[CP2K:3722] Memory Issue QMMM Cray XE6
Teodoro Laino
teodor... at gmail.com
Thu Jan 26 17:50:17 UTC 2012
I have no experience on the new configuration of Rosa. Nonetheless, from the info I was able to collect, I found that each node has 32 GB of memory.
This means that running 32 mpi tasks per node, each cp2k task has ~ 1GB of memory (maybe something less.. because of OS, IO, etc..).
Depending on your system this is definitely not too much.
You can try to change the parallelization inside QM/MM - switching to grid instead of atomic may help you to avoid an additional memory allocation which may cause the problem you see.
-----
Now the thought of the evening:
a machine with 32 cores per node is not designed to sustain 32 mpi tasks.
Clearly, there will be the need (more and more, looking at the machines of the next years) to move to hybrid parallel schemes on such a platform.
So, I would encourage you to try a mixed omp/mpi for cp2k.
Unfortunately, not all pieces of cp2k support omp, and unfortunately^2 qm/mm is not one of those few parts that supports it.
But you may still take advantage of the few parts that use it and avoid at the same time the memory issues that you observe.
Teo
On Jan 26, 2012, at 3:36 PM, marco.stenta wrote:
> Hello,
> I have a memory issue when running QM/MM-MD on a Cray XE6 machine (our
> dear rosa at CSCS, 16-core AMD Opteron 6272 2.1 GHz Interlagos
> processors).
> I did not do the compilation myself but infer it is gfortran (if you
> need I can ask the SA for more info)
> Below I attach both input and output (sorry: it is super long but I
> cannot attach zip files).
> The system used to run smoothly on an IBM-SP6 machine (SP6 at CINECA).
>
> On the Cray the job crashes while in the QM/MM module. the last thing
> it prints is
> QMMM| QM/MM Coupling computed collocating the Gaussian Potential
> Functions.
>
> and then:
> Application 347501 exit signals: Killed
> Application 347501 resources: utime ~8s, stime ~0s
>
> I use 128 MP processes.
> Now on the Cray if I create 128 tasks and use 32 tasks per node (fully
> packed nodes) the job crashes the very first time it performs the QMMM
> operation
> If, instead, I use half the tasks per node (16 out of a max of 32),
> thus leaving half node empty, but still use 128 tasks, the job goes on
> for a couple of cycles and then it crashes at the same time.
>
> With 256 tasks with fully packed nodes It crashes, but when I leave
> node half empty (16 tasks per node) it goes on for a while.
>
> Did any one experience something like that? I've seen in the forum
> some option to reduce the memory consumption and I used some of them
> to no avail.
>
> Would a different compilation solve the problem? Can you tell me which
> libraries could be critical for this issue (if all is OK in the
> input)? Would in your opinion a MPI-openMP solve the problem?
>
>
> Thank you very much in advance
>
>
> ################################################################
> @SET NSTEPS 500000
> @SET SOLNAME MOL69
> @SET QMCHARGE -1
> @SET QMPOISSON MT
>
> @SET FREQ 1
> @INCLUDE ../data/boxes.inc
>
> &GLOBAL
> PRINT_LEVEL LOW
> PROJECT system
> PROGRAM CP2K
> RUN_TYPE MD
> WALLTIME 82800
> SAVE_MEM TRUE
> #TRACE TRUE
> &END GLOBAL
>
> &MOTION
> &MD
> ENSEMBLE NVT
> STEPS ${NSTEPS}
> TIMESTEP 0.50
> TEMPERATURE 300.0
> &THERMOSTAT
> TYPE CSVR
> REGION DEFINED
> &DEFINE_REGION
> MM_SUBSYS ATOMIC
> &END DEFINE_REGION
> &DEFINE_REGION
> QM_SUBSYS ATOMIC
> &END DEFINE_REGION
> &CSVR
> TIMECON 50
> &END CSVR
> &END THERMOSTAT
> &PRINT
> FORCE_LAST T
> &ENERGY
> &EACH
> MD 1
> &END EACH
> FILENAME =system.ene
> &END ENERGY
> &END PRINT
> &END MD
> &PRINT
> &TRAJECTORY SILENT
> &EACH
> MD ${FREQ}
> &END EACH
> FILENAME =system.dcd
> FORMAT DCD
> &END TRAJECTORY
> &VELOCITIES OFF
> &EACH
> MD ${FREQ}
> &END EACH
> FILENAME =system.vel
> &END VELOCITIES
> &FORCES
> &EACH
> MD ${FREQ}
> &END EACH
> FILENAME =system.for.DCD
> FORMAT DCD
> &END FORCES
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
> &RESTART SILENT
> ADD_LAST NUMERIC
> &EACH
> MD ${FREQ}
> &END EACH
> FILENAME =system.restart
> &END RESTART
> &END PRINT
> &CONSTRAINT
> &G3X3
> MOLNAME ${SOLNAME}
> DISTANCES 1.7958 1.7958 2.85444
> ATOMS 1 2 3
> EXCLUDE_QM
> &END G3X3
> # @INCLUDE ../data/fix_qm_heavy.inc
> &END CONSTRAINT
> # @INCLUDE ../data/FREE_ENERGY.inc
> &END MOTION
>
> &FORCE_EVAL
> METHOD QMMM
> &DFT
> BASIS_SET_FILE_NAME ../data/BASIS_SET
> POTENTIAL_FILE_NAME ../data/GTH_POTENTIALS
> CHARGE ${QMCHARGE}
> &SCF
> MAX_SCF 40
> EPS_SCF 1.0E-7
> SCF_GUESS ATOMIC
> &OUTER_SCF
> EPS_SCF 1.0E-7
> MAX_SCF 10
> &END OUTER_SCF
> &OT
> PRECONDITIONER FULL_ALL
> MINIMIZER DIIS
> N_DIIS 7
> &END OT
> &PRINT
> &RESTART
> ADD_LAST NUMERIC
> &EACH
> MD ${FREQ}
> &END EACH
> FILENAME =RESTART
> &END RESTART
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
> &END PRINT
> &END SCF
> &QS
> EPS_DEFAULT 1.0E-12
> EXTRAPOLATION ASPC
> EXTRAPOLATION_ORDER 3
> &END QS
> &MGRID
> CUTOFF 320
> COMMENSURATE
> &END MGRID
> &POISSON
> POISSON_SOLVER ${QMPOISSON}
> PERIODIC NONE
> &END POISSON
> &XC
> &XC_FUNCTIONAL BLYP
> &END XC_FUNCTIONAL
> &END XC
> &END DFT
>
> &MM
> &FORCEFIELD
> PARMTYPE AMBER
> PARM_FILE_NAME ../data/molbox.prmtop
