exercises:2015_pitt:aimd
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exercises:2015_pitt:aimd [2015/03/03 11:58] – vondele | exercises:2015_pitt:aimd [2015/03/03 12:10] – [g(r)] vondele | ||
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The second goal to understand the produced .ener file and do some basic analysis of the trajectory with VMD. | The second goal to understand the produced .ener file and do some basic analysis of the trajectory with VMD. | ||
- | ====== AIMD of water ====== | + | ====== AIMD of bulk liquid |
< | < | ||
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How many neighbors does a given water molecule have on average (3, 3-4, 4, 4-5, 5)? | How many neighbors does a given water molecule have on average (3, 3-4, 4, 4-5, 5)? | ||
- | === IR spectrum === | + | ==== IR spectrum |
Based on the time evolution of the dipole of the system, the IR spectral density can be estimated. To estimate the dipole from AIMD, wannier centers need to be computed. This is out of scope of the current tutorial (TODO: find link). We employ a simple approximation, | Based on the time evolution of the dipole of the system, the IR spectral density can be estimated. To estimate the dipole from AIMD, wannier centers need to be computed. This is out of scope of the current tutorial (TODO: find link). We employ a simple approximation, | ||
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< | < | ||
+ | ====== AIMD of simle ions in water solution ====== | ||
===== 4th task: simple ions in solution ===== | ===== 4th task: simple ions in solution ===== | ||
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The easiest way to do so is to replace one or more water molecules (depending on the size of the ion) by the ion in question. Obviously, the configuration produced in this way is far from equilibrium, | The easiest way to do so is to replace one or more water molecules (depending on the size of the ion) by the ion in question. Obviously, the configuration produced in this way is far from equilibrium, | ||
- | Entertaining is to turn one H2O in H+, do you see Eigen and Zundel states and [[wp> | + | Entertaining is to turn one H2O into H+, do you see Eigen and Zundel states and [[wp> |
====== Required files ====== | ====== Required files ====== | ||
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H -4.1388543582 | H -4.1388543582 | ||
H -4.3955669691 | H -4.3955669691 | ||
+ | </ | ||
+ | The following file should be the result of your edits to '' | ||
+ | <code - water_cheating.inp> | ||
+ | &GLOBAL | ||
+ | ! the project name is made part of most output files... useful to keep order | ||
+ | PROJECT WATER | ||
+ | ! various runtypes (energy, geo_opt, etc.) available. | ||
+ | RUN_TYPE MD | ||
+ | ! limit the runs to 5min | ||
+ | WALLTIME 1800 | ||
+ | ! reduce the amount of IO | ||
+ | IOLEVEL | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | ! the electronic structure part of CP2K is named Quickstep | ||
+ | METHOD Quickstep | ||
+ | &DFT | ||
+ | ! basis sets and pseudopotential files can be found in cp2k/data | ||
+ | BASIS_SET_FILE_NAME HFX_BASIS | ||
+ | POTENTIAL_FILE_NAME GTH_POTENTIALS | ||
+ | |||
+ | ! Charge and multiplicity | ||
+ | CHARGE 0 | ||
+ | MULTIPLICITY 1 | ||
+ | |||
+ | &MGRID | ||
+ | ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect. | ||
+ | ! certain calculations (e.g. geometry optimization, | ||
+ | ! NPT and cell optimizations, | ||
+ | | ||
+ | &END | ||
+ | |||
+ | &QS | ||
+ | ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme). | ||
+ | | ||
+ | ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron, | ||
+ | ! sets reasonable values for all other thresholds. | ||
+ | | ||
+ | ! used for MD, the method used to generate the initial guess. | ||
+ | | ||
+ | &END | ||
+ | |||
+ | & | ||
+ | | ||
+ | &END | ||
+ | |||
+ | |||
+ | ! at the end of the SCF procedure generate cube files of the density | ||
+ | & | ||
+ | & | ||
+ | ! compute eigenvalues and homo-lumo gap each 10nd MD step | ||
+ | & | ||
+ | NLUMO 4 | ||
+ | NHOMO 4 | ||
+ | WRITE_CUBE .FALSE. | ||
+ | &EACH | ||
+ | MD 10 | ||
+ | &END | ||
+ | & | ||
+ | &END | ||
+ | |||
+ | ! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems. | ||
+ | & | ||
+ | SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation | ||
+ | MAX_SCF 30 | ||
+ | EPS_SCF 1.0E-6 ! accuracy of the SCF procedure typically 1.0E-6 - 1.0E-7 | ||
+ | &OT | ||
+ | ! an accurate preconditioner suitable also for larger systems | ||
+ | PRECONDITIONER FULL_SINGLE_INVERSE | ||
+ | ! the most robust choice (DIIS might sometimes be faster, but not as stable). | ||
+ | MINIMIZER DIIS | ||
+ | &END OT | ||
+ | & | ||
+ | MAX_SCF 10 | ||
+ | EPS_SCF 1.0E-6 ! must match the above | ||
+ | &END | ||
+ | ! do not store the wfn during MD | ||
+ | |||
+ | & | ||
+ | &END | ||
+ | &END | ||
+ | &END SCF | ||
+ | |||
+ | ! specify the exchange and correlation treatment | ||
+ | &XC | ||
+ | ! use a PBE functional | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | &END XC_FUNCTIONAL | ||
+ | ! adding Grimme' | ||
+ | & | ||
+ | | ||
+ | & | ||
+ | PARAMETER_FILE_NAME dftd3.dat | ||
+ | TYPE DFTD3 | ||
+ | REFERENCE_FUNCTIONAL PBE | ||
+ | R_CUTOFF [angstrom] 16 | ||
+ | & | ||
+ | &END VDW_POTENTIAL | ||
+ | &END XC | ||
+ | &END DFT | ||
+ | |||
+ | ! description of the system | ||
+ | &SUBSYS | ||
+ | & | ||
+ | ! unit cells that are orthorhombic are more efficient with CP2K | ||
+ | ABC [angstrom] 12.42 12.42 12.42 | ||
+ | &END CELL | ||
+ | |||
+ | ! atom coordinates can be in the &COORD section, | ||
+ | ! or provided as an external file. | ||
+ | & | ||
+ | COORD_FILE_NAME water.xyz | ||
+ | COORD_FILE_FORMAT XYZ | ||
+ | &END | ||
+ | |||
+ | ! MOLOPT basis sets are fairly costly, | ||
+ | ! but in the ' | ||
+ | ! their contracted nature makes them suitable | ||
+ | ! for condensed and gas phase systems alike. | ||
+ | &KIND H | ||
+ | BASIS_SET DZVP-GTH | ||
+ | POTENTIAL GTH-PBE-q1 | ||
+ | &END KIND | ||
+ | &KIND O | ||
+ | BASIS_SET DZVP-GTH | ||
+ | POTENTIAL GTH-PBE-q6 | ||
+ | &END KIND | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | ! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section | ||
+ | &MOTION | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | STEPS 1000 | ||
+ | # GLE thermostat as generated at http:// | ||
+ | # GLE provides an effective NVT sampling. | ||
+ | & | ||
+ | | ||
+ | TYPE GLE | ||
+ | & | ||
+ | NDIM 5 | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | |||
+ | & | ||
+ | & | ||
+ | MD 1 | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | MD 500 | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | & | ||
+ | MD 1 | ||
+ | & | ||
+ | & | ||
+ | &END PRINT | ||
+ | &END | ||
+ | & | ||
+ | RESTART_FILE_NAME WATER-1.restart | ||
+ | &END | ||
</ | </ | ||
exercises/2015_pitt/aimd.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1