Am I overspecifying my input file for liquid metal/CO2 MD?
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Michela Benazzi
May 5, 2024, 7:33:03 PM5/5/24
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Hello everyone,
please find below my CP2K input. I made an Al crystal with a single molecule of CO2 on Avogadro software, and wrote this input file below. I am running it above melting temperature of Al. Can anyone tell me if I am overspecifying anything? I am a little confused by the Open MPI error I get (also below the code). Thank you kindly in advance!
&GLOBALplease find below my CP2K input. I made an Al crystal with a single molecule of CO2 on Avogadro software, and wrote this input file below. I am running it above melting temperature of Al. Can anyone tell me if I am overspecifying anything? I am a little confused by the Open MPI error I get (also below the code). Thank you kindly in advance!
PROJECT_NAME Al_CO2_C1
RUN_TYPE MD
PRINT_LEVEL LOW
SAVE_MEM T
&END GLOBAL
&MOTION
&MD
ENSEMBLE NPT_F
STEPS 25000
TEMPERATURE 1.2000000000000000E+03
&BAROSTAT
PRESSURE 1.0100000000000000E+00
&END BAROSTAT
&END MD
&END MOTION
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data//BASIS_MOLOPT
POTENTIAL_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data//POTENTIAL
CHARGE 0
&SCF
EPS_SCF 1.0E-6 # convergence threshold for total energy
SCF_GUESS ATOMIC
&END SCF
&MGRID
CUTOFF 250 # plane-wave cutoff for the charge density [Rydbergs]
COMMENSURATE
&END MGRID
&XC # parameters for exchange-correlation functional
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&XC_GRID # some tricks to speed up the calculation of the xc potential
XC_DERIV SPLINE2_smooth
XC_SMOOTH_RHO NN10
&END XC_GRID
&END XC
&END DFT
&SUBSYS
&KIND Al
ELEMENT Al
BASIS_SET SZV-GTH
POTENTIAL GTH-PBE-q3
&END KIND
&KIND C
ELEMENT C
BASIS_SET SZV-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND O
ELEMENT O
BASIS_SET SZV-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&CELL
A 15.0000000 0.0000000 0.0000000
B 0.0000000 15.0000000 0.0000000
C 0.0000000 0.0000000 15.0000000
PERIODIC XYZ
MULTIPLE_UNIT_CELL 1 1 1
&END CELL
&COORD
Al 0.00000 0.00000 0.00000
Al 7.50000 3.75000 2.50000
Al 3.75000 0.00000 2.50000
Al 3.75000 3.75000 0.00000
Al 7.50000 0.00000 0.00000
Al 7.50000 7.50000 0.00000
Al 7.50000 0.00000 5.00000
Al 0.00000 7.50000 0.00000
Al 0.00000 7.50000 5.00000
Al 0.00000 0.00000 5.00000
Al 7.50000 7.50000 5.00000
Al 0.00000 3.75000 2.50000
Al 3.75000 7.50000 2.50000
Al 3.75000 3.75000 5.00000
Al 7.50000 0.00000 0.00000
Al 15.00000 3.75000 2.50000
Al 11.25000 0.00000 2.50000
Al 11.25000 3.75000 0.00000
Al 15.00000 0.00000 0.00000
Al 15.00000 7.50000 0.00000
Al 15.00000 0.00000 5.00000
Al 7.50000 7.50000 0.00000
Al 7.50000 7.50000 5.00000
Al 7.50000 0.00000 5.00000
Al 15.00000 7.50000 5.00000
Al 7.50000 3.75000 2.50000
Al 11.25000 7.50000 2.50000
Al 11.25000 3.75000 5.00000
Al 0.00000 7.50000 0.00000
Al 7.50000 11.25000 2.50000
Al 3.75000 7.50000 2.50000
Al 3.75000 11.25000 0.00000
Al 7.50000 7.50000 0.00000
Al 7.50000 15.00000 0.00000
Al 7.50000 7.50000 5.00000
Al 0.00000 15.00000 0.00000
Al 0.00000 15.00000 5.00000
Al 0.00000 7.50000 5.00000
Al 7.50000 15.00000 5.00000
Al 0.00000 11.25000 2.50000
Al 3.75000 15.00000 2.50000
Al 3.75000 11.25000 5.00000
Al 7.50000 7.50000 0.00000
Al 15.00000 11.25000 2.50000
Al 11.25000 7.50000 2.50000
Al 11.25000 11.25000 0.00000
Al 15.00000 7.50000 0.00000
Al 15.00000 15.00000 0.00000
Al 15.00000 7.50000 5.00000
Al 7.50000 15.00000 0.00000
Al 7.50000 15.00000 5.00000
Al 7.50000 7.50000 5.00000
Al 15.00000 15.00000 5.00000
Al 7.50000 11.25000 2.50000
Al 11.25000 15.00000 2.50000
Al 11.25000 11.25000 5.00000
Al 0.00000 0.00000 5.00000
Al 7.50000 3.75000 7.50000
Al 3.75000 0.00000 7.50000
Al 3.75000 3.75000 5.00000
Al 7.50000 0.00000 5.00000
Al 7.50000 7.50000 5.00000
Al 7.50000 0.00000 10.00000
Al 0.00000 7.50000 5.00000
Al 0.00000 7.50000 10.00000
Al 0.00000 0.00000 10.00000
Al 7.50000 7.50000 10.00000
Al 0.00000 3.75000 7.50000
Al 3.75000 7.50000 7.50000
Al 3.75000 3.75000 10.00000
Al 7.50000 0.00000 5.00000
Al 15.00000 3.75000 7.50000
Al 11.25000 0.00000 7.50000
Al 11.25000 3.75000 5.00000
