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input.inp

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

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 that you want use for simulations)
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 consisten 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)
input.mdl

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.

********* 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
input.cor

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

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
. . . . . . . . . . .
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out.prp

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.

trj.xyz

The out.xyz file contains the total trajectory for all particles of the system. The format in wich is writed the trajectory files is .xyz.

final.out

In the final.out file shwos the final configuration on the last step of simulations, written in the same fortmat fo .cor.