SPICA: Surface Property fItting Coarse grAined model

TutorialtSPICA

tSPICA

tSPICA is an extension of the SPICA FF for temperature and pressure dependence. To apply the T and P correction to the SPICA FF, the Lennard-Jones ε parameter for each interaction is scaled as a function of T and P (A brief summary of the model is given here, and the publication with full details here ). For simulations with LAMMPS, there is already a script to scale the parameters in the LAMMPS parameter file to the correct T and P dependent values. The tutorial for generating LAMMPS parameter files can be found here.

download tSPICA script
download Coefficients file

tSPICA.py useage:


$ tSPICA.py Temperature Pressure Parameter_file Coefficients_file

Temperature in Kelvin
Pressure in MPa
Parameter_file = Path to parameter_file . File in LAMMPS format
Coefficients_file = Path to coefficient_file . File format given here

Example:

Files for tutorial: Input SPICA Parameter fileOutput tSPICA parameter file

A simulation of n-dodecane* at 363 K and 25 MPa. Here we will only concern ourselves with generating the tSPICA parameter file for the simulation. Details for running the simulations can be found here
*Contains CM and CT SPICA beads

First we start with a LAMMPS parameter file for SPICA in this case PARM.FILE
The pair coefficents section of the parameter file should look like:

...
pair_coeff   1   1   lj9_6   0.4690   4.5850 # CT   CT
pair_coeff   1   2   lj9_6   0.4440   4.5850 # CT   CM
pair_coeff   2   2   lj9_6   0.4200   4.5850 # CM   CM
...


Note: For "# type1type2" type1 and type2 have to match the corresponding ID's in the coeffecient file.

Next we run the tSPICA.py script with the arguments for the temperature, pressure, parameter_file, and coefficent_file. In this example temperature = 363, pressure = 25, parameter_file = PARM.FILE and coefficient_file = tSPICA_Coeffs.txt, so the command is:

$ tSPICA.py 363 25 PARM.FILE tSPICA_Coeffs.txt

The output will be written to t-parameter_file, in this case t-PARM.FILE.
The pair coefficents section of the new parameter file should look like:

...
pair_coeff   1   1   lj9_6   0.4232   4.5850 # CT   CT
pair_coeff   1   2   lj9_6   0.3982   4.5850 # CT   CM
pair_coeff   2   2   lj9_6   0.3742   4.5850 # CM   CM
...

The LAMMPS simulation can now be run using t-PARM.FILE instead of PARM.FILE ( tutorial for SPICA simulations in LAMMPS)

tSPICA Coefficient file format

The coefficient file provides the coefficients for the T,P, and cross terms of tSPICA that have been derived for each interacting pair. For a brief outline of the coefficents see here or the see the original publication here

Format:
Type1 Type2 e1 e2 e3 e4 a1 a2

Type1 = Bead1 type
Type2 = Bead2 type
e1 and e2 = Temperature dependent coefficients
e3 and e4 = Pressure dependent coefficients
a1 and a2 = Cross coefficients

# Comment line

CM   CT   -0.036   0.0   -3.6E-5   7.4E-8   1.0005   1.03080
...

SPICA Force Field

Nagoya University