dftpy 2.0.2__tar.gz → 2.0.3__tar.gz

{dftpy-2.0.2/src/dftpy.egg-info → dftpy-2.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dftpy
-Version: 2.0.2
+Version: 2.0.3
 Summary: Python3 packages for Density Functional Theory
 Home-page: http://dftpy.rutgers.edu
 Author: Pavanello Research Group

{dftpy-2.0.2 → dftpy-2.0.3}/examples/test/test_ase_md.py

@@ -5,12 +5,10 @@ import numpy as np
 
 from dftpy.config import DefaultOption, OptionFormat
 from dftpy.api.api4ase import DFTpyCalculator
-import pytest
 
 
 class Test(unittest.TestCase):
     def test_md(self):
-        pytest.importorskip("ase")
         from ase.md.langevin import Langevin
         from ase.md.verlet import VelocityVerlet
         from ase.md.velocitydistribution import MaxwellBoltzmannDistribution

{dftpy-2.0.2 → dftpy-2.0.3}/examples/test/test_ase_opt.py

@@ -2,14 +2,12 @@
 import os
 import unittest
 import numpy as np
-import pytest
 
 from dftpy.config import DefaultOption, OptionFormat
 from dftpy.api.api4ase import DFTpyCalculator
 
 class Test(unittest.TestCase):
     def test_opt(self):
-        pytest.importorskip("ase")
         from ase.optimize import BFGS, LBFGS, FIRE
         from ase.optimize.sciopt import SciPyFminBFGS, SciPyFminCG
         from ase.constraints import StrainFilter, UnitCellFilter

{dftpy-2.0.2 → dftpy-2.0.3}/examples/test/test_ase_pmg_io.py

@@ -8,7 +8,6 @@ import pytest
 
 class Test(unittest.TestCase):
     def test_io_ase(self):
-        pytest.importorskip("ase")
         dftpy_data_path = os.environ.get('DFTPY_DATA_PATH')
         a1 = dftpy_io.read(dftpy_data_path + '/fcc.vasp', driver='ase')
         a2 = dftpy_io.read(dftpy_data_path + '/fcc.vasp')

{dftpy-2.0.2 → dftpy-2.0.3}/src/dftpy/__init__.py

@@ -1,8 +1,8 @@
 __author__ = "Pavanello Research Group"
 __contact__ = "m.pavanello@rutgers.edu"
 __license__ = "MIT"
-__version__ = "2.0.2"
-__date__ = "2023-06-28"
+__version__ = "2.0.3"
+__date__ = "2023-08-08"
 
 from .config import *
 from .mpi import mp, sprint

dftpy-2.0.3/src/dftpy/api/api4ase.py

@@ -0,0 +1,58 @@
+import numpy as np
+from dftpy.constants import ENERGY_CONV, FORCE_CONV, STRESS_CONV
+from dftpy.interface import ConfigParser, OptimizeDensityConf
+from dftpy.ions import Ions
+from ase.calculators.calculator import Calculator, all_changes
+
+class DFTpyCalculator(Calculator):
+    """DFTpy calculator for ase"""
+    implemented_properties = ['energy', 'forces', 'stress']
+
+    def __init__(self, config = None, mp = None, **kwargs):
+        Calculator.__init__(self, **kwargs)
+        self.config = config
+        self.mp = mp
+        self.dftpy_results = {}
+
+    def calculate(self, atoms=None, properties=['energy'], system_changes=all_changes):
+        Calculator.calculate(self, atoms, properties, system_changes)
+
+        if len(system_changes) > 0 :
+            self.run(system_changes)
+
+        energy = self.dftpy_results["energypotential"]["TOTAL"].energy * ENERGY_CONV["Hartree"]["eV"]
+        self.energy = self.dftpy_results["density"].grid.mp.asum(energy)
+        self.results['energy'] = self.energy
+        if 'forces' in properties:
+            self.forces = self.dftpy_results["forces"]["TOTAL"] * FORCE_CONV["Ha/Bohr"]["eV/A"]
+            self.results['forces'] = self.forces
+
+        if 'stress' in properties:
+            stress_voigt = np.zeros(6)
+            if "TOTAL" in self.dftpy_results["stress"]:
+                for i in range(3):
+                    stress_voigt[i] = self.dftpy_results["stress"]["TOTAL"][i, i]
+                    stress_voigt[3] = self.dftpy_results["stress"]["TOTAL"][1, 2]  # yz
+                    stress_voigt[4] = self.dftpy_results["stress"]["TOTAL"][0, 2]  # xz
+                    stress_voigt[5] = self.dftpy_results["stress"]["TOTAL"][0, 1]  # xy
+            else:
+                self.mp.sprint("!WARN : NOT calculate the stress, so return zeros")
+            self.stress = stress_voigt * STRESS_CONV["Ha/Bohr3"]["eV/A3"]
+            self.results['stress'] = self.stress
+
+    def run(self, system_changes=all_changes):
+        pseudo = self.dftpy_results.get('pseudo', None)
+        rho = self.dftpy_results.get('density', None)
+
+        grid = None
+        if 'cell' not in system_changes:
+            if rho is not None: grid = rho.grid
+        if not self.config["MATH"]["reuse"]:
+            rho = None
+
+        ions = Ions.from_ase(self.atoms)
+
+        config, others = ConfigParser(self.config, ions=ions, rhoini=rho, pseudo=pseudo, grid=grid, mp = self.mp)
+        self.dftpy_results = OptimizeDensityConf(config, **others)
+        if self.mp is None :
+            self.mp = self.dftpy_results["density"].grid.mp

