# Open SourceMolecular Dynamics

### Site Tools

exercises:2015_ethz_mmm:monte_carlo_ice

# Differences

This shows you the differences between two versions of the page.

 exercises:2015_ethz_mmm:monte_carlo_ice [2015/03/18 14:53]sclelia exercises:2015_ethz_mmm:monte_carlo_ice [2015/03/18 15:23] (current)sclelia Both sides previous revision Previous revision 2015/03/18 15:23 sclelia 2015/03/18 15:18 sclelia [Main Input-File (run this)] 2015/03/18 15:12 sclelia [Initial Coordinates] 2015/03/18 15:11 sclelia 2015/03/18 14:53 sclelia 2015/02/06 17:49 external edit Next revision Previous revision 2015/03/18 15:23 sclelia 2015/03/18 15:18 sclelia [Main Input-File (run this)] 2015/03/18 15:12 sclelia [Initial Coordinates] 2015/03/18 15:11 sclelia 2015/03/18 14:53 sclelia 2015/02/06 17:49 external edit Line 36: Line 36: ⇒ It will create a file ''​tmc_trajectory_T200.00.dip_cl'',​ which contains the dipole moment for each accepted step. ⇒ It will create a file ''​tmc_trajectory_T200.00.dip_cl'',​ which contains the dipole moment for each accepted step. - You should run these calculations on 3 cores with ''​bsub -n 3''​. + You should run these calculations on 3 cores with : \\ + ''​bsub ​-W 01:00 -n 3 mpirun cp2k.popt -i mc_exercise.inp -o mc_exercise.out''​ ​ * Plot the histogram of the z-component of the dipole moment. \\ * Plot the histogram of the z-component of the dipole moment. \\ Line 88: Line 89: Before you can run the python-script you have to load a newer python-module and set the executable-bit:​ Before you can run the python-script you have to load a newer python-module and set the executable-bit:​ <​code>​ <​code>​ - you@brutusX ​~$module load new python/​2.7.6 + you@eulerX ​~$ module load python/​2.7.6 - you@brutusX ​~$chmod +x calc_dielectric_constant.py + you@eulerX ​~$ chmod +x calc_dielectric_constant.py - you@brutusX ​~$./​calc_dielectric_constant.py 200 tmc_trajectory_T200.00.dip_cl + you@eulerX ​~$ ./​calc_dielectric_constant.py 200 tmc_trajectory_T200.00.dip_cl ​ Line 97: Line 98: You can gather more samples by launching multiple independent runs in parallel with different random number seeds. The seed is given by the ''​RND_DETERMINISTIC''​ keyword. The gathered trajectories can then be analyzed collectively with the python-script:​ You can gather more samples by launching multiple independent runs in parallel with different random number seeds. The seed is given by the ''​RND_DETERMINISTIC''​ keyword. The gathered trajectories can then be analyzed collectively with the python-script:​ <​code>​ <​code>​ - you@brutusX ​~$./​calc_dielectric_constant.py 200 trj_1_T200.00.dip_cl trj_1_T200.00.dip_cl ... + you@eulersX ​~$ ./​calc_dielectric_constant.py 200 trj_1_T200.00.dip_cl trj_1_T200.00.dip_cl ... Line 106: Line 107: ===== Required Files ===== ===== Required Files ===== ==== Initial Coordinates ==== ==== Initial Coordinates ==== + This file contains the initial ice coordinates. ​ {{ice_ih_96.xyz.gz| Download here}} {{ice_ih_96.xyz.gz| Download here}} ==== Main Input-File (run this) ==== ==== Main Input-File (run this) ==== + This file specifies the type of algorithm do adopt and the simulation parameters. ​ &GLOBAL &GLOBAL PROJECT H2O_MC PROJECT H2O_MC - PROGRAM TMC + PROGRAM TMC         ! Tree Monte Carlo algorithm ​ RUN_TYPE TMC RUN_TYPE TMC - PRINT_LEVEL LOW + PRINT_LEVEL LOW     ! Low amount of information written in the output - WALLTIME 1:00:00 + WALLTIME 1:​00:​00 ​   ! The simulation will last one hour and then will stop &END GLOBAL &END GLOBAL &MOTION &MOTION &TMC &TMC RND_DETERMINISTIC 42 !<=== Change this number to obtain different samplings RND_DETERMINISTIC 42 !<=== Change this number to obtain different samplings - PRINT_COORDS .FALSE. !this avoids the file-size ​problem + PRINT_COORDS .FALSE. !this avoids the printing of all coordinates and file-size ​problems GROUP_CC_SIZE 0 GROUP_CC_SIZE 0 NUM_MC_ELEM 100000 NUM_MC_ELEM 100000 - ENERGY_FILE_NAME H2O_ice.inp + ENERGY_FILE_NAME H2O_ice.inp ​! refers to the auxiliary input for the force specification TEMPERATURE 200 TEMPERATURE 200 - &​MOVE_TYPE ​     MOL_TRANS + &​MOVE_TYPE ​     MOL_TRANS ​      ! specifies "​proton moves" for better sampling SIZE          0.05 SIZE          0.05 PROB          3 PROB          3 Line 146: Line 149: &END &END PRESSURE 0.01 PRESSURE 0.01 - ESIMATE_ACC_PROB .TRUE. + ESIMATE_ACC_PROB .TRUE. ​       ​!accuracy parameters, do not change RESTART_OUT 0 RESTART_OUT 0 NUM_MV_ELEM_IN_CELL 5 NUM_MV_ELEM_IN_CELL 5 Line 166: Line 169: ​ - ==== Auxiliary Input-File (do not run this directly) ==== + ==== Auxiliary Input-File (do NOT run this directly) ==== + This auxiliary input specifies the system properties ​ Line 251: Line 255: ==== Topology File ==== ==== Topology File ==== + This file specifies the topology of the system (which atoms, bonds, angles in the water molecule). It allows the program to distinguish which atoms belong to which water molecule, and therefore discriminate between inter and intramolecular interactions. ​ PSF PSF