Example RC Files

Ccaffeine Resource Configuration or RC files provide the framework directives needed to compose a working component application. Several example RC files are given to illustrate usage of the framework directives. Description of additional input files are given elsewhere. While interacting with the framework at this level allows a high-level of user customization, it is admittedly quite cumbersome. Embedded framework capabilities within MPQC and the PyView GUI demonstrate that the user can be insulated from these low-level interactions. Note that configuration has not been standardized between various component implementations. Standardization of calculation capabilities is an area of active research.

Examples using MPQC

This simplest example computes the energy and gradient at the HF/STO-3G level of theory for the molecule given in /home/fred/h2o.xyz. A calculation of this type can be performed without installing NWChem or TAO/PETSc. This RC file assumes cca-chem-generic, cca-chem-apps, and mpqc where installed to /usr/local/cca-chem-generic, /usr/local/cca-chem-apps, and /usr/local/mpqc, respectively. Refer to the MoleculeFactory documentation for the format of the .xyz molecule files.

#!ccaffeine bootstrap file.
# ------- don't change anything ABOVE this line.-------------
path set /usr/local/cca-chem-generic/lib
path append /usr/local/cca-chem-apps/lib
path append /usr/local/mpqc/lib/cca

repository get-global Chemistry.Chemistry_MoleculeFactory
repository get-global MPQC.Chemistry_QC_ModelFactory
repository get-global ChemDrivers.SimpleDriver

create Chemistry.Chemistry_MoleculeFactory molfactory
create MPQC.Chemistry_QC_ModelFactory mpqcfactory
create ChemDrivers.SimpleDriver driver

connect driver ModelFactory mpqcfactory ModelFactory
connect mpqcfactory MoleculeFactory molfactory MoleculeFactory

parameter mpqcfactory configure basis STO-3G
parameter mpqcfactory configure theory HF
parameter mpqcfactory configure molecule_filename /home/fred/h2o.xyz 
parameter driver configure do_gradient true

go driver go

This is a more complicated example, using the TAO solver component and generic coordinate model component to perform a geometry optimization in Cartesian coordiantes. This RC file assumes TAO is installed to /usr/local/tao-devel.

#!ccaffeine bootstrap file.
# ------- don't change anything ABOVE this line.-------------
path set /usr/local/cca-chem-generic/lib
path append /usr/local/cca-chem-apps/lib
path append /usr/local/tao-devel/lib/libO_c++/linux

repository get-global Chemistry.Chemistry_MoleculeFactory
repository get-global TaoAdaptors.ModelPort
repository get-global ChemistryOpt.ChemistryOpt_CoordinateModel
repository get-global MPQC.Chemistry_QC_ModelFactory
repository get-global TaoDriver.Component
repository get-global TaoSolver.Component
repository get-global PetscLA.Factory

create Chemistry.Chemistry_MoleculeFactory molfactory
create TaoAdaptors.ModelPort adaptor
create ChemistryOpt.ChemistryOpt_CoordinateModel coormodel
create MPQC.Chemistry_QC_ModelFactory mpqcfactory
create TaoDriver.Component driver
create TaoSolver.Component solver
create PetscLA.Factory factory

connect driver OptimizationSolver solver OptimizationSolver
connect solver OptimizationModel  adaptor OptimizationModel
connect adaptor CoordinateModel coormodel CoordinateModel
connect solver LAFactory factory LAFactory
connect coormodel ModelFactory mpqcfactory ModelFactory
connect mpqcfactory MoleculeFactory molfactory MoleculeFactory

parameter mpqcfactory configure basis STO-3G
parameter mpqcfactory configure theory HF
parameter mpqcfactory configure molecule_filename /home/fred/h2o.xyz

# TAO parameters
parameter solver configure method tao_lmvm
parameter solver configure tao_max_its 10

go driver go
exit

This example uses the TAO solver component and MPQC coordinate model component to perform an optimization in internal coordinates. The Hessian approximation capabilities in the MPQC coordiante model (not available in the generic implementation) are used by the solver component.