> EI_SCALE14 0.8333
> VDW_SCALE14 0.5
> &SPLINE
> RCUT_NB 12.0
> &END SPLINE
>
> &BOND
> KIND AMBER
> ATOMS ZN SH
> K [angstrom^-2kcalmol] 68.05
> R0 [angstrom] 2.311
> &END BOND
> &BOND
> KIND AMBER
> ATOMS ZN NB
> K [angstrom^-2kcalmol] 45.58
> R0 [angstrom] 1.957
> &END BOND
>
> &END FORCEFIELD
> &POISSON
> &EWALD
> EWALD_TYPE SPME
> ALPHA .35
> GMAX ${EWALDA} ${EWALDB} ${EWALDC}
> &END EWALD
> &END POISSON
> &END MM
>
> &QMMM
> NOCENTER T
> NOCENTER0 T
> USE_GEEP_LIB 7
> ECOUPL GAUSS
> &CELL
> ABC ${QMBOXA} ${QMBOXB} ${QMBOXC}
> PERIODIC NONE
> &END CELL
>
> @INCLUDE ../data/QM_KIND-LINK.inc
>
> &WALLS
> WALL_SKIN [angstrom] 2.0 2.0 2.0
> TYPE REFLECTIVE
> &END WALLS
>
> &PRINT
> &PROGRAM_RUN_INFO SILENT
> &END PROGRAM_RUN_INFO
> &PERIODIC_INFO SILENT
> &END PERIODIC_INFO
> &QMMM_LINK_INFO SILENT
> &END QMMM_LINK_INFO
> &END PRINT
> &END QMMM
>
> &SUBSYS
> &CELL
> ABC ${MMBOXA} ${MMBOXB} ${MMBOXC}
> PERIODIC XYZ
> &END CELL
> &TOPOLOGY
> &MOL_SET
> &MERGE_MOLECULES
> &BONDS
> 1520 8881
> 11567 16020
> &END BONDS
> &END MERGE_MOLECULES
> &END MOL_SET
>
> &GENERATE
> &BOND ADD
> ATOMS 1520 8881
> &END BOND
> &BOND ADD
> ATOMS 1476 8881
> &END BOND
> &BOND ADD
> ATOMS 961 8881
> &END BOND
> &BOND ADD
> ATOMS 905 8881
> &END BOND
> &BOND ADD
> ATOMS 11567 16020
> &END BOND
> &BOND ADD
> ATOMS 11611 16020
> &END BOND
> &BOND ADD
> ATOMS 11052 16020
> &END BOND
> &BOND ADD
> ATOMS 10996 16020
> &END BOND
> &END GENERATE
>
>
> # COORD_FILE_NAME ../data/molbox.rst7
> # COORD_FILE_FORMAT CRD
> CONN_FILE_FORMAT psf
> CONN_FILE_NAME ../data/molbox_mod.psf
> MOL_CHECK T
> &END TOPOLOGY
> @INCLUDE ../data/KIND_BASIS_POTENTIAL.inc
> &END SUBSYS
> &END FORCE_EVAL
>
> &EXT_RESTART
> RESTART_FILE_NAME system.restart
> RESTART_DEFAULT T
> RESTART_POS T
> RESTART_QMMM T
> RESTART_CELL T
> RESTART_VEL T
> RESTART_CONSTRAINT F
> &END EXT_RESTART
>
> ################################################################
> 128 task 32 task /node
>
> *******************************************************************************
> * RESTART
> INFORMATION *
>
> *******************************************************************************
>
> *
> *
> * RESTART FILE NAME:
> system.restart *
>
> *
> *
> * RESTARTED
> QUANTITIES: *
> *
> CELL *
> *
> COORDINATES *
> * RANDOM NUMBER
> GENERATOR *
> *
> VELOCITIES *
> * QMMM TRANSLATION
> VECTOR *
> * MD
> COUNTERS *
> * MD
> AVERAGES *
> * PARTICLE
> THERMOSTAT *
> * REAL TIME
> PROPAGATION *
> * PINT BEAD
> POSITIONS *
> * PINT BEAD
> VELOCITIES *
> * PINT NOSE
> THERMOSTAT *
> * PINT GLE
> THERMOSTAT *
> * HELIUM BEAD
> POSITIONS *
> * HELIUM PERMUTATION
> STATE *
> * HELIUM FORCES ON
> SOLUTE *
> * HELIUM RNG
> STATE *
>
> *******************************************************************************
>
> DBCSR| Multiplication
> driver SMM
> DBCSR| Multiplication stack
> size 1000
> DBCSR| Multiplication size
> stacks 0
> DBCSR| Use
> subcommunicators F
> DBCSR| Use MPI combined
> types F
> DBCSR| Use MPI memory
> allocation T
> DBCSR| Use Communication
> thread T
> DBCSR| Communication thread
> load 100
>
>
> **** **** ****** ** PROGRAM STARTED AT 2012-01-26
> 10:01:28.566
> ***** ** *** *** ** PROGRAM STARTED
> ON nid01132
> ** **** ****** PROGRAM STARTED
> BY root ;-)
> ***** ** ** ** ** PROGRAM PROCESS
> ID 23112
> **** ** ******* ** PROGRAM STARTED IN /scratch/rosa/mstenta/
> integrase/integ
> rase_reac_new/prod_1
>
> CP2K| version string: CP2K version 2.3.29
> (Development Version)
> CP2K| is freely available from http://cp2k.berlios.de/
> CP2K| Program compiled at Mon Nov 21
> 10:22:36 CET 2011
> CP2K| Program compiled
> on gele2
> CP2K| Program compiled for CRAY-
> XE6-gfortran
> CP2K| Last CVS
> entry
> CP2K| Input file name
> system_prod_trace.inp
>
> GLOBAL| Force Environment
> number 1
> GLOBAL| Basis set file name ../data/
> BASIS_SET
> GLOBAL| Geminal file name
> BASIS_GEMINAL
> GLOBAL| Potential file name ../data/
> GTH_POTENTIALS
> GLOBAL| MM Potential file name
> MM_POTENTIAL
> GLOBAL| Coordinate file name
> __STD_INPUT__
> GLOBAL| Method
> name CP2K
> GLOBAL| Project
> name system
> GLOBAL| Preferred FFT
> library FFTW3
> GLOBAL| Run
> type MD
> GLOBAL| All-to-all communication in single
> precision F
> GLOBAL| FFTs using library dependent
> lengths F
> GLOBAL| Global print
> level LOW
> GLOBAL| Total number of message passing
> processes 128
> GLOBAL| Number of threads for this
> process 1
> GLOBAL| This output is from
> process 0
>
> MEMORY| system memory details [Kb]
> MEMORY| rank 0 min
> max average
> MEMORY| MemTotal 33083456 33083456
> 33083456 33083456
> MEMORY| MemFree 25030868 25030868
> 25076528 25064135
> MEMORY| Buffers 0 0
> 0 0
> MEMORY| Cached 100412 59880
> 100412 70112
> MEMORY| Slab 169372 164880
> 169372 166280
> MEMORY| SReclaimable 3824 3556
> 3824 3703
> MEMORY| MemLikelyFree 25135104 25135104
> 25140480 25137950
>
>
>
> SPLINE_INFO| Generating 73920 splines for the NONBONDED interactions
> due to 384 different atomic kinds
> 000000:000128>> 9 424 init_genpot
> start 3671 Mb
> 000000:000128<< 9 424 init_genpot
> 0.014 3671 Mb
> ...7392
> ...14784
> ...22176
> ...29568
> ...36960
> ...44352
> ...51744
> ...59136
> ...66528
> ...73920
>
> ....
