Adapt to changed API in spglib

Unpin spglib<2.3
jochym · Mar 1, 2024 · fc464cf · fc464cf
1 parent 004589b
commit fc464cf
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Showing 17 changed files with 152 additions and 116 deletions.
diff --git a/11_core.ipynb b/11_core.ipynb
diff --git a/15_monitor.ipynb b/15_monitor.ipynb
@@ -42,7 +42,7 @@
     "import sys\n",
     "from spglib import find_primitive, get_symmetry_dataset\n",
     "from collections import Counter\n",
-    "from hecss.util import load_dfset, get_dfset_len"
+    "from hecss.util import load_dfset, get_dfset_len, get_cell_data"
    ]
   },
   {
@@ -630,7 +630,7 @@
     "#| export\n",
     "\n",
     "def plot_dofmu_stat(cryst, dofmu, skip=10, window=10, normal=False):\n",
-    "    symm = get_symmetry_dataset(cryst)\n",
+    "    symm = get_symmetry_dataset(get_cell_data(cryst))\n",
     "    dofmap = symm['mapping_to_primitive']\n",
     "    dof = set(dofmap)\n",
     "    dofmul = Counter(symm['mapping_to_primitive'])\n",
@@ -692,7 +692,7 @@
     "#| export\n",
     "\n",
     "def plot_xs_stat(cryst, xsl, skip=10, window=10):\n",
-    "    symm = get_symmetry_dataset(cryst)\n",
+    "    symm = get_symmetry_dataset(get_cell_data(cryst))\n",
     "    dofmap = symm['mapping_to_primitive']\n",
     "    dof = set(dofmap)\n",
     "    dofmul = Counter(symm['mapping_to_primitive'])\n",

diff --git a/16_util.ipynb b/16_util.ipynb
@@ -30,7 +30,7 @@
    "outputs": [],
    "source": [
     "#| exporti\n",
-    "from numpy import dot, loadtxt, allclose\n",
+    "from numpy import dot, loadtxt, allclose, array\n",
     "from spglib import find_primitive, get_symmetry_dataset\n",
     "from ase import units as un\n",
     "import itertools"
@@ -345,7 +345,19 @@
    "id": "c6e20685-a0d2-4759-84b3-1cbe6f1bff9f",
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "#| exporti\n",
+    "def get_cell_data(cell):\n",
+    "    '''\n",
+    "    Create new spglib style of cell data from ase cell.\n",
+    "    '''\n",
+    "    \n",
+    "    lattice = array(cell.get_cell().T, dtype=\"double\", order=\"C\")\n",
+    "    positions = array(cell.get_scaled_positions(), dtype=\"double\", order=\"C\")\n",
+    "    numbers = array(cell.get_atomic_numbers(), dtype=\"intc\")\n",
+    "    \n",
+    "    return (lattice, positions, numbers)"
+   ]
   }
  ],
  "metadata": {

diff --git a/17_xscale.ipynb b/17_xscale.ipynb
diff --git a/72_DOF_map.ipynb b/72_DOF_map.ipynb
@@ -42,7 +42,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ase import spacegroup as sg"
+    "from ase import spacegroup as sg\n",
+    "from hecss.util import get_cell_data"
    ]
   },
   {
@@ -76,11 +77,11 @@
     }
    ],
    "source": [
-    "puc = spg.find_primitive(cryst)\n",
+    "puc = spg.find_primitive(get_cell_data(cryst))\n",
     "cryst_pc = ase.Atoms(cell=puc[0], scaled_positions=puc[1], numbers=puc[2], pbc=True)\n",
-    "sym = spg.get_symmetry(cryst_pc)\n",
-    "symds = spg.get_symmetry_dataset(cryst_pc)\n",
-    "spg.get_spacegroup(cryst_pc)"
+    "sym = spg.get_symmetry(get_cell_data(cryst_pc))\n",
+    "symds = spg.get_symmetry_dataset(get_cell_data(cryst_pc))\n",
+    "spg.get_spacegroup(get_cell_data(cryst_pc))"
    ]
   },
   {
@@ -223,7 +224,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "at_map = symds['equivalent_atoms'][spg.get_symmetry_dataset(cryst)['mapping_to_primitive']]"
+    "at_map = symds['equivalent_atoms'][spg.get_symmetry_dataset(get_cell_data(cryst))['mapping_to_primitive']]"
    ]
   },
   {

