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--- howto:gemc [2015/07/13 22:44] – [Sample of output files] 130.18.127.135
+++ howto:gemc [2020/08/21 10:15] – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-==== What is GEMC ====
+==== What is GEMC ?====
-In a Gibbs Ensemble Monte Carlo (GEMC) simulation, 2 boxes are utilized containing a vapor and liquid phase. In order to equilibrate the system, a molecule is allowed to perform 3 types of moves:
+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:
-\\ 1)Translations, rotations, and conformational changes \\
+\\ 1) Translations, rotations, and conformational changes \\
-)Volume exchanges \\
+) Volume exchanges \\
-)Particle Swaps. \\
+) Particle swaps. \\
-These 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 observed without a physical interface using a unified partition function. Thus, we used GEMC simulations to determined vapor-liquid coexistence curves for a system.
+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.zip}}{{gemc_nvt_box2.inp.zip}}, a topology file{{topology_atoms_wat.psf.zip}} for the particular component, and a bias file that contain information of the approximate potential for that component.{{bias_template.inp.zip}}. For example, we have provided sample files for 64 water molecules.
+In order to run GEMC certain input files are needed; the two main input files for each box {{gemc_nvt_box1.inp.zip}}{{gemc_nvt_box2.inp.zip}}, a topology file{{topology_atoms_wat.psf.zip}} for the particular component, and a bias file that contain information of the approximate potential for that component.{{bias_template.inp.zip}}. For example, we have provided here the sample files for 64 water molecules.
 ==== Sample of input files====
-Starting with the input gem_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 need to calculate the energy and forces to describe your system. The Quickstep method is used in order to declare the use of electronic structure methods.
+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
@@ Line 25: / Line 25: @@
       SCF_GUESS ATOMIC
     &END SCF
-One can increase the SCF iteration by including the <code>MAX_SCF</code> command. Adding <code>EPS_SCF</code> 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 function applies derivatives.
+One can increase the SCF iterations by including the ''MAX_SCF'' function. 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'' function specifies about method used to compute derivatives.
     &XC
       &XC_FUNCTIONAL BLYP
@@ Line 42: / Line 42: @@
       &END XC_GRID
     &END XC
-The code snippet below declares the cell and cell ref size.
+The cell and cell ref of the box 1 in angstorms.
     &CELL
       ABC 13.7151207699 13.7151207699 13.7151207699
@@ Line 54: / Line 54: @@
       POTENTIAL GTH-BLYP-q1
     &END KIND
-declares the basis set intended to be used for the simulation.
+declares the basis set(TZV2P) intended to be used for the simulation.
 The following code
   &GLOBAL
@@ Line 60: / Line 60: @@
     RUN_TYPE MC
     PRINT_LEVEL LOW
-is intended to described the type of run. Consequently, RUN_TYPE should be set to MC, as this is what we are running.
+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
@@ Line 76: / Line 76: @@
       RESTART_FILE_NAME mc_restart_2
-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 in a different potential. The LSTOP function determines whether the simulation increment will be in cycles (yes), or in steps (no). The NSTEP feature gives the number of MC cycles in a particular simulation run, and should be adjusted according to the length of the simulation.
+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'' function determines whether the simulation increment will be in cycles (no), or in steps (yes). The ''NSTEP'' feature 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 line BOX2_FILE_NAME GEMC_NVT_box2.inp 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, shown below
+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 line ''BOX2_FILE_NAME GEMC_NVT_box2.inp'' 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''.
-      BOX2_FILE_NAME GEMC_NVT_box1.inp
  ==== Sample of output files====
-Sample output files for 64 H<sub>2</sub>O molecules are provided below.
+Sample output files for 64 H<sub>2</sub>O molecules are provided below. The input file for Box 1 and Box2 has already been explained above. We additionally include a sample output file,{{output4.out.zip}}. Information used to calculate the density at the end of the run is towards the end of the file and looks like the following:
-As the input file for Box 1 and Box2 has already been explained above, we will not go into further detail{{gemc_nvt_box1.inp.zip}}{{gemc_nvt_box2.inp.zip}}. We include a topology file,{{topology_atoms_WAT.psf.zip}}. This file is molecule specific and will change accordingly. We additionally include a sample output file,{{output4.out.zip}}. 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                      |
   ------------------------------------------------