poly_qmdff
This program can be used to set up force field descriptions of liquid or gaseous mixtures of one or several different molecular species. The user must provide the QMDFF files of the different molecules (monomers). No keyfile is needed, the program works fully interactive.
List of examples:
- 1: Ethanol (QMDFF for liquid ethanol from an ethanol molecule): poly_qmdff/ethanol
- 2: [EMIM][OTf] (QMDFF for an ionic liquid from ions): poly_qmdff/emim_otf
Folder: poly_qmdff/ethanol
The only input file needed is the QMDFF of an ethanol molecule: ethanol.qmdff.
The polymerization is started by simply invoking:
poly_qmdff.x
Then, a dialogue starts:
Welcome to the program POLY_QMDFF.X!
Here you can build up QMDFF of multi-molecule systems
by copying QMDFFs of different single molecules!
How many different molecules (and their QMDFFs) are present?: 1
Prefix of the first QMDFF (name.qmdff must be in this folder!): ethanol
Give the size of the box! (number of mols per dimension): 5
Give the distance between two mols. in the grid (def: 2 A): 2
The system will contain the following randomly placed molecules:
125 units from ethanol.qmdff
The molecular configuration of the system was written to 'box.xyz'...
The size of the box (for periodic calculations) is 26.5699 Angstroms.
The new QMDFF was generated successfully! It is named 'box.qmdff'
The calculation needed a time of 0.012 seconds.
Here, the number of different molecules must be given first (1), then, the prefix of the available QMDFF file (ethanol).
After this, the setup of the periodic system is defined. Currently, only cubic crystalline cells can be setup. The shape of the cell has of course no influence on the performance of the new polymerized QMDFF, since noncovalent interactions are defined independently of the minimum structure given in the QMDFF!
Here, 5 ethanol molecules are placed per dimension, resulting in a total number of 125 molecules.
The minimum distance between the units is 2 Angstroms (considering the maximum elongation of the molecule in the three coordinate directions).
Two output files are generated: box.qmdff and box.xyz.
In the following, a single ethanol molecule (the QMDFF reference local minimum) and the generated box.xyz structure are shown:
The QMDFF file box.qmdff can be used in the other programs like dynamic as an usual QMDFF file.
It has only two small modifications:
1125 125.0000 0.0000
CM5*1.15
1 0.000000000000 2.621676594756 1.925802510977 0.096949126052 1
6 1.627750489999 1.360506083437 1.776800091639 -0.269869678795 1
1 1.507377432800 0.000000000000 3.328038974565 0.089905188483 1
6 4.072598958014 2.840891506239 1.893014655982 -0.062832550081 1
8 6.235924998285 1.305940096682 1.586746781473 -0.534609760311 1
1 4.175574308022 3.913814138920 3.666603650947 0.093852747532 1
1 6.262521411154 0.081613864871 2.921326965325 0.375574023499 1
1 4.148805875217 4.213614343523 0.354805063429 0.113748399428 1
1 1.489579648368 0.323227215328 0.000000000000 0.097260654192 1
1 0.000000000000 2.621676594756 11.967776171261 0.096949126052 2
6 1.627750489999 1.360506083437 11.818773751923 -0.269869678795 2
1 1.507377432800 0.000000000000 13.370012634849 0.089905188483 2
....
The second entry in the first line, usually a dummy parameter, now indicates the total number of monomers included into the box (125), and after each coordinate line, an additional number (also a dummy parameter in usual QMDFF files) indicates to which monomer molecule the current atom belongs (1, 2, ...)
Folder: poly_qmdff/emim_otf
This example can be set up with similar ease as the former one.
Here, two different QMDFFs are present: emim.qmdff and otf.qmdff.
The objective is to set up a ionic liquid simulation box.
Since EMIM has the charge +1 and OTf has the charge -1, it would be advantageous if the total charge is zero, thus having equal numbers of EMIM and OTf molecules.
This can be achieved by building a box with 4x4x4 molecules.
poly_qmdff.x
With the following dialogue:
....
How many different molecules (and their QMDFFs) are present?: 2
Prefix of the first QMDFF (name.qmdff must be in this folder!): emim
Prefix of the second QMDFF (name.qmdff must be in this folder!): otf
Give the size of the box! (number of mols per dimension): 4
Give the distance between two mols. in the grid (def: 2 A): 2
Relative abundancy of the first QMDFF (arbitrary number): 1
Relative abundancy of the second QMDFF (arbitrary number): 1
The system will contain the following randomly placed molecules:
32 units from emim.qmdff
32 units from otf.qmdff
The molecular configuration of the system was written to 'box.xyz'...
The size of the box (for periodic calculations) is 32.2493 Angstroms.
The new QMDFF was generated successfully! It is named 'box.qmdff'
....
You could of course also build larger boxes with 6x6x6 or 8x8x8 molecules. The monomers and the initial box look like this:
Note that the actual placement of the species in the box grid is done by chance, therefore, the arragement of EMIM and OTf will usually be different for each calculation! Further, the box.qmdff file is different, since the ordering of the molecules in it is important (in contrast to their relative spacial position).