exercises:2016_uzh_cmest:geometry_optimization
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exercises:2016_uzh_cmest:geometry_optimization [2016/10/12 08:54] – [1. Step: Setting up a calculation] tmueller | exercises:2016_uzh_cmest:geometry_optimization [2016/10/20 15:53] – [1. Step: Single point energy calculation with separate coordinate file] tmueller | ||
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MAX_SCF 300 | MAX_SCF 300 | ||
&END SCF | &END SCF | ||
- | & | + | & |
& | & | ||
&END XC_FUNCTIONAL | &END XC_FUNCTIONAL | ||
Line 98: | Line 98: | ||
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): | ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): | ||
</ | </ | ||
+ | |||
+ | You can also directly open a XYZ file in VMD: | ||
+ | |||
+ | < | ||
+ | $ vmd ethane1.xyz | ||
+ | </ | ||
+ | |||
+ | |||
+ | ===== 2. Step: Optimizing the geometry ===== | ||
+ | |||
+ | The only thing you have to change to get a geometry optimization instead of a single point energy calculation is the following: | ||
+ | |||
+ | <code - ethane1_opt.inp > | ||
+ | &GLOBAL | ||
+ | PROJECT ethane1_opt | ||
+ | RUN_TYPE GEO_OPT | ||
+ | PRINT_LEVEL MEDIUM | ||
+ | &END GLOBAL | ||
+ | [...] | ||
+ | </ | ||
+ | |||
+ | Note the different '' | ||
+ | |||
+ | After running this, you will have the following files: | ||
+ | |||
+ | < | ||
+ | $ ls ethane1_opt* | ||
+ | ethane1_opt-1.restart | ||
+ | ethane1_opt-1.restart.bak-1 | ||
+ | ethane1_opt-1.restart.bak-2 | ||
+ | </ | ||
+ | |||
+ | Take a look at the output file, especially the following section (repeated the number of cycles it took to reach convergence): | ||
+ | |||
+ | < | ||
+ | | ||
+ | Optimization Method | ||
+ | Total Energy | ||
+ | Real energy change | ||
+ | Predicted change in energy = -0.1885432833 | ||
+ | Scaling factor | ||
+ | Step size = | ||
+ | Trust radius | ||
+ | Decrease in energy | ||
+ | Used time = | ||
+ | |||
+ | Convergence check : | ||
+ | Max. step size | ||
+ | Conv. limit for step size = | ||
+ | Convergence in step size | ||
+ | RMS step size = | ||
+ | Conv. limit for RMS step | ||
+ | Convergence in RMS step = NO | ||
+ | Max. gradient | ||
+ | Conv. limit for gradients | ||
+ | Conv. for gradients | ||
+ | RMS gradient | ||
+ | Conv. limit for RMS grad. = | ||
+ | Conv. for gradients | ||
+ | | ||
+ | </ | ||
+ | |||
+ | For each convergence criterion you see the value which is used to check whether convergence is reached and convergence is only reached if all of them are satisfied simultaneously. | ||
+ | |||
+ | |||
+ | From the output file, extract the following data and generate 3 plots with the values vs the iteration number: | ||
+ | |||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | |||
+ | |||
+ | ===== 3. Step: Optimizing the geometry with an alternative geometry ===== | ||
+ | |||
+ | Now change the used coordinate file to '' | ||
+ | |||
+ | * Compare the final energy reached for both structures and the total number of optimization steps required | ||
+ | * Open the two output XYZ files (''< | ||
+ | * Which one is likely to be more stable and why? | ||
+ | |||
+ | |||
+ | ===== 4. Step: Visualize the geometry optimization ===== | ||
+ | |||
+ | Append the following section to your input file (does not matter for which structure) and run the simulation again. | ||
+ | |||
+ | < | ||
+ | &MOTION | ||
+ | |||
+ | & | ||
+ | LOG_PRINT_KEY T | ||
+ | FORMAT XYZ | ||
+ | ADD_LAST NUMERIC | ||
+ | &END TRAJECTORY | ||
+ | &END PRINT | ||
+ | &END MOTION | ||
+ | </ | ||
+ | |||
+ | If you check the output XYZ file now (''< | ||
+ | |||
+ | < | ||
+ | [...] | ||
+ | | ||
+ | [...] | ||
+ | </ | ||
+ | |||
+ | Open this new XYZ file again with VMD, choose an appropriate drawing method (// | ||
+ | |||
+ | {{ vmd_play.png |}} | ||
+ |
exercises/2016_uzh_cmest/geometry_optimization.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1