exercises:2018_ethz_mmm:index
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exercises:2018_ethz_mmm:index [2018/02/22 14:22] – dpasserone | exercises:2018_ethz_mmm:index [2018/05/18 02:59] – dpasserone | ||
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- [[lennard_jones_cluster_2018| 3D 38 Atom Lennard-Jones cluster - optimization ]] | - [[lennard_jones_cluster_2018| 3D 38 Atom Lennard-Jones cluster - optimization ]] | ||
- [[c2h2_bond_energy_2018|Bond Strength in a molecule]] | - [[c2h2_bond_energy_2018|Bond Strength in a molecule]] | ||
- | - [[alanine_dipeptide_2018|Alanine dipeptide: Ramachandran plot]] | ||
- | |||
- | ====== m_ bash functions ====== | + | ===== Lecture 2 ===== |
+ | - [[H2O_MD| Molecular dynamics of water ]] | ||
- | We have programmed in the virtual machine some useful bash functions. They all start with **m_** and can be called from the command line. | + | |
+ | ===== Lecture 3 ===== | ||
+ | - [[MC2018| Monte Carlo simulations for the estimation of pair interactions ]] | ||
+ | - [[KMC2018| Kinetic Monte Carlo simulations for the diffusion of molecules @Ag(111) ]] | ||
+ | |||
+ | ===== Lecture 4 ===== | ||
+ | - [[BF3| BF3 Hartree Fock calculation and orbitals ]] | ||
+ | |||
+ | ===== Lecture 5 ===== | ||
+ | - [[Ethanol_2018| Dehydration of ethanol ]] | ||
+ | |||
+ | ===== Lecture 6 ===== | ||
+ | - [[Adsorption_2018| Adsoprtion of acetylene on PdGa ]] | ||
+ | |||
+ | |||
+ | ===== Lecture 7 ===== | ||
+ | - [[Infrared_2018| Infrared spectroscopy with cp2k ]] | ||
+ | |||
+ | ===== Lecture 8 ===== | ||
+ | - [[Bands_I_2018| Crystallographic point groups, free electron model ]] | ||
+ | |||
+ | ===== Lecture 9 ===== | ||
+ | - [[Bands_II_2018| Bandstructure calculations | ||
+ | |||
+ | ===== Lecture 10 ===== | ||
+ | - [[STM_2018| STM and AFM simulations | ||
+ | |||
+ | ===== Lecture 11 ===== | ||
+ | - [[QMMM_2018| QM/MM and Replica exchange disordering of a cluster | ||
+ | |||
+ | < | ||
+ | --> | ||
+ | |||
+ | ===== note on the Quantum Mobile ===== | ||
+ | |||
+ | Remember that the Quantum Mobile VM is a Linux environment. As such, copy/paste operations are sometimes application-dependent. | ||
+ | |||
+ | <note tip> | ||
+ | * In a browser or other graphical programs: use CTRL+C/ | ||
+ | * In a terminal: use SHIFT+CTRL+C/ | ||
+ | </ | ||
+ | |||
+ | ===== m_ bash functions ===== | ||
+ | |||
+ | We have programmed in the virtual machine some useful bash functions. They all start with **m_** and can be called from the command line. To see the usage of one of them, use the -h flag. | ||
Here the list and usage of all of them: | Here the list and usage of all of them: | ||
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Usage: | Usage: | ||
m_distance x1 y1 z1 x2 y2 z2 | m_distance x1 y1 z1 x2 y2 z2 | ||
- | ================================================================== | ||
- | |||
- | |||
- | ================================================================== | ||
- | m_functions.bash | ||
================================================================== | ================================================================== | ||
Line 367: | Line 405: | ||
- | Download the 1.1 exercise into your $HOME folder and unzip it. | ||
- | < | ||
- | you@eulerX ~$ wget http:// | ||
- | you@eulerX ~$ unzip exercises: | ||
- | </ | ||
- | <!-- | ||
- | <note tip> | ||
