TB2Jflows 0.0.1__py3-none-any.whl → 0.2__py3-none-any.whl

TB2Jflows/ase_siesta.py

@@ -24,6 +24,7 @@ class SiestaFlow:
         restart=True,
         metadata={},
         fdf_arguments={},
+        relax_arguments={},
         split_soc=False,
         **kwargs,
     ):
@@ -50,6 +51,7 @@ class SiestaFlow:
         self.root_path = root_path
         self.restart = restart
         self.kwargs = kwargs
+        self.relax_args = relax_arguments
 
         # paths
         self.metadata_path = os.path.join(self.root_path, "metadata.json")
@@ -158,6 +160,7 @@ class SiestaFlow:
         MaxStressTol=0.1,
         NumCGSteps=200,
     ):
+        print(f"Relaxation in {path}")
         if (
             self.restart
             and self.metadata["already_relaxed"]
@@ -169,20 +172,20 @@ class SiestaFlow:
             old_spin = self.spin
             if use_collinear:
                 self.spin = "collinear"
-                calc = self.get_calculator(atoms, path=self.relax_path, label=label)
-                calc.atoms = atoms
-                atoms = calc.relax(
-                    atoms,
-                    TypeOfRun=TypeOfRun,
-                    VariableCell=VariableCell,
-                    ConstantVolume=ConstantVolume,
-                    RelaxCellOnly=RelaxCellOnly,
-                    MaxForceTol=MaxForceTol,
-                    MaxStressTol=MaxStressTol,
-                    NumCGSteps=NumCGSteps,
-                )
-                self.spin = old_spin
-                self.relaxed_atoms = atoms
+            calc = self.get_calculator(atoms, path=self.relax_path, label=label)
+            calc.atoms = atoms
+            atoms = calc.relax(
+                atoms,
+                TypeOfRun=TypeOfRun,
+                VariableCell=VariableCell,
+                ConstantVolume=ConstantVolume,
+                RelaxCellOnly=RelaxCellOnly,
+                MaxForceTol=MaxForceTol,
+                MaxStressTol=MaxStressTol,
+                NumCGSteps=NumCGSteps,
+            )
+            self.spin = old_spin
+            self.relaxed_atoms = atoms
             self.update_metadata(
                 {
                     "already_relaxed": True,
@@ -227,19 +230,20 @@ class SiestaFlow:
     def scf_calculatoin_split_soc(self, atoms, label="siesta", nscf=False):
         fdf_args = {
             "SOC_split_SR_SO": True,
-            #"Spin.OrbitStrength": 3,
+            # "Spin.OrbitStrength": 3,
             "SaveHS.so": True,
             "SaveHS": True,
-            "Spin.Fix": False, 
+            "Spin.Fix": False,
+        }
+        nscf_args = {
+            "SCF.DM.Converge": True,
+            "SCF.DM.Tolerance": 1e4,
+            "SCF.H.Converge": False,
+            "SCF.EDM.Converge": False,
+            "SCF.Mix.First": False,
+            "SCF.Mix": "density",
+            "MaxSCFIterations": 1,
         }
-        nscf_args={"SCF.DM.Converge": True, 
-                "SCF.DM.Tolerance": 1e4, 
-                "SCF.H.Converge": False, 
-                "SCF.EDM.Converge": False, 
-                "SCF.Mix.First": False, 
-                "SCF.Mix": "density", 
-                "MaxSCFIterations": 1,
-                }
         if nscf:
             fdf_args.update(nscf_args)
 
@@ -288,14 +292,17 @@ class SiestaFlow:
         )
 
     def set_nonscf_params(self):
-        nscf_params={"SCF.DM.Converge": False, 
-                "SCF.DM.Tolerance": 1e4, 
-                "SCF.H.Converge": False, 
-                "SCF.EDM.Converge": False, 
-                "SCF.Mix.First": False, 
-                "SCF.Mix": "density", 
-                "MaxSCFIterations": 1,
-                }
+        nscf_params = {
+            "SCF.DM.Converge": False,
+            "SCF.DM.Tolerance": 1e4,
+            "SCF.H.Converge": False,
+            "SCF.EDM.Converge": False,
+            "SCF.Mix.First": False,
+            "SCF.Mix": "density",
+            "MaxSCFIterations": 1,
+        }
+
+        self.fdf_arguments.update(nscf_params)
 
     def run_TB2J_split_soc(self, **kwargs):
         path = os.path.join(self.scf_path, "split_soc")
@@ -352,9 +359,9 @@ class SiestaFlow:
             write_path=os.path.join(self.root_path, "TB2J_results_merged"),
         )
 
