sampledoc

simulationGaussian Class API

Derived class for simulation object

class simulationGaussian1.SimulationGaussian1(name, verbose=False)[source]

Bases: simulation.Simulation

Dervied class implementing input/output methods specific to an application The Gaussian input file has two links 1.) one ground-state 2). TD DFT for excited state calc e.g.

%chk=acc1_D1_eff_R3R300_A84___n1.chk #P opt b3lyp/6-31g(d) geom=check guess=check pop=full density=current

acc1_D1_eff_R3R300_A84___n1 ground-state

0 1
<atoms>

–Link1– %chk=acc1_D1_eff_R3R300_A84___n1.chk #P b3lyp td=nstates=12/6-31g(d) geom=check guess=check pop=full density=current

NOTE: lc-wpbe removes ‘density=current’ from input lines

getBareTag()[source]

Return ‘bare tag’ without accuracy label eg D1_R2R200_Sp2_00_A48__Sp2_00__n2

getDBBasisStr()[source]

Return dbBasisStr

getOligomerNum()[source]

Return oligomer number string from run name. Assuming run name for contains n1,n2....

setCoeffs(fct, bsOPT, bsEXT=None)[source]

Set the main model parameters of functional and basis

Args:
fct (str): Gaussian functional bsOPT (str): Basis set to determine accuracy for geo opt. bsEXT (str): Basis set to determine accuracy for TD-DFT step. If not specified, then set to bsOPT
setDBBasisStr(s)[source]

Set dbBasisStr

Args:
s (str) basis string in database
setMetaData(mdDict)[source]

Set dictionary containing metadata (from json file info)

setRepoLocation(rL)[source]

Set repo location path so PBS file can be constructed from a template

Args:
rL (str) full path to repo location
writeInput()[source]

Write out a Gaussian input data file from all available held data (particles, bonds-zmatrix) Assumptions about one ‘link’ step made and naming convention of referenced ‘chk’ files and input file name

Args:
inputName (str): name of Gaussian input file (.com) to write out
Assumes that structure of input name is acc.functional.basis_D1_R300....