[CP2K-user] [CP2K:14060] Force calculation in CELL_OPT vs MD
mar...@gmail.com
martin.... at gmail.com
Fri Oct 16 07:54:58 UTC 2020
Hello,
Below are the inputs and timings for the cell opt and 20 subsequent md
steps:
*CELL_OPT:*
&GLOBAL
PROJECT uio66-half
RUN_TYPE CELL_OPT
PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
METHOD QS
&SUBSYS
&CELL
ABC 14.8 14.8 20.910
ALPHA_BETA_GAMMA 90 90 90
&END CELL
&TOPOLOGY
COORD_FILE_FORMAT CIF
COORD_FILE_NAME uio66-pristine-half-cell.cif
&END TOPOLOGY
&KIND O
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&KIND Zr
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q12
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&END SUBSYS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
&QS
EPS_DEFAULT 1.0E-12
&END QS
&MGRID
CUTOFF 600
NGRIDS 5
REL_CUTOFF 50
&END MGRID
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-08
MAX_SCF 30
&OT
MINIMIZER DIIS
PRECONDITIONER FULL_KINETIC
LINESEARCH 2PNT
&END OT
&OUTER_SCF
EPS_SCF 1.0E-08
MAX_SCF 25
&END OUTER_SCF
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
CALCULATE_C9_TERM TRUE
PARAMETER_FILE_NAME dftd3.dat
REFERENCE_FUNCTIONAL PBE
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&END DFT
STRESS_TENSOR ANALYTICAL
&END FORCE_EVAL
&MOTION
&CELL_OPT
KEEP_ANGLES TRUE
TYPE DIRECT_CELL_OPT
MAX_DR 4.5E-04
MAX_FORCE 1.0E-04
RMS_DR 4.5E-04
RMS_FORCE 4.5E-04
MAX_ITER 400
OPTIMIZER BFGS
&END CELL_OPT
&END MOTION
*MD*
&GLOBAL
PRINT_LEVEL LOW
PROJECT_NAME uio66-defect-md
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 20
TIMESTEP 4.9999999999999989E-01
STEP_START_VAL 20
TIME_START_VAL 1.0000000000000002E+01
ECONS_START_VAL -2.2805855491897287E+03
TEMPERATURE 3.0000000000000000E+02
&THERMOSTAT
TYPE CSVR
&CSVR
TIMECON 9.9999999999999978E-01
&THERMOSTAT_ENERGY
-3.1503507886676752E-01
&END THERMOSTAT_ENERGY
&RNG_INIT
Wiener process for Thermostat # 1 1 F T F
-5.2769235486593846E-01 1600409560.0 760341491.0
3744745813.0 3560625215.0 548769459.0
3217800586.0 12345.0 12345.0
12345.0 12345.0 12345.0
12345.0 12345.0 12345.0
12345.0 12345.0 12345.0 12345.0
&END RNG_INIT
&END CSVR
&END THERMOSTAT
&AVERAGES T
&RESTART_AVERAGES
ITIMES_START 1
AVECPU 9.3657589755114145E+01
AVEHUGONIOT 0.0000000000000000E+00
AVETEMP_BARO 0.0000000000000000E+00
AVEPOT -2.1740421539898202E+03
AVEKIN 3.2332755503992078E-01
AVETEMP 2.9984917723950269E+02
AVEKIN_QM 0.0000000000000000E+00
AVETEMP_QM 0.0000000000000000E+00
AVEVOL 3.0842651782127203E+04
AVECELL_A 2.7971726218973288E+01
AVECELL_B 2.7971726218973288E+01
AVECELL_C 3.9419687131994479E+01
AVEALPHA 9.0000000000000000E+01
AVEBETA 9.0000000000000000E+01
AVEGAMMA 9.0000000000000000E+01
AVE_ECONS 1.4016569135616819E+05
AVE_PRESS -1.6562449007126843E+03
AVE_PXX -3.4950333563135082E+03
&END RESTART_AVERAGES
&END AVERAGES
&END MD
&PRINT
&TRAJECTORY SILENT
&EACH
MD 1
&END EACH
&END TRAJECTORY
&VELOCITIES SILENT
&EACH
MD 500
&END EACH
&END VELOCITIES
&RESTART SILENT
&EACH
MD 1
&END EACH
&END RESTART
&RESTART_HISTORY SILENT
&EACH
MD 50
&END EACH
&END RESTART_HISTORY
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD QS
STRESS_TENSOR ANALYTICAL
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
&SCF
MAX_SCF 30
EPS_SCF 1.0000000000000000E-08
SCF_GUESS RESTART
&OT T
MINIMIZER DIIS
LINESEARCH 2PNT
PRECONDITIONER FULL_ALL
&END OT
&OUTER_SCF T
EPS_SCF 1.0000000000000000E-08
MAX_SCF 100
&END OUTER_SCF
&END SCF
&QS
EPS_DEFAULT 1.0000000000000002E-12
