Refactor pymatgen calls, improve config loading in MPInterfaces, and make examples/hetero_interface.py works.

README.rst

@@ -99,7 +99,7 @@ Note: on using virtual environments on your own machine, we recommend to use Min
    and update the file so that you at least have the following
    environment variables :
 
-   - MAPI_KEY=the_key_obtained_from_materialsproject
+   - PMG_MAPI_KEY=the_key_obtained_from_materialsproject
 
    - PMG_VASP_PSP_DIR=path_to_vasp_potcar_files
 

dev_scripts/grain_boundary.py

@@ -21,7 +21,7 @@ def get_grain_boundary_interface(structure=None,
         tilt:      tilt in degrees
     """
 
-    structure = get_struct_from_mp(structure, MAPI_KEY="")
+    structure = get_struct_from_mp(structure, PMG_MAPI_KEY="")
     sa = SpacegroupAnalyzer(structure)
     structure_conventional = sa.get_conventional_standard_structure()
     structure = structure_conventional.copy()

dev_scripts/hetero_interface.py

@@ -211,12 +211,12 @@ def get_matching_lattices(iface1, iface2, max_area=100,
 
 
     # structure from materials project, use your own key
-    # gaas = get_struct_from_mp('GaAs', MAPI_KEY="")
+    # gaas = get_struct_from_mp('GaAs', PMG_MAPI_KEY="")
     # sa_gaas = SpacegroupAnalyzer(gaas)
     # gaas_cvn = sa_gaas.get_conventional_standard_structure()
     # gaas_cvn.to(fmt='poscar', filename='POSCAR_GaAs.vasp')
 
-    # cdte = get_struct_from_mp('CdTe', MAPI_KEY="")
+    # cdte = get_struct_from_mp('CdTe', PMG_MAPI_KEY="")
     # sa_cdte = SpacegroupAnalyzer(cdte)
     # cdte_cvn = sa_cdte.get_conventional_standard_structure()
     # cdte_cvn.to(fmt='poscar', filename='POSCAR_CdTe.vasp')

dev_scripts/ligand_workflow.py

@@ -183,7 +183,7 @@ def get_measurement_task(structure, sol_add={}):
     bulk_fireworks = []
     bulk_firetasks = []
     # pull from matproj, use your own key
-    bulk = get_struct_from_mp('PbS', MAPI_KEY="")
+    bulk = get_struct_from_mp('PbS', PMG_MAPI_KEY="")
     #    primitive --> conventional cell
     sa = SpacegroupAnalyzer(bulk)
     structure_conventional = sa.get_conventional_standard_structure()

examples/CdS_mp-2469_primitive.cif

@@ -0,0 +1,28 @@
+# generated using pymatgen
+data_CdS
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.20080401
+_cell_length_b   4.20080401
+_cell_length_c   4.20080401
+_cell_angle_alpha   60.00000000
+_cell_angle_beta   60.00000000
+_cell_angle_gamma   60.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   CdS
+_chemical_formula_sum   'Cd1 S1'
+_cell_volume   52.41821899
+_cell_formula_units_Z   1
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Cd  Cd0  1  0.00000000  0.00000000  0.00000000  1
+  S  S1  1  0.75000000  0.75000000  0.75000000  1

examples/GaTe_mp-10009_primitive.cif

@@ -0,0 +1,34 @@
+# generated using pymatgen
+data_GaTe
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.13459973
+_cell_length_b   4.13459973
+_cell_length_c   18.42557000
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   120.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   GaTe
+_chemical_formula_sum   'Ga4 Te4'
+_cell_volume   272.78375687
+_cell_formula_units_Z   4
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Ga  Ga0  1  0.66666667  0.33333333  0.68295900  1
+  Ga  Ga1  1  0.33333333  0.66666667  0.18295900  1
+  Ga  Ga2  1  0.33333333  0.66666667  0.31704100  1
+  Ga  Ga3  1  0.66666667  0.33333333  0.81704100  1
+  Te  Te4  1  0.66666667  0.33333333  0.38620400  1
+  Te  Te5  1  0.33333333  0.66666667  0.88620400  1
+  Te  Te6  1  0.33333333  0.66666667  0.61379600  1
+  Te  Te7  1  0.66666667  0.33333333  0.11379600  1

examples/create_interface.py

@@ -13,7 +13,7 @@
 
 Note: Before using the script, make sure that you do have a valid 
 api key obtained  from the materialsproject website. 
-Use that to set the MAPI_KEY variable below
+Use that to set the PMG_MAPI_KEY variable below
 """
 