diff --git a/99_mh.ipynb b/99_mh.ipynb
diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
 # HECSS
 
+
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
 HECSS is a Monte-Carlo, configuration space sampler using sample

diff --git a/hecss/__init__.py b/hecss/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.5.18"
+__version__ = "0.5.19"
 
 from .core import *
 
diff --git a/hecss/_modidx.py b/hecss/_modidx.py
@@ -56,6 +56,7 @@
             'hecss.planner': {'hecss.planner.plan_T_scan': ('planner.html#plan_t_scan', 'hecss/planner.py')},
             'hecss.util': { 'hecss.util.calc_init_xscale': ('util.html#calc_init_xscale', 'hecss/util.py'),
                             'hecss.util.create_asap_calculator': ('util.html#create_asap_calculator', 'hecss/util.py'),
+                            'hecss.util.get_cell_data': ('util.html#get_cell_data', 'hecss/util.py'),
                             'hecss.util.get_dfset_len': ('util.html#get_dfset_len', 'hecss/util.py'),
                             'hecss.util.load_dfset': ('util.html#load_dfset', 'hecss/util.py'),
                             'hecss.util.normalize_conf': ('util.html#normalize_conf', 'hecss/util.py'),

diff --git a/hecss/core.py b/hecss/core.py
@@ -23,6 +23,7 @@
 import ase.units as un
 from ase.calculators import calculator
 from ase.data import chemical_symbols
+from hecss.util import get_cell_data
 import spglib
 from spglib import find_primitive, get_symmetry_dataset
 
@@ -358,8 +359,10 @@ def _sampler(self: HECSS, T_goal, N=None, delta_sample=0.01, sigma=2,
 
     nat = len(self.cryst)
     dim = (nat, 3)
-
-    symm = get_symmetry_dataset(self.cryst, symprec=symprec)
+    # lattice = np.array(cell.get_cell().T, dtype="double", order="C")
+    # positions = np.array(cell.get_scaled_positions(), dtype="double", order="C")
+    # numbers = np.array(cell.get_atomic_numbers(), dtype="intc")
+    symm = get_symmetry_dataset(get_cell_data(self.cryst), symprec=symprec)
     dofmap = symm['mapping_to_primitive']
     dof = list(sorted(set(dofmap)))
     dofmu = np.ones((len(dof), 3))

diff --git a/hecss/mh.py b/hecss/mh.py
@@ -17,6 +17,7 @@
 from itertools import islice
 from spglib import find_primitive, get_symmetry_dataset
 import spglib
+from hecss.util import get_cell_data
 from collections import Counter
 from ase.data import chemical_symbols
 from matplotlib import pyplot as plt
@@ -190,7 +191,7 @@ def print_xs(c, s):
     nat = len(cryst)
     dim = (nat, 3)
 
-    symm = get_symmetry_dataset(cryst, symprec=symprec)
+    symm = get_symmetry_dataset(get_cell_data(cryst), symprec=symprec)
     dofmap = symm['mapping_to_primitive']
     dof = list(sorted(set(dofmap)))
     dofmu = np.ones((len(dof), 3))

diff --git a/hecss/monitor.py b/hecss/monitor.py
@@ -19,7 +19,7 @@
 import sys
 from spglib import find_primitive, get_symmetry_dataset
 from collections import Counter
-from hecss.util import load_dfset, get_dfset_len
+from hecss.util import load_dfset, get_dfset_len, get_cell_data
 