> ....
> ....
> ....
> ....
> ....
>
>
> SPLINE_INFO| Number of unique splines computed: 211
>
> SPLINE_INFO| Done
> 000000:000128<< 8 2
> spline_nonbond_control 0.047 3671 Mb
> 000000:000128<< 7 2
> force_field_pack_splines 4.011 3671 Mb
> 000000:000128>> 7 1 force_field_pack_eicut
> start 3674 Mb
> 000000:000128<< 7 1 force_field_pack_eicut
> 0.151 3677 Mb
> 000000:000128<< 6 1 force_field_pack 30.658
> 3677 Mb
> 000000:000128>> 6 1 force_field_qeff_output
> start 3677 Mb
> 000000:000128<< 6 1 force_field_qeff_output
> 0.061 3677 Mb
> 000000:000128>> 6 1 clean_intra_force_kind
> start 3677 Mb
> 000000:000128<< 6 1 clean_intra_force_kind
> 0.018 3677 Mb
> 000000:000128<< 5 1 force_field_control 66.176
> 3677 Mb
> 000000:000128>> 5 1 fist_init_subsys start 3677
> Mb
> 000000:000128>> 6 1 write_molecule_kind_set
> start 3677 Mb
> 000000:000128<< 6 1 write_molecule_kind_set
> 0.000 3677 Mb
> 000000:000128>> 6 1 write_particle_distances
> start 3677 Mb
> 000000:000128<< 6 1 write_particle_distances
> 0.000 3677 Mb
> 000000:000128>> 6 1 write_structure_data
> start 3677 Mb
> 000000:000128<< 6 1 write_structure_data
> 0.000 3677 Mb
> 000000:000128>> 6 1 write_symmetry start 3677
> Mb
> 000000:000128<< 6 1 write_symmetry 0.000 3677
> Mb
> 000000:000128>> 6 1 distribute_molecules_1d
> start 3677 Mb
> 000000:000128<< 6 1 distribute_molecules_1d
> 0.056 3677 Mb
> 000000:000128>> 6 1 ewald_pw_init start 3677
> Mb
> 000000:000128>> 7 1 pw_grid_setup start
> 3677 Mb
> 000000:000128>> 8 1 pw_grid_distribute
> start 3683 Mb
> 000000:000128<< 8 1 pw_grid_distribute
> 0.004 3683 Mb
> 000000:000128>> 8 1 pw_grid_allocate
> start 3683 Mb
> 000000:000128<< 8 1 pw_grid_allocate
> 0.001 3683 Mb
> 000000:000128>> 8 1 pw_grid_assign
> start 3683 Mb
> 000000:000128<< 8 1 pw_grid_assign
> 0.001 3683 Mb
> 000000:000128>> 8 1 pw_grid_sort start
> 3683 Mb
> 000000:000128>> 9 1 sort_shells
> start 3683 Mb
> 000000:000128<< 9 1 sort_shells
> 0.002 3683 Mb
> 000000:000128<< 8 1 pw_grid_sort 0.003
> 3683 Mb
> 000000:000128>> 8 1 pw_grid_remap start
> 3683 Mb
> 000000:000128<< 8 1 pw_grid_remap 0.006
> 3691 Mb
> 000000:000128<< 7 1 pw_grid_setup 0.021
> 3691 Mb
> 000000:000128>> 7 1
> rs_grid_create_descriptor start 3691 Mb
> 000000:000128<< 7 1
> rs_grid_create_descriptor 0.001 3691 Mb
> 000000:000128>> 7 1 rs_grid_create start
> 3691 Mb
> 000000:000128<< 7 1 rs_grid_create 0.001
> 3691 Mb
> 000000:000128<< 6 1 ewald_pw_init 0.373 3691
> Mb
> 000000:000128>> 6 1 ewald_pw_release start
> 3691 Mb
> 000000:000128<< 6 1 ewald_pw_release 0.000
> 3691 Mb
> 000000:000128>> 6 2 ewald_pw_release start
> 3691 Mb
> 000000:000128<< 6 2 ewald_pw_release 0.000
> 3691 Mb
> 000000:000128<< 5 1 fist_init_subsys 0.432 3691
> Mb
> 000000:000128<< 4 1 fist_init 95.746 3691 Mb
> 000000:000128>> 4 2 cp_result_create start 3691 Mb
> 000000:000128<< 4 2 cp_result_create 0.000 3691 Mb
> 000000:000128<< 3 1 fist_create_force_env 95.748 3691
> Mb
> Number of QM atoms: 87
> Number of MM atoms: 232348
> QM cell ::
>
>
> -------------------------------------------------------------------------
>
> QM/MM LINKS
>
>
> -------------------------------------------------------------------------
>
> IMOMM TYPE LINK
> TYPE: IMOMM QM INDEX: 12075 MM INDEX: 12073 ALPHA:
> 1.410000
> TYPE: IMOMM QM INDEX: 12952 MM INDEX: 12950 ALPHA:
> 1.410000
> TYPE: IMOMM QM INDEX: 13493 MM INDEX: 13490 ALPHA:
> 1.410000
> TYPE: IMOMM QM INDEX: 20093 MM INDEX: 20090 ALPHA:
> 1.410000
> TYPE: IMOMM QM INDEX: 20096 MM INDEX: 20098 ALPHA:
> 1.410000
> TYPE: IMOMM QM INDEX: 20128 MM INDEX: 20130 ALPHA:
> 1.410000
> TYPE: IMOMM QM INDEX: 20154 MM INDEX: 20157 ALPHA:
> 1.410000
>
>
> -------------------------------------------------------------------------
>
> 000000:000128>> 3 2 connectivity_control start 3697 Mb
> 000000:000128>> 4 2
> connectivity_control_check_element_name start 3697 Mb
> 000000:000128<< 4 2
> connectivity_control_check_element_name 0.001 3697 Mb
> 000000:000128>> 4 1 topology_set_atm_mass start
> 3697 Mb
> 000000:000128<< 4 1 topology_set_atm_mass 0.000
> 3697 Mb
> 000000:000128>> 4 1 topology_generate_bend start
> 3697 Mb
> GENERATE| Number of Bends
> generated: 0
> 000000:000128<< 4 1 topology_generate_bend 0.000
> 3697 Mb
> 000000:000128>> 4 1 topology_generate_ub start 3697
> Mb
> GENERATE| Number of UB
> generated: 0
> 000000:000128<< 4 1 topology_generate_ub 0.000 3697
> Mb
> 000000:000128>> 4 1 topology_generate_dihe start
> 3697 Mb
> GENERATE| Number of Torsions
> generated: 0
> 000000:000128<< 4 1 topology_generate_dihe 0.000
> 3697 Mb
> 000000:000128>> 4 1 topology_generate_impr start
> 3697 Mb
> GENERATE| Number of Impropers
> generated: 0
> 000000:000128<< 4 1 topology_generate_impr 0.000
> 3697 Mb
> 000000:000128>> 4 1 topology_generate_onfo start
> 3697 Mb
> GENERATE| Number of 1-4 interactions
> generated: 0
> 000000:000128<< 4 1 topology_generate_onfo 0.000
> 3697 Mb
> 000000:000128>> 4 2 topology_muc start 3697 Mb
> 000000:000128<< 4 2 topology_muc 0.000 3697 Mb
> 000000:000128>> 4 2 topology_generate_molecule
> start 3697 Mb
> 000000:000128>> 5 2
> topology_generate_molecule_PARA_RES start 3697 Mb
> 000000:000128<< 5 2
> topology_generate_molecule_PARA_RES 0.000 3697 Mb
> 000000:000128<< 4 2 topology_generate_molecule
> 0.001 3697 Mb
> 000000:000128<< 3 2 connectivity_control 0.004 3697 Mb
> 000000:000128>> 3 2 topology_connectivity_pack start
> 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_1
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_1
