Fix GFN-FF energy - redirect GFN-FF output through a hack

avogadro/qtplugins/forcefield/scripts/gfnff.py

@@ -4,16 +4,59 @@
 import argparse
 import json
 import sys
+import os
 
 try:
     import numpy as np
     from xtb.libxtb import VERBOSITY_MUTED
-    from xtb.interface import Calculator, Param
+    from xtb.interface import Calculator, Param, Environment
 
     imported = True
 except ImportError:
     imported = False
 
+# we need to redirect stdout
+# this is from https://eli.thegreenplace.net/2015/redirecting-all-kinds-of-stdout-in-python/
+from contextlib import contextmanager
+import ctypes
+import io
+import tempfile
+
+libc = ctypes.CDLL(None)
+
+@contextmanager
+def stdout_redirector(stream):
+    # The original fd stdout points to. Usually 1 on POSIX systems.
+    original_stdout_fd = sys.stdout.fileno()
+
+    def _redirect_stdout(to_fd):
+        """Redirect stdout to the given file descriptor."""
+        # Flush the C-level buffer stdout
+        #libc.fflush(c_stdout)
+        # Flush and close sys.stdout - also closes the file descriptor (fd)
+        sys.stdout.close()
+        # Make original_stdout_fd point to the same file as to_fd
+        os.dup2(to_fd, original_stdout_fd)
+        # Create a new sys.stdout that points to the redirected fd
+        sys.stdout = io.TextIOWrapper(os.fdopen(original_stdout_fd, 'wb'))
+
+    # Save a copy of the original stdout fd in saved_stdout_fd
+    saved_stdout_fd = os.dup(original_stdout_fd)
+    try:
+        # Create a temporary file and redirect stdout to it
+        tfile = tempfile.TemporaryFile(mode='w+b')
+        _redirect_stdout(tfile.fileno())
+        # Yield to caller, then redirect stdout back to the saved fd
+        yield
+        _redirect_stdout(saved_stdout_fd)
+        # Copy contents of temporary file to the given stream
+        tfile.flush()
+        tfile.seek(0, io.SEEK_SET)
+        stream.write(tfile.read())
+    finally:
+        tfile.close()
+        os.close(saved_stdout_fd)
+
 
 def getMetaData():
     # before we return metadata, make sure xtb is in the path
@@ -57,25 +100,30 @@
         if "totalSpinMultiplicity" in mol_cjson["properties"]:
             spin = mol_cjson["properties"]["totalSpinMultiplicity"]
 
-    calc = Calculator(Param.GFNFF, atoms, coordinates, 
+    # xtb doesn't properly mute
+    # so we redirect stdout to a StringIO
+    #  and then just ignore it
+    f = io.BytesIO()
+    with stdout_redirector(f):
+        calc = Calculator(Param.GFNFF, atoms, coordinates, 
                         charge=charge, uhf=spin)
-    calc.set_verbosity(VERBOSITY_MUTED)
-    res = calc.singlepoint()
+        calc.set_verbosity(VERBOSITY_MUTED)
+        res = calc.singlepoint()
 
     # we loop forever - Avogadro will kill our process when done
     while True:
         # read new coordinates from stdin
         for i in range(len(atoms)):
-            coordinates[i] = np.fromstring(input())
+            coordinates[i] = np.fromstring(input(), sep=' ')
         # .. convert from Angstrom to Bohr
         coordinates /= 0.52917721067
 
         # update the calculator and run a new calculation
         calc.update(coordinates)
         calc.singlepoint(res)
 
-        # first print the energy of these coordinates
         print("AvogadroEnergy:", res.get_energy())  # in Hartree
+        # times 2625.5 kJ/mol
 
         # now print the gradient
         # .. we don't want the "[]" in the output
@@ -87,7 +135,7 @@
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser("GFN2 calculator")
+    parser = argparse.ArgumentParser("GFN-FF calculator")
     parser.add_argument("--display-name", action="store_true")
     parser.add_argument("--metadata", action="store_true")
     parser.add_argument("-f", "--file", nargs=1)