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Created August 3, 2024 13:04
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MD.inp
&GLOBAL
PROJECT MD_BF4_NVT
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
!! MD
&MOTION
&MD
ENSEMBLE NPT_I
STEPS 8000 ! 4.0 ps
TIMESTEP 0.5
TEMPERATURE 298
&THERMOSTAT
&NOSE
TIMECON 50
&END NOSE
&END
&BAROSTAT
PRESSURE 1.0
TIMECON [fs] 100.
&END
&END MD
!! print stuffs
&PRINT
&TRAJECTORY
FORMAT DCD_ALIGNED_CELL
&EACH
MD 10
&END EACH
&END TRAJECTORY
&VELOCITIES OFF
&END VELOCITIES
&FORCES OFF
&END FORCES
&RESTART_HISTORY
&EACH
MD 500
&END EACH
&END RESTART_HISTORY
&RESTART
BACKUP_COPIES 0
&EACH
MD 10
&END EACH
&END RESTART
&END PRINT
&FREE_ENERGY # Section to print out the values of CVs every step
&METADYN
DO_HILLS
NT_HILLS 100
WW 5.0e-3
&METAVAR
SCALE 0.2
COLVAR 1
&END
&METAVAR
SCALE 0.2
COLVAR 2
&WALL !! avoid negative CN
POSITION 0.0
TYPE QUARTIC
&QUARTIC
DIRECTION WALL_MINUS
K 100.0
&END
&END
&END
&METAVAR
SCALE 0.2
COLVAR 3
&WALL !! avoid negative CN
POSITION 0.0
TYPE QUARTIC
&QUARTIC
DIRECTION WALL_MINUS
K 100.0
&END
&END
&END
&PRINT
&COLVAR
COMMON_ITERATION_LEVELS 3
&EACH
MD 1
&END
&END COLVAR
&HILLS # print hills as well
COMMON_ITERATION_LEVELS 3
&EACH
MD 1
&END
&END
&END PRINT
&END METADYN
&END FREE_ENERGY
&END MOTION
!! DFT: PBE-D3 (and OT)
&FORCE_EVAL
METHOD Quickstep
STRESS_TENSOR ANALYTICAL
&DFT
BASIS_SET_FILE_NAME BASIS_SETS
POTENTIAL_FILE_NAME GTH_POTENTIALS
CHARGE 0 # neutral cell
&QS
EPS_DEFAULT 1.0E-12
&END QS
&MGRID
NGRIDS 5
CUTOFF 600
REL_CUTOFF 60
&END MGRID
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
! adding Grimme's D3 correction (by default without C9 terms)
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
PARAMETER_FILE_NAME dftd3.dat
TYPE DFTD3
REFERENCE_FUNCTIONAL PBE
R_CUTOFF [angstrom] 10
&END
&END VDW_POTENTIAL
&END XC
&SCF
MAX_SCF 10
EPS_SCF 1.0E-7
SCF_GUESS ATOMIC
&OT ON
PRECONDITIONER FULL_KINETIC
MINIMIZER BROYDEN
&END
&OUTER_SCF
MAX_SCF 50
EPS_SCF 1.0E-7 ! must match the above
&END
! do not store the wfn during MD
&PRINT
&RESTART OFF
&END
&END
&END SCF
&END DFT
&SUBSYS
&CELL !! from opt
A 1.9856590809357442E+01 0.0000000000000000E+00 0.0000000000000000E+00
B 0.0000000000000000E+00 2.0646459688144901E+01 0.0000000000000000E+00
C 0.0000000000000000E+00 0.0000000000000000E+00 1.9884808537494933E+01
MULTIPLE_UNIT_CELL 1 1 1
SYMMETRY ORTHORHOMBIC
&END CELL
&TOPOLOGY
COORD_FILE_NAME box2BF4.xyz
COORD_FILE_FORMAT XYZ
&END
&KIND C
BASIS_SET ORB DZVP-MOLOPT-SR-GTH-q4
POTENTIAL GTH-PBE-q4
&END KIND
&KIND O
BASIS_SET ORB DZVP-MOLOPT-SR-GTH-q6
POTENTIAL GTH-PBE-q6
&END KIND
&KIND H
BASIS_SET ORB DZVP-MOLOPT-SR-GTH-q1
POTENTIAL GTH-PBE-q1
&END KIND
&KIND B
BASIS_SET ORB DZVP-MOLOPT-SR-GTH-q3
POTENTIAL GTH-PBE-q3
&END KIND
&KIND Ca
BASIS_SET ORB DZVP-MOLOPT-SR-GTH-q10
POTENTIAL GTH-PBE-q10
&END KIND
&KIND F
BASIS_SET ORB DZVP-MOLOPT-SR-GTH-q7
POTENTIAL GTH-PBE-q7
&END KIND
&COLVAR # CV definitions
&DISTANCE # Ca-Ca
ATOMS 739 802
&END
&END COLVAR
&COLVAR
&COORDINATION
ATOMS_FROM 802
KINDS_TO B
R_0 [angstrom] 3.7
NN 20
ND 30
&END COORDINATION
&END COLVAR
&COLVAR
&COORDINATION
ATOMS_FROM 739
KINDS_TO B
R_0 [angstrom] 3.7
NN 20
ND 30
&END COORDINATION
&END COLVAR
&END SUBSYS
&END FORCE_EVAL
Raw
MD.out
DBCSR| CPU Multiplication driver XSMM (U)
DBCSR| Multrec recursion limit 512 (U)
DBCSR| Multiplication stack size 1000 (D)
DBCSR| Maximum elements for images UNLIMITED (U)
DBCSR| Multiplicative factor virtual images 1 (U)
DBCSR| Use multiplication densification T (D)
DBCSR| Multiplication size stacks 3 (U)
