Monte Carlo
In the most common set up of Gibbs Ensemble Monte Carlo (GEMC) simulation, 2 boxes are utilized to represent vapor and liquid phases. In order to equilibrate the system, different types of moves are used:
Translations, rotations, and conformational changes
Volume exchanges
Particle swaps.
The particles are swapped between boxes to equilibrate the chemical potential, volume moves equilibrate pressure, and the rest of the moves within a box are performed to maintain thermal equilibrium. The main advantage of the GEMC simulation is that coexisting phases can be simulated without a physical interface using a unified partition function. Thus, we used GEMC simulations to determined vapor-liquid coexistence curves for a system.
Files required to run GEMC
In order to run GEMC certain input files are needed; the two main input files for each box
GEMC_NVT_box1.inp, GEMC_NVT_box2.inp, a topology file topology_atoms_WAT.psf
for the particular component, and a bias file that contain information of the approximate potential
for that component bias_template.inp. For example, we have provided here the sample files for
64 water molecules.
Sample of input files
Starting with the input GEMC_NVT_box1.inp file first, we note that the location of the basis set
file, as well as the potential file, is declared (in this case these two files are present in the
current working directory). FORCE_EVAL initializes the parameters needed
to calculate the energy and forces to describe your system. The Quickstep module is used in order
to use of electronic structure methods.
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME GTH_BASIS_SETS
POTENTIAL_FILE_NAME POTENTIAL
...
The SCF section in the code below generates atomic density.
&SCF
SCF_GUESS ATOMIC
&END SCF
One can increase the SCF iterations by including the MAX_SCF keyword. Also, EPS_SCF declares the expected SCF convergence. Continuing down the code of the input file, the section shown below details which functional we intend on using, in our case BLYP. We also use the DFTD2 dispersion correction. Additionally, the XC_DERIV keyword specifies about method used to compute derivatives.
&XC
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
R_CUTOFF 40.0
TYPE DFTD2
REFERENCE_FUNCTIONAL BLYP
&END PAIR_POTENTIAL
&END VDW_POTENTIAL
&XC_GRID
XC_DERIV SPLINE2
XC_SMOOTH_RHO NONE
&END XC_GRID
&END XC
The cell and cell ref of the box 1 in angstorms.
&CELL
ABC 13.7151207699 13.7151207699 13.7151207699
&CELL_REF
ABC 13.7151207699 13.7151207699 13.7151207699
&END CELL_REF
&END CELL
After the above section of code, there is a listing of coordinates for each atom. After this, the section
&KIND H
BASIS_SET TZV2P-GTH
POTENTIAL GTH-BLYP-q1
&END KIND
declares the basis set(TZV2P) intended to be used for the simulation. The following code
&GLOBAL
PROJECT H2O_MC
RUN_TYPE MC
PRINT_LEVEL LOW
&END GLOBAL
is intended to described the type of run. Consequently, RUN_TYPE
should be set to MC, as this is what we are running.
&MOTION
&MC
ENSEMBLE GEMC_NVT
TEMPERATURE 398.0
IPRINT 1
LBIAS yes
LSTOP yes
NMOVES 8
NSWAPMOVES 640
NSTEP 5
PRESSURE 1.013
RESTART no
BOX2_FILE_NAME GEMC_NVT_box1.inp
RESTART_FILE_NAME mc_restart_2
...
&END MC
&END MOTION
The ENSEMBLE GEMC_NVT illustrates the particular type of
simulation. It should be noted that the condition LBIAS YES must be
true, as we pre sample moves with a classical potential. The LSTOP
keyword determines whether the simulation increment will be in cycles (no), or in steps (yes). The
NSTEP keyword gives the number of MC cycles in a particular
simulation run, and should be adjusted according to the length of the simulation. The line
RESTART NO should only be set to ‘no’ for the initial run, then
switched to ‘yes’ after the first simulation run is complete. The keyword
BOX2_FILE_NAME gives the file name of the input for Box2 and
uses it as a reference such that the two input files are read together. GEMC_NVT_box2.inp has a
similar line that references Box 1, for example: BOX2_FILE_NAME GEMC_NVT_box1.inp.
Sample of output files
Sample output files for 64 \(H_2O\) molecules are provided below. The input file for Box 1 and Box2
has already been explained above. We additionally include a sample output file,
GEMC_NVT_box1.out. Information used to calculate the density at the end of the run is towards
the end of the file and looks like the following:
| BOX 1 |
------------------------------------------------
********************************************************************************
Average Energy [Hartrees]: -1085.04223205
Average number of molecules: 63.00000000
Average Volume [angstroms**3]: 2579.876452
--------------------------------------------------------------------------------
Quickstep Moves Attempted Accepted Percent
4 1 25.000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Move Data for Molecule Type 1
--------------------------------------------------------------------------------
Conformational Moves Attempted Accepted Percent
9 2 22.222
Bond Changes Attempted Accepted Percent
5 2 40.000
--------------------------------------------------------------------------------
Angle Changes Attempted Accepted Percent
4 0 0.000
--------------------------------------------------------------------------------
Conformational Moves Rejected BecauseBox Was Empty: 0
-------------------------------------------------------------------------------
Translation Moves Attempted Accepted Percent
12 1 8.333
--------------------------------------------------------------------------------
Rotation Moves Attempted Accepted Percent
11 1 9.091
--------------------------------------------------------------------------------
Biased Move Data
--------------------------------------------------------------------------------
Bond Changes Attempted Accepted Percent
5 5 100.000
--------------------------------------------------------------------------------
Angle Changes Attempted Accepted Percent
4 4 100.000
--------------------------------------------------------------------------------
Translation Moves Attempted Accepted Percent
12 8 66.667
--------------------------------------------------------------------------------
Rotation Moves Attempted Accepted Percent
11 5 45.455
--------------------------------------------------------------------------------
********************************************************************************
------------------------------------------------
| BOX 2 |
------------------------------------------------
********************************************************************************
Average Energy [Hartrees]: -17.20378753
Average number of molecules: 1.00000000
Average Volume [angstroms**3]: 2579.876452
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Move Data for Molecule Type 1
--------------------------------------------------------------------------------
Swap Moves into this box Attempted Empty Percent
1 0 0.000
Growths Attempted Sucessful Percent
1 1 100.000
Total Attempted Accepted Percent
1 0 0.000
-------------------------------------------------------------------------------
Biased Move Data
--------------------------------------------------------------------------------
********************************************************************************
Additionally, other relevant information is included in this file, such as the percentage of accepted moves.