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howto:gemc [2020/08/21 10:15] – external edit 127.0.0.1howto: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 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 \\  +
-2) Volume exchanges \\  +
-3) 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.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 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.  +
-    &MGRID +
-      CUTOFF 280 +
-    &END MGRID +
-    &QS +
-    &END QS +
-    &SCF +
-      SCF_GUESS ATOMIC +
-    &END SCF +
-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 +
-      &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 +
- +
-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 +
-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 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, for example: ''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. 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: +
-  |                   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.1598004913.txt.gz · Last modified: 2020/08/21 10:15 by 127.0.0.1