Memory Issue QMMM Cray XE6
marco.stenta
marco.... at gmail.com
Thu Jan 26 14:36:20 UTC 2012
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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