diff --git a/sphinxman/master/_modules/index.html b/sphinxman/master/_modules/index.html index 256420fc15..9a77e287dd 100644 --- a/sphinxman/master/_modules/index.html +++ b/sphinxman/master/_modules/index.html @@ -46,7 +46,7 @@ - + @@ -92,7 +92,7 @@
missing_enabled_return_qm=missing_enabled_return_qm,
missing_enabled_return_efp=missing_enabled_return_efp,
verbose=verbose)
+
+ qmol = core.Molecule.from_dict(molrec['qm'])
+
+ if "geom" in molrec["qm"]:
+ geom = np.array(molrec["qm"]["geom"]).reshape((-1, 3))
+ if molrec["qm"]["units"] == "Angstrom":
+ # beware if qcel and psi4 choose different sets of constants
+ geom = geom / constants.bohr2angstroms
+ qmol._initial_cartesian = core.Matrix.from_array(geom)
+
if return_dict:
- return core.Molecule.from_dict(molrec['qm']), molrec
+ return qmol, molrec
else:
- return core.Molecule.from_dict(molrec['qm'])
+ return qmol
@classmethod
@@ -292,8 +302,13 @@ Source code for psi4.driver.molutil
verbose=verbose)
qmol = core.Molecule.from_dict(molrec)
- geom = np.array(molrec["geom"]).reshape((-1, 3))
- qmol._initial_cartesian = core.Matrix.from_array(geom)
+
+ if "geom" in molrec:
+ geom = np.array(molrec["geom"]).reshape((-1, 3))
+ if molrec["units"] == "Angstrom":
+ # beware if qcel and psi4 choose different sets of constants
+ geom = geom / constants.bohr2angstroms
+ qmol._initial_cartesian = core.Matrix.from_array(geom)
if return_dict:
return qmol, molrec
@@ -330,6 +345,8 @@ Source code for psi4.driver.molutil
qmol = core.Molecule.from_dict(molrec)
geom = np.array(molrec["geom"]).reshape((-1, 3))
+ # presently molschema are formats required to be in Bohr Cartesian
+ # if the format expands, convert _initial_cartesian to Bohr and conditionalize setting the prop
qmol._initial_cartesian = core.Matrix.from_array(geom)
if return_dict:
@@ -391,6 +408,11 @@ Source code for psi4.driver.molutil
molecule = core.Molecule.from_dict(molrec['qm'])
if "geom" in molrec["qm"]:
+ # for fully-specified w/frame (dtype="psi4" passed in "geom", not Zmat or
+ # vars for dtype="psi4+" passed in "geom_unsettled"), save frame in
+ # Bohr in `_initial_cartesian` for resetting through `Molecule.set_geometry`
+ # if nocom/noreorient/c1 needs to be set retroactively in driver for
+ # alignment with other data (e.g., point charges, polarizable embedding).
geom = np.array(molrec["qm"]["geom"]).reshape((-1, 3))
if molrec["qm"]["units"] == "Angstrom":
# beware if qcel and psi4 choose different sets of constants
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:srcsample:`dfep2-1` Compute three IP and 2 EA's for the PH3 molecule
:srcsample:`scf4` RHF cc-pVDZ energy for water, automatically scanning the symmetric stretch and bending coordinates using Python's built-in loop mechanisms. The geometry is specified using a Z-matrix with variables that are updated during the potential energy surface scan, and then the same procedure is performed using polar coordinates, converted to Cartesian coordinates.
:srcsample:`ci-multi` BH single points, checking that program can run multiple instances of DETCI in a single input, without an intervening clean() call
+:srcsample:`extern5` External potential sanity check with 0 charge far away Checks if all units behave the same and energy is same as no potential
:srcsample:`dfmp2-freq2` DF-MP2 frequency by difference of energies for H2O
:srcsample:`dft-custom-hybrid` DFT (hybrids) test of implementations in: hybrid_superfuncs.py
:srcsample:`mints4` A demonstration of mixed Cartesian/ZMatrix geometry specification, using variables, for the benzene-hydronium complex. Atoms can be placed using ZMatrix coordinates, whether they belong to the same fragment or not. Note that the Cartesian specification must come before the ZMatrix entries because the former define absolute positions, while the latter are relative.
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