 # %% ../15_monitor.ipynb 3
 from ase.data import chemical_symbols
@@ -433,7 +433,7 @@ def plot_acceptance_history(smpl):
 
 # %% ../15_monitor.ipynb 22
 def plot_dofmu_stat(cryst, dofmu, skip=10, window=10, normal=False):
-    symm = get_symmetry_dataset(cryst)
+    symm = get_symmetry_dataset(get_cell_data(cryst))
     dofmap = symm['mapping_to_primitive']
     dof = set(dofmap)
     dofmul = Counter(symm['mapping_to_primitive'])
@@ -487,7 +487,7 @@ def plot_dofmu_stat(cryst, dofmu, skip=10, window=10, normal=False):
 
 # %% ../15_monitor.ipynb 23
 def plot_xs_stat(cryst, xsl, skip=10, window=10):
-    symm = get_symmetry_dataset(cryst)
+    symm = get_symmetry_dataset(get_cell_data(cryst))
     dofmap = symm['mapping_to_primitive']
     dof = set(dofmap)
     dofmul = Counter(symm['mapping_to_primitive'])

diff --git a/hecss/util.py b/hecss/util.py
@@ -4,7 +4,7 @@
 __all__ = ['normalize_conf', 'load_dfset', 'get_dfset_len', 'write_dfset', 'calc_init_xscale']
 
 # %% ../16_util.ipynb 2
-from numpy import dot, loadtxt, allclose
+from numpy import dot, loadtxt, allclose, array
 from spglib import find_primitive, get_symmetry_dataset
 from ase import units as un
 import itertools
@@ -169,3 +169,15 @@ def calc_init_xscale(cryst, xsl, skip=None):
     for i, el in enumerate(set(elmap)):
         xscale[elmap==el] = xs[:,elmap==el,:].mean()
     return xscale
+
+# %% ../16_util.ipynb 15
+def get_cell_data(cell):
+    '''
+    Create new spglib style of cell data from ase cell.
+    '''
+
+    lattice = array(cell.get_cell().T, dtype="double", order="C")
+    positions = array(cell.get_scaled_positions(), dtype="double", order="C")
+    numbers = array(cell.get_atomic_numbers(), dtype="intc")
+
+    return (lattice, positions, numbers)
diff --git a/hecss/xscale.py b/hecss/xscale.py
@@ -15,7 +15,7 @@
 from spglib import find_primitive, get_symmetry_dataset
 from glob import glob
 from matplotlib import pyplot as plt
-from hecss.util import normalize_conf
+from hecss.util import normalize_conf, get_cell_data
 from hecss.monitor import plot_hist
 from hecss import *
 

diff --git a/index.ipynb b/index.ipynb
diff --git a/index_files/figure-commonmark/cell-5-output-1.png b/index_files/figure-commonmark/cell-5-output-1.png
diff --git a/settings.ini b/settings.ini
@@ -8,14 +8,14 @@ author = Paweł T. Jochym
 author_email = pawel.jochym@ifj.edu.pl
 copyright = Paweł T. Jochym
 branch = devel
-version = 0.5.18
+version = 0.5.19
 min_python = 3.7
 audience = Science/Research
 language = English
 custom_sidebar = False
 license = gpl3
 status = 3
-requirements = fastcore>=1.5 numpy scipy ase spglib<2.3 tqdm click matplotlib ipython
+requirements = fastcore>=1.5 numpy scipy ase spglib tqdm click matplotlib ipython
 console_scripts = hecss_sampler=hecss.cli:hecss_sampler plot_stats=hecss.cli:plot_stats plot_bands=hecss.cli:plot_bands calculate_xscale=hecss.cli:calculate_xscale reshape_sample=hecss.cli:reshape_sample
 tst_flags = vasp interactive slow quick asap vaspx
 nbs_path = .