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_1.1
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_1.1
> 0.001 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_2
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_2
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_3
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_3
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_4
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_4
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_5
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_5
> 0.001 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_6
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_6
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_7
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_7
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_8
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_8
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_9
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_9
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_10
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_10
> 0.000 3697 Mb
> 000000:000128>> 4 2
> topology_connectivity_pack_11_pre start 3697 Mb
> 000000:000128<< 4 2
> topology_connectivity_pack_11_pre 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_11
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_11
> 0.000 3697 Mb
> 000000:000128>> 4 2
> topology_connectivity_pack_12_pre start 3697 Mb
> 000000:000128<< 4 2
> topology_connectivity_pack_12_pre 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_12
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_12
> 0.000 3697 Mb
> 000000:000128>> 4 2
> topology_connectivity_pack_13_pre start 3697 Mb
> 000000:000128<< 4 2
> topology_connectivity_pack_13_pre 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_13
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_13
> 0.000 3697 Mb
> 000000:000128>> 4 2
> topology_connectivity_pack_14_pre start 3697 Mb
> 000000:000128<< 4 2
> topology_connectivity_pack_14_pre 0.000 3697 Mb
> 000000:000128>> 4 2 topology_connectivity_pack_14
> start 3697 Mb
> 000000:000128<< 4 2 topology_connectivity_pack_14
> 0.001 3697 Mb
> 000000:000128<< 3 2 topology_connectivity_pack 0.004
> 3697 Mb
> 000000:000128>> 3 2 topology_coordinate_pack start
> 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_1
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_1
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_2
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_2
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_3
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_3
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_4
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_4
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_5
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_5
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_6
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_6
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_7a
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_7a
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_7b
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_7b
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_89
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_89
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_10
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_10
> 0.000 3697 Mb
> 000000:000128>> 4 2 topology_coordinate_pack_11
> start 3697 Mb
> 000000:000128<< 4 2 topology_coordinate_pack_11
> 0.000 3697 Mb
> 000000:000128<< 3 2 topology_coordinate_pack 0.001
> 3697 Mb
> 000000:000128>> 3 1 quickstep_create_force_env start
> 3697 Mb
> 000000:000128>> 4 3 cp_result_create start 3697 Mb
> 000000:000128<< 4 3 cp_result_create 0.000 3697 Mb
> 000000:000128>> 4 1 read_atomic_kind_set start 3697
> Mb
> 000000:000128>> 5 1 read_atomic_kind start 3697
> Mb
> 000000:000128>> 6 824 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 824
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 824
> broadcast_input_information 0.005 3701 Mb
> 000000:000128<< 6 824 parser_read_line_low
> 0.030 3701 Mb
> 000000:000128>> 6 825 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 825
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 825
> broadcast_input_information 0.005 3701 Mb
> 000000:000128<< 6 825 parser_read_line_low
> 0.011 3701 Mb
> 000000:000128>> 6 826 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 826
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 826
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 826 parser_read_line_low
> 0.010 3701 Mb
> 000000:000128>> 6 827 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 827
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 827
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 827 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128<< 5 1 read_atomic_kind 0.107 3701
> Mb
> 000000:000128>> 5 2 read_atomic_kind start 3701
> Mb
> 000000:000128>> 6 828 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 828
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 828
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 828 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128>> 6 829 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 829
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 829
> broadcast_input_information 0.005 3701 Mb
> 000000:000128<< 6 829 parser_read_line_low
> 0.010 3701 Mb