 from pymatgen.core import Molecule, Structure
@@ -23,7 +23,7 @@
 
 if __name__ == '__main__':
     # PbS 100 surface with single hydrazine as ligand
-    # strt=get_struct_from_mp("PbS",MAPI_KEY=MAPI_KEY) 
+    # strt=get_struct_from_mp("PbS",PMG_MAPI_KEY=PMG_MAPI_KEY) 
     # using smiles_to_xyz.py you can obtain molecule xyz
     # using openbabel.  
     # example structure files are provided and set in dev_scripts

examples/hetero_interface.py

@@ -17,12 +17,14 @@
 from mpinterfaces.interface import Interface
 from mpinterfaces.transformations import *
 from mpinterfaces.utils import *
+from mpinterfaces.old_transformations import generate_all_configs
 
 separation = 3  # in angstroms
 nlayers_2d = 2
 nlayers_substrate = 2
 
-substrate_bulk = Structure.from_file('POSCAR_substrate')
+#substrate_bulk = Structure.from_file('POSCAR_substrate')
+substrate_bulk = Structure.from_file('CdS_mp-2469_primitive.cif')
 # substrate_bulk = get_struct_from_mp('Ag')
 sa_sub = SpacegroupAnalyzer(substrate_bulk)
 substrate_bulk = sa_sub.get_conventional_standard_structure()
@@ -32,7 +34,9 @@
                            min_vac=25,
                            primitive=False, from_ase=True)
 # substrate_slab = slab_from_file([0,0,1], 'POSCAR_substrate')
-mat2d_slab = slab_from_file([0, 0, 1], 'POSCAR_2D')
+#mat2d_slab = slab_from_file([0, 0, 1], 'POSCAR_2D')
+mat2d_slab = slab_from_file([0, 0, 1], 'GaTe_mp-10009_primitive.cif')
+
 # get the in-plane lattice aligned slabs
 # substrate_slab.to(fmt='poscar', filename='POSCAR_substrate_slab.vasp')
 mat2d_slab.to(fmt='poscar', filename='POSCAR_mat2d_slab.vasp')

examples/naf.yaml

@@ -6,9 +6,9 @@ FORMULA: NaF
 # below
 # if no poscar file is provided, structure will be 
 # downloaded from the materialsproject database
-# note: must set MAPI_KEY evironment variable to
+# note: must set PMG_MAPI_KEY evironment variable to
 # your key for obtaining data from materialproject
-# export MAPI_KEY="key_value"
+# export PMG_MAPI_KEY="key_value"
 #------------------------------------------------
 INCAR: 
  NSW: 0

examples/nanoparticle.py

@@ -29,7 +29,7 @@
 # -----------------------------------
 # caution: set the structure wrt which the the miller indices are
 # specified. use your own key
-structure = get_struct_from_mp('PbS', MAPI_KEY="")
+structure = get_struct_from_mp('PbS', PMG_MAPI_KEY="")
 # primitive ---> conventional cell
 sa = SpacegroupAnalyzer(structure)
 structure_conventional = sa.get_conventional_standard_structure()

examples/vasp_jobs.py

@@ -23,9 +23,9 @@
 from mpinterfaces.interface import Interface
 from mpinterfaces.utils import get_run_cmmnd
 
-MAPI_KEY = os.environ.get("MAPI_KEY", "")
+PMG_MAPI_KEY = os.environ.get("PMG_MAPI_KEY", "")
 # get structure from materialsproject, use your own key
-strt = get_struct_from_mp('PbS', MAPI_KEY=MAPI_KEY)
+strt = get_struct_from_mp('PbS', PMG_MAPI_KEY=PMG_MAPI_KEY)
 # convert from fcc primitive to conventional cell
 # the conventional unit cell is used to create the slab
 # this is important becasue the hkl specification for the required slab

mpinterfaces/__init__.py

@@ -9,45 +9,35 @@
 import operator
 import warnings
 
-from pymatgen.ext.matproj import MPRester
-
-from monty.serialization import loadfn
-
 __author__ = "Kiran Mathew, Joshua J. Gabriel, Michael Ashton, " \
              "Arunima K. Singh, Joshua T. Paul, Seve G. Monahan, " \
              "Richard G. Hennig"
 __date__ = "March 3 2017"
 __version__ = "1.7.0"
 
-PACKAGE_PATH = os.path.dirname(__file__)
+PACKAGE_PATH = os.path.dirname(os.path.abspath(__file__))
 
