large water system calculation with cp2k
Phil G.
phil... at aol.com
Fri Sep 9 11:27:39 UTC 2016
Dear CP2K group,
before the MD simulation of the interfacial arrangement of water molecules
near the ferroelectric lithium niobate single crystal (here the positive
polar surface site), I had performed the geometry optimization of the
LiNbO3 slab (consisting of 8 unit cells) with fixing all atoms of the lower
unit cells to get reconstructed LiNbO3 surface (Nb-O2 surface termination).
(the comparison between surface reconstruction with only the lowest atom
layers fixed and that with all atoms of lower unit cells fixed shows no
remarkable difference, only small energy difference of about 0.014 a.u.)
For the next step I build a large system consisting of 24 LiNbO3 unit cells
(6x6x2) and 478 water molecules (solvated by VMD package solvate 1.5) in
the volume cell box of size 30.888 x 26.7498 x 100.0 Angstrom^3. Like the
geometry optimization above I set all atoms of the lower unit cells of
LiNbO3 fixed and I want to start the geometry optimization of the large
system (of about 3600 atoms), but short time after submitting the
simulation files I got the error message that the required memory exceeds
the memory size available (of a small part of super computer system at our
institute).
After searching for the alternate way I found some interesting articles
about new linear scaling methods:
a) J. Chem. Theory Comput. 9 (2013), 4421
[http://pubs.acs.org/doi/abs/10.1021/ct400595k]
b) J. Chem. Theory Comput. 8 (2012), 3565
[http://pubs.acs.org/doi/abs/10.1021/ct200897x]
Now I would like to rewrite the input code but because I am beginner and I
don't really know how to write correct codes into the input file for
geometry optimization and then MD simulation (one input file for geom.-opt.
and one for MD sim.) on the basis of the linear scaling SCF method. Is it
possible to write an efficient method for DFT calculation on a part of
super computer system in the order of 10^2 cores?
As additional information of the energies after geometry optimization of
the LiNbO3 slabs an additional file is attached here also.
For a better overview of the input code (this is for geometry optimization
for LiNbO3 slab) and of the large system the files are attached here.
Kind regards,
Phil
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Electronic density on regular grids: -1631.9999999700 0.0000000300
Core density on regular grids: 1631.9999999138 -0.0000000862
Total charge density on r-space grids: -0.0000000561
Total charge density g-space grids: -0.0000000561
Overlap energy of the core charge distribution: 0.00000001896601
Self energy of the core charge distribution: -11259.11652246923404
Core Hamiltonian energy: 2845.48164216265741
Hartree energy: 3920.04473187577923
Exchange-correlation energy: -931.67969460663187
Dispersion energy: -3.07256467191988
Electronic entropic energy: -0.00448116158218
Fermi energy: 0.04252472899742
Total energy: -5428.34688533529243
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -5428.352050368117489
*** BRENT run terminated - exceeded requested execution time: 172800.000 seconds.
*** Execution time now: 172810.448 seconds.
*******************************************************************************
*** BRENT - NUMBER OF ENERGY EVALUATIONS : 1 ***
*******************************************************************************
*** GEO run terminated - exceeded requested execution time: 172800.000 seconds.
*** Execution time now: 172810.454 seconds.
-------------------------------------------------------------------------------
- -
- DBCSR STATISTICS -
- -
-------------------------------------------------------------------------------
COUNTER CPU ACC ACC%
number of processed stacks 388044753 0 0.0
matmuls inhomo. stacks 392765078 0 0.0
matmuls total 17075438864 0 0.0
flops 6 x 24 x 6 11481937920 0 0.0
flops 26 x 24 x 6 49461235200 0 0.0
flops 6 x 24 x 26 49461235200 0 0.0
flops 6 x 24 x 17 89189898336 0 0.0
flops 17 x 24 x 6 89189898336 0 0.0
flops 26 x 24 x 26 210512240640 0 0.0
flops 26 x 24 x 17 391582035936 0 0.0
flops 17 x 24 x 26 391582035936 0 0.0
flops 6 x 6 x 64 579242926080 0 0.0
flops 17 x 24 x 17 669807023040 0 0.0
flops 6 x 32 x 6 857318031360 0 0.0
flops 6 x 6 x 96 1737728778240 0 0.0
flops 6 x 26 x 64 2432820289536 0 0.0
flops 26 x 6 x 64 2442474338304 0 0.0
flops 26 x 32 x 6 3693105561600 0 0.0
flops 6 x 32 x 26 3693105561600 0 0.0
flops 17 x 6 x 64 4391449208832 0 0.0
flops 6 x 17 x 64 4399647071232 0 0.0
flops 6 x 32 x 17 6659512409088 0 0.0
flops 17 x 32 x 6 6659512409088 0 0.0
flops 6 x 26 x 96 7298460868608 0 0.0
flops 26 x 6 x 96 7327423014912 0 0.0
flops 26 x 26 x 64 10625889677312 0 0.0
flops 17 x 6 x 96 13174347626496 0 0.0
flops 6 x 17 x 96 13198941213696 0 0.0
flops 26 x 32 x 26 15718247301120 0 0.0
flops 17 x 26 x 64 19234507918080 0 0.0
flops 26 x 17 x 64 19366021828608 0 0.0
flops 26 x 32 x 17 29238125349888 0 0.0
flops 17 x 32 x 26 29238125349888 0 0.0
flops 26 x 26 x 96 31877669031936 0 0.0
flops 17 x 17 x 64 33332691987840 0 0.0
flops 17 x 32 x 17 50012257720320 0 0.0
flops 17 x 26 x 96 57703523754240 0 0.0
flops 26 x 17 x 96 58098065485824 0 0.0
flops 17 x 17 x 96 99998075963520 0 0.0
flops total 585918323221568 0 0.0
marketing flops 646631550908928
-------------------------------------------------------------------------------
Warning: using a non-square number of MPI ranks might lead to poor performance.
