howto:geometry_optimisation
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
howto:geometry_optimisation [2014/02/09 14:59] – geometry_optimisation renamed to howto:geometry_optimisation oschuett | howto:geometry_optimisation [2024/01/15 09:23] (current) – oschuett | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ====== Introduction ====== | + | This page has been moved to: https:// |
- | + | ||
- | This tutorial is designed | + | |
- | of a system (without changing the cell dimensions) using '' | + | |
- | use the relaxation of a water (H\(_2\)O) molecule as an example. | + | |
- | + | ||
- | The example files are contained in {{:geometry_optimisation.tgz|geometry_optimisation.tgz}} that comes with this tutorial. The calculation was carried out with '' | + | |
- | 2.4. | + | |
- | + | ||
- | It should be noted that before running the geometry optimisation, | + | |
- | the reader should have already know how to perform a simple | + | |
- | Kohn-Sham Density Functional Theory energy and force calculation | + | |
- | (this is covered in tutorial [[static_calculation|Calculating Energy and Forces using | + | |
- | QUICKSTEP]]), | + | |
- | grid cutoff for the static energy calculations (this is covered in | + | |
- | tutorial [[converging_cutoff|Converging the CUTOFF and REL_CUTOFF]]). | + | |
- | + | ||
- | ====== Input Files ====== | + | |
- | + | ||
- | The input file for a geometry calculation is shown below: | + | |
- | + | ||
- | <code cp2k> | + | |
- | & | + | |
- | PROJECT H2O | + | |
- | RUN_TYPE GEO_OPT | + | |
- | PRINT_LEVEL LOW | + | |
- | &END GLOBAL | + | |
- | & | + | |
- | METHOD QS | + | |
- | & | + | |
- | &CELL | + | |
- | ABC 12.4138 12.4138 12.4138 | + | |
- | &END CELL | + | |
- | & | + | |
- | O 12.235322 | + | |
- | H 12.415139 | + | |
- | H 11.922476 | + | |
- | &END COORD | + | |
- | &KIND H | + | |
- | BASIS_SET DZVP-GTH-PADE | + | |
- | POTENTIAL GTH-PADE-q1 | + | |
- | &END KIND | + | |
- | &KIND O | + | |
- | BASIS_SET DZVP-GTH-PADE | + | |
- | POTENTIAL GTH-PADE-q6 | + | |
- | &END KIND | + | |
- | &END SUBSYS | + | |
- | &DFT | + | |
- | BASIS_SET_FILE_NAME ./ | + | |
- | POTENTIAL_FILE_NAME ./ | + | |
- | &QS | + | |
- | EPS_DEFAULT 1.0E-7 | + | |
- | &END QS | + | |
- | & | + | |
- | CUTOFF 200 | + | |
- | NGRIDS 4 | + | |
- | REL_CUTOFF 30 | + | |
- | &END MGRID | + | |
- | &SCF | + | |
- | SCF_GUESS ATOMIC | + | |
- | EPS_SCF 1.0E-05 | + | |
- | MAX_SCF 200 | + | |
- | & | + | |
- | ALGORITHM STANDARD | + | |
- | &END DIAGONALIZATION | + | |
- | &MIXING T | + | |
- | ALPHA 0.5 | + | |
- | METHOD PULAY_MIXING | + | |
- | NPULAY 5 | + | |
- | &END MIXING | + | |
- | & | + | |
- | & | + | |
- | &END RESTART | + | |
- | &END PRINT | + | |
- | &END SCF | + | |
- | &XC | + | |
- | & | + | |
- | &END XC_FUNCTIONAL | + | |
- | &END XC | + | |
- | &END DFT | + | |
- | &END FORCE_EVAL | + | |
- | & | + | |
- | & | + | |
- | TYPE MINIMIZATION | + | |
- | MAX_DR | + | |
- | MAX_FORCE 1.0E-03 | + | |
- | RMS_DR | + | |
- | RMS_FORCE 1.0E-03 | + | |
- | MAX_ITER 200 | + | |
- | OPTIMIZER CG | + | |
- | &CG | + | |
- | MAX_STEEP_STEPS | + | |
- | RESTART_LIMIT 9.0E-01 | + | |
- | &END CG | + | |
- | &END GEO_OPT | + | |
- | & | + | |
- | & | + | |
- | COMPONENTS_TO_FIX XYZ | + | |
- | LIST 1 | + | |
- | &END FIXED_ATOMS | + | |
- | &END CONSTRAINT | + | |
- | &END MOTION | + | |
- | </ | + | |
- | + | ||
- | The reader should already be familiar with the [[http:// | + | |
- | [[http:// | + | |
- | must set [[http:// | + | |
- | + | ||
- | <code cp2k> | + | |
- | RUN_TYPE GEO_OPT | + | |
- | </ | + | |
- | + | ||
- | In this example, we note that we have chosen diagonalisation of the | + | |
- | Kohn-Sham Hamiltonian for the evaluation of wavefunctions, | + | |
