Differences

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

--- exercises:2017_ethz_mmm:qmmm [2017/06/02 03:33] – dpasserone
+++ exercises:2017_ethz_mmm:qmmm [2017/06/02 03:43] – dpasserone
@@ Line 19: / Line 19: @@
 <note important>
    *  Make three copies of **input.inp** and call them **qm_1l.inp**, **qm_2l.inp** and **qm.inp**.
-   * **qm_1l.inp** should have ''PROJECT KCl_1'' and one QM layer. Modify accordingly by looking first at the ''kcl.xyz'' coordinate files.
+   * **qm_1l.inp** should have ''PROJECT KCl_1'' and one QM layer. Modify accordingly the MM_INDEX lines by looking first at the ''kcl.xyz'' coordinate files.
-   * **qm_2l.inp** should have ''PROJECT KCl_2'' and two QM layers. Modify accordingly by looking first at the ''kcl.xyz'' coordinate files.
+   * **qm_2l.inp** should have ''PROJECT KCl_2'' and two QM layers. Modify accordingly the MM_INDEX lines by looking first at the ''kcl.xyz'' coordinate files.
-   * **qm.inp** should have ''PROJECT KCl_QM'' and the full QM treatment. For this, it is sufficient to change ''QMMM'' at the beginning to ''QS''.
+   * **qm.inp** should have ''PROJECT KCl_QM'' and the full QM treatment. For this, it is sufficient to change ''QMMM'' at the beginning to ''QS''. Change also the input coordinates from kcl.xyz to kcl_opt.xyz: these are the already optimized coordinates for the full QM treatment. In this way you will spare time.
 </note>
+===== 2. Task: Run the jobs  =====
+<note important>
+  * Run the jobs by giving the command: ''qsub run -v INP=qm_1l'' and similarly for the other input files.
+  * You will also get cube files for hartree potential and electronic density. They can be examined with vmd.
+  * For each job, a ''*pos*xyz'' optimization file is produced, as well as two PDOS files, one for the species 1 (K), the other for the species 2 (Cl).
+</note>
@@ Line 69: / Line 75: @@
     #but should be treated as parameters in general
     #fit to some physical property
-    &MM_KIND K
-      RADIUS 1.52
-    &END MM_KIND
     &MM_KIND Cl
-      RADIUS 1.67
-    &END MM_KIND
-    #define the model
-    &QM_KIND K
-      MM_INDEX 25..32 41..48
-    &END QM_KIND
-        &MM_KIND Cl
       RADIUS 1.67
     &END MM_KIND