> 000000:000128>> 6 830 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 830
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 830
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 830 parser_read_line_low
> 0.010 3701 Mb
> 000000:000128>> 6 831 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 831
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 831
> broadcast_input_information 0.003 3701 Mb
> 000000:000128<< 6 831 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128<< 5 2 read_atomic_kind 0.069 3701
> Mb
> 000000:000128>> 5 3 read_atomic_kind start 3701
> Mb
> 000000:000128>> 6 832 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 832
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 832
> broadcast_input_information 0.003 3701 Mb
> 000000:000128<< 6 832 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128>> 6 833 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 833
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 833
> broadcast_input_information 0.005 3701 Mb
> 000000:000128<< 6 833 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128>> 6 834 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 834
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 834
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 834 parser_read_line_low
> 0.010 3701 Mb
> 000000:000128>> 6 835 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 835
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 835
> broadcast_input_information 0.003 3701 Mb
> 000000:000128<< 6 835 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128<< 5 3 read_atomic_kind 0.069 3701
> Mb
> 000000:000128>> 5 4 read_atomic_kind start 3701
> Mb
> 000000:000128>> 6 836 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 836
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 836
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 836 parser_read_line_low
> 0.008 3701 Mb
> 000000:000128>> 6 837 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 837
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 837
> broadcast_input_information 0.005 3701 Mb
> 000000:000128<< 6 837 parser_read_line_low
> 0.010 3701 Mb
> 000000:000128>> 6 838 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 838
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 838
> broadcast_input_information 0.003 3701 Mb
> 000000:000128<< 6 838 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128>> 6 839 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 839
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 839
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 839 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128<< 5 4 read_atomic_kind 0.071 3701
> Mb
> 000000:000128>> 5 5 read_atomic_kind start 3701
> Mb
> 000000:000128>> 6 840 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 840
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 840
> broadcast_input_information 0.003 3701 Mb
> 000000:000128<< 6 840 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128>> 6 841 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 841
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 841
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 841 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128>> 6 842 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 842
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 842
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 842 parser_read_line_low
> 0.009 3701 Mb
> 000000:000128>> 6 843 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 843
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 843
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 843 parser_read_line_low
> 0.008 3701 Mb
> 000000:000128>> 6 844 parser_read_line_low
> start 3701 Mb
> 000000:000128>> 7 844
> broadcast_input_information start 3701 Mb
> 000000:000128<< 7 844
> broadcast_input_information 0.004 3701 Mb
> 000000:000128<< 6 844 parser_read_line_low
> 0.008 3701 Mb
> 000000:000128<< 5 5 read_atomic_kind 0.083 3701
> Mb
> 000000:000128>> 5 6 read_atomic_kind start 3701
> Mb
> 000000:000128<< 5 6 read_atomic_kind 0.001 3701
> Mb
> 000000:000128<< 4 1 read_atomic_kind_set 0.400 3701
> Mb
> 000000:000128>> 4 1 qs_init_subsys start 3701 Mb
>
>
> *******************************************************************************
>
> *******************************************************************************
>
> **
> **
> ** ##### ##
> ## **
> ** ## ## ## ##
> ## **
> ** ## ## ##
> ###### **
> ** ## ## ## ## ## ##### ## ## #### ## #####
> ##### **
> ** ## ## ## ## ## ## ## ## ## ## ## ##
> ## ## **
> ** ## ## ## ## ## ## ## #### ### ## ######
> ###### **
> ** ## ### ## ## ## ## ## ## ## ## ##
> ## **
> ** ####### ##### ## ##### ## ## #### ## #####
> ## **
> ** ##
> ## **
>
> **
> **
> ** ... make the atoms
> dance **
>
> **
> **
> ** Copyright (C) by CP2K Developers Group (2000 -
> 2011) **
>
> **
> **
>
> *******************************************************************************
> 000000:000128>> 5 1 read_qs_section start 3701
> Mb
> 000000:000128<< 5 1 read_qs_section 0.003 3701
> Mb
> 000000:000128>> 5 1 read_mgrid_section start
> 3701 Mb
> 000000:000128<< 5 1 read_mgrid_section 0.000
> 3701 Mb
> 000000:000128>> 5 1 check_atomic_kind_set start
> 3701 Mb
> 000000:000128<< 5 1 check_atomic_kind_set 0.000
> 3701 Mb
> 000000:000128>> 5 1 init_atomic_kind_set start
> 3701 Mb
> 000000:000128>> 6 1 init_atomic_kind start
> 3701 Mb
> 000000:000128<< 6 1 init_atomic_kind 0.000
> 3733 Mb
> 000000:000128>> 6 2 init_atomic_kind start
