exercises:2017_ethz_mmm:benzene_dimer
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— | exercises:2017_ethz_mmm:benzene_dimer [2020/08/21 10:15] (current) – created - external edit 127.0.0.1 | ||
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+ | ====== Binding Energy of the Benzene Dimer ====== | ||
+ | |||
+ | The goal of this exercise is to compute the interaction energy for a π-stacked benzene dimer, with three different methods: | ||
+ | |||
+ | * PBE with no dispersion interaction | ||
+ | * PBE with parametrized dispersion interaction (PBE-DFTD3) | ||
+ | * MP2 (Møller-Plesset perturbation theory) | ||
+ | |||
+ | The formula to compute the interaction energy is: | ||
+ | \[E_\text{interaction}= E_\text{dimer}- 2 E_\text{benzene}\] | ||
+ | |||
+ | <note important> | ||
+ | The equilibrium distance between the $\pi$-stacked benzene rings has to be obtained through geometry optimization for every level of theory separately. Since the cost of MP2 calculations are very hight, we provide you with the readily optimized geometry for this method. For the other two methods (PBE, PBE-DFTD3) this provided geometry has to be **re-optimized**.</ | ||
+ | |||
+ | You will also require energy calculations of the single benzene molecule. You can extract the coordinates of a single benzene ring with VMD or a text editor. Again, the geometry has to be optimized separately for each method. The correct geometry for MP2-benzene can be found at the end of the exercise and, due to time issues, should not be re-optimized. | ||
+ | |||
+ | ===== Questions ===== | ||
+ | * Report interaction energy and equilibrium distance for each method | ||
+ | |||
+ | ===== Required files ===== | ||
+ | |||
+ | ==== DFT-D3 Parameters ==== | ||
+ | |||
+ | {{dftd3.dat.gz| Download here}} | ||
+ | < | ||
+ | < | ||
+ | $ gunzip dftd3.dat.gz | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | ==== Input File ==== | ||
+ | <code - benzene_dimer.inp> | ||
+ | &GLOBAL | ||
+ | PROJECT | ||
+ | RUN_TYPE | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | METHOD | ||
+ | &DFT | ||
+ | |||
+ | !specification of external basis and potential files | ||
+ | BASIS_SET_FILE_NAME | ||
+ | POTENTIAL_FILE_NAME | ||
+ | |||
+ | !section to ensure stable and correct simulations | ||
+ | &MGRID | ||
+ | CUTOFF | ||
+ | &END MGRID | ||
+ | &QS | ||
+ | METHOD GPW | ||
+ | EPS_DEFAULT | ||
+ | EPS_PGF_ORB | ||
+ | &END QS | ||
+ | &SCF | ||
+ | SCF_GUESS ATOMIC | ||
+ | EPS_SCF 1.0E-6 | ||
+ | MAX_SCF 40 | ||
+ | &OT | ||
+ | MINIMIZER | ||
+ | PRECONDITIONER | ||
+ | &END | ||
+ | & | ||
+ | EPS_SCF 1.0E-6 | ||
+ | MAX_SCF 10 | ||
+ | &END | ||
+ | &END SCF | ||
+ | | ||
+ | & | ||
+ | PERIODIC NONE | ||
+ | PSOLVER | ||
+ | &END POISSON | ||
+ | |||
+ | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
+ | !!This is the section for PBE calculations | ||
+ | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
+ | !&XC | ||
+ | ! & | ||
+ | ! & | ||
+ | !&END XC | ||
+ | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
+ | |||
+ | |||
+ | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
+ | !!This is the section for PBE-DFTD3 calculations | ||
+ | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
+ | !&XC | ||
+ | ! & | ||
+ | ! & | ||
+ | ! & | ||
+ | ! | ||
+ | ! & | ||
+ | ! TYPE DFTD3 ! computed with the DFTD3 method | ||
+ | ! REFERENCE_FUNCTIONAL PBE | ||
+ | ! ! that requires the following parameters (in external file, specified here) | ||
+ | ! PARAMETER_FILE_NAME ./ | ||
+ | ! R_CUTOFF 15 ! cutoff raddius for the dispersion interactions | ||
+ | ! & | ||
+ | ! & | ||
+ | !&END XC | ||
+ | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
+ | |||
+ | |||
+ | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
+ | !!This is the section for MP2 calculations | ||
+ | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
+ | ! &XC | ||
+ | ! & | ||
+ | ! &END XC_FUNCTIONAL | ||
+ | ! & | ||
+ | ! | ||
+ | ! & | ||
