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--- exercises:2018_ethz_mmm:index [2018/02/22 13:28] – dpasserone
+++ exercises:2018_ethz_mmm:index [2018/05/25 10:04] – dpasserone
@@ Line 6: / Line 6: @@
   - [[lennard_jones_cluster_2018| 3D 38 Atom Lennard-Jones cluster - optimization ]]
   - [[c2h2_bond_energy_2018|Bond Strength in a molecule]]
-  - [[alanine_dipeptide_2018|Alanine dipeptide: Ramachandran plot]]
-<!--
-===== Lecture 1 =====
-  - [[lennard_jones_cluster| 3D 38 Atom Lennard-Jones cluster - optimization ]]
-  - [[lennard_jones_cluster_neb| 3D 38 Atom Lennard-Jones cluster - transition paths ]]
 ===== Lecture 2 =====
-  - [[pythonmd| 3D 38 Atom Lennard-Jones Molecular dynamics ]]
+  - [[H2O_MD| Molecular dynamics of water ]]
 ===== Lecture 3 =====
-  - [[MC and KMC| Monte Carlo  simulations for the diffusion of "sumanene" molecules on the Ag(111) surface ]]
+  - [[MC2018| Monte Carlo simulations for the estimation of pair interactions ]]
-  - [[MC and KMC 2| Kinetic Monte Carlo simulations for the diffusion of Hexaiodobenzene molecules on noble metal substrates ]]
+  - [[KMC2018| Kinetic Monte Carlo simulations for the diffusion of molecules @Ag(111) ]]
 ===== Lecture 4 =====
-  - [[surface_Cu|surface energy of Cu(111), Cu(110), Cu(100) and Wulff plot]]
+  - [[BF3| BF3 Hartree Fock calculation and orbitals ]]
-  - [[surface_Au|surface energy of Au(110): perfect and reconstructed and other faces]]
 ===== Lecture 5 =====
-  - [[T_melting_2017|Determination of melting temperature of a copper system from molecular dynamics]]
+  - [[Ethanol_2018| Dehydration of ethanol ]]
+===== Lecture 6 =====
+  - [[Adsorption_2018| Adsoprtion of acetylene on PdGa  ]]
 ===== Lecture 7 =====
-  - [[replica_2017|Sampling the disordering of a cluster using replica exchange]]
+  - [[Infrared_2018| Infrared spectroscopy with cp2k  ]]
 ===== Lecture 8 =====
-  - [[Reaction_energy_2017|Dehydration of ethanol]]
+  - [[Bands_I_2018| Crystallographic point groups, free electron model  ]]
 ===== Lecture 9 =====
-  - [[c2h2_PdGa|Adsorption energy of acetylene on PdGa]]
+  - [[Bands_II_2018| Bandstructure calculations  ]]
 ===== Lecture 10 =====
-  - [[bands_1|Crystallographic point groups, free electron model]]
+  - [[STM_2018| STM and AFM simulations  ]]
 ===== Lecture 11 =====
-  - [[bands_2|Bandstructure calculations]]
+  - [[RE_2018| Replica Exchange molecular dynamics  ]]
+  - [[QMMM_2018| QM/MM for a slab  ]]
 ===== Lecture 12 =====
-  - [[STM|Scanning Tunnelling Microscopy]]
+  - [[PMF| Potential of mean force  ]]
-===== Lecture 13 =====
-  - [[QMMM|Validation of a QM/MM model for KCl]]
- ===== Lecture 1 (tentative) =====
+<!--  - [[alanine_dipeptide_2018|Alanine dipeptide: Ramachandran plot]]
-  - [[single_point_calculation|Single Point Energy Calculation]]
+-->
-  - [[geometry_optimization|Geometry Optimization]]
-  - [[nudged_elastic_band|Nudged Elastic Band]]
-===== Lecture 2 (tentative) =====
+===== note on the Quantum Mobile =====
-  - [[c2h2_bond_energy|Bond Strength in a molecule]]
-  - [[alanine_dipeptide|Alanine dipeptide: Ramachandran plot]]
-  - [[alanine_modify|Alanine dipeptide: Modifying the parameters of the force field]]
+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/CTRL+V
+  * In a terminal: use SHIFT+CTRL+C/SHIFT+CTRL+V
+</note>
-===== Lecture 4 (tentative) =====
+===== m_ bash functions =====
-  - [[MD_ala|Molecular dynamics of alanine dipeptide]]
-  - [[MD_slab|Molecular dynamics of Au 100 slab]]
-===== Lecture 5 (tentative) =====
+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.