- | All files of this exercise be downloaded from the wiki: {{exercise_1.1.zip|}} | ||
- | </ | ||
- | |||
- | In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following paper about the energy landscape of the 38 atom Lennard-Jones cluster: | ||
- | <note tip>{{ : | ||
- | </ | ||
- | Login to euler using your nethz credentials. | ||
- | Then go to the directory " | ||
- | < | ||
- | you@eulerX ~$ cd exercise_1.1 | ||
- | |||
- | |||
- | </ | ||
- | |||
- | ===== Geometry optimization | ||
- | In this first part you will perform a simple energy optimization, | ||
- | |||
- | The input file structure of the template is the following: | ||
- | |||
- | <code - geo_opt.inp> | ||
- | &GLOBAL | ||
- | | ||
- | | ||
- | | ||
- | | ||
- | | ||
- | &END GLOBAL | ||
- | |||
- | &MOTION | ||
- | & | ||
- | OPTIMIZER BFGS | ||
- | MAX_ITER | ||
- | MAX_DR | ||
- | RMS_DR | ||
- | MAX_FORCE 0.0001 | ||
- | RMS_FORCE 0.00003 | ||
- | &BFGS | ||
- | | ||
- | &END BFGS | ||
- | & | ||
- | & | ||
- | & | ||
- | | ||
- | & | ||
- | GEO_OPT 1 | ||
- | & | ||
- | &END TRAJECTORY | ||
- | & | ||
- | &END MOTION | ||
- | |||
- | & | ||
- | | ||
- | | ||
- | & | ||
- | & | ||
- | &CHARGE | ||
- | ATOM Ar | ||
- | CHARGE 0.0 | ||
- | &END | ||
- | & | ||
- | & | ||
- | atoms Ar Ar | ||
- | EPSILON 119.8 | ||
- | SIGMA 3.405 | ||
- | RCUT 8.4 | ||
- | &END LENNARD-JONES | ||
- | &END NONBONDED | ||
- | &CHARGE | ||
- | ATOM Kr | ||
- | CHARGE 0.0 | ||
- | &END CHARGE | ||
- | &END FORCEFIELD | ||
- | & | ||
- | | ||
- | & | ||
- | EWALD_TYPE none | ||
- | & | ||
- | &END POISSON | ||
- | |||
- | & | ||
- | SPLINE_DATA | ||
- | SPLINE_INFO | ||
- | & | ||
- | &END PRINT | ||
- | & | ||
- | & | ||
- | &FORCES off | ||
- | &END FORCES | ||
- | & | ||
- | &END GRID_INFORMATION | ||
- | & | ||
- | & | ||
- | GEO_OPT 1 | ||
- | & | ||
- | &END PROGRAM_RUN_INFO | ||
- | & | ||
- | & | ||
- | GEO_OPT 1 | ||
- | & | ||
- | &END STRESS_TENSOR | ||
- | & | ||
- | & | ||
- | &CELL | ||
- | | ||
- | | ||
- | | ||
- | | ||
- | &END CELL | ||
- | & | ||
- | COORD_FILE_NAME in.xyz | ||
- | COORDINATE xyz | ||
- | &END | ||
- | |||
- | & | ||
- | & | ||
- | & | ||
- | & | ||
- | & | ||
- | & | ||
- | & | ||
- | & | ||
- | &END PRINT | ||
- | & | ||
- | &END FORCE_EVAL | ||
- | | ||
- | </ | ||
- | <note important> | ||
- | **1 Hartree=27.2114 eV**. | ||
- | In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in " | ||
- | </ | ||
- | <note tip> | ||
- | - load the module with the special m_* bash functions and initialize the module: < | ||
- | - randomize the coordinate files **fcc.xyz** | ||
- | - extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values.< | ||
- | python stein.py file.xyz </ | ||
- | - before running the simulation, copy the input coordinate file into in.xyz < | ||
- | - run cp2k < | ||
- | - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)** | ||
- | - load vmd module and play with the optimization trajectory < | ||
- | - apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. < | ||
- | - plot q4 and energies with **gnuplot** (ask the teacher) | ||
- | - have a look at the myq4 script < | ||
- | - repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example: < | ||
- | - finally, run the bash script < | ||
- | |||
- | </ | ||
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exercises/2018_ethz_mmm/index.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1