Add qe print

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.13
+current_version = 0.6.14
 commit = True
 tag = False
 

CITATION.cff

@@ -20,4 +20,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.6.13
+version: 0.6.14

atomrdf/graph.py

@@ -34,6 +34,7 @@
 import logging
 import warnings
 import re
+import pickle
 
 # from pyscal3.core import System
 from pyscal3.atoms import Atoms
@@ -803,6 +804,21 @@ def write(self, filename, format="json-ld"):
         with open(filename, "w") as fout:
             fout.write(self.graph.serialize(format=format))
 
+    def close(self, filename, format="json-ld"):
+        """
+        Close the graph and write to a file
+
+        Parameters
+        ----------
+        filename: string
+            name of output file
+
+        Returns
+        -------
+        None
+        """
+        self.write(filename, format=format)
+
     def archive(self, package_name, format="turtle", compress=True, add_simulations=False):
         """
         Publish a dataset from graph including per atom quantities.
@@ -1215,7 +1231,11 @@ def get_system_from_sample(self, sample):
         sys.graph = self
         return sys
 
-    def to_file(self, sample, filename=None, format="poscar", add_sample_id=True):
+    def to_file(self, sample, filename=None, format="poscar", add_sample_id=True,
+        input_data=None, pseudopotentials=None, 
+                kspacing=None, kpts=None, 
+                koffset=(0, 0, 0), 
+                crystal_coordinates=False):
         """
         Save a given sample to a file
 
@@ -1227,9 +1247,28 @@ def to_file(self, sample, filename=None, format="poscar", add_sample_id=True):
         filename: string
             name of output file
 
-        format: string, {"lammps-dump","lammps-data", "poscar"}
+        format: string, {"lammps-dump","lammps-data", "poscar", 'cif', 'quantum-espresso'}
             or any format supported by ase
 
+        input_data : str, optional
+            Additional input data to include in the output file. Defaults to None.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        pseudopotentials : str, optional
+            The path to the pseudopotentials file. Defaults to None.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        kspacing : float, optional
+            The k-spacing value to include in the output file. Defaults to None.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        kpts : list, optional
+            A list of k-points to include in the output file. Defaults to None.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        koffset : tuple, optional
+            The k-offset values to include in the output file. Defaults to (0, 0, 0).
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        crystal_coordinates : bool, optional
+            Whether to include crystal coordinates in the output file. Defaults to False.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+
         Returns
         -------
         None
@@ -1239,32 +1278,17 @@ def to_file(self, sample, filename=None, format="poscar", add_sample_id=True):
             filename = os.path.join(os.getcwd(), "out")
 
         sys = self.get_system_from_sample(sample)
-
-        if format == "ase":
-            return sys.write.ase()
-        elif format == "poscar":
-            asesys = sys.write.ase()
-            write(filename, asesys, format="vasp")
-            if add_sample_id:
-                lines = []
-                with open(filename, "r") as fin:
-                    for line in fin:
-                        lines.append(line)
-                lines[0] = sample.toPython() + "\n"
-                with open(filename, "w") as fout:
-                    for line in lines:
-                        fout.write(line)
-        else:
-            asesys = sys.write.ase()
-            write(filename, asesys, format=format)
+        sys.to_file(filename, format=format, add_sample_id=add_sample_id, input_data=input_data, 
+                pseudopotentials=pseudopotentials, kspacing=kspacing, 
+                kpts=kpts, koffset=koffset, crystal_coordinates=crystal_coordinates)
 
     def enable_workflow(self, workflow_object, workflow_environment=None, workflow_module=None):
         self.workflow.inform_graph(workflow_object, 
                         workflow_environment=workflow_environment, 
                         workflow_module=workflow_module)
 
     def add_workflow(self, job, workflow_environment=None, workflow_module=None, job_dicts=None,
-                     add_intermediate_jobs=False):
+                    add_intermediate_jobs=False):
         self.workflow.to_graph(job, workflow_environment=workflow_environment, 
                             workflow_module=workflow_module, 
                             job_dicts=job_dicts,

atomrdf/structure.py

@@ -16,7 +16,7 @@
 import shutil
 import tarfile
 import warnings
-
+from ase.io import write
 
 import pyscal3.structure_creator as pcs
 from pyscal3.grain_boundary import GrainBoundary
@@ -1083,22 +1083,104 @@ def __delitem__(self, val):
         # now the graph has to be updated accordingly
         self.delete(indices=list(val))
 
+    def write_poscar_id(self, outfile):
+        lines = []
+        with open(outfile, "r") as fin:
+            for line in fin:
+                lines.append(line)
+        lines[0] = self.sample.toPython() + "\n"
+        with open(outfile, "w") as fout:
+            for line in lines:
+                fout.write(line)
+
+    def write_quatum_espresso_id(self, outfile):
+        lines = []
+        lines.append(f"! {self.sample.toPython()}\n") 
+        with open(outfile, "r") as fin:
+            for line in fin:
+                lines.append(line)
+        with open(outfile, "w") as fout:
+            for line in lines:
+                fout.write(line)
+
     def to_file(self, outfile, format='lammps-dump', customkeys=None, customvals=None,
-            compressed=False, timestep=0, species=None,  add_sample_id=True):
+                compressed=False, timestep=0, species=None,  add_sample_id=True,
+                input_data=None, pseudopotentials=None, 
+                kspacing=None, kpts=None, 
+                koffset=(0, 0, 0), 
+                crystal_coordinates=False):
+        """
+        Write the structure to a file in the specified format.
 
