emmet-builders 0.48.3__py3-none-any.whl → 0.48.5__py3-none-any.whl

emmet/builders/abinit/phonon.py

@@ -56,7 +56,8 @@ class PhononBuilder(Builder):
         standard MongoDB document.
 
         Args:
-            materials (Store): source Store of materials documents.
+            phonon_materials (Store): source Store of phonon materials documents
+                containing abinit_input and abinit_output.
             ddb_source (Store): source Store of ddb files. Matching the data in the materials Store.
             phonon (Store): target Store of the phonon properties
             phonon_bs (Store): target Store for the phonon band structure. The document may

emmet/builders/abinit/sound_velocity.py

@@ -1,5 +1,4 @@
 import tempfile
-import gridfs
 import traceback
 from typing import Optional, Dict, List, Iterator
 
@@ -16,7 +15,8 @@ from emmet.core.utils import jsanitize
 class SoundVelocityBuilder(Builder):
     def __init__(
         self,
-        materials: Store,
+        phonon_materials: Store,
+        ddb_source: Store,
         sound_vel: Store,
         query: Optional[dict] = None,
         manager: Optional[TaskManager] = None,
@@ -27,14 +27,17 @@ class SoundVelocityBuilder(Builder):
         the phonon calculations.
 
         Args:
-            materials (Store): source Store of materials documents
+            phonon_materials (Store): source Store of phonon materials documents
+                containing abinit_input and abinit_output.
+            ddb_source (Store): source Store of ddb files. Matching the data in the materials Store.
             sound_vel (Store): target Store of the sound velocity
             query (dict): dictionary to limit materials to be analyzed
             manager (TaskManager): an instance of the abipy TaskManager. If None it will be
                 generated from user configuration.
         """
 
-        self.materials = materials
+        self.phonon_materials = phonon_materials
+        self.ddb_source = ddb_source
         self.sound_vel = sound_vel
         self.query = query or {}
 
@@ -43,7 +46,7 @@ class SoundVelocityBuilder(Builder):
         else:
             self.manager = manager
 
-        super().__init__(sources=[materials], targets=[sound_vel], **kwargs)
+        super().__init__(sources=[phonon_materials], targets=[sound_vel], **kwargs)
 
     def get_items(self) -> Iterator[Dict]:
         """
@@ -71,15 +74,12 @@ class SoundVelocityBuilder(Builder):
         # file ids to be fetched
         projection["abinit_output.ddb_id"] = 1
 
-        # initialize the gridfs
-        ddbfs = gridfs.GridFS(self.materials.collection.database, "ddb_fs")
-
         for m in mats:
-            item = self.materials.query_one(properties=projection, criteria={self.materials.key: m})
+            item = self.phonon_materials.query_one(properties=projection, criteria={self.phonon_materials.key: m})
 
             # Read the DDB file and pass as an object. Do not write here since in case of parallel
             # execution each worker will write its own file.
-            item["ddb_str"] = ddbfs.get(item["abinit_output"]["ddb_id"]).read().decode("utf-8")
+            item["ddb_str"] = self.ddb_source.get(item["abinit_output"]["ddb_id"]).read().decode("utf-8")
 
             yield item
 

emmet/builders/vasp/materials.py

@@ -310,7 +310,7 @@ class MaterialsBuilder(Builder):
                 if (
                     transmuter is None
                 ):  # Do not include deformed tasks without transmuter information
-                    self.logger.warn(
+                    self.logger.debug(
                         "Cannot find transmuter for deformation task {}. Excluding task.".format(
                             task.task_id
                         )

{emmet_builders-0.48.3.dist-info → emmet_builders-0.48.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emmet-builders
-Version: 0.48.3
+Version: 0.48.5
 Summary: Builders for the Emmet Library
 Home-page: https://github.com/materialsproject/emmet
 Author: The Materials Project

{emmet_builders-0.48.3.dist-info → emmet_builders-0.48.5.dist-info}/RECORD

@@ -2,8 +2,8 @@ emmet/builders/__init__.py,sha256=y-ZREtieuFK3MaYvCBDMPf3YLxnsZG1VNho9lMjnRDU,22
 emmet/builders/settings.py,sha256=xVIqpQjSxn--m6mbKJIr7g-nqoqZr1Vcxi3YNa3etOg,2766
 emmet/builders/utils.py,sha256=VtA_77cBqzKBaA747FBbcPX3M0QmQE-l2nMLzlQwijw,5775
 emmet/builders/abinit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-emmet/builders/abinit/phonon.py,sha256=ECMd6jdw_OXcuezqqQJt90qNTADUcMdC0_0Tt5W3D6E,29853
-emmet/builders/abinit/sound_velocity.py,sha256=bwoHd-8RBEOKdb2NFashxZrzTPSqiwAwsN42uO6iAM4,5817
+emmet/builders/abinit/phonon.py,sha256=PvWoSf6ZeMuO6jE1vL6iYXoWZCEyFucd2W0x7B8ELsY,29925
+emmet/builders/abinit/sound_velocity.py,sha256=mqUVrHmmK2B7pLPhNcPlQIOAOM6IUdCgGTzUu5AD77A,5984
 emmet/builders/feff/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 emmet/builders/feff/xas.py,sha256=JZAU69tZXI_JEkzNxwVruebcRVcTZJnQON3H0cbrnvg,2093
 emmet/builders/materials/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -40,9 +40,9 @@ emmet/builders/molecules/vibration.py,sha256=C_2itk6hfCVrSQieYxNWAmArJ8zx385gs3A
 emmet/builders/qchem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 emmet/builders/qchem/molecules.py,sha256=ew1dT0JDvoIP1yUTWfoRkYox9g49fkOnAc636niK-Nk,25379
 emmet/builders/vasp/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-emmet/builders/vasp/materials.py,sha256=uIsIzIhDCqYVkZrep1MUP0riECUBUAbiGkF235pheZ0,13333
+emmet/builders/vasp/materials.py,sha256=JnV_5Kd0qCU0hsqAcyhZwgMTYVcs54NmYKS9kNS9bhI,13334
 emmet/builders/vasp/task_validator.py,sha256=9hiYdnG_Wz4zxzG6mrxjPIJbZTm_N-22UwpYPT5zXFE,3601
-emmet_builders-0.48.3.dist-info/METADATA,sha256=b6eTdVSVrGlxF2LRtQ2TUrqqZSEXxvmI362qVhj8Eps,1449
-emmet_builders-0.48.3.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-emmet_builders-0.48.3.dist-info/top_level.txt,sha256=6GcpbmWPeFhNCTfDFilb8GQ4T1UQu4z9c5jpobjwE-Q,6
-emmet_builders-0.48.3.dist-info/RECORD,,
+emmet_builders-0.48.5.dist-info/METADATA,sha256=5TQMSHHR7JpdYZ1FEysdYn3kM2OVyxcvkLAUns_emqI,1449
+emmet_builders-0.48.5.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+emmet_builders-0.48.5.dist-info/top_level.txt,sha256=6GcpbmWPeFhNCTfDFilb8GQ4T1UQu4z9c5jpobjwE-Q,6
+emmet_builders-0.48.5.dist-info/RECORD,,