smeagol_usage
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| After finishing H-chain tutorial (wich computational time ~20 second is short enought for learning purpose ), you can approach to much more computationaly demanding task of computation of transmission coefficient for molecule between gold electrodes. The computationl time of this example would be arround 1 day, but can by shotened by setting shorter and less densly sampled energy region in smeagol optional by | After finishing H-chain tutorial (wich computational time ~20 second is short enought for learning purpose ), you can approach to much more computationaly demanding task of computation of transmission coefficient for molecule between gold electrodes. The computationl time of this example would be arround 1 day, but can by shotened by setting shorter and less densly sampled energy region in smeagol optional by | ||
| - | </code> | + | <code> |
| 1000 NeneT | 1000 NeneT | ||
| -20.0 TEnergI | -20.0 TEnergI | ||
| Line 398: | Line 398: | ||
| If you are going to run it interactively outside the PBS front system, remove the line | If you are going to run it interactively outside the PBS front system, remove the line | ||
| - | </code> | + | <code> |
| cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
| </code> | </code> | ||
| Line 481: | Line 481: | ||
| </code> | </code> | ||
| + | We recommand you to follow the script order line by line, watching on the description of manual succesive executing of each steps which is described in H-chain tutorial section above. | ||
| + | We also recommand you to examine imput files like | ||
| + | |||
| + | <code> | ||
| + | Au100-LEADS-1k/fireball.in-scf | ||
| + | Au100-LEADS-1k/fireball.in-leads | ||
| + | Au100-LEADS-1k/answer.bas | ||
| + | AuBTB-1k/fireball.in-scf | ||
| + | AuBTB-1k/fireball.in-smeagol | ||
| + | AuBTB-1k/smeagol.optional | ||
| + | AuBTB-1k/answer.bas | ||
| + | </code> | ||
| + | |||
| + | which determine the computation. | ||
| + | |||
| + | We provide this script as a template for furter modification for specific computations you are going to do. | ||
| + | |||
| + | finally, after the computation is successfully finished, you should plot the outputfile with transmission coefficient | ||
| + | |||
| + | AuBTB-1k/**smeagol.TRC** | ||
| + | |||
| + | the plot for our basis set looks like this, but it can differ slightly with basiset | ||
| + | |||
| + | Transmussion coefficient for Dithiobenzene between gold 100 electrodes with 1 k-point. Basis used was | ||
| + | H_s3.8 C_s4.0_p4.5_d5.40 S_s4.2_p4.7_d5.5 Au_s5.0_p5.6_d4.7 | ||
| - | | + | {{:smeagol:au-dtb-trcoef.png| Transmussion coefficient for Dithiobenzene between gold 100 electrodes with 1 k-point. Basis used was |
| + | H_s3.8 C_s4.0_p4.5_d5.40 S_s4.2_p4.7_d5.5 Au_s5.0_p5.6_d4.7 | ||
| + | }} | ||
smeagol_usage.1335953818.txt.gz · Last modified: 2012/05/02 12:16 (external edit)
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