-        inputmethods.to_file(self, outfile, format=format, customkeys=customkeys, customvals=customvals,
-            compressed=compressed, timestep=timestep, species=species)
-        if format == 'poscar':
-            if add_sample_id and (self.sample is not None):
-                lines = []
-                with open(outfile, "r") as fin:
-                    for line in fin:
-                        lines.append(line)
-                lines[0] = self.sample.toPython() + "\n"
-                with open(outfile, "w") as fout:
-                    for line in lines:
-                        fout.write(line)
+        Parameters
+        ----------
+        outfile : str
+            The path to the output file.
+        format : str, optional
+            The format of the output file. Defaults to 'lammps-dump'.
+        customkeys : list, optional
+            A list of custom keys to include in the output file. Defaults to None.
+            Only valid if format is 'lammps-dump'.
+        customvals : list, optional
+            A list of custom values corresponding to the custom keys. Defaults to None.
+            Only valid if format is 'lammps-dump'.
+        compressed : bool, optional
+            Whether to compress the output file. Defaults to False.
+        timestep : int, optional
+            The timestep value to include in the output file. Defaults to 0.
+            Only valid if format is 'lammps-dump'.
+        species : list, optional
+            A list of species to include in the output file. Defaults to None.
+            Only valid for ASE, if species is not specified.
+        add_sample_id : bool, optional
+            Whether to add a sample ID to the output file. Defaults to True.
+            Only valid for poscar and quantum-espresso formats.
+        input_data : str, optional
+            Additional input data to include in the output file. Defaults to None.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        pseudopotentials : str, optional
+            The path to the pseudopotentials file. Defaults to None.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        kspacing : float, optional
+            The k-spacing value to include in the output file. Defaults to None.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        kpts : list, optional
+            A list of k-points to include in the output file. Defaults to None.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        koffset : tuple, optional
+            The k-offset values to include in the output file. Defaults to (0, 0, 0).
+            Only valid for quantum-espresso format. See ASE write docs for more information.
+        crystal_coordinates : bool, optional
+            Whether to include crystal coordinates in the output file. Defaults to False.
+            Only valid for quantum-espresso format. See ASE write docs for more information.
 
+        Returns
+        -------
+        None
+        """
+        if format == "ase":
+            return self.write.ase()
+        elif format == "poscar":
+            asesys = self.write.ase()
+            write(outfile, asesys, format="vasp")
+            if add_sample_id and (self.sample is not None):
+                self.write_poscar_id(outfile)
+        elif format == "lammps-dump":
+            inputmethods.to_file(self, outfile, format='lammps-dump', customkeys=customkeys, customvals=customvals,
+                compressed=compressed, timestep=timestep, species=species)
+        elif format == "lammps-data":
+            asesys = self.write.ase()
+            write(outfile, asesys, format='lammps-data', atom_style='atomic')
+        elif format == "quantum-espresso":
+            asesys = self.write.ase()
+            write(outfile, asesys, format='espresso-in', input_data=input_data, 
+                pseudopotentials=pseudopotentials, kspacing=kspacing, 
+                kpts=kpts, koffset=koffset, crystal_coordinates=crystal_coordinates)
+            if add_sample_id and (self.sample is not None):
+                self.write_quatum_espresso_id(outfile)
+        else:
+            asesys = self.write.ase()
+            write(outfile, asesys, format=format)
 
     def to_graph(self):
         """

examples/08_write_qe.ipynb

@@ -0,0 +1,108 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from atomrdf import KnowledgeGraph, System"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "kg = KnowledgeGraph()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "s = System.create.element.Fe(graph = kg)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "s.write.file('qe_input', format='quantum-espresso')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "! sample:f2b5122e-7458-40e2-a197-4275dde7ed77\n",
+      "&CONTROL\n",
+      "/\n",
+      "&SYSTEM\n",
+      "   ntyp             = 1\n",
+      "   nat              = 2\n",
+      "   ibrav            = 0\n",
+      "/\n",
+      "&ELECTRONS\n",
+      "/\n",
+      "&IONS\n",
+      "/\n",
+      "&CELL\n",
+      "/\n",
+      "\n",
+      "ATOMIC_SPECIES\n",
+      "Fe 55.845 None\n",
+      "\n",
+      "K_POINTS gamma\n",
+      "\n",
+      "CELL_PARAMETERS angstrom\n",
+      "2.87000000000000 0.00000000000000 0.00000000000000\n",
+      "0.00000000000000 2.87000000000000 0.00000000000000\n",
+      "\u001b[Km--More--(67%)\u001b[m"
+     ]
+    }
+   ],
+   "source": [
+    "! more qe_input"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "workflow-rdf",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name='atomrdf',
-    version='0.6.13',
+    version='0.6.14',
     author='Abril Azocar Guzman, Sarath Menon',
     author_email='[email protected]',
     description='Ontology based structural manipulation and quering',