> 3733 Mb
> 000000:000128<< 6 2 init_atomic_kind 0.000
> 3733 Mb
> 000000:000128>> 6 3 init_atomic_kind start
> 3733 Mb
> 000000:000128<< 6 3 init_atomic_kind 0.000
> 3733 Mb
> 000000:000128>> 6 4 init_atomic_kind start
> 3733 Mb
> 000000:000128<< 6 4 init_atomic_kind 0.000
> 3733 Mb
> 000000:000128>> 6 5 init_atomic_kind start
> 3733 Mb
> 000000:000128<< 6 5 init_atomic_kind 0.000
> 3733 Mb
> 000000:000128>> 6 6 init_atomic_kind start
> 3733 Mb
> 000000:000128<< 6 6 init_atomic_kind 0.000
> 3733 Mb
> 000000:000128<< 5 1 init_atomic_kind_set 0.003
> 3733 Mb
> 000000:000128>> 5 1 init_interaction_radii start
> 3733 Mb
> 000000:000128<< 5 1 init_interaction_radii 0.001
> 3733 Mb
> 000000:000128>> 5 2 distribute_molecules_1d
> start 3733 Mb
> 000000:000128<< 5 2 distribute_molecules_1d
> 0.001 3733 Mb
> 000000:000128>> 5 1 scf_c_create start 3733 Mb
> 000000:000128<< 5 1 scf_c_create 0.000 3733 Mb
> 000000:000128>> 5 1 scf_c_read_parameters start
> 3733 Mb
> 000000:000128<< 5 1 scf_c_read_parameters 0.001
> 3733 Mb
> 000000:000128>> 5 1 allocate_qs_energy start
> 3733 Mb
> 000000:000128<< 5 1 allocate_qs_energy 0.000
> 3733 Mb
> 000000:000128>> 5 1 wfi_create start 3733 Mb
> 000000:000128<< 5 1 wfi_create 0.001 3733 Mb
> 000000:000128>> 5 1 write_dft_control start 3733
> Mb
> 000000:000128<< 5 1 write_dft_control 0.000 3733
> Mb
> 000000:000128>> 5 1 write_dispersion start 3733
> Mb
> 000000:000128<< 5 1 write_dispersion 0.001 3733
> Mb
> 000000:000128>> 5 1 write_qs_control start 3733
> Mb
> 000000:000128<< 5 1 write_qs_control 0.001 3733
> Mb
> 000000:000128>> 5 1 write_gto_basis_sets start
> 3733 Mb
> 000000:000128<< 5 1 write_gto_basis_sets 0.000
> 3733 Mb
> 000000:000128>> 5 1 write_atomic_kind_set start
> 3733 Mb
> 000000:000128<< 5 1 write_atomic_kind_set 0.000
> 3733 Mb
> 000000:000128>> 5 2 write_molecule_kind_set
> start 3733 Mb
> 000000:000128<< 5 2 write_molecule_kind_set
> 0.001 3733 Mb
> 000000:000128>> 5 1
> write_qs_particle_coordinates start 3733 Mb
> 000000:000128<< 5 1
> write_qs_particle_coordinates 0.000 3733 Mb
> 000000:000128>> 5 2 write_particle_distances
> start 3733 Mb
> 000000:000128<< 5 2 write_particle_distances
> 0.000 3733 Mb
> 000000:000128>> 5 2 write_structure_data start
> 3733 Mb
> 000000:000128<< 5 2 write_structure_data 0.000
> 3733 Mb
> 000000:000128>> 5 2 write_symmetry start 3733 Mb
> 000000:000128<< 5 2 write_symmetry 0.000 3733 Mb
> 000000:000128>> 5 1 scf_c_write_parameters start
> 3733 Mb
>
>
> SCF PARAMETERS Density
> guess: ATOMIC
>
> --------------------------------------------------------
>
> max_scf: 40
>
> max_scf_history: 0
>
> max_diis: 4
>
> --------------------------------------------------------
>
> eps_scf: 1.00E-07
>
> eps_scf_history: 0.00E+00
>
> eps_diis: 1.00E-01
>
> eps_eigval: 1.00E-05
>
> --------------------------------------------------------
> level_shift
> [a.u.]: 0.00
>
> --------------------------------------------------------
> Outer loop SCF in use
> No variables optimised in outer loop
>
> eps_scf 1.00E-07
>
> max_scf 10
> No outer loop optimization
>
> step_size 5.00E-01
> 000000:000128<< 5 1 scf_c_write_parameters 0.004
> 3733 Mb
> 000000:000128>> 5 1 qs_env_setup start 3733 Mb
> 000000:000128>> 6 1 qs_env_rebuild_pw_env
> start 3733 Mb
> 000000:000128>> 7 1 pw_env_rebuild start
> 3733 Mb
> 000000:000128>> 8 2 pw_grid_setup start
> 3733 Mb
> 000000:000128>> 9 2
> pw_grid_distribute start 3743 Mb
> 000000:000128<< 9 2
> pw_grid_distribute 0.026 3743 Mb
> 000000:000128>> 9 2 pw_grid_allocate
> start 3743 Mb
> 000000:000128<< 9 2 pw_grid_allocate
> 0.001 3792 Mb
> 000000:000128>> 9 2 pw_grid_assign
> start 3792 Mb
> 000000:000128<< 9 2 pw_grid_assign
> 0.203 3792 Mb
> 000000:000128>> 9 2 pw_grid_sort
> start 3792 Mb
> 000000:000128>> 10 2 sort_shells
> start 3796 Mb
> 000000:000128<< 10 2 sort_shells
> 0.173 3796 Mb
> 000000:000128<< 9 2 pw_grid_sort
> 0.461 3815 Mb
> 000000:000128>> 9 2 pw_grid_remap
> start 3815 Mb
> 000000:000128<< 9 2 pw_grid_remap
> 0.039 3825 Mb
> 000000:000128<< 8 2 pw_grid_setup 0.772
> 3825 Mb
> 000000:000128>> 8 3 pw_grid_setup start
> 3825 Mb
> 000000:000128>> 9 3
> pw_grid_distribute start 3835 Mb
> 000000:000128<< 9 3
> pw_grid_distribute 0.012 3835 Mb
> 000000:000128>> 9 3 pw_grid_allocate
> start 3835 Mb
> 000000:000128<< 9 3 pw_grid_allocate
> 0.001 3836 Mb
> 000000:000128>> 9 3 pw_grid_assign
> start 3836 Mb
> 000000:000128<< 9 3 pw_grid_assign
> 0.027 3836 Mb
> 000000:000128>> 9 3 pw_grid_sort
> start 3836 Mb
> 000000:000128>> 10 3 sort_shells
> start 3837 Mb
> 000000:000128<< 10 3 sort_shells
> 0.076 3837 Mb
> 000000:000128<< 9 3 pw_grid_sort
> 0.231 3846 Mb
> 000000:000128>> 9 3 pw_grid_remap
> start 3846 Mb
> 000000:000128<< 9 3 pw_grid_remap
> 0.025 3856 Mb
> 000000:000128<< 8 3 pw_grid_setup 0.318
> 3856 Mb
> 000000:000128>> 8 4 pw_grid_setup start
> 3856 Mb
> 000000:000128>> 9 4
> pw_grid_distribute start 3862 Mb
> 000000:000128<< 9 4
> pw_grid_distribute 0.004 3862 Mb
> 000000:000128>> 9 4 pw_grid_allocate
> start 3862 Mb
> 000000:000128<< 9 4 pw_grid_allocate
> 0.001 3862 Mb
> 000000:000128>> 9 4 pw_grid_assign
> start 3862 Mb
> 000000:000128<< 9 4 pw_grid_assign
> 0.003 3862 Mb
> 000000:000128>> 9 4 pw_grid_sort
> start 3862 Mb
> 000000:000128>> 10 4 sort_shells
> start 3862 Mb
> 000000:000128<< 10 4 sort_shells
> 0.008 3862 Mb
> 000000:000128<< 9 4 pw_grid_sort
> 0.025 3862 Mb
> 000000:000128>> 9 4 pw_grid_remap
> start 3862 Mb
> 000000:000128<< 9 4 pw_grid_remap
> 0.006 3872 Mb
> 000000:000128<< 8 4 pw_grid_setup 0.045