Al 15.00000 0.00000 5.00000
Al 15.00000 7.50000 5.00000
Al 15.00000 0.00000 10.00000
Al 7.50000 7.50000 5.00000
Al 7.50000 7.50000 10.00000
Al 7.50000 0.00000 10.00000
Al 15.00000 7.50000 10.00000
Al 7.50000 3.75000 7.50000
Al 11.25000 7.50000 7.50000
Al 11.25000 3.75000 10.00000
Al 0.00000 7.50000 5.00000
Al 7.50000 11.25000 7.50000
Al 3.75000 7.50000 7.50000
Al 3.75000 11.25000 5.00000
Al 7.50000 7.50000 5.00000
Al 7.50000 15.00000 5.00000
Al 7.50000 7.50000 10.00000
Al 0.00000 15.00000 5.00000
Al 0.00000 15.00000 10.00000
Al 0.00000 7.50000 10.00000
Al 7.50000 15.00000 10.00000
Al 0.00000 11.25000 7.50000
Al 3.75000 15.00000 7.50000
Al 3.75000 11.25000 10.00000
Al 7.50000 7.50000 5.00000
Al 15.00000 11.25000 7.50000
Al 11.25000 7.50000 7.50000
Al 11.25000 11.25000 5.00000
Al 15.00000 7.50000 5.00000
Al 15.00000 15.00000 5.00000
Al 15.00000 7.50000 10.00000
Al 7.50000 15.00000 5.00000
Al 7.50000 15.00000 10.00000
Al 7.50000 7.50000 10.00000
Al 15.00000 15.00000 10.00000
Al 7.50000 11.25000 7.50000
Al 11.25000 15.00000 7.50000
Al 11.25000 11.25000 10.00000
Al 0.00000 0.00000 10.00000
Al 7.50000 3.75000 12.50000
Al 3.75000 0.00000 12.50000
Al 3.75000 3.75000 10.00000
Al 7.50000 0.00000 10.00000
Al 7.50000 7.50000 10.00000
Al 8.37531 3.33323 14.03022
Al 0.00000 7.50000 10.00000
Al 0.00000 7.50000 15.00000
Al 0.00000 0.00000 15.00000
Al 7.50000 7.50000 15.00000
Al 0.00000 3.75000 12.50000
Al 3.75000 7.50000 12.50000
Al 3.75000 3.75000 15.00000
Al 7.50000 0.00000 10.00000
Al 15.00000 3.75000 12.50000
Al 11.25000 0.00000 12.50000
Al 11.25000 3.75000 10.00000
Al 15.00000 0.00000 10.00000
Al 15.00000 7.50000 10.00000
Al 15.00000 0.00000 15.00000
Al 7.50000 7.50000 10.00000
Al 7.50000 7.50000 15.00000
Al 7.50000 0.00000 15.00000
Al 15.00000 7.50000 15.00000
Al 7.50000 3.75000 12.50000
Al 11.25000 7.50000 12.50000
Al 11.25000 3.75000 15.00000
Al 0.00000 7.50000 10.00000
Al 7.50000 11.25000 12.50000
Al 3.75000 7.50000 12.50000
Al 3.75000 11.25000 10.00000
Al 7.50000 7.50000 10.00000
Al 7.50000 15.00000 10.00000
Al 7.50000 7.50000 15.00000
Al 0.00000 15.00000 10.00000
Al 0.00000 15.00000 15.00000
Al 0.00000 7.50000 15.00000
Al 7.50000 15.00000 15.00000
Al 0.00000 11.25000 12.50000
Al 3.75000 15.00000 12.50000
Al 3.75000 11.25000 15.00000
Al 7.50000 7.50000 10.00000
Al 15.00000 11.25000 12.50000
Al 11.25000 7.50000 12.50000
Al 11.25000 11.25000 10.00000
Al 15.00000 7.50000 10.00000
Al 15.00000 15.00000 10.00000
Al 15.00000 7.50000 15.00000
Al 7.50000 15.00000 10.00000
Al 7.50000 15.00000 15.00000
Al 7.50000 7.50000 15.00000
Al 15.00000 15.00000 15.00000
Al 7.50000 11.25000 12.50000
Al 11.25000 15.00000 12.50000
Al 11.25000 11.25000 15.00000
C 6.31336 7.90494 6.67474
O 7.25666 8.30983 7.29041
O 5.37005 7.50005 6.05906
UNIT armstrong
&END COORD
&END SUBSYS
&FORCES ON
&END FORCES
&END PRINT
&END FORCE_EVAL
$END
______________________________________________________________________________
[[57845,1],0]: A high-performance Open MPI point-to-point messaging module was unable to find any relevant network interfaces: Module: OpenFabrics (openib) Host: c0279 Another transport will be used instead, although this may result in lower performance. NOTE: You can disable this warning by setting the MCA parameter btl_base_warn_component_unused to 0. -------------------------------------------------------------------------- -------------------------------------------------------------------------- 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. --------------------------------------------------------------------------
[[57845,1],0]: A high-performance Open MPI point-to-point messaging module was unable to find any relevant network interfaces: Module: OpenFabrics (openib) Host: c0279 Another transport will be used instead, although this may result in lower performance. NOTE: You can disable this warning by setting the MCA parameter btl_base_warn_component_unused to 0. -------------------------------------------------------------------------- -------------------------------------------------------------------------- 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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