update ase dependency

MaterSim · Aug 12, 2024 · 7f07a19 · 7f07a19
1 parent 9603b96
commit 7f07a19
Show file tree

Hide file tree

Showing 4 changed files with 29 additions and 30 deletions.
diff --git a/pyxtal/interface/ani.py b/pyxtal/interface/ani.py
@@ -3,9 +3,9 @@
 
 import numpy as np
 import torchani
-from ase.constraints import ExpCellFilter
+from ase.constraints import UnitCellFilter, FixSymmetry
 from ase.optimize.fire import FIRE
-from ase.spacegroup.symmetrize import FixSymmetry
+#from ase.spacegroup.symmetrize import FixSymmetry
 
 
 def ANI_relax(struc, opt_cell=False, step=500, fmax=0.1, logfile=None, max_time=6.0):
@@ -20,7 +20,7 @@ def ANI_relax(struc, opt_cell=False, step=500, fmax=0.1, logfile=None, max_time=
     struc.set_calculator(calc)
     struc.set_constraint(FixSymmetry(struc))
     if opt_cell:
-        ecf = ExpCellFilter(struc)
+        ecf = UnitCellFilter(struc)
         dyn = FIRE(ecf, a=0.1, logfile=logfile) if logfile is not None else FIRE(ecf, a=0.1)
     else:
         dyn = FIRE(struc, a=0.1, logfile=logfile) if logfile is not None else FIRE(struc, a=0.1)
@@ -55,26 +55,28 @@ def __init__(self, struc, opt_lat=True, logfile=None):
         self.optimized = True
         self.positions = None
         self.cell = None
-        self.group = self.structure.group
         self.cputime = 0
-        self.calculator = torchani.models.ANI2x().ase()
         self.logfile = logfile
 
-    def run(self):
+    def run(self, steps=10):
         t0 = time()
         s = self.structure.to_ase(resort=False)
         s.set_constraint(FixSymmetry(s))
-        s.set_calculator(self.calculator)
-        dyn = FIRE(s, a=0.1, logfile=self.logfile)
-        dyn.run(fmax=0.1, steps=10)
-        # print(s)
-        if self.opt_lat:
-            ecf = ExpCellFilter(s)
-            dyn = FIRE(ecf, a=0.1, logfile=self.logfile)
-            dyn.run(fmax=0.1, steps=10)
+        s.set_calculator(torchani.models.ANI2x().ase())#; print("Setup Fire")
+
+        if not self.opt_lat:
+            dyn = FIRE(s, a=0.1, logfile=self.logfile)#, force_consistent=False)
+            dyn.run(fmax=0.1, steps=steps)
+        else:
+            #ecf = FrechetCellFilter(s)
+            ecf = UnitCellFilter(s)
+            dyn = FIRE(ecf, a=0.1, logfile=self.logfile)#, force_consistent=False)
+            dyn.run(fmax=0.1, steps=steps)
             self.structure.lattice.set_matrix(s.get_cell())
+
         positions = s.get_scaled_positions()
-        try:
+        #try:
+        if True:
             # s.write('../1.cif', format='cif')
             count = 0
             for _i, site in enumerate(self.structure.mol_sites):
@@ -89,21 +91,20 @@ def run(self):
                         coords1[j] = coords0[j] + diff
                     else:
                         print(coords1[j], coords1[j], np.linalg.norm(abs_diff))
-                        import sys
-
-                        sys.exit()
+                        import sys; sys.exit()
 
                 site.update(coords1, self.structure.lattice)
                 count += len(site.molecule.mol) * site.wp.multiplicity
             self.structure.optimize_lattice()
             self.structure.energy = s.get_potential_energy()
             self.cell = s.get_cell()
             # print(self.structure.lattice)
-        except:
-            self.structure.energy = 10000
-            self.optimized = False
-            print("Structure is wrong after optimization")
-
+        #except:
+        #    self.structure.energy = 10000
+        #    self.optimized = False
+        #    print("Structure is wrong after optimization")
+        s.set_calculator()
+        s.set_constraint()
         self.cputime = time() - t0
 
 

diff --git a/pyxtal/interface/dftb.py b/pyxtal/interface/dftb.py
@@ -7,10 +7,9 @@
     kpts2ndarray,
     kpts2sizeandoffsets,
 )
-from ase.constraints import ExpCellFilter
+from ase.constraints import UnitCellFilter, FixSymmetry
 from ase.io import read
 from ase.optimize.fire import FIRE
-from ase.spacegroup.symmetrize import FixSymmetry
 from ase.units import Bohr, Hartree
 
 from pyxtal.util import Kgrid
@@ -220,7 +219,7 @@ def DFTB_relax(
 
     # impose cell constraints
     if opt_cell:
-        ecf = ExpCellFilter(struc, mask=mask)
+        ecf = UnitCellFilter(struc, mask=mask)
         dyn = FIRE(ecf, logfile=logfile)
     else:
         dyn = FIRE(struc, logfile=logfile)

diff --git a/pyxtal/interface/lammpslib.py b/pyxtal/interface/lammpslib.py
@@ -6,10 +6,9 @@
 import ase.units
 import numpy as np
 from ase.calculators.calculator import Calculator
-from ase.constraints import ExpCellFilter
+from ase.constraints import UnitCellFilter, FixSymmetry
 from ase.optimize import LBFGS
 from ase.optimize.fire import FIRE
-from ase.spacegroup.symmetrize import FixSymmetry
 from lammps import lammps
 
 
@@ -65,7 +64,7 @@ def opt_lammpslib(
     struc.set_calculator(lammps)
     struc.set_constraint(FixSymmetry(struc))
     if opt_cell:
-        ecf = ExpCellFilter(struc, mask)
+        ecf = UnitCellFilter(struc, mask)
         dyn = FIRE(ecf, logfile=logfile, a=a) if method == "FIRE" else LBFGS(ecf, logfile=logfile)
     else:
         dyn = FIRE(struc, logfile=logfile) if method == "FIRE" else LBFGS(struc, logfile=logfile)

diff --git a/setup.py b/setup.py
@@ -46,7 +46,7 @@
         "pymatgen>=2024.3.1",
         "pandas>=2.0.2",
         "networkx>=2.3",
-        "ase>=3.18.0",  # covered by pymatgen
+        "ase>=3.23.0",
         "scipy>=1.7.3",
         "numpy>=1.26,<2",  # prevent the use of numpy2
         "importlib_metadata>=1.4",