Example:
The transformation as translation,T, or rotation, R, operation in a format:
where the is a 3D-vector of translation, or the is a 3D-vector of rotation if the [ x y z angle] angle parameter is presented, and the angle is an optional parameter which is an angle of rotation around this vector in degrees. Generally, translation and rotation operation do not commute, since that the first applys transformation from left to right, i.e.: product means that the MkNemo will apply first rotation and then translation.
MkNemo
The input of **Mole**cules,**Clus**ters, and**Disp**lacement,**GetE**energy,**Next**,**Test**.
.
MkNemo
Finally the structure of a standard input file for
* Loop over configurations >>>>>>>>>>>>>>>>>>> Do While <<<<<<<<<<<<<<<<<<<< &MkNemo&End * Molecules definitions Mole : MoleculeName AtomLabel x y z ......... .. .. .. AtomLabel x y z End .................... Mole : MoleculeName AtomLabel x y z ......... .. .. .. AtomLabel x y z End * Clus : ClusterName ClusterTransformation MoleculeName MoleculeTransformation ............ ...................... MoleculeName MoleculeName End Clus : ClusterName ClusterTransformation MoleculeName MoleculeTransformation ............ MoleculeName End Disp ClusterName NumberOfSteps [x y z alpha] ClusterName NumberOfSteps [x y z] ........... ............. ............. ClusterName NumberOfSteps [x y z alpha] End End Of Input *************** SUPER-SYSTEM CALCULATION ********************* * Calculation of integrals &Seward coord=$Project.MkNemo.Axyz coord=$Project.MkNemo.Bxyz basis=........ ................................ * Energy calculation on the first level of the theory &Scf ............................... * Save energy &MkNemo GetE=S1 * Energy calculation on the second level of the theory &MBPT2 ............................... * Save energy &MkNemo GetE=S2 *************** A-SUBSYSTEM CALCULATION ********************* * Calculation of integrals &Seward coord=$Project.MkNemo.Axyz coord=$Project.MkNemo.Bxyz * the B-subsytem has charge equal to zero BSSE=2 basis=........ ................................ * Energy calculation on the first level of the theory &Scf ............................... * Save energy &MkNemo&End GetE=A1 * Energy calculation on the second level of the theory &MBPT2 ............................... * Save energy &MkNemo GetE=A2 *************** B-SUBSYSTEM CALCULATION ********************* * Calculation of integrals &Seward coord=$Project.MkNemo.Axyz coord=$Project.MkNemo.Bxyz * the A-subsytem has charge equal to zero BSSE=1 basis=........ ................................ * Energy calculation on the first level of the theory &Scf ............................... * Save energy &MkNemo GetE=B1 * Energy calculation on the second level of the theory &MBPT2 ............................... * Save energy and take next configuration &MkNemo GetE=B2; Next >>>>>>>>>>>>>>>>>>> EndDo <<<<<<<<<<<<<<<<<<<<
Example:
In this example we calculate potential energy curve for interaction between two water clusters. The A-cluster, H2O, was rotated around Y-axis about 180 degrees. The B-subsystem, h2o,has been translated along Z-axis by 2 a.u.. In the Next of , we save all informations about potential for given configuration and we generate new configuration. This procedure will be repeated for all translations and rotations defined in the Displacement block.
MkNemo
## 6.31.2.2 Input filesApart from the standard input unit will use the following input files.
MkNemo
Files of the , SCF, RASSCF, MBPT2, MOTRA, and CCSDT modules are needed to get total energy on each level of theory for subsystems and super-system.
CASPT2
## 6.31.2.3 Output filesIn addition to the standard output unit will generate the following files.
MkNemo
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