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howto:gemc [2015/07/13 22:37] – [Sample of output files] 130.18.127.135howto:gemc [2024/01/03 13:07] (current) – oschuett
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-==== What is GEMC ==== +This page has been moved to: https://manual.cp2k.org/trunk/methods/sampling/monte_carlo.html
-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:  +
-\\ 1)Translations, rotations, and conformational changes \\  +
-2)Volume exchanges \\  +
-3)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.  +
- +
-==== 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. +
- +
-==== 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. +
-  &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.  +
-    &MGRID +
-      CUTOFF 280 +
-    &END MGRID +
-    &QS +
-    &END QS +
-    &SCF +
-      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.  +
-    &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 code snippet below declares the cell and cell ref size.  +
-    &CELL +
-      ABC 13.7151207699 13.7151207699 13.7151207699 +
-      &CELL_REF +
-        ABC 13.7151207699 13.7151207699 13.7151207699 +
-      &END CELL_REF +
- +
-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 intended to be used for the simulation. +
-The following code +
-  &GLOBAL +
-    PROJECT H2O_MC +
-    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. +
-  &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 +
- +
-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 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. Box 2 has a similar line that references Box 1, shown below +
-      BOX2_FILE_NAME GEMC_NVT_box1.inp +
-==== Sample of output files==== +
-Sample input files for 64 H<sub>2</sub>O molecules are provided and explained below. +
-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 consequently 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                      | +
-  ------------------------------------------------ +
-   +
-  ******************************************************************************** +
-  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.+
howto/gemc.1436827040.txt.gz · Last modified: 2020/08/21 10:15 (external edit)