Code cleanup in qha_aproximation.py

.gitignore

@@ -3,7 +3,9 @@ abinit_vars.pickle
 Profile.prof
 abipy/examples/flows/flow_*
 abipy/examples/flows/develop/flow_*
+__abipy_import.log
 _debug
+abipy/scripts/tests/test-output/
 #__abinb_workdir__
 #abinb_*.ipynb
 $*.pickle

abipy/dfpt/tests/test_qha_approximation.py

@@ -45,17 +45,20 @@ def test_v_ZSIZA(self):
         self.assert_almost_equal(data.min_vol, 40.05665096)
         self.assert_almost_equal(data.temp, 0)
 
+        e2d_v = qha.second_derivative_energy_v(41)
+        self.assert_almost_equal(e2d_v, 0.0128727)
+
         f = qha.get_thermal_expansion_coeff(tstart=0, tstop=1000, num=7, tref=None)
         self.assert_almost_equal(f.values, [-0.0000000e+00,  5.1944952e-07,  7.0431284e-06,  9.4401141e-06,
                                              1.0630764e-05,  1.1414897e-05,  1.2035432e-05])
 
         vols, fits = qha.vol_Einf_Vib4(num=2, tstop=tstop, tstart=tstart)
-        aas, bbs, ccs = qha.get_abc(tstart=tstart, tstop=tstop, num=2, volumes=vols)
+        aas, bbs, ccs = qha.get_abc(volumes=vols, num=2)
         self.assert_almost_equal(aas, [3.8466098, 3.8530056])
         self.assert_almost_equal(bbs, [3.8466098, 3.8530056])
         self.assert_almost_equal(ccs, [3.8466098, 3.8530056])
 
-        alphas, betas, gammas = qha.get_angles(tstart=tstart, tstop=tstop, num=2, volumes=vols)
+        alphas, betas, gammas = qha.get_angles(vols, num=2)
         self.assert_almost_equal(alphas, [60., 60.])
         self.assert_almost_equal(betas, [60., 60.])
         self.assert_almost_equal(gammas, [60., 60.])

abipy/embedding/tests/test_embedding_ifc.py

@@ -157,11 +157,11 @@ def test_embedding_interstitial(self):
         ########
         ### model of the split-interstitial as one vacancy + 2 inter.
 
-        stru=abiopen(abidata.ref_file("refs/embedding_ifc/C_sc.cif"))
+        stru= abiopen(abidata.ref_file("refs/embedding_ifc/C_sc.cif"))
         stru.remove_sites(indices=[14])
-        stru.append(species="C",coords=[0.600, 0.5000, 0.2500])
-        stru.append(species="C",coords=[0.400, 0.5000, 0.2500])
-        structure_defect_wo_relax=stru
+        stru.append(species="C", coords=[0.600, 0.5000, 0.2500])
+        stru.append(species="C", coords=[0.400, 0.5000, 0.2500])
+        structure_defect_wo_relax = stru
 
         # main defect is
         main_defect_coords_in_pristine=get_pmg_structure(ph_pristine.supercell)[31].coords
@@ -184,8 +184,7 @@ def test_embedding_interstitial(self):
 
 
         freqs, vecs = ph_emb.get_gamma_freq_with_vec_abipy_fmt()
-
-        self.assert_almost_equal(freqs[-1],0.212826358519,decimal=5)
+        self.assert_almost_equal(freqs[-1], 0.212826358519, decimal=5)
 
         ratio = localization_ratio(vecs)
-        self.assert_almost_equal(ratio[650],78.76445591,decimal=5)
+        self.assert_almost_equal(ratio[650], 78.76445591, decimal=5)

abipy/scripts/abiview.py

@@ -53,6 +53,15 @@ def abiview_structure(options):
     return 0
 
 
+def abiview_input(options):
+    """Read input file from netcdf file and print it to terminal."""
+    from abipy.iotools import ETSF_Reader
+    with ETSF_Reader(options.filepath) as r:
+        input_str = r.read_string("input_string")
+        print(input_str)
+    return 0
+
+
 def abiview_hist(options):
     """
     Visualize structural relaxation/molecular-dynamics run
@@ -701,6 +710,9 @@ def add_args(p, *args):
         help=("Application name. Default: vesta. "
               "Possible options: %s, mayavi, vtk" % ", ".join(Visualizer.all_visunames())))
 
+    # Subparser for input command.
+    p_input = subparsers.add_parser('input', parents=[copts_parser], help=abiview_input.__doc__)
+
     # Subparser for hist command.
     p_hist = subparsers.add_parser('hist', parents=[copts_parser], help=abiview_hist.__doc__)
     p_hist.add_argument("-a", "--appname", nargs="?", default=None, const="ovito",

pyproject.toml

@@ -57,10 +57,11 @@ dependencies = [
     "numpy<2.0.0",
     "packaging",
     "pandas",
-    "phonopy",
+    "phonopy<=2.31.2",
     "plotly",
     "pydispatcher>=2.0.5",
-    "pymatgen>=2022.0.14",
+    "pymatgen==v2024.10.29",
+    "monty==v2024.10.21",
     "pyyaml>=3.11",
     "scipy",
     "seaborn",

tasks.py

@@ -2,8 +2,8 @@
 Deployment file to facilitate AbiPy releases.
 Use invoke --list to get list of tasks
 """
-
 import os
+import shutil
 
 from invoke import task
 from monty.os import cd
@@ -128,6 +128,53 @@ def update_vars(ctx, abinit_repo_path):
         os.system(cmd)
 
 
+@task
+def pyclean(ctx):
+    """remove all pyc files and all __pycache__ directory."""
+
+    def rm_pycaches(top: str) -> None:
+        """remove __pycache__ directory."""
+        count = 0
+        for dirpath, dirnames, filenames in os.walk(top):
+            for d in dirnames:
+                if not d ==  "__pycache__": continue
+                path = os.path.join(dirpath, d)
+                #print("Will remove %s" % path)
+                shutil.rmtree(path)
+                count += 1
+
+        print("Removed %d __pycache__ directories" % count)
+
+
+    def rm_pycfiles(top: str) -> int:
+        """remove all pyc files."""
+        count = 0
+        for dirpath, dirnames, filenames in os.walk(top):
+            for f in filenames:
+                if not f.endswith(".pyc"): continue
+                path = os.path.join(dirpath, f)
+                #print("Will remove %s" % path)
+                os.remove(path)
+                count += 1
+
+        print("Removed %d .pyc files" % count)
+        return count
+
+    top = ABIPY_ROOTDIR
+    rm_pycaches(top)
+    rm_pycfiles(top)
+
+
+@task
+def tuna(ctx):
+    """Execute tuna import profiler."""
+    cmd = 'python -X importtime -c "import abipy" 2> __abipy_import.log'
+    print("Executing:", cmd)
+    ctx.run(cmd, pty=True)
+    cmd = "tuna __abipy_import.log"
+    ctx.run(cmd, pty=True)
+
+
 #@task
 #def move_to_master(ctx):
 #    ctx.run("git tag -a v%s -m \"v%s release\"" % (NEW_VER, NEW_VER))