-  - [[T_melting|Determination of melting temperature of a Lennard-Jones system from molecular dynamics]]
+Here the list and usage of all of them:
-===== Lecture 5 (tentative) =====
+<code>
-  - [[T_melting|Determination of melting temperature of a Lennard-Jones system from molecular dynamics]]
+==================================================================
+m_addcolumn
+Description:
+        add a column at the left of a file, the same string in every line.
+Usage:
+        m_addcolumn string < file > file.out
+==================================================================
-===== Lecture 6 (tentative) ===
-  - [[exercises:2015_ethz_mmm:monte_carlo_ice|Properties of Ice from Monte Carlo Simulations]]
-  - [[nacl_md | Observer NaCl dissociation in water ]]
-  - [[nacl_free_energy | Free Energy Profile of NaCl Dissociation ]]
-===== Lecture 7 (tentative) =====
+==================================================================
-  - [[basis_sets|Basis Sets]]
+m_cutlines
-  - [[reaction_energy|Reaction Energy]]
+Description:
-  - [[mo_ethene|Molecular orbitals of Ethene]]
+        Cuts lines l1..l2, l3..l4, l5..l6 away from a file
+Usage:
+        m_cutlines l1 l2 l3 l4 l5 l6 ...  < file > modified_file
+==================================================================
-===== Lecture 8 (tentative) =====
-  - [[dye_tio|Dye anchoring to TiO$_2$]]
-===== Lecture 9 (tentative)  =====
+==================================================================
-  - [[hfx_h2ion|Hartree-Fock exchange for the dihydrogen cation]]
+m_domyslab
-  - [[tio2_gap|TiO$_2$ Band Gap as a function of %hfx]]
+Description:
-  - [[benzene_dimer|Binding Energy of the Benzene Dimer]]
+        starting from a unit cell file with Element x y z columns, generate a nx ny nz cell. The parameter d is the nearest neighbor distance, and the cell lengths Lx, Ly, Lz are in the same units as in the unit cell file. Since d is used to multiply all coordinates, the unit cell coordinates are meant to be in nearest neighbor units.
+Usage:
+        m_domyslab Lx Ly Lz d nx ny nz < unitcell > slab.xyz
+==================================================================
-===== Lecture 10 (tentative)  =====
-  - [[ls_scf| Linear scaling SCF]]
-  - [[wannier | Maximally Localized Wannier Functions]]
-===== Lecture 11 (tentative) =====
+==================================================================
-  - [[infra_red | Infrared spectroscopy with MD ]]
+m_interpolate
-  - [[simple_stm | Simple STM images ]]
+Description:
+        Returns a list of real numbers that interpolates two given extremes A and B with n+1 points (from A=0 to B=n)
+Usage:
+        m_interpolate xa xb n
+==================================================================
-===== Lecture 12 (tentative) =====
-  - [[bs | band structure and DOS of graphene ]] ...
-====== Euler Cheat Sheet ======
+==================================================================
+m_multiply
+Description:
+        Returns the product of two numbers
+Usage:
+        m_multiply num1 num2
+==================================================================
+==================================================================
+m_overlayer
+Description:
+        Replaces the 4th column (z coordinate) of a file with a user-given new z coordinate.
+Usage:
+        m_overlayer newz < overlayer.xyz > newoverlayer.xyz
+==================================================================
+==================================================================
+m_replace
+Description:
+        Replaces all occurrencies of an "oldstring" in a file with a "newstring" string
+Usage:
+        m_replace "oldstring" "newstring" < oldfile > newfile
+==================================================================
+==================================================================
+m_trimlines
+Description:
+        trims around lines l1..l2, l3..l4, l5..l6 of
+Usage:
+        m_trimlines l1 l2 l3 l4 l5 l6 ...  < file > modified_file
+==================================================================
+==================================================================
+m_xyzcenter
+Description:
+        Centers a sample in the directions specified by a 1, and not in those specified by a 0
+Usage:
+        m_xyzcenter flagx flagy flagz < cell.xyz > cell_center.xyz
+==================================================================
+==================================================================
+m_xyzminmax
+Description:
+        This function returns the maximum and minimum X (or Y, or Z) value from a XYZ file
+Usage:
+        m_xyzminmax x|y|z < file.xyz
+==================================================================
+==================================================================
+m_xyzrefold
+Description:
+        Refolds a sample according to periodic boundary conditions in all directions marked by 1
+        The cell is defined by a,b,c in the second line of the xyz file
+Usage:
+        m_xyzrefold markx marky markz < filein.xyz > fileout.xyz
+==================================================================
+==================================================================
+m_xyztranslate
+Description:
+        Translates all coordinates of a xyz file by a given vector.