EPS_PGF_ORB 1.0000000000000001E-18
&END QS
&MGRID
NGRIDS 5
CUTOFF 6.0000000000000000E+02
REL_CUTOFF 5.0000000000000000E+01
&END MGRID
&XC
DENSITY_CUTOFF 1.0000000000000000E-10
GRADIENT_CUTOFF 1.0000000000000000E-10
TAU_CUTOFF 1.0000000000000000E-10
&XC_FUNCTIONAL NO_SHORTCUT
&PBE T
&END PBE
&END XC_FUNCTIONAL
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
PARAMETER_FILE_NAME dftd3.dat
REFERENCE_FUNCTIONAL PBE
CALCULATE_C9_TERM T
&END PAIR_POTENTIAL
&END VDW_POTENTIAL
&END XC
&END DFT
&SUBSYS
&CELL
A 1.4802000000000001E+01 0.0000000000000000E+00
0.0000000000000000E+00
B 0.0000000000000000E+00 1.4802000000000001E+01
0.0000000000000000E+00
C 0.0000000000000000E+00 0.0000000000000000E+00
2.0859999999999999E+01
MULTIPLE_UNIT_CELL 1 1 1
&END CELL
&KIND H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND Zr
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q12
&END KIND
&TOPOLOGY
COORD_FILE_FORMAT XYZ
COORD_FILE_NAME half-cell-optimised.xyz
NUMBER_OF_ATOMS 228
MULTIPLE_UNIT_CELL 1 1 1
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
The latter is a restart file from which ive removed coordinates and
velocities to reduce cluttering. The preconditioner changes from
full_kinetic to full_all for md, but using full_kinetic for both leads to
no major difference. The timings are attached as text files to preserve
sensible formatting.
Best regards,
Martin
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SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.021 0.031 1873.540 1873.541
qs_mol_dyn_low 1 2.0 0.003 0.003 1873.162 1873.170
qs_forces 21 4.0 0.004 0.004 1872.283 1872.284
velocity_verlet 20 3.0 0.003 0.003 1779.757 1779.763
qs_energies 21 5.0 0.001 0.002 1020.519 1020.533
build_core_hamiltonian_matrix_ 21 5.0 0.001 0.001 520.398 806.313
qs_energies_init_hamiltonians 21 6.0 0.000 0.000 576.531 576.532
build_core_hamiltonian_matrix 21 7.0 0.001 0.001 328.416 542.657
build_core_ppnl_forces 21 6.0 328.220 500.648 328.220 500.648
mp_sum_d 4698 11.8 319.666 448.046 319.666 448.046
build_core_ppnl 21 8.0 260.626 428.325 260.626 428.325
calculate_ecore_overlap 42 6.0 0.001 0.001 286.017 426.724
scf_env_do_scf 21 6.0 0.001 0.002 423.899 423.900
scf_env_do_scf_inner_loop 202 6.9 0.012 1.120 369.883 370.512
rs_pw_transfer 2272 12.3 0.029 0.044 240.629 369.532
mp_waitany 37056 14.1 213.624 343.425 213.624 343.425
rs_pw_transfer_RS2PW_300 244 11.9 2.627 4.491 210.793 340.136
qs_env_update_s_mstruct 21 7.0 0.000 0.000 218.454 330.194
calculate_rho_core 21 8.0 0.045 0.099 215.365 327.178
build_core_ppl_forces 21 6.0 175.423 280.243 175.423 280.243
rebuild_ks_matrix 223 8.7 0.001 0.001 255.898 256.176
qs_ks_build_kohn_sham_matrix 223 9.7 0.028 0.032 255.897 256.175
qs_ks_update_qs_env 223 7.9 0.002 0.002 211.004 211.259
sum_up_and_integrate 223 10.7 0.091 0.119 197.266 197.355
integrate_v_rspace 223 11.7 157.621 166.157 197.174 197.268
qs_rho_update_rho 223 8.0 0.001 0.002 170.050 170.186
calculate_rho_elec 223 9.0 131.387 140.921 170.048 170.185
build_core_ppl 21 8.0 62.932 107.101 62.932 107.101
pw_transfer 4704 12.4 0.268 0.374 61.020 62.376
fft_wrap_pw1pw2 4258 13.4 0.036 0.049 60.444 61.809
fft_wrap_pw1pw2_300 2474 14.5 2.346 2.905 56.278 57.752
fft3d_ps 4258 15.4 14.505 19.849 54.494 56.005
init_scf_loop 21 7.0 0.001 0.001 53.281 53.282
density_rs2pw 223 10.0 0.014 0.017 33.750 50.535
qs_vxc_create 223 10.7 0.005 0.007 47.992 48.273
