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--- exercises:2015_ethz_mmm:monte_carlo_ice [2015/03/18 14:53] – sclelia
+++ exercises:2015_ethz_mmm:monte_carlo_ice [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 36: / Line 36: @@
 ⇒ It will create a file ''tmc_trajectory_T200.00.dip_cl'', which contains the dipole moment for each accepted step.
 <note tip>
-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''
 </note>
     * 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:
 <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
 </code>
 </note>
@@ 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:
 <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 ...
 </code>
 <note tip>
@@ Line 106: / Line 107: @@
 ===== Required Files =====
 ==== Initial Coordinates ====
+This file contains the initial ice coordinates.
 {{ice_ih_96.xyz.gz| Download here}}
 ==== Main Input-File (run this) ====
+This file specifies the type of algorithm do adopt and the simulation parameters.
 <code - mc_exercise.inp>
 &GLOBAL
   PROJECT H2O_MC
-  PROGRAM TMC
+  PROGRAM TMC         ! Tree Monte Carlo algorithm
   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
 &MOTION
   &TMC
       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
       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
-      &MOVE_TYPE      MOL_TRANS
+      &MOVE_TYPE      MOL_TRANS       ! specifies "proton moves" for better sampling
         SIZE          0.05
         PROB          3
@@ Line 146: / Line 149: @@
       &END
       PRESSURE 0.01
-      ESIMATE_ACC_PROB .TRUE.
+      ESIMATE_ACC_PROB .TRUE.        !accuracy parameters, do not change
       RESTART_OUT 0
       NUM_MV_ELEM_IN_CELL 5
@@ Line 166: / Line 169: @@
 </code>
-==== Auxiliary Input-File (do not run this directly) ====
+==== Auxiliary Input-File (do NOT run this directly) ====
+This auxiliary input specifies the system properties
 <code - H2O_ice.inp>
@@ Line 251: / Line 255: @@
 ==== 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.
 <code - topology_H2O.psf>
  PSF