[CP2K-user] CP2K V6.1/V8.1 Using Input Files in &TOPOLOGY section
Ubi Ubu
karam... at gmail.com
Sun Mar 28 10:36:12 UTC 2021
Dear all,
tried to run a CELL_OPT calculation using an input file in &Topology
section. Got the error message file not found.
The file is definitely in the directory and is copied to the working
directory. Tried it with and without file extension. Same result in both
cases. Also tried different formats (CIF, XYZ). Nothing changed. It would
be fine if somebody has an idea what went wrong.
Kind regards
Dirk
PS. Please find enclosed three files a)the INPUT b) the Bash-Script c) the
Output
The Bash-Script used v6.1. But same results with recently installed 8.1
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DBCSR| Multiplication driver XSMM
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Maximum elements for images UNLIMITED
DBCSR| Multiplicative factor virtual images 1
DBCSR| Multiplication size stacks 3
DBCSR| Number of 3D layers SINGLE
DBCSR| Use MPI memory allocation T
DBCSR| Use RMA algorithm F
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
**** **** ****** ** PROGRAM STARTED AT 2021-03-28 12:10:04.349
***** ** *** *** ** PROGRAM STARTED ON dbu-virtual-machine
** **** ****** PROGRAM STARTED BY dbu
***** ** ** ** ** PROGRAM PROCESS ID 4461
**** ** ******* ** PROGRAM STARTED IN /home/dbu/cp2k_tmp
CP2K| version string: CP2K version 6.1
CP2K| source code revision number: svn:18464
CP2K| cp2kflags: libint fftw3 libxc parallel mpi3 scalapack xsmm libderiv_max_a
CP2K| m1=5 libint_max_am=6
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Sa 29. Jun 13:06:55 CEST 2019
CP2K| Program compiled on dbu-virtual-machine
CP2K| Program compiled for local
CP2K| Data directory path /home/dbu/CP2K_61/cp2k-6.1/data
CP2K| Input file name /home/dbu/cp2k_tmp/3_Thiobenzamid_UC_CP2K_Basis_2M
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name ./GTH_BASIS_SETS
GLOBAL| Potential file name ./GTH_POTENTIALS
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name 3_Thiobenzamid_ERWEITERT-pos-1
GLOBAL| Method name CP2K
GLOBAL| Project name 3_Thiobenzamid_BASIS_UC_ERWEITERT_270321
GLOBAL| Preferred FFT library FFTW3
GLOBAL| Preferred diagonalization lib. SL
GLOBAL| Run type CELL_OPT
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Global print level MEDIUM
GLOBAL| Total number of message passing processes 16
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
GLOBAL| CPU model name : AMD Ryzen Threadripper 1950X 16-Core Processor
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 16369580 16369580 16369580 16369580
MEMORY| MemFree 12929752 12929752 12929752 12929752
MEMORY| Buffers 262664 262664 262664 262664
MEMORY| Cached 1088504 1088504 1088504 1088504
MEMORY| Slab 310480 310480 310480 310480
MEMORY| SReclaimable 198648 198648 198648 198648
MEMORY| MemLikelyFree 14479568 14479568 14479568 14479568
*** Fundamental physical constants (SI units) ***
*** Literature: B. J. Mohr and B. N. Taylor,
*** CODATA recommended values of the fundamental physical
*** constants: 2006, Web Version 5.1
*** http://physics.nist.gov/constants
Speed of light in vacuum [m/s] 2.99792458000000E+08
Magnetic constant or permeability of vacuum [N/A**2] 1.25663706143592E-06
Electric constant or permittivity of vacuum [F/m] 8.85418781762039E-12
Planck constant (h) [J*s] 6.62606896000000E-34
Planck constant (h-bar) [J*s] 1.05457162825177E-34
Elementary charge [C] 1.60217648700000E-19
Electron mass [kg] 9.10938215000000E-31
Electron g factor [ ] -2.00231930436220E+00
Proton mass [kg] 1.67262163700000E-27
Fine-structure constant 7.29735253760000E-03
Rydberg constant [1/m] 1.09737315685270E+07
Avogadro constant [1/mol] 6.02214179000000E+23
Boltzmann constant [J/K] 1.38065040000000E-23
Atomic mass unit [kg] 1.66053878200000E-27
Bohr radius [m] 5.29177208590000E-11
*** Conversion factors ***
[u] -> [a.u.] 1.82288848426455E+03
[Angstrom] -> [Bohr] = [a.u.] 1.88972613288564E+00
[a.u.] = [Bohr] -> [Angstrom] 5.29177208590000E-01
[a.u.] -> [s] 2.41888432650478E-17
[a.u.] -> [fs] 2.41888432650478E-02
[a.u.] -> [J] 4.35974393937059E-18
[a.u.] -> [N] 8.23872205491840E-08