xc_vxc_pw_create 223 11.7 0.883 1.284 47.987 48.267
qs_ks_update_qs_env_forces 21 5.0 0.000 0.000 45.325 45.350
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SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.014 0.028 7564.232 7564.232
cp_cell_opt 1 2.0 0.000 0.000 7563.461 7563.463
geoopt_bfgs 1 3.0 0.040 1.609 7563.461 7563.463
cp_eval_at 237 4.0 0.035 0.060 7514.141 7514.151
qs_forces 236 5.0 0.048 0.053 7495.872 7495.872
qs_energies 237 6.0 0.014 0.019 6797.890 6798.056
scf_env_do_scf 237 7.0 0.013 0.023 6207.261 6207.275
scf_env_do_scf_inner_loop 4360 8.0 0.604 89.772 5953.545 5963.173
rebuild_ks_matrix 4596 9.8 0.015 0.016 3759.543 3765.027
qs_ks_build_kohn_sham_matrix 4596 10.8 0.550 0.634 3759.528 3765.011
qs_ks_update_qs_env 4628 9.0 0.044 0.056 3496.388 3502.063
sum_up_and_integrate 4596 11.8 1.884 2.378 2606.707 2607.406
integrate_v_rspace 4596 12.8 1954.877 2100.764 2604.815 2605.639
qs_rho_update_rho 4597 9.0 0.023 0.034 2386.804 2389.798
calculate_rho_elec 4597 10.0 1755.135 1875.699 2386.781 2389.776
pw_transfer 96759 13.5 5.524 6.638 1165.587 1184.984
fft_wrap_pw1pw2 87567 14.6 0.724 0.820 1153.681 1173.145
fft_wrap_pw1pw2_300 50795 15.7 47.369 55.966 1093.612 1113.724
fft3d_ps 87567 16.6 292.728 398.824 1034.180 1057.864
qs_vxc_create 4596 11.8 0.085 0.108 960.930 965.922
xc_vxc_pw_create 4596 12.8 18.571 26.948 960.845 965.840
rs_pw_transfer 46438 13.4 0.623 0.887 689.319 762.994
mp_alltoall_z22v 87567 18.6 636.128 686.585 636.128 686.585
density_rs2pw 4597 11.0 0.291 0.383 539.828 610.588
xc_rho_set_and_dset_create 4596 13.8 3.442 3.597 441.669 537.304
potential_pw2rs 4596 13.8 0.326 0.362 451.991 453.135
mp_sum_d 95117 14.3 372.317 447.993 372.317 447.993
qs_energies_init_hamiltonians 237 7.0 0.003 0.004 431.564 431.574
dbcsr_multiply_generic 68495 13.8 3.052 3.431 412.573 427.060
yz_to_x 23218 17.6 18.494 19.667 380.209 418.594
qs_scf_new_mos 4360 9.0 0.023 0.038 369.891 377.591
qs_scf_loop_do_ot 4360 10.0 0.026 0.040 369.868 377.564
mp_waitany 742598 15.3 256.120 370.678 256.120 370.678
qs_ks_update_qs_env_forces 236 6.0 0.001 0.002 352.848 353.128
ot_scf_mini 4360 11.0 0.184 0.211 341.089 345.339
multiply_cannon 68495 14.8 17.122 18.497 293.106 329.804
mp_waitall_1 ******* 16.5 204.780 323.771 204.780 323.771
rs_pw_transfer_RS2PW_300 4834 12.9 86.166 110.211 243.600 320.951
build_core_hamiltonian_matrix_ 236 6.0 0.008 0.010 239.562 320.254
calculate_dispersion_pairpot 237 8.0 152.893 317.997 319.043 319.044
x_to_yz 27577 17.7 41.676 53.852 311.601 318.336
mp_alltoall_d11v 63084 15.0 229.464 317.072 229.464 317.072
rs_distribute_matrix 9429 12.4 4.066 8.581 224.599 309.410
xc_functional_eval 4596 14.8 0.051 0.087 146.027 249.006
pbe_lda_eval 4596 15.8 145.976 248.975 145.976 248.975
init_scf_loop 268 8.0 0.006 0.008 243.826 243.856
rs_pw_transfer_PW2RS_300 4832 15.6 125.842 137.526 219.001 232.205
multiply_cannon_metrocomm3 1643880 15.8 4.677 5.063 85.776 225.570
ot_mini 4360 12.0 0.024 0.027 211.959 217.857
build_core_ppnl_forces 236 7.0 141.122 167.812 141.122 167.812
qs_ot_get_derivative 4360 13.0 0.036 0.040 161.644 165.947
init_scf_run 237 7.0 0.004 0.010 155.115 155.123
scf_env_initial_rho_setup 237 8.0 0.002 0.007 155.110 155.118
multiply_cannon_multrec 1643880 15.8 87.730 154.695 88.003 154.999
wfi_extrapolate 237 9.0 0.017 0.022 153.987 153.987
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