> 3872 Mb
> 000000:000128>> 8 5 pw_grid_setup start
> 3872 Mb
> 000000:000128>> 9 5
> pw_grid_distribute start 3874 Mb
> 000000:000128<< 9 5
> pw_grid_distribute 0.003 3874 Mb
> 000000:000128>> 9 5 pw_grid_allocate
> start 3874 Mb
> 000000:000128<< 9 5 pw_grid_allocate
> 0.001 3874 Mb
> 000000:000128>> 9 5 pw_grid_assign
> start 3874 Mb
> 000000:000128<< 9 5 pw_grid_assign
> 0.001 3874 Mb
> 000000:000128>> 9 5 pw_grid_sort
> start 3874 Mb
> 000000:000128>> 10 5 sort_shells
> start 3874 Mb
> 000000:000128<< 10 5 sort_shells
> 0.001 3874 Mb
> 000000:000128<< 9 5 pw_grid_sort
> 0.002 3874 Mb
> 000000:000128>> 9 5 pw_grid_remap
> start 3874 Mb
> 000000:000128<< 9 5 pw_grid_remap
> 0.003 3876 Mb
> 000000:000128<< 8 5 pw_grid_setup 0.011
> 3876 Mb
> 000000:000128>> 8 6 pw_grid_setup start
> 3876 Mb
> 000000:000128>> 9 6
> pw_grid_distribute start 3876 Mb
> 000000:000128<< 9 6
> pw_grid_distribute 0.003 3876 Mb
> 000000:000128>> 9 6 pw_grid_allocate
> start 3876 Mb
> 000000:000128<< 9 6 pw_grid_allocate
> 0.000 3876 Mb
> 000000:000128>> 9 6 pw_grid_assign
> start 3876 Mb
> 000000:000128<< 9 6 pw_grid_assign
> 0.001 3876 Mb
> 000000:000128>> 9 6 pw_grid_sort
> start 3876 Mb
> 000000:000128>> 10 6 sort_shells
> start 3876 Mb
> 000000:000128<< 10 6 sort_shells
> 0.001 3876 Mb
> 000000:000128<< 9 6 pw_grid_sort
> 0.002 3876 Mb
> 000000:000128>> 9 6 pw_grid_remap
> start 3876 Mb
> 000000:000128<< 9 6 pw_grid_remap
> 0.001 3876 Mb
> 000000:000128<< 8 6 pw_grid_setup 0.008
> 3876 Mb
> 000000:000128>> 8 1 compute_max_radius
> start 3876 Mb
> 000000:000128<< 8 1 compute_max_radius
> 0.203 3876 Mb
> 000000:000128>> 8 1 init_cube_info
> start 3876 Mb
> 000000:000128<< 8 1 init_cube_info
> 0.002 3876 Mb
> 000000:000128>> 8 2
> rs_grid_create_descriptor start 3876 Mb
> 000000:000128<< 8 2
> rs_grid_create_descriptor 0.001 3876 Mb
> 000000:000128>> 8 2 rs_grid_create
> start 3876 Mb
> 000000:000128<< 8 2 rs_grid_create
> 0.000 3885 Mb
> 000000:000128>> 8 2 init_cube_info
> start 3885 Mb
> 000000:000128<< 8 2 init_cube_info
> 0.003 3885 Mb
> 000000:000128>> 8 3
> rs_grid_create_descriptor start 3885 Mb
> 000000:000128<< 8 3
> rs_grid_create_descriptor 0.000 3885 Mb
> 000000:000128>> 8 3 rs_grid_create
> start 3885 Mb
> 000000:000128<< 8 3 rs_grid_create
> 0.000 3890 Mb
> 000000:000128>> 8 3 init_cube_info
> start 3890 Mb
> 000000:000128<< 8 3 init_cube_info
> 0.002 3890 Mb
> 000000:000128>> 8 4
> rs_grid_create_descriptor start 3890 Mb
> 000000:000128<< 8 4
> rs_grid_create_descriptor 0.000 3890 Mb
> 000000:000128>> 8 4 rs_grid_create
> start 3890 Mb
> 000000:000128<< 8 4 rs_grid_create
> 0.000 3896 Mb
> 000000:000128>> 8 4 init_cube_info
> start 3896 Mb
> 000000:000128<< 8 4 init_cube_info
> 0.007 3896 Mb
> 000000:000128>> 8 5
> rs_grid_create_descriptor start 3896 Mb
> 000000:000128<< 8 5
> rs_grid_create_descriptor 0.000 3896 Mb
> 000000:000128>> 8 5 rs_grid_create
> start 3896 Mb
> 000000:000128<< 8 5 rs_grid_create
> 0.002 3897 Mb
> 000000:000128<< 7 1 pw_env_rebuild 1.384
> 3897 Mb
> 000000:000128>> 7 1 pw_pool_create_pw
> start 3897 Mb
> 000000:000128>> 8 1 pw_create start
> 3897 Mb
> 000000:000128<< 8 1 pw_create 0.001
> 3903 Mb
> 000000:000128<< 7 1 pw_pool_create_pw
> 0.001 3903 Mb
> 000000:000128<< 6 1 qs_env_rebuild_pw_env
> 1.385 3903 Mb
> 000000:000128>> 6 1 mpools_rebuild_fm_pools
> start 3903 Mb
> 000000:000128<< 6 1 mpools_rebuild_fm_pools
> 0.001 3903 Mb
> 000000:000128>> 6 1 distribute_molecules_2d
> start 3903 Mb
> 000000:000128>> 7 1
> make_basic_distribution start 3903 Mb
> 000000:000128<< 7 1
> make_basic_distribution 0.001 3903 Mb
> 000000:000128<< 6 1 distribute_molecules_2d
> 0.002 3903 Mb
> 000000:000128<< 5 1 qs_env_setup 1.388 3903 Mb
> 000000:000128<< 4 1 qs_init_subsys 1.415 3903 Mb
> 000000:000128>> 4 4 cp_result_create start 3903 Mb
> 000000:000128<< 4 4 cp_result_create 0.000 3903 Mb
> 000000:000128<< 3 1 quickstep_create_force_env 1.824
> 3903 Mb
>
>
> *******************************************************************************
>
> *******************************************************************************
>
> **
> **
> ** ####### ## ## ## ## ##
> ## **
> ** ## ## ### ### ### ### ###
> ### **
> ** ## ## #### #### #### #### ####
> #### **
> ** ## ## ## ### ## ## ### ## ## ###
> ## **
> ** ## ## ## ## ## ## ## ##
> ## **
> ** ## ## ## ## ## ## ## ## T.Laino and
> F.Mohamed **
> ** ##### ## ## ## ## ## ## ##
> 2005-2011 **
>
> **
> **
> ** Calculation
> Started.. **
>
> *******************************************************************************
>
> *******************************************************************************
> 000000:000128>> 3 5 cp_result_create start 3905 Mb
> 000000:000128<< 3 5 cp_result_create 0.000 3905 Mb
> 000000:000128<< 2 1 qmmm_create_force_env 265.651 3905 Mb
> 000000:000128>> 2 1 metadyn_read start 3905 Mb
> 000000:000128<< 2 1 metadyn_read 0.000 3905 Mb
> 000000:000128>> 2 1 fp_env_create start 3905 Mb
> 000000:000128<< 2 1 fp_env_create 0.000 3905 Mb
> 000000:000128>> 2 1 fp_env_read start 3905 Mb
> 000000:000128<< 2 1 fp_env_read 0.000 3905 Mb
> 000000:000128>> 2 1 fp_env_write start 3905 Mb
> 000000:000128<< 2 1 fp_env_write 0.001 3905 Mb
> 000000:000128>> 2 1 fp_env_release start 3905 Mb
> 000000:000128<< 2 1 fp_env_release 0.001 3905 Mb
> 000000:000128>> 2 2 fp_env_release start 3905 Mb
> 000000:000128<< 2 2 fp_env_release 0.000 3905 Mb
> 000000:000128>> 2 1 qs_mol_dyn_low start 3905 Mb
>
> MD| Molecular Dynamics Protocol
> MD| Ensemble
> Type NVT
> MD| Number of Time
