, outcar: Outcar, verbose: int = 1) -> bool:
     """
     Check if a VASP calculation completed successfully.
 
@@ -223,22 +222,7 @@ def to_string(self, verbose=0) -> str:
 
         return "\n".join(lines)
 
-    #def get_custom_incar_settings():
-    #    # Define custom INCAR settings
-    #    custom_incar_settings = {
-    #        'ENCUT': 600,         # Override plane-wave cutoff energy
-    #        'ISMEAR': -5,         # Use tetrahedron method with Blöchl corrections
-    #        'SIGMA': 0.01,        # Smearing width
-    #        'EDIFF': 1E-8,        # Electronic energy convergence criterion
-    #        'NSW': 0,             # Number of ionic steps (static calculation)
-    #        'ISIF': 2,            # Stress tensor calculation
-    #        'LREAL': 'Auto',      # Projection operators (automatic)
-    #        'LWAVE': False,       # Do not write WAVECAR
-    #        'LCHARG': True        # Write CHGCAR
-    #    }
-    #    return custom_incar_settings
-
-    def sbatch(self, max_jobs: int=100) -> list[int]:
+    def sbatch(self, max_jobs: int = 100) -> list[int]:
         """
         """
         if not self.topdir.exists(): self.topdir.mkdir()
@@ -247,7 +231,7 @@ def sbatch(self, max_jobs: int=100) -> list[int]:
         for index in self.traj_range:
             workdir = self.topdir / f"SINGLEPOINT_{index}"
             if workdir.exists():
-                print(f"{workdir=} already exists. Ignoring it")
+                print(f"{str(workdir)} already exists. Ignoring it")
                 continue
 
             try:
@@ -262,9 +246,12 @@ def sbatch(self, max_jobs: int=100) -> list[int]:
             if self.code == "vasp":
                 # Generate VASP input files using the Materials Project settings for a single-point calculation
                 from pymatgen.io.vasp.sets import MPStaticSet
-                user_incar_settings = {"NCORE": 2}
+                user_incar_settings = {
+                    "NCORE": 2
+                    'LWAVE': False,       # Do not write WAVECAR
+                    'LCHARG': False,      # Do not Write CHGCAR
+                }
                 vasp_input_set = MPStaticSet(structure, user_incar_settings=user_incar_settings)
-
                 vasp_input_set.write_input(workdir)
                 with open(workdir / "run_custodian.py", "wt") as fh:
                     fh.write(self.custodian_script_str)
@@ -282,7 +269,7 @@ def sbatch(self, max_jobs: int=100) -> list[int]:
 
         return job_ids
 
-    def write_xyz(self, xyz_filepath: PathLike, dryrun=False) -> None:
+    def write_xyz(self, xyz_filepath: PathLike, dry_run=False) -> None:
         """
         """
         ext = {
@@ -292,4 +279,3 @@ def write_xyz(self, xyz_filepath: PathLike, dryrun=False) -> None:
 
         writer = ExtxyzIOWriter.from_top(self.topdir, ext)
         writer.write(xyz_filepath)
-

abipy/scripts/abistruct.py

@@ -199,7 +199,7 @@ def add_primitive_options(parser):
         group.add_argument('--primitive-standard', default=False, action='store_true',
                            help="Enforce primitive standard cell.")
 
-    supported_formats = "(abivars, cif, xsf, poscar, qe, siesta, wannier90, cssr, json, None)"
+    supported_formats = "(abivars, cif, xsf, poscar, qe, siesta, wannier90, cssr, json, lammps, fleur-inpgen, None)"
 
     def add_format_arg(parser, default, option=True, formats=None):
         """