improved xtb driver and testing suite

molli/external/xtb.py

@@ -1,7 +1,5 @@
 from typing import Any, Generator, Callable
 from ..chem import Molecule
-from ..config import BACKUP_DIR
-from ..config import SCRATCH_DIR
 from subprocess import run, PIPE
 from pathlib import Path
 import attrs
@@ -134,6 +132,8 @@ def __contains__(self, key):
 
 class XTBDriver:
     def __init__(self, nprocs: int = 1) -> None:
+        from ..config import BACKUP_DIR
+        from ..config import SCRATCH_DIR        
         self.nprocs = nprocs
         self.backup_dir = BACKUP_DIR
         self.scratch_dir = SCRATCH_DIR
@@ -152,14 +152,11 @@ def optimize(
         crit: str = "normal",
         xtbinp: str = "",
         maxiter: int = 50,
-        # xyz_name: str = "mol", # do we need this anymore?
-
         ):
         assert isinstance(M, Molecule), "User did not pass a Molecule object!"
-        # print(self.nprocs)
         inp = JobInput(
             M.name,
-            command=f"""xtb input.xyz --{method} --opt {crit} --charge {M.charge} {"--input param.inp" if xtbinp else ""} -P {self.nprocs}""",
+            command=f"""xtb input.xyz --{method} --opt {crit} --charge {M.charge} --iterations {maxiter} {"--input param.inp" if xtbinp else ""} -P {self.nprocs}""",
             files={"input.xyz": M.dumps_xyz().encode()}
         )
 

molli_test/test_external_xtb.py

@@ -2,33 +2,51 @@
 
 import numpy as np
 import molli as ml
+import subprocess
+import os
+from pathlib import Path
+import shutil
 
 from joblib import delayed,Parallel
 from molli.external import XTBDriver
+from molli.config import BACKUP_DIR
+from molli.config import SCRATCH_DIR
 
-# how to handle this?
-# try:
-#     from rdkit.Chem.PropertyMol import PropertyMol
-# except:
-#     _RDKIT_INSTALLED = False
-# else:
-#     _RDKIT_INSTALLED = True
-# try:
-#     from rdkit.Chem.Draw import IPythonConsole
-# except:
-#     _IPYTHON_INSTALLED = False
-# else:
-#     from molli.external import _rdkit
-#     _IPYTHON_INSTALLED = True
 
+# a little clunky but will check if xTB is installed
+try:
+    out = subprocess.run(['xtb', '--version'], capture_output=True)
+    if out.stderr == b'normal termination of xtb\n':
+        _XTB_INSTALLED = True
+except FileNotFoundError:
+    _XTB_INSTALLED = False
+
+_CURRENT_BACKUP_DIR = BACKUP_DIR
+_CURRENT_SCRATCH_DIR = SCRATCH_DIR
+_TEST_BACKUP_DIR: Path  = ml.config.HOME / "test_backup"
+_TEST_SCRATCH_DIR: Path  = ml.config.HOME / "test_scratch"
+
+def prep_dirs():
+    ml.config.BACKUP_DIR = _TEST_BACKUP_DIR
+    ml.config.SCRATCH_DIR = _TEST_SCRATCH_DIR 
+
+def cleanup_dirs():
+    shutil.rmtree(_TEST_BACKUP_DIR)
+    shutil.rmtree(_TEST_SCRATCH_DIR)
+    ml.config.BACKUP_DIR = _CURRENT_BACKUP_DIR
+    ml.config.SCRATCH_DIR = _CURRENT_SCRATCH_DIR
 
 class XTBTC(ut.TestCase):
     """This test suite is for the basic installation stuff"""
 
-    # @ut.skipUnless(_RDKIT_INSTALLED, "RDKit is not installed in current environment.")
-    # @ut.skipUnless(_IPYTHON_INSTALLED, "IPython is not installed in current environment.")
+
+    @ut.skipUnless(_XTB_INSTALLED, "xtb is not installed in current environment.")
     def test_xtb_optimize(self):
+
+        prep_dirs()
+
         # test with cinchonidine library
+
         mlib1 = ml.MoleculeLibrary(ml.files.cinchonidines)
         #Cinchonidine Charges = 1
         for m in mlib1:
@@ -52,4 +70,32 @@ def test_xtb_optimize(self):
             for m1, m2 in zip(mlib1, res):
                 self.assertNotAlmostEqual(np.linalg.norm(m1.coords - m2.coords), 0) # make sure the atom coordinates have moved
 
+        cleanup_dirs()
+
+    @ut.skipUnless(_XTB_INSTALLED, "xtb is not installed in current environment.")
+    def test_xtb_energy(self):
+
+        prep_dirs()
+
+        # test with cinchonidine library
+        mlib1 = ml.MoleculeLibrary(ml.files.cinchonidines)
+        #Cinchonidine Charges = 1
+        for m in mlib1:
+            m.charge = 1
+
+        # testing in serial works fine
+        xtb = XTBDriver(nprocs=4)
+        res = [xtb.energy(m) for m in mlib1]
+
+        # we will spot check several of these based on output from separate call to xtb
+        for i, energy in enumerate(res):
+            if mlib1[i].name == '1_5_c':
+                self.assertEqual(energy, -105.591624613587)
+            if mlib1[i].name == '2_12_c':
+                self.assertEqual(energy, -102.911928497077)
+            if mlib1[i].name == '10_5_c':
+                self.assertEqual(energy, -116.035733938867)
+
+        cleanup_dirs()
+