#!ccaffeine bootstrap file.
# ------- don't change anything ABOVE this line.-------------

path set /usr/local/cca-chem-generic/lib
path append /usr/local/cca-chem-apps/lib
path append /usr/local/tao-devel/lib/libO_c++/linux

repository get-global Chemistry.Chemistry_MoleculeFactory
repository get-global TaoAdaptors.ModelPort
repository get-global MPQC.ChemistryOpt_CoordinateModel
repository get-global MPQC.Chemistry_QC_ModelFactory
repository get-global TaoDriver.Component
repository get-global TaoSolver.Component
repository get-global PetscLA.Factory

create Chemistry.Chemistry_MoleculeFactory molfactory
create TaoAdaptors.ModelPort adaptor
create MPQC.ChemistryOpt_CoordinateModel coormodel
create MPQC.Chemistry_QC_ModelFactory mpqcfactory
create TaoDriver.Component driver
create TaoSolver.Component solver
create PetscLA.Factory factory

connect driver OptimizationSolver solver OptimizationSolver
connect solver OptimizationModel  adaptor OptimizationModel
connect adaptor CoordinateModel coormodel CoordinateModel
connect solver LAFactory factory LAFactory
connect coormodel ModelFactory mpqcfactory ModelFactory
connect mpqcfactory MoleculeFactory molfactory MoleculeFactory

parameter mpqcfactory configure basis STO-3G
parameter mpqcfactory configure theory HF
parameter mpqcfactory configure molecule_filename /home/fred/h2o.xyz

# specify coordinate type
parameter coormodel configure coordinates symmetrized

# TAO parameters
parameter solver configure method tao_lmvm
parameter solver configure tao_max_its 10

# turn on hessianSolve
parameter solver configure tao_options -tao_lmvmh

# force convergence checking within the CoordianteModel
parameter solver configure tao_gatol 0
parameter solver configure tao_grtol 0
parameter solver configure tao_gttol 0
parameter solver configure tao_fatol 0
parameter solver configure tao_frtol 0

go driver go
exit

Example using NWChem component

(out-of-date???)

This is a an example, using the TAO solver component and generic coordinate model component to perform a geometry optimization in Cartesian coordiantes. One needs to set three files (examples are located in ccachem/nwchem/Tests):

*.xyz - coordinate file for Molecule Factory; format of the file is similar to xyz and same for NWChem and MPQC; set coordinates and units only. Example h2o.xyz:
```
# comments
# more comments if desired
angstroms
8 0.000 0.000 0.000
1 1.000 0.000 0.000
1 0.000 1.000 0.000
```

config.cmp - configuration file for NWChem input parser; set all NWChem specific parameters which are same for all runs. Example config.cmp:

permanent_dir /home/yuri/scratch
geometry units angstrom noautosym noautoz nocenter;
H 0.000 0.000 0.000;
end
set loadbalancing:dynamic f;
scf;
  maxiter 200;
  tol2e 1e-13;
end

*.rc - in this file, components are properly connected and configured. Example test.rc:

#!ccaffeine bootstrap file.
# ------- don't change anything ABOVE this line.-------------
path set /home/yuri/cca-chem/lib
path append /home/yuri/cca-chem/nwchem/lib
path append /home/sarich/tao_babel92/lib/libO_c++/linux-rh72

repository get-global Chemistry.Chemistry_MoleculeFactory
repository get-global OptimizationModelAdaptor.Adaptor
repository get-global ChemistryOpt.ChemistryOpt_CoordinateModel
repository get-global NWChemFactory.ChemistryQCModelFactory
repository get-global TaoDriver.Component
repository get-global TaoSolver.Component
repository get-global PetscLA.Factory

create Chemistry.Chemistry_MoleculeFactory molfactory
create TaoDriver.Component driver
create TaoSolver.Component solver
create PetscLA.Factory factory
create OptimizationModelAdaptor.Adaptor adaptor
create ChemistryOpt.ChemistryOpt_CoordinateModel coormodel
create NWChemFactory.ChemistryQCModelFactory nwchemfactory

connect driver OptimizationSolver solver OptimizationSolver
connect solver OptimizationModel  adaptor OptimizationModel
connect adaptor CoordinateModel coormodel CoordinateModel
connect solver LAFactory factory LAFactory
connect coormodel ModelFactory nwchemfactory ModelFactory
connect coormodel CoordinateType coordinates string
connect nwchemfactory MoleculeFactory molfactory MoleculeFactory

# TAO parameters
parameter solver configure method tao_lmvm
parameter solver configure tao_options -tao_lmmax%20%-log_summary
parameter solver configure tao_gatol 0
parameter solver configure tao_grtol 0
parameter solver configure tao_gttol 0
parameter solver configure tao_fatol 0
parameter solver configure tao_frtol 0
parameter solver configure tao_max_its 100

# NWChem parameters
parameter nwchemfactory configure scratchParam /pvfs/scratch/yuri
parameter nwchemfactory configure theoryParam scf
parameter nwchemfactory configure basisSetParam 6-31g
parameter nwchemfactory configure configParam /home/yuri/cca-chem/nwchem/Tests/config.cmp
parameter nwchemfactory configure coordParam /home/yuri/cca-chem/nwchem/Tests/h2o.xyz

go driver go
exit

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