Add abi_kwargs kwargs to new_with_structure

abinit · Nov 15, 2024 · 7331b76 · 7331b76
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commit 7331b76
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Showing 16 changed files with 934 additions and 237 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -36,7 +36,7 @@ jobs:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
 
     steps:
-      - name: Check out Abipy repo
+      - name: Checkout Abipy repo
         uses: actions/checkout@v4
 
       - name: Set up Miniconda

diff --git a/abipy/abio/inputs.py b/abipy/abio/inputs.py
@@ -675,7 +675,7 @@ def runlevel(self):
             # DTE run.
             runlevel.add(atags.DFPT)
             runlevel.add(atags.DTE)
-    
+
         elif optdriver == 99:
             # BSE run
             runlevel.update([atags.MANY_BODY, atags.BSE])
@@ -1502,7 +1502,7 @@ def new_with_vars(self, *args, **kwargs) -> AbinitInput:
         new.set_vars(*args, **kwargs)
         return new
 
-    def new_with_structure(self, new_structure, scdims=None, verbose=1) -> AbinitInput:
+    def new_with_structure(self, new_structure, scdims=None, verbose=1, **abi_vars) -> AbinitInput:
         """
         Return a new |AbinitInput| with a different structure.
         See notes below for the constraints that must be fulfilled by the new structure
@@ -1514,6 +1514,7 @@ def new_with_structure(self, new_structure, scdims=None, verbose=1) -> AbinitInp
                 Must be used when `new_structure` represents a supercell of the initial structure defined
                 in the input file.
             verbose: Verbosity level.
+            abi_vars: Abinit variables added to the Abinit input.
 
         .. warning::
 
@@ -1522,11 +1523,15 @@ def new_with_structure(self, new_structure, scdims=None, verbose=1) -> AbinitInp
             When structure represents a supercell, `scdims` must be coherent with the `new_structure` passed
             as argument.
         """
+        new_structure = Structure.as_structure(new_structure)
+
         # Check structure
         if scdims is None:
             # Assume same value of natom and typat
             if len(self.structure) != len(new_structure):
-                raise ValueError("Structures must have same value of natom")
+                raise ValueError(f"Structures must have same value of natom." +
+                                 f"new_structure has {len(new_structure)} atoms." +
+                                 f"input.structure has {len(self.structure)}")
             errors = []
             for i, (site1, site2) in enumerate(zip(self.structure, new_structure)):
                 if site1.specie.symbol != site2.specie.symbol:
@@ -1610,6 +1615,8 @@ def new_with_structure(self, new_structure, scdims=None, verbose=1) -> AbinitInp
             # Add chkprim if not yet done.
             new.set_vars_ifnotin(chkprim=0)
 
+        new.set_vars(**abi_vars)
+
         return new
 
     def new_with_decorators(self, decorators) -> AbinitInput:
@@ -1929,7 +1936,7 @@ def make_ph_inputs_qpoint(self, qpt, tolerance=None,
     def make_ddkpert_input(self, perturbation, kptopt=2, only_vk=False, use_symmetries=False, tolerance=None, manager=None) -> AbinitInput:
         """
         Returns |AbinitInput| for the calculation of an electric field perturbation.
-        This function should be called with an input that represents a GS run and 
+        This function should be called with an input that represents a GS run and
         an electric field perturbation.
 
         Args:
@@ -1973,7 +1980,7 @@ def make_ddkpert_input(self, perturbation, kptopt=2, only_vk=False, use_symmetri
 
         if only_vk:
             inp.set_vars(nstep=1, nline=1)
-        
+
         # TODO: to implement
         #if not use_symmetries:
         #    inp.set_vars(
@@ -2073,11 +2080,11 @@ def make_dkdk_input(self, tolerance=None, kptopt=2, manager=None) -> AbinitInput
         dkdk_input.set_vars(tolerance)
 
         return dkdk_input
-    
+
     def make_ddepert_input(self, perturbation, use_symmetries=True, tolerance=None, manager=None) -> AbinitInput:
         """
         Returns |AbinitInput| for the calculation of an electric field perturbation.
-        This function should be called with an input that represents a GS run and 
+        This function should be called with an input that represents a GS run and
         an electric field perturbation.
 
         Args:
@@ -2111,7 +2118,7 @@ def make_ddepert_input(self, perturbation, use_symmetries=True, tolerance=None,
             qpt=(0, 0, 0),  # q-wavevector.
             kptopt=2,       # Take into account time-reversal symmetry.
         )
-        
+
         if not use_symmetries:
             inp.set_vars(
                 comment="Input file for DDE calculation without symmetries.",
@@ -2122,7 +2129,7 @@ def make_ddepert_input(self, perturbation, use_symmetries=True, tolerance=None,
         inp.set_vars(tolerance)
 
         return inp
-    
+
     def make_dde_inputs(self, tolerance=None, use_symmetries=True, manager=None) -> MultiDataset:
         """
         Return |MultiDataset| inputs for the calculation of electric field perturbations.