- | Pulay mixing for the self-consistency loops. 5 histories are used | + | |
- | for Pulay mixing. | + | |
- | + | ||
- | The important section for geometry optimisation settings are | + | |
- | contained in subsection [[http:// | + | |
- | '' | + | |
- | dimensions do not change. Calculations which allows the relaxation | + | |
- | of the cell are covered in a separate tutorial. | + | |
- | + | ||
- | <code cp2k> | + | |
- | & | + | |
- | TYPE MINIMIZATION | + | |
- | MAX_DR | + | |
- | MAX_FORCE 1.0E-03 | + | |
- | RMS_DR | + | |
- | RMS_FORCE 1.0E-03 | + | |
- | MAX_ITER 200 | + | |
- | OPTIMIZER CG | + | |
- | &CG | + | |
- | MAX_STEEP_STEPS | + | |
- | RESTART_LIMIT 9.0E-01 | + | |
- | &END CG | + | |
- | &END GEO_OPT | + | |
- | </ | + | |
- | + | ||
- | The [[http:// | + | |
- | finding the local minima ('' | + | |
- | point transition state ('' | + | |
- | [[http:// | + | |
- | optimised geometry is reached. '' | + | |
- | the tolerance on the maximum and root-mean-square of atomic | + | |
- | displacements from the previous geometry optimisation iteration; | + | |
- | '' | + | |
- | the maximum and root-mean-square of atomic forces. The geometry is | + | |
- | considered to be optimised //only when all four criteria are | + | |
- | satisfied// | + | |
- | geometry optimisation iterations. [[http:// | + | |
- | finding the stationary points; in this example we have chosen the | + | |
- | conjugate gradients ('' | + | |
- | + | ||
- | The [[http:// | + | |
- | algorithm. In this case, we have configured it so that no steepest | + | |
- | descent steps are to be performed before the start of the conjugate | + | |
- | gradients algorithm; and the CG algorithm should be reset (and one | + | |
- | steepest descent step is performed) if the cosine of the angles | + | |
- | between two consecutive searching directions is less than 0.9. | + | |
- | + | ||
- | <code cp2k> | + | |
- | & | + | |
- | & | + | |
- | COMPONENTS_TO_FIX XYZ | + | |
- | LIST 1 | + | |
- | &END FIXED_ATOMS | + | |
- | &END CONSTRAINT | + | |
- | </ | + | |
- | + | ||
- | We can add constraints to atomic movements by using the [[http:// | + | |
- | subsection in '' | + | |
- | particular atoms using the [[http:// | + | |
- | [[http:// | + | |
- | be fixed, and in this case, the atoms will be completely pinned in | + | |
- | all directions ('' | + | |
- | given by the [[http:// | + | |
- | + | ||
- | <code cp2k> | + | |
- | LIST 1 2 3 ... N | + | |
- | </ | + | |
- | + | ||
- | The numbers to the right of '' | + | |
- | and correspond to the order (from top to bottom) of the atoms given | + | |
- | in the [[http:// | + | |
- | example, we have fixed the oxygen atom during geometry optimisation, | + | |
- | so that the water molecule will not move around while its structure | + | |
- | is being relaxed. | + | |
- | ====== Results ====== | + | |
- | + | ||
- | The example is run using the serial version of the '' | + | |
- | + | ||
- | < | + | |
- | cp2k.sopt -o H2O.out H2O.inp & | + | |
- | </ | + | |
- | + | ||
- | After the job has finished, you should obtain the following files: | + | |
- | + | ||
- | * '' | + | |
- | * '' | + | |
- | * '' | + | |
- | * '' | + | |
- | * '' | + | |
- | * '' | + | |
- | + | ||
- | Again, the file '' | + | |
- | job. '' | + | |
- | each geometry optimisation step in the '' | + | |
- | set of atomic coordinates corresponds to the relaxed | + | |
- | structure. '' | + | |
- | '' | + | |
- | molecule. Should the job die for some reason, you can continue the | + | |
- | job using the latest atomic coordinates by using command: | + | |
- | + | ||
- | < | + | |
- | cp2k.sopt -o H2O.out H2O-1.restart & | + | |
- | </ | + | |
- | + | ||