{dftpy-2.0.2 → dftpy-2.0.3}/src/dftpy/constants.py

@@ -86,10 +86,7 @@ ZERO = 1E-30
 
 environ = {} # You can change it anytime you want
 environ['STDOUT'] = sys.stdout # file descriptor of sprint
-try:
-    environ['LOGLEVEL'] = int(os.environ.get('DFTPY_LOGLEVEL', 2)) # The level of sprint
-except Exception :
-    environ['LOGLEVEL'] = 2 # The level of sprint
+environ['LOGLEVEL'] = int(os.environ.get('DFTPY_LOGLEVEL', 2)) # The level of sprint
 """
     0 : all
     1 : debug

{dftpy-2.0.2 → dftpy-2.0.3}/src/dftpy/field.py

@@ -62,7 +62,12 @@ class BaseField(np.ndarray):
             input_values = np.asarray(data)
             input_values = np.reshape(input_values, nr, order=order)
 
-        obj = np.asarray(input_values).view(cls)
+        obj = np.asarray(input_values)
+        if order == 'C' and not obj.flags['C_CONTIGUOUS']:
+            obj = np.ascontiguousarray(obj)
+        elif order == 'F' and not obj.flags['F_CONTIGUOUS']:
+            obj = np.asfortranarray(obj)
+        obj = obj.view(cls)
         # add the new attribute to the created instance
         obj.grid = grid
         obj.span = (grid.nr > 1).sum()

{dftpy-2.0.2 → dftpy-2.0.3}/src/dftpy/grid.py

@@ -24,9 +24,9 @@ class BaseGrid:
     """
 
     def __init__(self, lattice, nr = None, origin=np.array([0.0, 0.0, 0.0]), full=True, direct=True,
-                 cplx=False, mp=None, ecut = None, **kwargs):
+                 cplx=False, mp=None, ecut = None, comm = None, **kwargs):
         if mp is None :
-            mp = MP()
+            mp = MP(comm)
         self._origin = np.asarray(origin)
         if not isinstance(lattice, Cell):
             cell=Cell(lattice)

{dftpy-2.0.2 → dftpy-2.0.3}/src/dftpy/mpi/mp_mpi4py.py

@@ -49,7 +49,7 @@ def get_mpi4py_fft(comm, nr, decomposition = 'Slab', backend = None, grid = None
     cplx = cplx or full
     if cplx :
         backend = 'numpy' # If cplx, use numpy for safe
-        dtype = np.complex
+        dtype = np.complex128
     else :
         dtype = np.float64
 

{dftpy-2.0.2 → dftpy-2.0.3}/src/dftpy/mpi/mpi.py

@@ -290,6 +290,11 @@ class MP :
         s = self._sum_1(a)
         return s
 
+    def sprint(self, *args, comm = None, **kwargs):
+        from .utils import sprint
+        if comm is None : comm = self.comm
+        sprint(*args, comm = comm, **kwargs)
+
 class PMI :
     """
     Detect mpi