diff --git a/abipy/dfpt/deformation_utils.py b/abipy/dfpt/deformation_utils.py
@@ -28,8 +28,8 @@ def generate_deformations_volumic(structure, eps_V=0.02, scales=None):
 
     return structures_new
 
-def generate_deformations(structure , eps=0.005):
-    spgrp = AbinitSpaceGroup.from_structure(structure ) 
+def generate_deformations(structure, eps=0.005):
+    spgrp = AbinitSpaceGroup.from_structure(structure )
     print (spgrp)
     spgrp_number=spgrp.spgid
     rprim= structure.lattice.matrix
@@ -39,11 +39,11 @@ def generate_deformations(structure , eps=0.005):
     structures_new = {}
 
     if 1 <= spgrp_number <= 2:
-        disp=[[1,1,1,1,1,1],  [0,1,1,1,1,1],  [2,1,1,1,1,1],  [1,0,1,1,1,1],  [1,2,1,1,1,1],  [1,1,0,1,1,1],  
-              [1,1,2,1,1,1],  [1,1,1,0,1,1],  [1,1,1,2,1,1],  [1,1,1,1,0,1],  [1,1,1,1,2,1],  [1,1,1,1,1,0],  
-              [1,1,1,1,1,2],  [0,0,1,1,1,1],  [1,0,0,1,1,1],  [1,1,0,0,1,1],  [1,1,1,0,0,1],  [1,1,1,1,0,0],  
-              [0,1,0,1,1,1],  [0,1,1,0,1,1],  [0,1,1,1,0,1],  [0,1,1,1,1,0],  [1,0,1,0,1,1],  [1,0,1,1,0,1],  
-              [1,0,1,1,1,0],  [1,1,0,1,0,1],  [1,1,0,1,1,0],  [1,1,1,0,1,0] , [0 ,0,0,0,0,0]]  
+        disp=[[1,1,1,1,1,1],  [0,1,1,1,1,1],  [2,1,1,1,1,1],  [1,0,1,1,1,1],  [1,2,1,1,1,1],  [1,1,0,1,1,1],
+              [1,1,2,1,1,1],  [1,1,1,0,1,1],  [1,1,1,2,1,1],  [1,1,1,1,0,1],  [1,1,1,1,2,1],  [1,1,1,1,1,0],
+              [1,1,1,1,1,2],  [0,0,1,1,1,1],  [1,0,0,1,1,1],  [1,1,0,0,1,1],  [1,1,1,0,0,1],  [1,1,1,1,0,0],
+              [0,1,0,1,1,1],  [0,1,1,0,1,1],  [0,1,1,1,0,1],  [0,1,1,1,1,0],  [1,0,1,0,1,1],  [1,0,1,1,0,1],
+              [1,0,1,1,1,0],  [1,1,0,1,0,1],  [1,1,0,1,1,0],  [1,1,1,0,1,0] , [0 ,0,0,0,0,0]]
         if abs(rprim[1, 0]) > 1e-9 or abs(rprim[2, 0]) > 1e-9 or abs(rprim[2, 1]) > 1e-9:
             print("Warning: The lattice is oriented such that xz =xy =yz =0 .")
         rprim0 = np.copy(rprim)
@@ -59,12 +59,12 @@ def generate_deformations(structure , eps=0.005):
         cos_ac = np.dot(a, c) / (norm_a * norm_c)
         cos_bc = np.dot(b, c) / (norm_b * norm_c)
 
-        rprim0[0,0] = 1.0 
-        rprim0[0,1] = 0.0 
-        rprim0[0,2] = 0.0 
+        rprim0[0,0] = 1.0
+        rprim0[0,1] = 0.0
+        rprim0[0,2] = 0.0
         rprim0[1,0] = cos_ab
         rprim0[1,1] = np.sqrt(1-cos_ab**2)
-        rprim0[1,2] = 0.0 
+        rprim0[1,2] = 0.0
         rprim0[2,0] = cos_ac
         rprim0[2,1] = (cos_bc-rprim0[1,0]*rprim0[2,0])/rprim0[1,1]
         rprim0[2,2] = np.sqrt(1.0-rprim0[2,0]**2-rprim0[2,1]**2)
@@ -92,7 +92,7 @@ def generate_deformations(structure , eps=0.005):
 
             structure2=structure.copy()
             structure2.lattice=Lattice(rprim2)
-            structures_new[formatted_namei] = structure2 
+            structures_new[formatted_namei] = structure2
 
         return structures_new
     elif 3 <= spgrp_number <= 15:
@@ -116,7 +116,7 @@ def generate_deformations(structure , eps=0.005):
             cos_bc = np.dot(b, c) / (norm_b * norm_c)
 
             rprim0[0,0] = norm_a
-            rprim0[0,2] = 0.0 
+            rprim0[0,2] = 0.0
             rprim0[1,1] = norm_b
             rprim0[2,0] = norm_c*cos_ac
             rprim0[2,2] = norm_c*np.sqrt(1-cos_ac**2)
@@ -139,7 +139,7 @@ def generate_deformations(structure , eps=0.005):
 
             structure2=structure.copy()
             structure2.lattice=Lattice(rprim2)
-            structures_new[formatted_namei] = structure2 
+            structures_new[formatted_namei] = structure2
 
         return structures_new
     elif 16 <= spgrp_number <= 74:
@@ -157,7 +157,7 @@ def generate_deformations(structure , eps=0.005):
 
             structure2=structure.copy()
             structure2.lattice=Lattice(rprim2)
-            structures_new[formatted_namei] = structure2 
+            structures_new[formatted_namei] = structure2
 
         return structures_new
     elif 75 <= spgrp_number <= 194:
@@ -175,7 +175,7 @@ def generate_deformations(structure , eps=0.005):
 
             structure2=structure.copy()
             structure2.lattice=Lattice(rprim2)
-            structures_new[formatted_namei] = structure2 
+            structures_new[formatted_namei] = structure2
 
         return structures_new
     elif 195 <= spgrp_number <= 230:
@@ -188,6 +188,6 @@ def generate_deformations(structure , eps=0.005):
 
             structure2=structure.copy()
             structure2.lattice=Lattice(rprim2)
-            structures_new[formatted_namei] = structure2 
+            structures_new[formatted_namei] = structure2
         return structures_new