- | You can of course also use '' | + | |
- | an input for further calculations using the relaxed atomic | + | |
- | structures. | + | |
- | + | ||
- | The files '' | + | |
- | atomic coordinates obtained from the previous 1, 2 and 3 geometry | + | |
- | optimisation iterations. '' | + | |
- | '' | + | |
- | + | ||
- | In the main output file '' | + | |
- | optimisation step, we will have the following information: | + | |
- | + | ||
- | < | + | |
- | -------- | + | |
- | | + | |
- | Total Energy | + | |
- | Real energy change | + | |
- | | + | |
- | Used time = | + | |
- | + | ||
- | | + | |
- | Max. step size | + | |
- | Conv. limit for step size = | + | |
- | | + | |
- | RMS step size = | + | |
- | Conv. limit for RMS step | + | |
- | | + | |
- | Max. gradient | + | |
- | Conv. limit for gradients | + | |
- | Conv. for gradients | + | |
- | RMS gradient | + | |
- | Conv. limit for RMS grad. = | + | |
- | Conv. for gradients | + | |
- | --------------------------------------------------- | + | |
- | </ | + | |
- | + | ||
- | The above output segment states that at the end of geometry | + | |
- | optimisation step 1, the total energy of the system is | + | |
- | -17.1643447508 (Ha) and none of the criteria for optimised geometry | + | |
- | has been reached. The iteration therefore will carry on, until all | + | |
- | criteria becomes "'' | + | |
- | + | ||
- | At the end of geometry optimisation, | + | |
- | like: | + | |
- | + | ||
- | < | + | |
- | -------- | + | |
- | | + | |
- | Total Energy | + | |
- | Real energy change | + | |
- | | + | |
- | Used time = | + | |
- | + | ||
- | | + | |
- | Max. step size | + | |
- | Conv. limit for step size = | + | |
- | | + | |
- | RMS step size = | + | |
- | Conv. limit for RMS step | + | |
- | | + | |
- | Max. gradient | + | |
- | Conv. limit for gradients | + | |
- | Conv. in gradients | + | |
- | RMS gradient | + | |
- | Conv. limit for RMS grad. = | + | |
- | Conv. in RMS gradients | + | |
- | --------------------------------------------------- | + | |
- | </ | + | |
- | + | ||
- | which clearly shows all criteria have been satisfied. | + | |
- | + | ||
- | The final Kohn-Sham energies can be obtained at the end of the | + | |
- | output: | + | |
- | + | ||
- | < | + | |
- | ******************************************************************************* | + | |
- | *** GEOMETRY OPTIMIZATION COMPLETED | + | |
- | ******************************************************************************* | + | |
- | + | ||
- | | + | |
- | + | ||
- | Number of electrons: | + | |
- | Number of occupied orbitals: | + | |
- | Number of molecular orbitals: | + | |
- | + | ||
- | Number of orbital functions: | + | |
- | Number of independent orbital functions: | + | |
- | + | ||
- | | + | |
- | + | ||
- | ASPC order: 3 | + | |
- | + | ||
- | B(1) = | + | |
- | B(2) = -3.428571 | + | |
- | B(3) = | + | |
- | B(4) = -0.571429 | + | |
- | B(5) = | + | |
- | + | ||
- | Extrapolation method: ASPC | + | |
- | + | ||
- | + | ||
- | SCF WAVEFUNCTION OPTIMIZATION | + | |
- | + | ||
- | | + | |
- | | + | |
- | 1 Pulay/Diag. 0.50E+00 | + | |
- | 2 Pulay/Diag. 0.50E+00 | + | |
- | + | ||
- | *** SCF run converged in 2 steps *** | + | |
- | + | ||
- | + | ||
- | | + | |
- | Core density on regular grids: | + | |
- | Total charge density on r-space grids: | + | |
- | Total charge density g-space grids: | + | |
- | + | ||
- | | + | |
- | Self energy of the core charge distribution: | + | |
- | Core Hamiltonian energy: | + | |
- | | + | |
- | | + | |
- | + | ||
- | Total energy: | + | |
- | + | ||
- | ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): | + | |
- | </ | + |
howto/geometry_optimisation.1391957942.txt.gz · Last modified: 2020/08/21 10:15 (external edit)