{dftpy-2.0.2 → dftpy-2.0.3}/src/dftpy/td/real_time_runner.py

@@ -135,7 +135,7 @@ class RealTimeRunner(Dynamics):
         if self.correction:
             correct_potential = self.correct_functionals(self.rho, calcType=['V'], current=self.j).potential
             self.correct_propagator.hamiltonian.v = correct_potential
-            self.predictor_corrector.psi_pred = self.correct_propagator(self.predictor_corrector.psi_pred)
+            self.predictor_corrector.psi_pred, info = self.correct_propagator(self.predictor_corrector.psi_pred)
             self.predictor_corrector.rho_pred = calc_rho(self.predictor_corrector.psi_pred)
             self.predictor_corrector.j_pred = calc_j(self.predictor_corrector.psi_pred)
 

{dftpy-2.0.2 → dftpy-2.0.3/src/dftpy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dftpy
-Version: 2.0.2
+Version: 2.0.3
 Summary: Python3 packages for Density Functional Theory
 Home-page: http://dftpy.rutgers.edu
 Author: Pavanello Research Group

dftpy-2.0.2/src/dftpy/api/api4ase.py

@@ -1,80 +0,0 @@
-import numpy as np
-from dftpy.constants import LEN_CONV, ENERGY_CONV, FORCE_CONV, STRESS_CONV
-from dftpy.interface import ConfigParser, OptimizeDensityConf
-from dftpy.ions import Ions
-
-
-class DFTpyCalculator(object):
-    """DFTpy calculator for ase"""
-
-    def __init__(self, config=None, mp = None, **kwargs):
-        self.config = config
-        self.results = None
-        self.atoms = {}
-        self.mp = mp
-
-    def check_restart(self, atoms=None):
-        if (
-            self.atoms
-            and np.allclose(self.atoms["lattice"], atoms.cell)
-            and np.allclose(self.atoms["positions"], atoms.positions)
-            and self.results is not None
-        ):
-            return False
-        else:
-            return True
-
-    def get_potential_energy(self, atoms=None, **kwargs):
-        if self.check_restart(atoms):
-            lattice = atoms.cell
-            pos = atoms.positions
-            if self.results is not None and len(self.atoms) > 0 :
-                pseudo = self.results["pseudo"]
-                if np.allclose(self.atoms["lattice"], atoms.cell[:]):
-                    grid = self.results["density"].grid
-                else :
-                    grid = None
-            else :
-                pseudo = None
-                grid = None
-
-            # Save the information of structure
-            self.atoms["lattice"] = lattice.copy()
-            self.atoms["positions"] = pos.copy()
-            #
-            ions = Ions.from_ase(atoms)
-            #
-            if self.results is not None and self.config["MATH"]["reuse"]:
-                config, others = ConfigParser(self.config, ions=ions, rhoini=self.results["density"], pseudo=pseudo, grid=grid, mp = self.mp)
-            else:
-                config, others = ConfigParser(self.config, ions=ions, pseudo=pseudo, grid=grid, mp = self.mp)
-            results = OptimizeDensityConf(config, **others)
-            self.results = results
-        energy = self.results["energypotential"]["TOTAL"].energy * ENERGY_CONV["Hartree"]["eV"]
-        energy = self.results["density"].grid.mp.asum(energy)
-        return energy
-
-    def get_forces(self, atoms):
-        if self.check_restart(atoms):
-            # if 'Force' not in self.config['JOB']['calctype'] :
-                # self.config['JOB']['calctype'] += ' Force'
-            self.get_potential_energy(atoms)
-        return self.results["forces"]["TOTAL"] * FORCE_CONV["Ha/Bohr"]["eV/A"]
-
-    def get_stress(self, atoms):
-        if self.check_restart(atoms):
-            # if 'Stress' not in self.config['JOB']['calctype'] :
-                # self.config['JOB']['calctype'] += ' Stress'
-            self.get_potential_energy(atoms)
-        # return self.results['stress']['TOTAL'] * STRESS_CONV['Ha/Bohr3']['eV/A3']
-        stress_voigt = np.zeros(6)
-        if "TOTAL" not in self.results["stress"]:
-            # print("!WARN : NOT calculate the stress, so return zeros")
-            return stress_voigt
-        for i in range(3):
-            stress_voigt[i] = self.results["stress"]["TOTAL"][i, i]
-        stress_voigt[3] = self.results["stress"]["TOTAL"][1, 2]  # yz
-        stress_voigt[4] = self.results["stress"]["TOTAL"][0, 2]  # xz
-        stress_voigt[5] = self.results["stress"]["TOTAL"][0, 1]  # xy
-        # stress_voigt  *= -1.0
-        return stress_voigt * STRESS_CONV["Ha/Bohr3"]["eV/A3"]