exercises:2016_uzh_cmest:path_optimization_neb
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exercises:2016_uzh_cmest:path_optimization_neb [2016/10/20 18:24] – [Visualize the trajectory] tmueller | exercises:2016_uzh_cmest:path_optimization_neb [2016/10/20 19:39] – [Vibrational analysis] tmueller | ||
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This may take a couple of hours. Continue with the exercises below once the calculation finishes. | This may take a couple of hours. Continue with the exercises below once the calculation finishes. | ||
- | ====== Visualize the trajectory ====== | + | ====== Visualize the trajectory |
When you take another peek at the input file you used to run the calculation, | When you take another peek at the input file you used to run the calculation, | ||
- | You should therefore find 8 files named '' | + | You should therefore find 8 files named '' |
< | < | ||
Line 215: | Line 215: | ||
</ | </ | ||
+ | Since CP2K writes the energy in the comment line of each frame in the XYZ file (see tip above), we can extract the energy values for each bead directly from the newly generated '' | ||
+ | |||
+ | < | ||
+ | awk '/E =/ {i=i+1; printf "%s %16.8f\n", | ||
+ | </ | ||
+ | |||
+ | Create a plot for this energy curve. | ||
+ | |||
+ | ====== Vibrational analysis ====== | ||
+ | |||
+ | To verify whether the point at the highest energy is actually a transition state, we will be doing a vibrational analysis. | ||
+ | |||
+ | First identify the bead with the highest energy (see exercise above) and create a new XYZ file named '' | ||
+ | |||
+ | Use the following input file: | ||
+ | |||
+ | <code - ethane_TS_va.inp> | ||
+ | &GLOBAL | ||
+ | PROJECT ethane_TS_va | ||
+ | RUN_TYPE NORMAL_MODES | ||
+ | PRINT_LEVEL MEDIUM | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | METHOD Quickstep | ||
+ | &DFT | ||
+ | BASIS_SET_FILE_NAME | ||
+ | POTENTIAL_FILE_NAME | ||
+ | |||
+ | & | ||
+ | PERIODIC XYZ | ||
+ | &END POISSON | ||
+ | & | ||
+ | SCF_GUESS ATOMIC | ||
+ | EPS_SCF 1.0E-7 | ||
+ | MAX_SCF 300 | ||
+ | &END SCF | ||
+ | & | ||
+ | & | ||
+ | &END XC_FUNCTIONAL | ||
+ | &END XC | ||
+ | &END DFT | ||
+ | |||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | ABC 12. 12. 12. | ||
+ | PERIODIC XYZ | ||
+ | &END CELL | ||
+ | & | ||
+ | & | ||
+ | &END | ||
+ | COORD_FILE_FORMAT xyz | ||
+ | COORD_FILE_NAME | ||
+ | &END | ||
+ | &KIND H | ||
+ | ELEMENT H | ||
+ | BASIS_SET DZVP-MOLOPT-GTH | ||
+ | POTENTIAL GTH-PBE-q1 | ||
+ | &END KIND | ||
+ | &KIND C | ||
+ | ELEMENT C | ||
+ | BASIS_SET DZVP-MOLOPT-GTH | ||
+ | POTENTIAL GTH-PBE-q4 | ||
+ | &END KIND | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | & | ||
+ | NPROC_REP 1 | ||
+ | DX 0.01 | ||
+ | FULLY_PERIODIC | ||
+ | |||
+ | & | ||
+ | &END | ||
+ | & | ||
+ | &END | ||
+ | & | ||
+ | &EACH | ||
+ | REPLICA_EVAL 1 | ||
+ | &END | ||
+ | &END | ||
+ | &END | ||
+ | &END | ||
+ | </ |
exercises/2016_uzh_cmest/path_optimization_neb.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1