used ranks: 96
suggested : 100 196
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- -
- MESSAGE PASSING PERFORMANCE -
- -
-------------------------------------------------------------------------------
ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]
MP_Group 6 0.000
MP_Bcast 33698 1.067 30001. 947.54
MP_Allreduce 410497 707.285 469. 0.27
MP_Gather 2628 1.430 1920. 3.53
MP_Sync 16945 63.365
MP_Alltoall 943370 12506.668 4261539. 321.45
MP_ISendRecv 9562320 76.272 39456. 4946.63
MP_Wait 14174504 5734.873
MP_comm_split 16940 73.824
MP_ISend 4926060 1676.555 296941. 872.47
MP_IRecv 4898066 56.286 291419. 25359.35
MP_Recv 60984 42.633 1019904. 1458.91
MP_Memory 1697910 8.566
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- -
- T I M I N G -
- -
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.1 0.1 172810.5 172810.5
cp_geo_opt 1 2.0 0.0 0.0 172808.2 172808.2
geoopt_cg 1 3.0 0.0 0.0 172808.1 172808.2
cp_cg_main 1 4.0 0.0 0.2 172808.1 172808.2
cp_eval_at 657 8.4 0.0 0.2 172806.7 172806.8
qs_energies_scf 657 9.9 0.1 0.1 170190.2 170191.5
scf_env_do_scf 657 10.9 0.1 0.4 165744.3 166157.0
scf_env_do_scf_inner_loop 16284 12.0 1.1 4.7 165739.8 166152.2
cg_linmin 97 5.0 0.0 0.0 148550.8 148550.8
linmin_gold 97 6.0 0.0 0.0 148550.8 148550.8
qs_forces 327 8.8 2.2 3.9 93387.0 93387.1
eigensolver 16284 13.0 0.3 0.4 93314.5 93327.3
cp_fm_syevd 16940 14.1 27286.0 87048.8 87025.4 87048.8
cp_fm_syevd_base 16940 15.0 59712.9 85201.0 59712.9 85201.0
cg_mnbrak 97 7.0 0.0 0.0 79419.6 79419.6
cg_eval1d 330 8.0 0.0 0.0 79419.6 79419.6
cg_dbrent 97 7.0 0.0 0.0 69131.2 69131.2
cg_deval1d 230 8.0 0.0 0.0 69130.1 69130.1
rebuild_ks_matrix 16611 13.9 0.1 0.1 41848.0 41910.4
qs_ks_build_kohn_sham_matrix 16611 14.9 4.4 6.7 41847.9 41910.3
qs_ks_update_qs_env 16284 13.0 0.2 0.2 40866.0 40928.7
sum_up_and_integrate 16611 15.9 81.8 87.2 27163.1 27226.0
integrate_v_rspace 16611 16.9 20159.3 21832.4 27081.3 27169.7
qs_rho_update_rho 16941 13.0 0.1 0.2 26126.3 26147.3
calculate_rho_elec 16941 14.0 18098.9 19559.9 26126.2 26147.2
fft_wrap_pw1pw2 350484 17.4 5.3 6.5 15488.9 16204.0
fft_wrap_pw1pw2_400 216276 18.4 1112.6 1250.7 14797.5 15473.3
fft3d_ps 350484 19.4 4861.0 5297.8 12769.9 13948.5
qs_vxc_create 16611 15.9 0.3 0.4 11627.9 11656.3
xc_vxc_pw_create 16611 16.9 197.1 333.1 11627.6 11655.8
rs_pw_transfer 168744 17.4 2.2 2.4 6983.5 8488.9
density_rs2pw 16941 15.0 0.8 0.9 6592.6 8138.8
cp_fm_cholesky_restore 48852 14.0 6673.3 6745.5 6673.3 6745.5
xc_rho_set_and_dset_create 16611 17.9 188.9 199.5 6335.1 6549.8
yz_to_x 100983 20.4 3093.4 5149.4 3093.4 5149.4
x_to_yz 148845 20.4 4603.3 5127.8 4603.3 5127.8
rs_distribute_matrix 33879 16.4 3528.7 5043.4 3560.7 5054.9
rs_pw_transfer_RS2PW_400 17598 16.9 2981.6 4514.0 2981.6 4514.0
potential_pw2rs 16611 17.9 7.3 11.0 4426.1 4456.0
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