Differences

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

--- exercises:2015_ethz_mmm:c2h2_bond_energy [2015/02/26 14:15] – yakutovich
+++ exercises:2015_ethz_mmm:c2h2_bond_energy [2015/03/03 22:26] – dpasserone
@@ Line 1: / Line 1: @@
 ====== C2H2 and C2H4 bond energy ======
+<note warning>
+TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE IN DANIELE PASSERONE DIR) IN THE INTERACTIVE SHELL:
+you@eulerX ~$ . ~danielep/Scripts/m_functions.bash
+</note>
 <note warning>
 Before you start it is **ABSOLUTELY NEСESSARY** to update the function library. So from you $HOME directory please run:
@@ Line 21: / Line 26: @@
 </note>
-<note important> **REMEMBER** to load the  module for the cp2k program:
+<note important> **REMEMBER: this is the command to load the  module for the cp2k program:**
 <code>
@@ Line 27: / Line 32: @@
 </code>
-**and to submit the job chain:**
+**and to submit the job:**
 <code>
-you@eulerX ~$ bsub < c2h2.a.chain
+you@eulerX ~$ bsub < jobname
 </code>
 </note>
@@ Line 47: / Line 52: @@
 In this exercise you will test the general AMBER force field, which is suitable for a large class of molecules. In this example you will compute the classical energy of a simple acetylene molecule and apply small variations to the C-C bond lengths.
-Please go to the directory "exercise_2.1/c2h2/".
+Then go to the directory "exercise_2.1/c2h2/".
 <code>
 you@eulerX ~$ cd exercise_2.1/c2h2/
@@ Line 53: / Line 58: @@
 The input file structure of the template is the following:
-<code - c2h2.amber.inp.templ>
+<code - c2h2.inp.templ>
 &FORCE_EVAL                     ! This section defines method for calculating energy and forces
   METHOD FIST                   ! Using Molecular Mechanics
@@ Line 113: / Line 118: @@
 The script to modify the C-C distance in the input and generate the curve is the following:
-<code bash c2h2.amber.chain>
+<code bash c2h2.chain>
 #
 # task 2.1 C2H2 bond strength
@@ Line 179: / Line 184: @@
 <code>
-you@brutusX mmm_exercise_2.1$ module load new cp2k
+you@eulerX c2h2$ module load new cp2k
-you@brutusX mmm_exercise_2.1$ bsub < c2h2.a.chain
+you@eulerX c2h2$ bsub < c2h2.chain
 </code>
@@ Line 188: / Line 193: @@
 <code>
-you@brutusX mmm_exercise_2.1$ gnuplot fit.triple.gnu
+you@eulerX c2h2$ gnuplot fit.gnu
 </code>
-<code - fit.triple.gnu>
+<code - fit.gnu>
 #!/usr/bin/gnuplot
 f(x)=k*(x-x0)*(x-x0)+e0         # definition of the function to be fitted
@@ Line 232: / Line 237: @@
 Now, perform the same exercise in another directory for the molecule C2H4.
+<code>
+you@eulerX c2h2$ cd ../c2h4
+</code>
-    * The input c2h4.amber.inp.templ is similar to the previous one, only with different project name (C2H4) and coordinates:
+    * The new input c2h4.inp.templ is similar to the previous one, only with different project name (C2H4) and coordinates:
 <code coo.ch4>
@@ Line 246: / Line 254: @@
    * The script to modify the bond lengths changes slightly as well
-<code bash c2h4.a.chain>
+<code bash c2h4.chain>
 #
 # task 2.2 C2H4 bond strength
@@ Line 312: / Line 320: @@
 <note tip>Assignment:
   - Report the values of the bond length and force constants in all cases.
-  - Discuss these values in view of the kind of molecules we are simulating
+  - Discuss these values in view of the kind of molecules we are simulating.
+</note>