Numerical Hessian Code

[bessvlai]

The implementation of the numerical Hessian and partial harmonic vibrational analysis (PHVA)

[shiozaki]

Just as a record: There is one TODO to be fixed before this is merged into the master branch. Also perhaps it's good to include a test (which I can do myself before merging)

[shiozaki]

@bessvlai I've added some stylistic changes and addressed the TODO. Please check that the code is still correct and comment here, otherwise I think it's ready for merge.

For purposes of record, the copyright associated with PR has been released in writing to QSimulate.

[bessvlai]

@shiozaki I have checked the code and it is ready to merge. We could include the following for testing. Perhaps also as an example in the manual. I believe I added keywords but I don't think I added an example.

{ "bagel" : [

{ "title" : "molecule", "basis" : "svp", "df_basis" : "cc-pvdz-jkfit", "geometry" : [ { "atom" : "H", "xyz" : [ 0.676914, 2.781690, 3.773783 ] }, { "atom" : "O", "xyz" : [ 0.064239, 1.944715, 2.324074 ] }, { "atom" : "H", "xyz" : [ -3.307624, 3.886786, 2.344879 ] }, { "atom" : "H", "xyz" : [ -3.312992, 1.002931, 4.011981 ] }, { "atom" : "C", "xyz" : [ -2.575001, 1.949136, 2.323306 ] }, { "atom" : "C", "xyz" : [ -3.491636, 0.596669, -0.021682 ] }, { "atom" : "H", "xyz" : [ -2.798895, -1.344513, -0.045732 ] }, { "atom" : "H", "xyz" : [ -2.795117, 1.545961, -1.713429 ] }, { "atom" : "H", "xyz" : [ -5.552636, 0.559870, -0.086997 ] } ] },

{ "title" : "hessian", "partial" : true, "atom_list" : [1,2], "method" : [ { "title" : "hf" } ] }

]}