-try:
-    MPINT_CONFIG = loadfn(os.path.join(PACKAGE_PATH, 'mpint_config.yaml'))
-except:
-    MPINT_CONFIG = {}
-    warnings.warn('mpint_config.yaml file not configured.')
+from .config_loader import CONFIG
+from pymatgen.ext.matproj import MPRester
 
-# set environ variables for MAPI_KEY and VASP_PSP_DIR
-if MPINT_CONFIG.get('potentials', ''):
-    os.environ['PMG_VASP_PSP_DIR'] = MPINT_CONFIG.get('potentials', '')
-MP_API = MPINT_CONFIG.get('mp_api', '')
-if MP_API:
-    os.environ['MAPI_KEY'] = MP_API
+# First, correctly fetch PMG_MAPI_KEY using .get() to handle cases where it might not be set
+PMG_MAPI_KEY = CONFIG.get('PMG_MAPI_KEY')
 
-MPR = MPRester(MP_API)
-USERNAME = MPINT_CONFIG.get('username', None)
-VASP_STD_BIN = MPINT_CONFIG.get('normal_binary', None)
-VASP_TWOD_BIN = MPINT_CONFIG.get('twod_binary', None)
-VDW_KERNEL = MPINT_CONFIG.get('vdw_kernel', None)
-VASP_PSP = MPINT_CONFIG.get('potentials', None)
-QUEUE_SYSTEM = MPINT_CONFIG.get('queue_system', None)
-QUEUE_TEMPLATE = MPINT_CONFIG.get('queue_template', None)
+MPR = MPRester(PMG_MAPI_KEY)
+
+# Other configurations
+USERNAME = CONFIG.get('username')
+VASP_STD_BIN = CONFIG.get('normal_binary')
+VASP_TWOD_BIN = CONFIG.get('twod_binary')
+VDW_KERNEL = CONFIG.get('vdw_kernel')
+VASP_PSP = CONFIG.get('potentials')
+QUEUE_SYSTEM = CONFIG.get('queue_system')
+QUEUE_TEMPLATE = CONFIG.get('queue_template')
 
 if not QUEUE_SYSTEM:
     QUEUE_SYSTEM = 'slurm'
-
-
-def get_struct_from_mp(formula, MAPI_KEY="", all_structs=False):
+
+def get_struct_from_mp(formula, PMG_MAPI_KEY="", all_structs=False):
     """
     fetches the structure corresponding to the given formula
     from the materialsproject database.
@@ -59,12 +49,12 @@ def get_struct_from_mp(formula, MAPI_KEY="", all_structs=False):
     this function returns the one with the lowest energy above the hull
     unless all_structs is set to True
     """
-    if not MAPI_KEY:
-        MAPI_KEY = os.environ.get("MAPI_KEY", "")
-        if not MAPI_KEY:
+    if not PMG_MAPI_KEY:
+        PMG_MAPI_KEY = os.environ.get("PMG_MAPI_KEY", "")
+        if not PMG_MAPI_KEY:
             print('API key not provided')
             print(
-                'get API KEY from materialsproject and set it to the MAPI_KEY environment variable. aborting ... ')
+                'get API KEY from materialsproject and set it to the PMG_MAPI_KEY environment variable. aborting ... ')
             sys.exit()
     with MPR as m:
         data = m.get_data(formula)

mpinterfaces/calibrate.py

@@ -35,7 +35,7 @@
 
 import numpy as np
 
-from pymatgen import Lattice
+from pymatgen.core import Lattice
 from pymatgen.core.structure import Structure
 from pymatgen.core.surface import SlabGenerator
 from pymatgen.io.vasp.inputs import Incar, Poscar

mpinterfaces/config_loader.py

@@ -0,0 +1,32 @@
+import os
+from monty.serialization import loadfn
+
+def load_configurations():
+    expected_keys = [
+        'PMG_MAPI_KEY', 'PMG_VASP_PSP_DIR', 'username', 'normal_binary',
+        'twod_binary', 'vdw_kernel', 'potentials', 'queue_system', 'queue_template'
+    ]
+    configurations = {}
+
+    # Attempt to load from .pmgrc.yaml
+    pmgrc_path = os.path.join(os.path.expanduser('~'), '.pmgrc.yaml')
+    if os.path.isfile(pmgrc_path):
+        try:
+            pmgrc_config = loadfn(pmgrc_path)
+            for key in expected_keys:
+                configurations[key] = pmgrc_config.get(key)
+        except Exception as e:
+            print(f"Error loading configurations from {pmgrc_path}: {e}")
+
+    # Override with environment variables or set to None if not found
+    for key in expected_keys:
+        configurations[key] = os.getenv(key.upper(), configurations.get(key))
+
+    # Ensure all expected keys are present, even if as None
+    for key in expected_keys:
+        if key not in configurations:
+            configurations[key] = None
+
+    return configurations
+
+CONFIG = load_configurations()

