CP2K Open Source Molecular Dynamics

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howto:running_qe_computation [2019/08/13 12:50] – mtaillefumierhowto:running_qe_computation [2019/08/20 06:17] – [Molecular dynamics] mtaillefumier
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 </code> </code>
  
-===== Cell relaxation ===== +===== Molecular dynamics =====
- +
-Quantum expresso supports many types of calculations that cp2k supports natively. For instance, it is possible to do cell relaxation in cp2k with the sirius backend, something that QE can do as well. The following QE input file +
-<code> +
-&control +
-calculation='scf', +
-restart_mode='from_scratch', +
-pseudo_dir = './', +
-outdir='./', +
-prefix = 'scf_', +
-tstress = false, +
-tprnfor = false, +
-verbosity = 'high', +
-wf_collect = false +
-/ +
-&system +
-ibrav=0, celldm(1)=1, ecutwfc=30, ecutrho = 300, +
-occupations = 'smearing', smearing = 'gauss', degauss = 0.001, +
-nat=8 ntyp=2 +
-/ +
-&electrons +
-conv_thr =  1.0d-11, +
-mixing_beta = 0.7, +
-electron_maxstep = 100 +
-/ +
-&IONS +
-ion_dynamics='bfgs', +
-/ +
-&CELL +
-cell_dynamics='bfgs', +
-/ +
-ATOMIC_SPECIES +
-Ge 0.0 ge_lda_v1.uspp.F.UPF +
-Si 0.0 si_lda_v1.uspp.F.UPF +
-CELL_PARAMETERS +
-       10.26253566        0.00000000        0.00000000 +
-        0.00000000       10.26253566        0.00000000 +
-        0.00000000        0.00000000       10.26253566 +
-ATOMIC_POSITIONS (crystal) +
-Ge          0.00000000         0.00000000         0.00000000 +
-Si          0.00000000         0.50000000         0.50000000 +
-Si          0.50000000         0.00000000         0.50000000 +
-Si          0.50000000         0.50000000         0.00000000 +
-Si          0.75000000         0.75000000         0.25000000 +
-Si          0.75000000         0.25000000         0.75000000 +
-Si          0.25000000         0.75000000         0.75000000 +
-Si          0.25000000         0.25000000         0.25000000 +
-K_POINTS (automatic) +
-2 2 2  0 0 0 +
-</code> +
- +
-describes the computation of the cell relaxation for Si7Ge for instance. The cp2k input file for the sirius backend will look like+
  
 +Quantum expresso supports many types of calculations that cp2k supports natively. For instance, it is possible to do molecular dynamics in cp2k with the sirius backend, something that QE can do as well. To do this, we can start from the previous cp2k input file for Si7Ge and add a small section for setting the parameters relevant for the molecular dynamics. The ''symmetry'' parameter **should be off** during molecular dynamics configurations. 
 + 
 <code> <code>
 &FORCE_EVAL &FORCE_EVAL
Line 519: Line 470:
        ELECTRONIC_STRUCTURE_METHOD  pseudopotential        ELECTRONIC_STRUCTURE_METHOD  pseudopotential
        SMEARING_WIDTH 0.01        SMEARING_WIDTH 0.01
-       USE_SYMMETRY true+       USE_SYMMETRY false
        NUM_MAG_DIMS 0        NUM_MAG_DIMS 0
        GK_CUTOFF 6.0        GK_CUTOFF 6.0
Line 581: Line 532:
       OPTIMIZER LBFGS       OPTIMIZER LBFGS
    &END GEO_OPT    &END GEO_OPT
 +   &MD
 +      ENSEMBLE NVE
 +      TIMESTEP 0.1 
 +      STEPS 125
 +      TEMPERATURE 300.0
 +   &END MD
 &END MOTION &END MOTION
 &GLOBAL &GLOBAL
   PROJECT Si7Ge   PROJECT Si7Ge
   PRINT_LEVEL MEDIUM   PRINT_LEVEL MEDIUM
-  RUN_TYPE GEO_OPT+  RUN_TYPE MD
 &END GLOBAL &END GLOBAL
 </code> </code>
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 </code> </code>
  
-you should obtain a file ''Si7Ge-pos-1.xyz'' that contains the positions of the atoms after relaxation. +you should obtain a file ''Si7Ge-pos-1.xyz'' that contains the positions of the atoms and ''Si7Ge-1.ener'' that contains the different energies and temperature as a function of time. The calculations are done in the micro-canonical ensemble which means that the total energy (the sum of the potential which is the total energy given by SIRIUS and the kinetic energy) is conserved during the integration process. It is possible to compare these results with QE, but instead of doing the molecular dynamics with QE, we take the positions of the atoms at each time step and compute the potential energy for this atom position with QE.  
 + 
 +{{:howto:qe-cp2k-sirius.png|}}<imgcaption image1|>Computation of the potential energy with cp2k/sirius and quantum expresso</imgcaption> 
howto/running_qe_computation.txt · Last modified: 2021/12/08 10:18 by mtaillefumier