# Open SourceMolecular Dynamics

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exercises:2017_ethz_mmm:ls_scf

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 — exercises:2017_ethz_mmm:ls_scf [2017/02/22 10:01] (current) Line 1: Line 1: + ====== Linear Scaling Self Consistent Field Methods ====== + + In this exercise we will compare linear scaling SCF [[doi>​10.1021/​ct200897x]] with normal SCF methods. We will run simulations on a 2D polymer system containing up to 2400 atoms. The 2D polymer system is described in more detail in this recent publication [[doi>​10.1002/​adma.201304705]]. To make this exercise computationally feasible, will us the efficient Density Functional based Tight Binding (DFTB) method [[doi>​10.1103/​PhysRevB.58.7260]]. It requires only a minima basis, but delivers nevertheless reasonable results due to an empirical correction term called //repulsion potential//​. + + + You should run these calculations on 4 nodes with ''​bsub -n 4''​. ​ + ​ + + ===== 1. Task: Scaling Behavior ===== + Calculate the energy of the 2D-polymer for three different system sizes, by using ''​NREP=1'',​ ''​2'',​ and ''​3''​. Perform each calculations with the linear scaling and the normal SCF method. Plot the time required for the last SCF cycle of each calculation vs. the system size. Extrapolate the time required for an SCF cycle of a system containing 10x10 unit cells. + + The number of seconds required of each SCF cycle is printed as part of the regular output. ​ + + For the normal SCF it's the 4th column in the following table: + <​code>​ + Step     ​Update method ​     Time    Convergence ​        Total energy ​   Change + ------------------------------------------------------------------------------ + 1 P_Mix/Diag. 0.40E+00 ​   3.7     ​0.15459443 ​     -957.7477897329 -9.58E+02 + 2 P_Mix/Diag. 0.40E+00 ​   5.6     ​0.06222675 ​     -957.8604155443 -1.13E-01 + 3 DIIS/​Diag. ​ 0.11E-01 ​   5.6     ​0.02839814 ​     -957.9170257078 -5.66E-02 + 4 DIIS/​Diag. ​ 0.11E-01 ​   5.6     ​0.02966521 ​     -957.9973636669 -8.03E-02 + 5 DIIS/​Diag. ​ 0.22E-01 ​   5.6     ​0.01746285 ​     -957.9863069368 ​ 1.11E-02 + ​ + + For the linear scaling SCF it's the last column in lines like these: + <​code>​ + ​SCF ​    ​1 ​     -957.747786827 ​     -957.747786827 ​  ​12.559000 + ... + ​SCF ​    ​2 ​     -957.970635063 ​       -0.222848235 ​  ​11.204000 + ... + ​SCF ​    ​3 ​     -957.994490590 ​       -0.023855528 ​  ​11.233000 + ​ + + ===== 2. Task: Filter Threshold ===== + Calculate the energy of the single unit-cell with the linear scaling method at different filter thresholds, by changing ''​EPS_FILTER''​. Plot the time required for the calculation and the obtained total energy vs the threshold. How does this compare with the total energy obtained from the normal SCF method? + + ===== Input File ===== + ​ + ! Number of unit cell replications,​ increase this to create a large polymer. + @SET NREPX 1 + @SET NREPY 1 + + &GLOBAL + PROJECT 2d_polymer + RUN_TYPE ENERGY + &END GLOBAL + + &​FORCE_EVAL + &DFT + ! linear scaling SCF + &LS_SCF + ! TRS4, does not need an estimate for the chemical potential + PURIFICATION_METHOD TRS4 + ! threshold used to determine sparsity and thus speed and accuracy + EPS_FILTER 1E-5  ​ + ! convergence for the SCF + EPS_SCF ​   1E-15 + MAX_SCF 30 + ! chemical potential, an energy from within in the HOMO-LUMO gap + MU         ​-0.15 ​ + S_PRECONDITIONER ATOMIC + &END + + ! traditional SCF, diagonalization by default + &SCF + &END + + &QS + LS_SCF ​ ! Turns on linear scaling DFT. Comment this line to run with standard SCF. + + ! ============================================================================================= + ! === Description of Hamiltonian (Density Functional Tight Binding + Smooth Particle Meshed Ewald) === + METHOD DFTB + &DFTB + HB_SR_GAMMA ​ + SELF_CONSISTENT ​   T + DO_EWALD ​          T + DISPERSION ​        T + &​PARAMETER + PARAM_FILE_PATH ​ ./​dftb_params/​scc + PARAM_FILE_NAME ​ scc_parameter + UFF_FORCE_FIELD ​ uff_table + &END PARAMETER + &END DFTB + &END QS + + &​POISSON + &EWALD + ​EWALD_TYPE SPME + ! scale the number of points with the system size, roughly 1pt/A. + GMAX 40*${NREPX} 40*${NREPY} 40 + ​O_SPLINE 5 + &END EWALD + &END POISSON + ! ==============================End of Hamiltonian Description ================================ + ! ============================================================================================= + &END DFT + + ​ + &SUBSYS + &CELL + ! a 2D system, z-direction is non-periodic + ABC 23.577999 40.8383 30 + MULTIPLE_UNIT_CELL ${NREPX}${NREPY} 1 + &END CELL + &​TOPOLOGY + MULTIPLE_UNIT_CELL ${NREPX}${NREPY} 1 + &END + &COORD + @INCLUDE '​2d_polymer.coord' ​ + &END COORD + &END SUBSYS + &END FORCE_EVAL + + ​ + + ===== Additional Files ===== + Download the following files into your project directory: + * {{dftb_params.tgz|}} + * {{2d_polymer.coord.gz|}} + + You can unpack them with the following commands: + <​code>​ + $tar -xvzf dftb_params.tgz +$ gunzip 2d_polymer.coord.gz +