[a.u.] -> [K] 3.15774647902944E+05
[a.u.] -> [kJ/mol] 2.62549961709828E+03
[a.u.] -> [kcal/mol] 6.27509468713739E+02
[a.u.] -> [Pa] 2.94210107994716E+13
[a.u.] -> [bar] 2.94210107994716E+08
[a.u.] -> [atm] 2.90362800883016E+08
[a.u.] -> [eV] 2.72113838565563E+01
[a.u.] -> [Hz] 6.57968392072181E+15
[a.u.] -> [1/cm] (wave numbers) 2.19474631370540E+05
[a.u./Bohr**2] -> [1/cm] 5.14048714338585E+03
CELL_TOP| Volume [angstrom^3]: 6219.128
CELL_TOP| Vector a [angstrom 21.584 0.000 0.000 |a| = 21.584
CELL_TOP| Vector b [angstrom 0.000 11.488 0.000 |b| = 11.488
CELL_TOP| Vector c [angstrom -1.372 0.000 25.081 |c| = 25.119
CELL_TOP| Angle (b,c), alpha [degree]: 90.000
CELL_TOP| Angle (a,c), beta [degree]: 93.132
CELL_TOP| Angle (a,b), gamma [degree]: 90.000
CELL_TOP| Requested initial symmetry: MONOCLINIC
CELL_TOP| Numerically orthorhombic: NO
*******************************************************************************
* ___ *
* / \ *
* [ABORT] *
* \___/ Coordinate file <3_Thiobenzamid_ERWEITERT-pos-1 > not found. *
* | *
* O/| *
* /| | *
* / \ topology.F:538 *
*******************************************************************************
===== Routine Calling Stack =====
3 coordinate_control
2 topology_control
1 CP2K
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
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! General CP2K Insput file setting global parameters
!
! General options
@SET SYSNAME 3_Thiobenzamid_BASIS_UC_ERWEITERT_270321_CIF
! Runtype GEO_OPT Optimization, MD Molecular dynamics, ENERGY Single point energy
@SET RTYPE Cell_Opt
! Internal CPU Time limit in sec
@SET CPUTIME 39600
! Restart options
@SET RESTART FALSE
!
! Files options
! Name of the file that contains the basis setting
!@SET BASISFILE GTH_BASIS_SETS
! Name of the file containing pseudo potentials
!@SET PSEUDOFILE GTH_POTENTIALS
! Name of the file that contains wave functions for restart
@SET WAVEFILE 3_Thiobenzamid-BASIS_UC_ERWEITERT_270321-CIF.wfn
@SET RESTARTFILE 3_Thiobenzamid-BASIS_UC_ERWEITERT_270321-CIF.restart
!
! Output options
!
@SET OUT_FORM XYZ
@SET OUT_UNIT angstrom
! Save results every OUT_STEPS
@SET OUT_STEPS 1
!
! DFT options
@SET CUTOFF 500
@SET RELCUTOFF 60
@SET GRIDS 5
@SET SCF_NCYCLES 500
@SET SCF_OCYCLES 100
@SET SCF_CONV 1E-6
@SET SCF_MINI CG
@SET GEO_MINI CG
!
! Molecular dynamics options
!
! Thermodynamical ensemble NVT or NVE
@SET MD_ENS NVE
! Number of MD steps
@SET MD_STEPS 10000
! Integration time step für Newtons equations of motion in fs
@SET MD_DT 0.5
! Target temperature in Kelvin
@SET MD_TEMP 100
! Output options
!
!!!!!!!!!!!!!!! RESTART !!!!!!!!!!!!!!!!
@IF ( $RESTART == TRUE )
@SET SCF_GUESS RESTART
@ENDIF
@IF ( $RESTART == FALSE )
@SET SCF_GUESS ATOMIC
@ENDIF
!
!@IF ( $RESTART == TRUE )
!&EXT_RESTART
! RESTART_DEFAULT FALSE
! RESTART_FILE_NAME $RESTARTFILE
! RESTART_POS TRUE
! RESTART_COUNTERS TRUE
! @IF ( $RTYPE == MD )
! RESTART_VEL TRUE
! @IF ( $MD_ENS == NVT )
! RESTART_THERMOSTAT TRUE
! @ENDIF
! @ENDIF
!&END EXT_RESTART
!@ENDIF
!
!The mandatory Global Section
&GLOBAL
PROJECT $SYSNAME
RUN_TYPE $RTYPE
PRINT_LEVEL MEDIUM
WALLTIME $CPUTIME
&TIMINGS
THRESHOLD 0.01
&END
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
STRESS_TENSOR ANALYTICAL
&PRINT
&STRESS_TENSOR
ADD_LAST NUMERIC
&EACH
GEO_OPT 1
CELL_OPT 1
&END
&END
&END PRINT
&DFT
! specification of basis and potential files (cp2k/data)
BASIS_SET_FILE_NAME ./GTH_BASIS_SETS
POTENTIAL_FILE_NAME ./GTH_POTENTIALS
&MGRID
CUTOFF $CUTOFF
REL_CUTOFF $RELCUTOFF
NGRIDS $GRIDS
&END MGRID
&QS
METHOD GPW
EPS_DEFAULT 1.0E-10
EXTRAPOLATION ASPC
EPS_PGF_ORB 1.0E-8
&END QS
! standard OT
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-6
MAX_SCF 400
! Orbital Transformation without pre-conditioning due to Cholesky-Transformation errors
&OT
MINIMIZER DIIS
PRECONDITIONER FULL_KINETIC
CHOLESKY REDUCE
&END
&MIXING T
METHOD BROYDEN_MIXING
&END
&OUTER_SCF
EPS_SCF 1.0E-6
MAX_SCF 200
&END
&END SCF
! Non periodic calculation needs Poisson solver: use wavelet solver
&POISSON
PERIODIC XYZ
PSOLVER PERIODIC
&END POISSON
&PRINT
&E_DENSITY_CUBE OFF
&END E_DENSITY_CUBE
&MO_CUBES
NLUMO 4
NHOMO 4
WRITE_CUBE .FALSE.