-    def runall_collinear(self, atoms, relax=True, scf=True, TB2J=True, **kwargs):
+    def runall_collinear(self, atoms, relax=True, scf=True, TB2J=True,  **kwargs):
         if relax:
-            atoms = self.relax(atoms)
+            atoms = self.relax(atoms, **self.relax_args)
         if scf:
             self.scf_calculation_collinear(atoms, label="siesta")
         if TB2J:
@@ -364,7 +371,7 @@ class SiestaFlow:
         self, atoms, relax=True, scf=True, TB2J=True, rotate_type="structure", **kwargs
     ):
         if relax:
-            atoms = self.relax(atoms)
+            atoms = self.relax(atoms, **self.relax_args)
         if scf:
             self.scf_calculation_with_rotations(
                 atoms, rotate_type=rotate_type, label="siesta"
@@ -375,7 +382,7 @@ class SiestaFlow:
 
     def runall_split_soc(self, atoms, relax=True, scf=True, TB2J=True, **kwargs):
         if relax:
-            atoms = self.relax(atoms)
+            atoms = self.relax(atoms, **self.relax_args)
         if scf:
             self.scf_calculatoin_split_soc(atoms, label="siesta")
         if TB2J:

TB2Jflows/auto_siesta_TB2J.py

@@ -52,6 +52,7 @@ def auto_siesta_TB2J(
     TB2J=True,
     rotate_type="structure",
     fincore=True,
+    relax_kwargs={},
     siesta_kwargs={},
     TB2J_kwargs={},
     fdf_kwargs={},
@@ -99,6 +100,7 @@ def auto_siesta_TB2J(
         fincore=fincore,
         Udict=Udict,
         split_soc=split_soc,
+        relax_arguments = relax_kwargs,
         **siesta_kwargs,
     )
     flow.write_metadata()

{tb2jflows-0.0.1.dist-info → tb2jflows-0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: TB2Jflows
-Version: 0.0.1
+Version: 0.2
 Summary: TB2Jflows: Workflows for automatically calculation of exchange parameters using TB2J
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -23,6 +23,7 @@ Dynamic: author-email
 Dynamic: classifier
 Dynamic: description
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

tb2jflows-0.2.dist-info/RECORD

@@ -0,0 +1,9 @@
+TB2Jflows/__init__.py,sha256=0aRVj9v-u64LxJl7Cyxcr4YUjpeMkBGPuv-nJbxbHOg,100
+TB2Jflows/ase_siesta.py,sha256=tHeiKWszra8sjcJ_7Pq0cOBUC1ZEluRNEeHGj35Oz6M,14476
+TB2Jflows/auto_siesta_TB2J.py,sha256=o1A5Qf0Ru35BY5jwSAIQ2rPXD1mb572LEAQfgNfEVnM,3174
+TB2Jflows/run_abacus.py,sha256=96tZ2n02FFLl8IZf4W_4TvkCcsd6oS1FVEIqhZpY76o,2692
+tb2jflows-0.2.dist-info/licenses/LICENSE,sha256=KNu68sa-XR_2jZJKhDcSnxoNve8jtHgkw_w9PjP1YOk,1315
+tb2jflows-0.2.dist-info/METADATA,sha256=l2Lsj-MqAlL7fizCsUsD94RaqGpg6D-F-1HtmaOesL8,967
+tb2jflows-0.2.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
+tb2jflows-0.2.dist-info/top_level.txt,sha256=iYRLHB7ZeHb59fEZLnbqJDymBKWPqfVgmvqd9S51Txw,10
+tb2jflows-0.2.dist-info/RECORD,,

{tb2jflows-0.0.1.dist-info → tb2jflows-0.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (76.1.0)
+Generator: setuptools (77.0.3)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

tb2jflows-0.0.1.dist-info/RECORD

@@ -1,9 +0,0 @@
-TB2Jflows/__init__.py,sha256=0aRVj9v-u64LxJl7Cyxcr4YUjpeMkBGPuv-nJbxbHOg,100
-TB2Jflows/ase_siesta.py,sha256=BagiujWCwUZ6Aj03oRFdAL1DzJ4pw1_upW4G5d9tMXw,14363
-TB2Jflows/auto_siesta_TB2J.py,sha256=c5dviznEbXyO3BJbh-LNBlC9efT7YbdC7ydWxyCJZ5E,3113
-TB2Jflows/run_abacus.py,sha256=96tZ2n02FFLl8IZf4W_4TvkCcsd6oS1FVEIqhZpY76o,2692
-tb2jflows-0.0.1.dist-info/LICENSE,sha256=KNu68sa-XR_2jZJKhDcSnxoNve8jtHgkw_w9PjP1YOk,1315
-tb2jflows-0.0.1.dist-info/METADATA,sha256=avwrwge2xfv6PgTUy92JCpBdqUFrJNbiNlQpurzX7Ss,947
-tb2jflows-0.0.1.dist-info/WHEEL,sha256=beeZ86-EfXScwlR_HKu4SllMC9wUEj_8Z_4FJ3egI2w,91
-tb2jflows-0.0.1.dist-info/top_level.txt,sha256=iYRLHB7ZeHb59fEZLnbqJDymBKWPqfVgmvqd9S51Txw,10
-tb2jflows-0.0.1.dist-info/RECORD,,