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PES templates

PES templates

General comments

A key piece of information which cde requires in order to perform energy evaluations or geometry optimization is a PES template file.

  • The input parameters pesfile and pesoptfile are header files which are used to direct external codes in which calculation to perform when they are called by cde. These header files must have the same format as input files required by the pesexecutable and pesoptexecutable.

  • However, in the pesfile and pesoptfile template files, there must be a line with XXX as follows:

    XXX

  • The XXX indicator tells cde where it should insert the atomic coordinates of the configuration at which the energy evaluation is requested. After inserting the coordinates, cde writes the input file then runs the relevant external executable to evaluate the energy. Once the energy evaluation (or geometry optimization) is complete, cde reads in the results.

  • The file pes.f90 can be consulted to see how this write/run/read process works for each external code.

  • An example header file for a PES evaluation by ORCA using PM3 semi-empirical method might be as follows:

    ! PM3
* xyz 0 1
XXX
*

  • An example header file for PES evaluation by DFTB+ might be as follows:

    Geometry = GenFormat {
XXX
}
Driver = {}
 Hamiltonian = DFTB {
 SCC = Yes
 SCCTolerance = 1e-3
 Mixer = Broyden{}
 Eigensolver = RelativelyRobust {}
MaxAngularMomentum {
C = "p"
O = "p"
H = "s"
}
SlaterKosterFiles = Type2FileNames {
Prefix = "/Users/scott/code/cde/src/SKfiles/"
Separator = "-"
Suffix = ".skf"
}
}
Analysis = {
CalculateForces = Yes
}

Warning

Note in the above examples that the only part of the file which is written by cde is in replacing the XXX with the coordinates at which the energy evaluation is being performed. All other aspects, such as the calculation type (e.g. DFT, Hartree-Fock, semi-empirical, DFTB+), basis sets, accuracy controls, and so on, are controlled by editing the pesfile and pesoptfile BEFORE the calculation starts.

Template file examples

This section gives several examples of template files for PES evaluation or geometry evaluation.

Tip

Note that a single PES template file is used for all energy evaluations in cde. There is no option to change the PES evaluation-type "on the fly".

ORCA examples

  • Example header file for a PES evaluation by ORCA using PM3 semi-empirical method:

    ! PM3
* xyz 0 1
XXX
*

  • Example header file for a PES evaluation by ORCA using DFT (B3LYP):

    ! DFT B3LYP aug-cc-pvtz
* xyz 0 1
XXX
*

  • Example header file for geometry optimization using PM3:

    ! PM3 OPT
* xyz 0 1
XXX
*

DFTB+ example

In the case of DFTB+, note that the input file must correctly specify the location of any Slater-Koster files required.

  • Example header file for PES evaluation by DFTB+:

     Geometry = GenFormat {
XXX
}
Driver = {}
 Hamiltonian = DFTB {
 SCC = Yes
 SCCTolerance = 1e-3
 Mixer = Broyden{}
 Eigensolver = RelativelyRobust {}
MaxAngularMomentum {
 C = "p"
O = "p"
H = "s"
 }
SlaterKosterFiles = Type2FileNames {
Prefix = "./SKfiles/"
 Separator = "-"
 Suffix = ".skf"
 }
}
Analysis = {
CalculateForces = Yes
 }

  • DFTB+ geometry optimization example (with constraints):

    Geometry = GenFormat {
XXX
}
Driver = ConjugateGradient{
MaxForceComponent = 1d-5
MaxSteps = 1000
Constraints = {
1 1.0 0.0 0.0
1 0.0 1.0 0.0
1 0.0 0.0 1.0
2 0.0 1.0 0.0
2 0.0 0.0 1.0
3 0.0 0.0 1.0
}
}
Hamiltonian = DFTB {
SCC = Yes
SCCTolerance = 1e-3
Mixer = Broyden{}
Eigensolver = RelativelyRobust {}
MaxAngularMomentum {
C = "p"
O = "p"
H = "s"
}
SlaterKosterFiles = Type2FileNames {
Prefix = "./SKfiles/"
Separator = "-"
Suffix = ".skf"
}
}
Analysis = {
CalculateForces = Yes
}

Psi-4 example

  • Hartree-Fock example using psi-4.
    ################
# INPUT SETUP #
################

molecule x {
0 1
XXX
}

set {
    basis def2-SVP
    fail_on_maxiter false
}

################
# OUTPUT SETUP #
################

energy = energy('scf')
grad = np.array(gradient('scf'))

e = open('e.out','w')
e.write(str(energy))
e.close()

f = open('f.out','w')
for i in grad:
    for j in i:
        f.write(str(j)+'\n')
f.close

Warning

Note that the python sections are required in the output section above to ensure that energies and forces can be correctly read back into cde.

LAMMPS/ReaxFF example

  • The following is an example of a LAMMPS input file (e.g. lmp.head) for running a ReaxFF calculation.

    #dimension      3
units          real
boundary       f f f
atom_style     charge
atom_modify    map array sort 0 0.0

# XXX replaced by mass labels and atom creation

XXX

pair_style     reax/c lmp_control
# Force file to be used, types added automatically
pair_coeff     * * CHOPtNiX.ff
fix            1 all qeq/reax 1 0.0 10.0 1.0e-8 reax/c  # new addition

neighbor       1.0 bin
neigh_modify   every 1 delay 0 check no

compute        reax all pair reax/c

dump           1 all custom 1 temp.force fx fy fz
dump_modify    1 format float "%14.8f"

thermo         0
thermo_style   custom pe

run            0

  • The following is an example of a geometry optimization calculation performed using ReaxFF through LAMMPS.

    # Intialization
dimension      3
units          real
boundary       f f f
atom_style     charge
atom_modify    map array sort 0 0.0

# XXX replaced by mass labels and atom creation
XXX

pair_style     reax/c lmp_control
# Force file to be used, atom types are added automatically for reax/c
pair_coeff     * * CHOPtNiX.ff
fix            1 all qeq/reax 1 0.0 10.0 1.0e-8 reax/c

neighbor       2.5 bin
neigh_modify   every 1 delay 0 check no

compute        reax all pair reax/c

thermo         1
thermo_style   custom pe

min_style quickmin # new addition
minimize 1.00e-10 1.00e-8 50000 50000

timestep 1

# output forces
dump           2 all custom 1 temp.force fx fy fz
dump_modify    2 format float "%14.8f"

  • Both of the files above also require two additional files to be present in the run directory. The first of these, lmp_control is an additional LAMMPS control file, which usually looks like the following:

    nbrhood_cutoff          5.0  ! near neighbors cutoff for bond calculations in A
hbond_cutoff            6.0  ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff       0.3  ! bond strength cutoff for bond graphs
thb_cutoff              0.001 ! cutoff value for three body interactions
atom_forces 1

  • The second additional file required is the ReaxFF parameter file. In this case, it is referred to as CHOPtNiX.ff, but this could be changed depending on the system under investigation and the parameters available. An example of these *.ff files can be found in Tutorial 2.