+ | ! | ||
+ | ! & | ||
+ | ! & | ||
+ | ! | ||
+ | ! & | ||
+ | ! & | ||
+ | ! & | ||
+ | ! | ||
+ | ! & | ||
+ | ! | ||
+ | ! & | ||
+ | ! & | ||
+ | ! & | ||
+ | ! | ||
+ | ! | ||
+ | ! & | ||
+ | ! &END XC | ||
+ | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
+ | |||
+ | |||
+ | &END DFT | ||
+ | | ||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | ABC [angstrom] | ||
+ | PERIODIC NONE ! Non periodic calculation. | ||
+ | &END CELL | ||
+ | | ||
+ | &COORD | ||
+ | ! specification of an external file with coordinates | ||
+ | @INCLUDE ' | ||
+ | &END | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | &END | ||
+ | &END TOPOLOGY | ||
+ | |||
+ | !specification of external basis sets and potentials. The name of the files is given above. | ||
+ | &KIND H | ||
+ | BASIS_SET | ||
+ | RI_AUX_BASIS_SET | ||
+ | POTENTIAL | ||
+ | &END KIND | ||
+ | &KIND C | ||
+ | BASIS_SET | ||
+ | RI_AUX_BASIS_SET | ||
+ | POTENTIAL | ||
+ | &END KIND | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | </ | ||
+ | |||
+ | ==== MP2 optimized Coordinates ==== | ||
+ | <code - benzene_dimer-MP2.xyz> | ||
+ | 24 | ||
+ | |||
+ | H | ||
+ | C | ||
+ | C | ||
+ | H | ||
+ | C | ||
+ | H | ||
+ | C | ||
+ | H | ||
+ | C | ||
+ | H | ||
+ | C | ||
+ | H | ||
+ | H | ||
+ | H | ||
+ | C | ||
+ | C | ||
+ | C | ||
+ | C | ||
+ | H | ||
+ | H 10.1283042427 | ||
+ | C | ||
+ | C | ||
+ | H | ||
+ | H | ||
+ | |||
+ | </ | ||
+ | |||
+ | <code - benzene_single-MP2.xyz> | ||
+ | 12 | ||
+ | |||
+ | H | ||
+ | H | ||
+ | C | ||
+ | C | ||
+ | C | ||
+ | C | ||
+ | H | ||
+ | H | ||
+ | C | ||
+ | C | ||
+ | H | ||
+ | H | ||
+ | |||
+ | |||
+ | |||
+ | </ | ||
+ | ==== Basis Set ==== | ||
+ | <code - BASIS> | ||
+ | # | ||
+ | H cc-TZ | ||
+ | 6 | ||
+ | 1 0 0 3 1 | ||
+ | | ||
+ | 3.0968750876 | ||
+ | 0.9874518162 | ||
+ | 1 0 0 1 1 | ||
+ | 0.3450687533 | ||
+ | 1 0 0 1 1 | ||
+ | 0.1492693554 | ||
+ | 2 1 1 1 1 | ||
+ | 1.4070000000 | ||
+ | 2 1 1 1 1 | ||
+ | 0.3880000000 | ||
+ | 3 2 2 1 1 | ||
+ | 1.0570000000 | ||
+ | # | ||
+ | C cc-TZ | ||
+ | 6 | ||
+ | 2 0 1 3 1 1 | ||
+ | 5.3685662937 | ||
+ | 1.9830691554 | ||
+ | 0.6978346167 | ||
+ | 2 0 1 1 1 1 | ||
+ | 0.2430968816 | ||
+ | 2 0 1 1 1 1 | ||
+ | 0.0812865018 | ||
+ | 3 2 2 1 1 | ||
+ | 1.0970000000 | ||
+ | 3 2 2 1 1 | ||
+ | 0.3180000000 | ||
+ | 4 3 3 1 1 | ||
+ | 0.7610000000 | ||
+ | # | ||
+ | # | ||
+ | | ||
+ | 10 | ||
+ | 1 0 0 1 1 | ||
+ | 8.5115919487 | ||
+ | 1 0 0 1 1 | ||
+ | 1.8744684087 | ||
+ | 1 0 0 1 1 | ||
+ | 0.5632515602 | ||
+ | 1 0 0 1 1 | ||
+ | 0.3698299759 | ||
+ | 1 1 1 1 1 | ||
+ | 2.3711712242 | ||
+ | 1 1 1 1 1 | ||
+ | 1.1794161391 | ||
+ | 1 1 1 1 1 | ||
+ | 0.6050431621 | ||
+ | 1 2 2 1 1 | ||
+ | 1.8092525711 | ||
+ | 1 2 2 1 1 | ||
+ | 1.1433220615 | ||
+ | 1 3 3 1 1 | ||
+ | 1.8065804513 | ||
+ | # | ||
+ | | ||
+ | 20 | ||
+ | 1 0 0 1 1 | ||
+ | | ||
+ | 1 0 0 1 1 | ||
+ | 7.1315246807 | ||
+ | 1 0 0 1 1 | ||
+ | 3.5380450775 | ||
+ | 1 0 0 1 1 | ||
+ | 1.2333453175 | ||
+ | 1 0 0 1 1 | ||
+ | 0.2821517353 | ||
+ | 1 0 0 1 1 | ||
+ | 0.3468258230 | ||
+ | 1 1 1 1 1 | ||
+ | 7.2975063903 | ||
+ | 1 1 1 1 1 | ||
+ | 3.7896065213 | ||
+ | 1 1 1 1 1 | ||
+ | 1.0633834831 | ||
+ | 1 1 1 1 1 | ||
+ | 0.2356430320 | ||
+ | 1 1 1 1 1 | ||
+ | 0.5078423493 | ||
+ | 1 2 2 1 1 | ||
+ | 9.9000557486 | ||
+ | 1 2 2 1 1 | ||
+ | 2.3408375066 | ||
+ | 1 2 2 1 1 | ||
+ | 1.5195338451 | ||
+ | 1 2 2 1 1 | ||
+ | 0.5788522388 | ||
+ | 1 2 2 1 1 | ||
+ | 0.3721345858 | ||
+ | 1 3 3 1 1 | ||
+ | 1.9332589728 | ||
+ | 1 3 3 1 1 | ||
+ | 1.1560553410 | ||
+ | 1 3 3 1 1 | ||
+ | 0.4987261239 | ||
+ | 1 4 4 1 1 | ||
+ | 1.2175667359 | ||
+ | # | ||
+ | |||
+ | </ | ||
+ | |||
+ | ==== Pseudo-Potentials ==== | ||
+ | <code - POTENTIALS> | ||
+ | # | ||
+ | H GTH-HF-q1 | ||
+ | 1 0 0 0 | ||
+ | 0.196680577426 | ||
+ | 0 | ||
+ | # | ||
+ | C GTH-HF-q4 | ||
+ | 2 2 0 0 | ||
+ | 0.315416975333 | ||
+ | 1 | ||
+ | 0.301022709314 | ||
+ | </ | ||