DBCSR| Use memory pool for CPU allocation F (U)
DBCSR| Number of 3D layers SINGLE (U)
DBCSR| Use MPI memory allocation F (U)
DBCSR| Use RMA algorithm F (U)
DBCSR| Use Communication thread T (U)
DBCSR| Communication thread load 87 (D)
DBCSR| MPI: My process id 0
DBCSR| MPI: Number of processes 256
DBCSR| OMP: Current number of threads 1
DBCSR| OMP: Max number of threads 1
DBCSR| Split modifier for TAS multiplication algorithm 1.0E+00 (U)
**** **** ****** ** PROGRAM STARTED AT 2024-08-03 12:28:55.273
***** ** *** *** ** PROGRAM STARTED ON lm4-w019
** **** ****** PROGRAM STARTED BY pbeaujea
***** ** ** ** ** PROGRAM PROCESS ID 3058203
**** ** ******* ** PROGRAM STARTED IN /home/users/p/b/pbeaujea/workdir/meta
dyn/eq_2BF4_1
CP2K| version string: CP2K version 2023.1
CP2K| source code revision number: git:b888bd8
CP2K| cp2kflags: omp libint fftw3 libxc parallel scalapack xsmm plumed2 libvori
CP2K| libbqb
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Tue Apr 30 15:44:28 CEST 2024
CP2K| Program compiled on lm4-w011
CP2K| Program compiled for Linux-x86-64-foss
CP2K| Data directory path /home/unamur/ucpts/pbeaujea/.local/easybuild/softw
CP2K| Input file name MD.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name BASIS_SETS
GLOBAL| Potential file name GTH_POTENTIALS
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name box2BF4.xyz
GLOBAL| Method name CP2K
GLOBAL| Project name MD_BF4_NVT
GLOBAL| Run type MD
GLOBAL| FFT library FFTW3
GLOBAL| Diagonalization library ScaLAPACK
GLOBAL| DGEMM library BLAS
GLOBAL| Orthonormality check for eigenvectors DISABLED
GLOBAL| Matrix multiplication library ScaLAPACK
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Grid backend AUTO
GLOBAL| Global print level LOW
GLOBAL| MPI I/O enabled T
GLOBAL| Total number of message passing processes 256
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
GLOBAL| Stack size for threads created by OpenMP (OMP_STACKSIZE) default
GLOBAL| CPU model name AMD EPYC 9534 64-Core Processor
GLOBAL| CPUID 1003
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 791619620 791619620 791619636 791619628
MEMORY| MemFree 626359036 622403588 626359036 624381334
MEMORY| Buffers 7416 7404 7416 7410
MEMORY| Cached 134070024 134070024 137629200 135849610
MEMORY| Slab 5105396 5105396 5431824 5268610
MEMORY| SReclaimable 2657012 2487484 2657012 2572248
MEMORY| MemLikelyFree 763093488 762527676 763093488 762810603
----------------------------------------------------------------------
COLVARS| COLVAR INPUT INDEX: 1
COLVARS| BOND >>> ATOMS: 739 802
----------------------------------------------------------------------
----------------------------------------------------------------------
COLVARS| COLVAR INPUT INDEX: 2
COLVARS| COORDINATION >>> FROM ATOMS: 802
COLVARS| COORDINATION >>> TO KINDS B
COLVARS| R0 6.99199
COLVARS| NN 20
COLVARS| ND 30
----------------------------------------------------------------------
----------------------------------------------------------------------
COLVARS| COLVAR INPUT INDEX: 3
COLVARS| COORDINATION >>> FROM ATOMS: 739
COLVARS| COORDINATION >>> TO KINDS B
COLVARS| R0 6.99199
COLVARS| NN 20
COLVARS| ND 30
----------------------------------------------------------------------
GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
* ___ *
* / \ *
* [ABORT] *
* \___/ CPASSERT failed *
* | *
* O/| *
* /| | *
* / \ colvar_utils.F:611 *
*******************************************************************************
===== Routine Calling Stack =====
2 topology_control
1 CP2K
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