Manual

The input.inp contains the general parameters for the simulations (time step, termodynamic conditions, ecc...).

Example input.inp file.

title:

Title of simulation

atoms:

200 (number of atoms in the system)

nl_cutoff:

1.20 (the cutoff distance for non-bonded interaction in nm)

nl_size:

1.60 (Size of list of particles included in cutoff)

time_step:

0.03 (time steps in fs)

number_of_steps:

1000 (number of steps)

velocity_read:

(yes/no) (read the velocity from the input.cor file)

simulated_ensemble:

NVT (type of ensemble)

target_temperature:

325 (temperature K)

collision_frequency:

7.00 (The collision frequency for the thermostat)

angle_funcion:

2 (type of function for the angle potential calculation)

mean_field:

SCF (The self-consistent field method is used in the simulation)

SCF_lattice_update:

100 (update frequency for the density field)

num_config_acc:

10 (accumulated num. of config. between two consecutive density update)

trj_print:

100 (output frequency for the trajectory file out.xyz)

The input.mdl contains the informations about the model used. The parameters for intramolecular interactions ( the bonds, angles, force constant, ecc..) and also for the intermolecular interactions (matrix interactions for the SCF ) are written in input.mdl.

Example input.mdl file.

********* model file ******************************

5 different atom types

*label mass charge

1 N 72.0000 1.0000

2 P 72.0000 -1.0000

3 G 72.0000 0.0000

4 C 72.0000 0.0000

5 W 72.0000 0.0000

****************************************************

5 different bond types

*atom 1 atom2 bond_length force_constant

1 2 0.47 1250.00

2 3 0.47 1250.00

3 3 0.37 1250.00

3 4 0.47 1250.00

4 4 0.47 1250.00

****************************************************

4 different bond angles

*atom1 atom2 atom3 theta0(deg) force_constant

2 3 3 120.00 25.000

2 3 4 180.00 25.000

3 4 4 180.00 25.000

4 4 4 180.00 25.000

****************************************************

0 different torsions

*atom1***atom2*** atom3***atom4***

****************************************************

5 different non-bonded interactions

*type 1 ** type 2 sigma epsilon

1 2 0.47 4.5

2 3 0.47 4.0

3 3 0.47 3.5

3 4 0.47 2.7

4 4 0.47 3.5

***** SCF settings **********************************

* mx my mz cells in X Y Z directions

14 14 12

* compressibility

0.1

*chi

0.00 -1.50 6.30 9.00 -8.13

-1.50 0.00 4.50 13.50 -3.60

6.30 4.50 0.00 6.30 4.50

9.00 13.50 6.30 0.00 40.50

-8.13 -3.60 4.50 40.50 0.00

The input.cor contains the coordinates and connectivity for the different molecules in the system.

Example input.cor file.

box:

8.176050 8.176050 6.949820 0.0000

Number of total molecules:

1808

molecule nr. 1

12 (number of particles for the molecules 1)

(index and label) (coordinates) (connectivity)

1 N 1 1 4.616 7.945 2.432 2 0 0 0

2 P 2 2 4.239 8.160 2.593 1 3 0 0

3 G 3 3 4.120 7.952 2.980 2 4 5 0

4 G 3 2 4.337 8.039 3.204 3 9 0 0

5 C 4 2 3.968 7.830 3.438 3 6 0 0

6 C 4 2 4.012 7.679 3.888 5 7 0 0

7 C 4 2 4.020 7.491 4.361 6 8 0 0

8 C 4 1 3.756 7.506 4.722 7 0 0 0

9 C 4 2 4.427 8.340 3.521 4 10 0 0

10 C 4 2 4.472 8.355 3.889 9 11 0 0

11 C 4 2 4.278 8.244 4.302 10 12 0 0

12 C 4 1 3.991 7.937 4.396 11 0 0 0

molecule nr. 2

12

13 N 1 1 2.032 0.932 6.459 14 0 0 0

14 P 2 2 2.275 0.537 6.319 13 15 0 0

. . . . . . . . . . .

. . . . . . . . . . .

. . . . . . . . . .

. . . . . . . . . . .

. . . . . . . . . . .

The out.prp file contains lots of information. In the first part of the file lists all the parameters about the simulations and any warning messages. In the second part of the file lists the values of different properties calculated by Occam.

In the out.xyz file, the trajectory is accumulated according to the frequency of writing value trj_print in the input.inp. The format of trajectory is xyz. The first row is left empty, while the second row indicates the total number of particles of the systems.

the final.out file is the restarting file, and it is written only after a successful run.