Tblite migrating.

lanl · Dec 19, 2024 · 9dae795 · 9dae795
1 parent a76cc1a
commit 9dae795
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Showing 3 changed files with 21 additions and 16 deletions.
diff --git a/architector/arch_xtb_text_ase_calc.py b/architector/arch_xtb_text_ase_calc.py
@@ -87,7 +87,7 @@ def calculate(self, atoms=None, *args, **kwargs):
                     file1.write("    gbsa=true\n")
 
                 # Run xtb
-                execStr = "{} structure.xyz {} --chrg {} --uhf {} --alpb {} -P 1 -a {} --etemp {} --iterations {} --grad -I solv_options.txt> output.xtb".format(
+                execStr = "{} structure.xyz {} --chrg {} --uhf {} --alpb {} -P 1 -a {} --etemp {} --iterations {} --grad -I solv_options.txt".format(
                     xtbPath,
                     methods_dict[self.parameters.get("xtb_method", "GFN2-xTB")],
                     int(charge),
@@ -98,7 +98,7 @@ def calculate(self, atoms=None, *args, **kwargs):
                     self.parameters["xtb_max_iterations"],
                 )
             else:
-                execStr = "{} structure.xyz {} --chrg {} --uhf {} -P 1 -a {} --etemp {} --iterations {} --grad> output.xtb".format(
+                execStr = "{} structure.xyz {} --chrg {} --uhf {} -P 1 -a {} --etemp {} --iterations {} --grad".format(
                     xtbPath,
                     methods_dict[self.parameters.get("xtb_method", "GFN2-xTB")],
                     int(charge),
@@ -108,9 +108,11 @@ def calculate(self, atoms=None, *args, **kwargs):
                     self.parameters["xtb_max_iterations"],
                 )
 
-            sub.run(
-                execStr, shell=True, check=True, stderr=sub.DEVNULL, stdout=sub.DEVNULL
-            )
+            with open('output.xtb', 'w') as file1:
+                sub.run(
+                    execStr.split(), check=True,
+                    stderr=sub.DEVNULL, stdout=file1
+                )
 
             outpath = pathlib.Path(".")
 

diff --git a/architector/io_calc.py b/architector/io_calc.py
@@ -315,15 +315,8 @@ def calculate(self):
                                   max_iterations=self.xtb_max_iterations,
                                   electronic_temperature=self.xtb_electronic_temperature,
                                   # spin_polarization=1.0, # Have spin polarization on if desired.
-                                  verbosity=self.parameters['debug'])
-                # No xtb-python
-                elif (not has_xtb_python) and (self.method != 'GFN-FF'):
-                    print('Warning: Defaulting to TBLite with no solvent since xtb-python is not installed.')
-                    calc = TBLite(method=self.method,
-                                  max_iterations=self.xtb_max_iterations,
-                                  electronic_temperature=self.xtb_electronic_temperature,
-                                  # spin_polarization=1.0, # Have spin polarization on if desired.
-                                  verbosity=self.parameters['debug'])
+                                #   verbosity=self.parameters['debug'])
+                                 verbosity=-1)
                 elif (not has_xtb_python):
                     calc = XTB_Calculator(
                         xtb_method=self.method,

diff --git a/architector/io_lig.py b/architector/io_lig.py
@@ -37,7 +37,14 @@
 from ase import Atom
 from ase.optimize.bfgslinesearch import BFGSLineSearch
 import ase.constraints as ase_con
-from xtb.ase.calculator import XTB
+has_xtb_python = False
+try:
+    from xtb.ase.calculator import XTB
+    has_xtb_python = True
+except:
+    pass
+
+from architector.arch_xtb_text_ase_calc import XTB_Calculator
 # from tblite.ase import TBLite -> No GFN-FF support yet.
 import warnings
 
@@ -107,7 +114,10 @@ def set_XTB_calc(ase_atoms):
     """
     ase_atoms.set_initial_charges(np.zeros(len(ase_atoms)))
     ase_atoms.set_initial_magnetic_moments(np.zeros(len(ase_atoms)))
-    calc = XTB(method="GFN-FF")
+    if has_xtb_python:
+        calc = XTB(method="GFN-FF")
+    else:
+        calc = XTB_Calculator(xtb_method="GFN-FF")
     # Default to only GFN-FF for ligand conformer relaxation.
     ase_atoms.calc = calc
     return ase_atoms