+Usage:
+        m_xyztranslate tx ty tz < filein.xyz > fileout.xyz
+==================================================================
+==================================================================
+m_atan2
+Description:
+        Returns the angle in degrees between the positive X-axis of a plane and the point given by the coordinates (x,y) on it:
+\
+ \
+  * (x,y)
+   \
+    \
+     \_______
+      \      |
+       \angle|
+      --\---------------------->
+         \                     X
+Usage:
+        m_atan2 x y
+==================================================================
+==================================================================
+m_distance
+Description:
+        Computes the distance between two points
+Usage:
+        m_distance x1 y1 z1 x2 y2 z2
+==================================================================
+==================================================================
+m_lattice
+Description:
+        Replicates a cell in 3 directions and generates a sample with the cell lengths a b c in the second line
+        IT ONLY READS THE LINES WITH EXACTLY 4 COLUMNS (atomic index, x, y, z)
+Usage:
+        m_lattice [Atom] cellx celly cellz nx ny nz < cell > sample.xyz
+==================================================================
+==================================================================
+m_norm
+Please specify three arguments
+Description:
+        Returns the norm of a vector
+Usage:
+        m_norm x y z
+==================================================================
+==================================================================
+m_pdbtorsion
+Description:
+        Returns torsion defined by 4 atoms in a pdb file
+                           Atom4
+                            /
+             <-.           /
+           angle\         /
+     Atom2-------|-----Atom3
+      /      \__/
+     /
+    /
+ Atom1
+Usage:
+        m_pdbtorsion n1 n2 n3 n4 file
+==================================================================
+==================================================================
+m_scalar
+Description:
+        Returns scalar product of two vectos
+Usage:
+        m_scalar x1 y1 z1 x2 y2 z2
+==================================================================
+==================================================================
+m_unitvec
+Description:
+        Returns a normalized input vector
+Usage:
+        m_unitvec x y z
+==================================================================
+==================================================================
+m_xyzcountframes
+Description:
+        This function counts the number of frames in a trajectory
+Usage:
+        m_xyzcountframes file.xyz
+==================================================================
+==================================================================
+m_xyznatoms
+Description:
+        This function returns the number of atoms in a given XYZ file
+Usage:
+        m_xyznatoms < file.xyz
+==================================================================
+==================================================================
+m_xyzrescale
+Description:
+        Rescales all coordinates of a xyz file by a given factor. If the cell is given in the second line it is multiplied by the same factor
+Usage:
+        m_xyzrescale factor < filein.xyz > fileout.xyz
+==================================================================
+==================================================================
+m_xyzzhistogram
+Description:
+        This function makes a z histogram of a trajectory
+Usage:
+        m_xyzzhistogram n_intervals n_atoms z_min z_max
+==================================================================
+==================================================================
+m_change
+Please specify three arguments
+Description:
+        Adds a delta times an integer to a central value
+Usage:
+        m_change x0 n delta
+==================================================================
+==================================================================
+m_divide
+Description:
+        Returns the ratio of two numbers
+Usage:
+        m_ratio num1 num2
+==================================================================
+==================================================================
+m_getcolumn
+Description:
+        Greps a string from a file and gets the last instance; then takes the nth column
+Usage:
+        m_getcolumn "STRING" column < file
+==================================================================
+==================================================================
+m_list
+Please specify two arguments
+Description:
+        Creates an ordered list of numbers between two integers
+Usage:
+        m_list nmin nmax
+==================================================================
+==================================================================
+m_onecolumn
+Description:
+        parse a file and write all words as a single column
+Usage:
+        m_onecolumn < file
+==================================================================
+==================================================================
+m_pdbvecjoin
+Description:
+        Returns a vector joining  two atoms in a pdb file
+Usage:
+        m_pdbvecjoin at1 at2 pdbfile
+==================================================================
+==================================================================
+m_sum
+Description:
+        Returns the sum of two numbers
+Usage:
+        m_sum num1 num2
+==================================================================
+==================================================================
+m_vecprod
+Description:
+        Returns vector product of two vectors
+Usage:
+        m_vecprod x1 y1 z1 x2 y2 z2
+==================================================================
+==================================================================
+m_xyzframes
+Description:
+        This function takes frames from a xyz file
+Usage:
+        m_takeslides first_frame last_frame file.xyz  (with last_frame=all, until the end)
+==================================================================
+==================================================================
+m_xyzrand
+Description:
+        Randomizes a file xyz from -delta/2 to delta/2
+Usage:
+        m_xyzrand delta < file.xyz
+==================================================================
+==================================================================
+m_xyzsort
+Description:
+        Sorts a xyz file according to z, y, x coordinates (z is inverted)
+Usage:
+        m_xyzsort < file.xyz > filesorted.xyz
+==================================================================
+</code>
+<!--
 For more information have a look at the [[http://www.clusterwiki.ethz.ch/brutus/Getting_started_with_Euler | cluster-wiki]].