mpinterfaces/mat2d/__init__.py

@@ -1,6 +1,8 @@
-from mpinterfaces import MPINT_CONFIG, VASP_PSP, VASP_STD_BIN, VASP_TWOD_BIN, \
-    USERNAME, VDW_KERNEL, QUEUE_SYSTEM, MPR
-
+from mpinterfaces import (
+    VASP_PSP, VASP_STD_BIN, VASP_TWOD_BIN,
+    USERNAME, VDW_KERNEL, QUEUE_SYSTEM, 
+    QUEUE_TEMPLATE, MPR
+)
 __author__ = "Michael Ashton, Joshua J. Gabriel, Joshua T. Paul, " \
              "Seve G. Monahan"
 __version__ = "1.7.0"

mpinterfaces/mat2d/electronic_structure/tests/test_electronic_structure.py

@@ -1,7 +1,11 @@
 import os
 import unittest
 
-from mpinterfaces import MPINT_CONFIG
+from mpinterfaces import (
+    VASP_PSP, VASP_STD_BIN, VASP_TWOD_BIN,
+    USERNAME, VDW_KERNEL, QUEUE_SYSTEM, 
+    QUEUE_TEMPLATE, MPR
+)
 from mpinterfaces.mat2d.electronic_structure import *
 from mpinterfaces.mat2d.electronic_structure.analysis import get_band_edges, \
     get_fermi_velocities, plot_band_alignments, plot_band_structure, \

mpinterfaces/mat2d/friction/tests/test_friction.py

@@ -1,7 +1,12 @@
 import os
 import unittest
 
-from mpinterfaces import MPINT_CONFIG
+from mpinterfaces import (
+    VASP_PSP, VASP_STD_BIN, VASP_TWOD_BIN,
+    USERNAME, VDW_KERNEL, QUEUE_SYSTEM, 
+    QUEUE_TEMPLATE, MPR
+)
+from mpinterfaces.config_loader import CONFIG
 from mpinterfaces.mat2d.friction import *
 from mpinterfaces.mat2d.friction.analysis import get_basin_and_peak_locations, \
     get_mu_vs_F_N

mpinterfaces/mat2d/pourbaix/tests/test_pourbaix.py

@@ -3,7 +3,7 @@
 
 from monty.serialization import loadfn
 
-from mpinterfaces import MP_API
+from mpinterfaces import PMG_MAPI_KEY
 from mpinterfaces.mat2d.pourbaix import *
 from mpinterfaces.mat2d.stability.startup import INCAR_DICT
 
@@ -32,7 +32,7 @@ def test_get_experimental_formation_energies(self):
         for elt in control_energies:
             self.assertEqual(test_energies[elt], control_energies[elt])
 
-    @unittest.skipIf(MP_API == None, "API key not set")
+    @unittest.skipIf(PMG_MAPI_KEY == None, "API key not set")
 #    def test_relax_references_for_Mo_and_S(self):
 #        os.chdir(ROOT)
 #        relax_references(['Mo_pv', 'S'], incar_dict=INCAR_DICT, submit=False)

mpinterfaces/mat2d/stability/tests/test_stability.py

@@ -1,7 +1,7 @@
 import os
 import unittest
 
-from mpinterfaces import MP_API
+from mpinterfaces import PMG_MAPI_KEY
 from mpinterfaces.mat2d.stability import *
 from mpinterfaces.mat2d.stability.analysis import get_competing_phases, \
     get_hull_distance
@@ -30,13 +30,13 @@ def test_relax_creates_files(self):
 
 class AnalysisTest(unittest.TestCase):
 
-    @unittest.skipIf(not MP_API, "API key not set")
+    @unittest.skipIf(not PMG_MAPI_KEY, "API key not set")
     def test_get_hull_distance_for_BiTeCl(self):
         os.chdir(ROOT)
         os.chdir('BiTeCl')
         self.assertEqual(get_hull_distance(), 0.10335952666666692)
 
-    @unittest.skipIf(not MP_API, "API key not set")
+    @unittest.skipIf(not PMG_MAPI_KEY, "API key not set")
     def test_get_competing_phases_for_BiTeCl(self):
         os.chdir(ROOT)
         os.chdir('BiTeCl')