&EACH
MD 10
&END EACH
&END MO_CUBES
&END
&XC
!XC functional
&XC_FUNCTIONAL
&PBE
&END PBE
&END XC_FUNCTIONAL
! VdWGrimme D3 Correction
&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
CALCULATE_C9_TERM .TRUE.
REFERENCE_C9_TERM .TRUE.
LONG_RANGE_CORRECTION .TRUE.
PARAMETER_FILE_NAME dftd3.dat
VERBOSE_OUTPUT .FALSE.
REFERENCE_FUNCTIONAL PBE
R_CUTOFF [angstrom] 10.0
EPS_CN 1.0E-6
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&END DFT
&SUBSYS
! sufficiently large non-periodic unit cell
&CELL
ABC [angstrom] 21.584 11.488 25.119
alpha_beta_gamma 90.00 93.132 90.00
&CELL_REF
ABC 21.584*1.1 11.488*1.1 25.119*1.1
&END
SYMMETRY Monoclinic
PERIODIC XYZ ! periodic calculation.
&END CELL
! specification of an (external) file with Coordinates
! keep atoms away from box borders,
! a requirement for the wavelet Poisson solver
&TOPOLOGY
COORD_FILE_FORMAT XYZ
COORD_FILE_NAME 3_Thiobenzamid_ERWEITERT-pos-1
&CENTER_Coordinates
&END
&END TOPOLOGY
! MP2 needs correlation consistent basis set
! RI-MP2 needs an auxiliary basis set
! We employ GTH pseudo potentials
&KIND H
BASIS_SET DZVP-GTH
! RI_AUX_BASIS_SET RI_DZ
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET DZVP-GTH
! RI_AUX_BASIS_SET RI_DZ
POTENTIAL GTH-PBE-q4
&END KIND
&KIND N
BASIS_SET DZVP-GTH
! RI_AUX_BASIS_SET RI_DZ
POTENTIAL GTH-PBE-q5
&END KIND
&KIND S
BASIS_SET DZVP-GTH
! RI_AUX_BASIS_SET RI_DZ
POTENTIAL GTH-PBE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section
&MOTION
&GEO_OPT
OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large systems)
MAX_ITER 600
MAX_DR [bohr] 0.003 ! adjust target as needed
&BFGS
&END
&END
&CELL_OPT
! KEEP_SYMMETRY 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 600
OPTIMIZER BFGS
&END CELL_OPT
&MD
ENSEMBLE $MD_ENS
TEMPERATURE [K] $MD_TEMP
TEMP_TOL [K] 0.1
TIMESTEP [fs] $MD_DT
STEPS $MD_STEPS
&THERMOSTAT
REGION MASSIVE
&END THERMOSTAT
&END
&PRINT
&RESTART
LOG_PRINT_KEY TRUE
&EACH
$RTYPE ${OUT_STEPS} !RESTART FILE will be printed every OUT_STEPS steps
QS_SCF $OUT_STEPS
&END EACH
ADD_LAST NUMERIC
&END RESTART
@IF ( $RTYPE == GEO_OPT )
&TRAJECTORY
LOG_PRINT_KEY TRUE
FORMAT $OUT_FORM
UNIT $OUT_UNIT
&EACH
$RTYPE ${OUT_STEPS} !Trajectory FILE will be printed every OUT_STEPS steps
&END EACH
ADD_LAST NUMERIC
&END TRAJECTORY
@ENDIF
@IF ( $RTYPE == CELL_OPT )
&TRAJECTORY
LOG_PRINT_KEY TRUE
FORMAT $OUT_FORM
UNIT $OUT_UNIT
&EACH
$RTYPE ${OUT_STEPS} !Trajectory FILE will be printed every OUT_STEPS steps
&END EACH
ADD_LAST NUMERIC
&END TRAJECTORY
@ENDIF
@IF ( $RTYPE == MD )
&TRAJECTORY
&EACH
MD 1
&END EACH
&END TRAJECTORY
&VELOCITIES OFF
&END VELOCITIES
&FORCES OFF
&END FORCES
&RESTART_HISTORY
&EACH
MD 500
&END EACH
&END RESTART_HISTORY
@ENDIF
&END PRINT
&END
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