5.1 MOL_1, MOL_2, …files for molecular crystals

Molecular Crystals, calculationType=310/311

For a molecular crystal, the MOL_1 file describes the structure of the molecule from which the structure is built. This file also defines which torsion angles will be mutated if the molecule is flexible. This file and its format differ from SIESTA’s Z_Matrix file (MOL_1 gives the Cartesian coordinates of the atoms, whereas Z_Matrix file defines the atomic positions from bond lengths, bond angles and torsion angles). The Z_Matrix file is created using the information given in the MOL_1 file, i.e., bond lengths and all necessary angles are calculated from the Cartesian coordinates. The lengths and angles that are important should be used for the creation of Z_Matrix — this is exactly what columns 5–7 specify. Let’s look at the MOL_1 file for benzene C$_6$H$_6$:

\includegraphics[scale=0.36]{pic/benzene}
Figure 8: Sample of MOL_1 file and illustration of the corresponding molecular structure.

The 1$^{st}$ atom is H, its coordinates are defined without reference to other atoms (“0 0 0”).

The 2$^{nd}$ atom is C, its coordinates (in molecular coordinate frame) in Z_matrix will be set only by its distance from the 1$^{st}$ atom (i.e. H described above), but no angles — (“1 0 0”).

The 3$^{rd}$ atom is C, its coordinates will be set by its distance from the 2$^{nd}$ atom, and the bond angle 3-2-1, but not by torsion angle — hence we use “2 1 0”.

The 4$^{th}$ atom is C, its coordinates will be set by its distance from the 3$^{rd}$ atom, bond angle 4-3-2, and torsion angle 4-3-2-1 — hence, we use “3 2 1” and so forth…until we reach the final, 12$^{th}$ atom, which is H, defined by its distance from the 7$^{th}$ atom (C), bond angle 12-7-6 and torsion angle 12-7-6-11 — hence “7-6-11”.

The final column is the flexibility flag for the torsion angle. For example, in C4, the tosion angle is defined by 4-3-2-1. Ideally, this flag should be 1 for the first three atoms, and 0 — for the others. If any other flexible torsion angle exists, specify 1 for this column.

Polymeric Crystals, calculationType=110 (“linear chain model”)

For polymers, the MOL_1 file is used to represent the geometry of a monomeric unit, in the same style as for molecular crystals, except that we use the last column to specify the reactive atoms as shown in the MOL_1 file for PVDF:

\includegraphics[scale=0.72]{pic/PVDF_MOL}
Figure 9: Sample of MOL_1 file of PVDF and illustration of the corresponding monomeric structure.

Additional inputs for classical forcefields

The above MOL_1 files can be used for general cases in USPEX. However, some classical forcefield based codes need additional information. For instance, GULP needs to specify the chemical labels and charge. The MOL_1 file for aspirin can be written in the following way:

Aspirin_charge
Number of atoms: 21
H_1     0.2310     3.5173     4.8778     0  0  0   1     0.412884
O_R     0.7821     4.3219     4.9649     1  0  0   1    -0.676228
C_R     0.4427     5.0883     6.0081     2  1  0   1     0.558537
O_2    -0.5272     4.5691     6.6020     3  2  1   0    -0.658770
C_R     1.0228     6.3146     6.3896     3  2  4   0     0.116677
C_R     2.1330     6.8588     5.6931     5  3  2   0     0.311483
C_R     0.4810     7.0546     7.4740     5  3  6   0    -0.119320
O_R     2.8023     6.2292     4.6938     6  5  3   0    -0.574557
C_R     2.6211     8.1356     6.0277     6  5  8   0    -0.083091
C_R     0.9966     8.3146     7.8237     7  5  3   0    -0.103442
H_2    -0.3083     6.6848     8.0128     7  5 10   0     0.198534
C_R     3.6352     5.1872     4.9079     8  6  5   0     0.609295
C_R     2.0623     8.8613     7.0940     9  6  5   0    -0.119297
H_2     3.3963     8.5283     5.4906     9  6 13   0     0.174332
H_2     0.5866     8.8412     8.6013    10  7 13   0     0.205960
O_2     3.9094     4.7941     6.0632    12  8  6   0    -0.588433
C_3     4.2281     4.5327     3.7638    12  8 16   0    -0.271542
H_2     2.4227     9.7890     7.3367    13  9 10   0     0.196738
H_2     3.4269     4.1906     3.1183    17 12  8   0     0.151315
H_2     4.8283     3.6848     4.0792    17 12 19   0     0.131198
H_2     4.8498     5.2464     3.2337    17 12 19   0     0.127726

Here, the keyword charge in the title tells the program to read the charge in the additional (last) column.

To work with Tinker, the additional column is used to specify the atomic label as follows:

Urea
Number of atoms: 8
C     0.000000    0.000000    0.000000   0 0 0 1  189  
O     0.000000    0.000000    1.214915   1 0 0 1  190  
N     1.137403    0.000000   -0.685090   1 2 0 1  191  
N    -1.137403    0.000000   -0.685090   1 2 3 0  191  
H     1.194247    0.000000   -1.683663   4 1 3 0  192  
H    -1.194247    0.000000   -1.683663   4 1 3 0  192  
H     1.998063    0.000000   -0.138116   2 1 3 0  192  
H    -1.998063    0.000000   -0.138116   2 1 3 0  192  

How to prepare the MOL files

There are plenty of programs which can generate Zmatrix style files, such as Molden, Avogadro, and so on. The experienced users might have their own way to prepare these files. For the users’ convenience, we have created an online utility to allow one to generate the USPEX-style MOL file just from a file in XYZ format. Please try this utility at http://han.ess.sunysb.edu/zmatrix.