> Steps 500000
> MD| Time Step
> [fs] 0.50
> MD| Temperature
> [K] 300.00
> MD| Temperature tolerance
> [K] 0.00
> MD| Constraints activated
> MD| Tolerance for shake
> 0.1000E-05
> MD| Print MD information every
> 1 step(s)
> MD| File type Print frequency[steps]
> File names
> MD| Coordinates 1
> system.dcd
> MD| Velocities 1
> system.vel
> MD| Energies 1
> system.ene
> MD| Dump 1
> system.restart
>
> 000000:000128>> 3 1 rot_ana start 3905 Mb
> 000000:000128>> 4 1 diamat_all start 3905 Mb
> 000000:000128<< 4 1 diamat_all 0.001 3905 Mb
> ROT| Rotational Analysis Info
> ROT| Principal axes and moments of inertia in atomic units:
> ROT| 1
> 2 3
> ROT| EIGENVALUES 0.202294878E+14 0.346096292E+14
> 0.394887163E+14
> ROT| X -0.005663006 0.999954168
> -0.007719647
> ROT| Y -0.006728067 0.007681496
> 0.999947863
> ROT| Z 0.999961331 0.005714649
> 0.006684259
> ROT| Numer of Rotovibrational vectors: 6
> 000000:000128<< 3 1 rot_ana 0.270 3935 Mb
>
> Calculation of degrees of freedom
> Number of
> atoms: 232428
> Number of Intramolecular
> constraints: 212169
> Number of Intermolecular
> constraints: 0
> Invariants(translation +
> rotations): 0
> Degrees of
> freedom: 485115
>
>
> Restraints Information
> Number of Intramolecular
> restraints: 0
> Number of Intermolecular
> restraints: 0
> 000000:000128>> 3 1 thermostat_mapping_region start
> 3935 Mb
> 000000:000128>> 4 1 mapping_region_evaluate start
> 3935 Mb
> 000000:000128<< 4 1 mapping_region_evaluate 0.027
> 3935 Mb
> 000000:000128>> 4 1 massive_list_generate start
> 3935 Mb
> 000000:000128<< 4 1 massive_list_generate 0.000
> 3935 Mb
> 000000:000128>> 4 1 thermostat_mapping_region_low
> start 3935 Mb
> 000000:000128<< 4 1 thermostat_mapping_region_low
> 0.001 3935 Mb
> 000000:000128<< 3 1 thermostat_mapping_region 0.030
> 3935 Mb
>
> THERMOSTAT| Thermostat Info for PARTICLES
> THERMOSTAT| Type of thermostat Canonical Sampling/Velocity
> Rescaling
> THERMOSTAT| CSVR time constant
> [ fs] 50.00
> THERMOSTAT| Initial Kinetic Energy
> -0.412238
> THERMOSTAT| End of Thermostat Info for PARTICLES
>
> 000000:000128>> 3 1 setup_velocities start 3935 Mb
> 000000:000128>> 4 1 initialize_velocities start
> 3935 Mb
> ************************** Velocities initialization
> **************************
> 000000:000128>> 5 1 read_binary_velocities start
> 3935 Mb
> 000000:000128<< 5 1 read_binary_velocities 0.000
> 3935 Mb
> Initial
> Temperature 299.69
> K
> COM velocity: -0.000000013862 0.000000131448
> -0.000000639613
>
> *******************************************************************************
>
> 000000:000128<< 4 1 initialize_velocities 0.213
> 3935 Mb
> 000000:000128<< 3 1 setup_velocities 0.215 3935 Mb
> 000000:000128>> 3 2 write_qs_particle_coordinates
> start 3935 Mb
> 000000:000128<< 3 2 write_qs_particle_coordinates
> 0.001 3935 Mb
> 000000:000128>> 3 1 qs_ks_qmmm_create start 3935 Mb
> 000000:000128>> 4 2 pw_pool_create_pw start 3935 Mb
> 000000:000128>> 5 2 pw_create start 3935 Mb
> 000000:000128<< 5 2 pw_create 0.001 3935 Mb
> 000000:000128<< 4 2 pw_pool_create_pw 0.001 3935 Mb
> 000000:000128>> 4 5 init_cube_info start 3935 Mb
> 000000:000128<< 4 5 init_cube_info 0.000 3935 Mb
> 000000:000128>> 4 6 init_cube_info start 3935 Mb
> 000000:000128<< 4 6 init_cube_info 0.000 3935 Mb
> 000000:000128>> 4 7 init_cube_info start 3935 Mb
> 000000:000128<< 4 7 init_cube_info 0.009 3935 Mb
> 000000:000128>> 4 8 init_cube_info start 3935 Mb
> 000000:000128<< 4 8 init_cube_info 0.009 3935 Mb
> 000000:000128<< 3 1 qs_ks_qmmm_create 0.020 3935 Mb
> 000000:000128>> 3 1 qmmm_el_coupling start 3935 Mb
> QMMM| Information on the QM/MM Electrostatic Potential:
> 000000:000128>> 4 1 pw_zero start 3935 Mb
> 000000:000128<< 4 1 pw_zero 0.002 3935 Mb
> QMMM| QM/MM Coupling computed collocating the Gaussian Potential
> Functions.
> 000000:000128>> 4 1 qmmm_elec_with_gaussian start
> 3935 Mb
> 000000:000128>> 5 3 pw_pool_create_pw start 3935
> Mb
> 000000:000128>> 6 3 pw_create start 3935 Mb
> 000000:000128<< 6 3 pw_create 0.000 4294 Mb
> 000000:000128<< 5 3 pw_pool_create_pw 0.001 4294
> Mb
> 000000:000128>> 5 4 pw_pool_create_pw start 4294
> Mb
> 000000:000128>> 6 4 pw_create start 4294 Mb
> 000000:000128<< 6 4 pw_create 0.000 4340 Mb
> 000000:000128<< 5 4 pw_pool_create_pw 0.000 4340
> Mb
> 000000:000128>> 5 5 pw_pool_create_pw start 4340
> Mb
> 000000:000128>> 6 5 pw_create start 4340 Mb
> 000000:000128<< 6 5 pw_create 0.000 4340 Mb
> 000000:000128<< 5 5 pw_pool_create_pw 0.000 4340
> Mb
> 000000:000128>> 5 6 pw_pool_create_pw start 4340
> Mb
> 000000:000128>> 6 6 pw_create start 4340 Mb
> 000000:000128<< 6 6 pw_create 0.000 4340 Mb
> 000000:000128<< 5 6 pw_pool_create_pw 0.000 4340
> Mb
> 000000:000128>> 5 2 pw_zero start 4340 Mb
> 000000:000128<< 5 2 pw_zero 0.769 4340 Mb
> 000000:000128>> 5 3 pw_zero start 4340 Mb
> 000000:000128<< 5 3 pw_zero 0.047 4340 Mb
> 000000:000128>> 5 4 pw_zero start 4340 Mb
> 000000:000128<< 5 4 pw_zero 0.003 4340 Mb
> 000000:000128>> 5 5 pw_zero start 4340 Mb
> 000000:000128<< 5 5 pw_zero 0.000 4340 Mb
> 000000:000128>> 5 1 qmmm_elec_with_gaussian_low
> start 4340 Mb
> 000000:000128>> 6 1 qmmm_elec_gaussian_low_G
> start 4340 Mb
> 000000:000128<< 6 1 qmmm_elec_gaussian_low_G
> 0.120 4340 Mb
> 000000:000128>> 6 1 qmmm_elec_gaussian_low_R
> start 4340 Mb
> 000000:000128>> 7 1
> qmmm_elec_with_gaussian_LR start 4340 Mb
> Application 350059 exit signals: Killed
> Application 350059 resources: utime ~4s, stime ~6s
>
> --
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