Method section
Here the user provides details of the method employed for sampling the reaction space. In our FA example, we have the following:
--Method--
sampling MD
ntraj 10
List of Keyword value(s) for this section:
sampling value
[value is one string with no blank spaces; default value: MD]
value can be: MD, MD-micro, BXDE, external, ChemKnow, association and vdW
MD and MD-micro refer to the type of initial conditions used to run the MD simulations. MD-micro _has not been implemented yet for qcore. With BXDE the rare-event acceleration method named BXDE is invoked.
MD allows the user to include partial constraints in the trajectories, which may be useful for large systems.
external allows trajectory data to be read from the results of an external MD program. The trajectory data in XYZ format must be stored in a directory named coordir using one file per trajectory which should be called name_dynX.xyz, where name is value[molecule], and X is the number of each trajectory, with X = 1 - ntraj. The keyword ntraj must be set accordingly.
ChemKnow makes all possible combinations of bond breakages/formations which are consistent with preset valencies of the atoms and with products lying below the maximum energy of the system. Once the combinations are known, the starting and ending points are obtained after a constrained MD simulation with external forces applied to break/form the selected bonds. Then, a NEB calculation tries to obtain a path connecting both states, and the highest point of the NEB is subjected to TS optimization. This sampling does not need to include the number of trajectories and has not been implemented yet for qcore.
To use MD-micro the initial structure needs to be fully optimized and a frequency calculation can not afford imaginary frequencies. Otherwise choose MD
association and vdW are employed to sample van der Waals structures, present some peculiarities and therefore are explained in detail in van der Waals complexes.
MD, MD-micro, external and BXDE samplings accept the following keywords (BXDE and ChemKnow also accept additional keywords as seen below):
barrierless value
[value is one string: yes or no; default value: no]
value can be yes, in which case barrierless processes are searched. The keyword neighbors explained below is related to this one.
neighbors values
[three values: first is a string and last two are floats; default values, see table below]
The first value is an atomic symbol and the two numbers are the minimum and maximum number of neighbors of the corresponding atoms. This keyword is needed if atoms other than those in the table below are present in your system and/or if you want to change the default values. The number of neighbors is employed to locate barrierless processes and are also employed by ChemKnow.
For instance, if you want to consider dissociations leading to atomic hydrogen, you must add the following line:
neighbors H 0 1
You can add as many lines as needed, one per atom. The default values are listed in this table:
| Atom | Min # of neighbors | Max # of neighbors | Atom | Min # of neighbors | Max # of neighbors |
|---|---|---|---|---|---|
| H | 1 | 1 | Mg | 0 | 2 |
| Li | 0 | 1 | Al | 1 | 3 |
| Be | 0 | 2 | Si | 1 | 4 |
| B | 1 | 3 | P | 1 | 5 |
| C | 1 | 4 | S | 1 | 6 |
| N | 1 | 3 | Cl | 0 | 1 |
| O | 1 | 2 | Br | 0 | 1 |
| F | 0 | 1 | I | 0 | 1 |
| Na | 0 | 1 | Â | Â | Â |
ntraj value
[value is an integer; default value: 1 ]
value is the number of trajectories. We strongly recommend here to avoid using big numbers of trajectories. Instead, the user should try to run different batches of trajectories as indicated below with a small number of trajectories each one. One trajectory is recommended for BXDE and about 10 for MD-based sampling.
seed value
[value is an integer; only valid for MD and MD-micro ; default value: 0 ]
value is the seed of the random number generator. It can be employed to run a test trajectory. See the FA_singletraj.dat file in the examples. Only use this keyword for testing.
BXDE specific keywords
This sampling (and the other BXDE-based sampling based: vdW) has a number of specific keywords as shown in this example:
sampling BXDE
Friction 0.5
AdaptiveLimit 100
Window 500
Hookean 1 2 2.5 10.
Friction value
[value is a float; default value: 0.5]
value is the friction coefficient in a.u. employed in the Langevin dynamics of a BXDE simulation.
AdaptiveLimit value
[value is an integer; default value: 100 ]
value determines how many MD steps are performed in a new box before the BXDE algorithm adaptively places a new box based upon the sampled energies.
Window value
[value is an integer; default value: 500 ]
value determines the number of consecutive MD steps before considering a reaction to have occurred.
Hookean values
[four values: first (i) and second (j) are integers, third (rt) and fourth (k) are floats]
Hookean keyword can be employed with any BXDE-based dynamics sampling. It employs ASE’s Hookean class to conserve molecular identity. A Hookean restorative force with spring constant given by the fourth value (in eV/Å2) is applied between two atoms of indices given by the first and second values if the distance between them exceeds a threshold, rt.
ChemKnow specific keywords
This sampling has a number of specific keywords as shown in this example:
sampling ChemKnow
Graphto3D POpt
active 1 2 3 4
startd 2.75
MaxBoF 2
MaxBoB 2
comb22 no
crossb no
BreakRing no
CK_minima all
Graphto3D value
[value is a string: POpt or Traj; default value: POpt]
value is the method employed to transform the product Graph into a 3D geometry. POpt performs a series of partial optimizations, with the bonds involved in the reaction coordinate frozen, where the geometry is smootly changed from reactant to product. In Traj, an external force is applied for the same purpose.
active values
[values are integers]
values are the labels of the atoms that participate in the reactions we are interested in. By default, all atoms in the system are active.
startd value
[value is a float; default value: 2.75]
value is the maximum distance between active atoms to be considered in a bond formation.
MaxBoF/MaxBoB value
[value is an integer; default value: 2]
value is the maximum number of bonds formed (nF)/broken (nB) to make all possible (nF,nB) combinations for Graph transformations.
comb22 value
[value is a string: yes or no; default value: no]
By default, the $\scriptstyle{(}$2,2$\scriptstyle{)}$ combination is not considered.
crossb value [value is a string: yes or no; default value: no]
A check can be done to see if the closest distance between the paths followed by the atoms in their rearrangements is lower that a threshold value, a potential problem in planar molecules or planar regions of a molecule. By default, this check is not done.
BreakRing value
[value is a string: yes or no; default value: no]
By default, a bond that belongs to a ring is not broken in $\scriptstyle{(}$0,1$\scriptstyle{)}$ transformations. However, there might be ring opening reactions of our interest.
CK_minima value
[value is a string: all or cg; default value: all]
By default, all minima are used for graph transformations including conformers. With the value cg, only the lowest energy member of each family of conformers is utilized.