[CP2K-user] Thermostat setup for ADIABATIC_DYNAMICS (CAFES)
chris...@pnnl.gov
cjm... at charter.net
Wed Feb 24 19:35:55 UTC 2021
The CAFES is used if you have a system that allows one to choose "fast"
and "slow" degrees of freedom.. Is this what you want?
On Monday, February 22, 2021 at 10:14:40 AM UTC-8 dl... at wisc.edu wrote:
> Hi,
>
> If anyone could point me to or share with me any example input files of
> CAFES with CP2K, that will also be very helpful.
>
> Thanks again.
>
> Best,
> Dongyue
>
> On Saturday, February 20, 2021 at 1:30:16 PM UTC-5 Dongyue Liang wrote:
>
>> Dear experts,
>>
>> I'm trying to apply adiabatic dynamics (CAFES) with DFT MD at an oxide
>> material - water interface system. Before CAFES, I have performed short (~2
>> ps) NVT simulation and it works fine. When I try to set up CAFES, I got the
>> following error:
>>
>>
>> *******************************************************************************
>> * ___
>> *
>> * / \
>> *
>> * [ABORT]
>> *
>> * \___/ CPASSERT failed
>> *
>> * |
>> *
>> * O/|
>> *
>> * /| |
>> *
>> * / \
>> motion/thermostat/thermostat_utils.F:507 *
>>
>> *******************************************************************************
>>
>>
>> ===== Routine Calling Stack =====
>>
>> 2 qs_mol_dyn_low
>> 1 CP2K
>>
>> I'm attaching my input file at the end of the message. One thing to
>> mention is that, this error message shows up even when I set the
>> ADIABATIC_DYNAMICS/THERMOSTAT_FAST/REGION to NONE. However, a regular NVT
>> setup with everything else identical initializes just fine.
>>
>> I'm new to CP2K and ab initio MD. Any suggestions will be appreciated.
>>
>> Best regards,
>> Dongyue
>>
>> Input file:
>>
>> &FORCE_EVAL
>> METHOD Quickstep
>> ! STRESS_TENSOR ANALYTICAL
>> &DFT
>> BASIS_SET_FILE_NAME BASIS_MOLOPT
>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>> &MGRID
>> COMMENSURATE
>> CUTOFF 500
>> REL_CUTOFF 40
>> NGRIDS 6
>> &END MGRID
>> &QS
>> METHOD GPW
>> EXTRAPOLATION ASPC
>> EXTRAPOLATION_ORDER 3
>> EPS_DEFAULT 1.0E-10
>> &END QS
>> &SCF
>> MAX_SCF 50
>> SCF_GUESS RESTART
>> EPS_SCF 1.0E-6
>> &OUTER_SCF
>> EPS_SCF 1.0E-6
>> MAX_SCF 500
>> &END
>> &OT
>> PRECONDITIONER FULL_SINGLE_INVERSE
>> MINIMIZER DIIS
>> &END
>> &END SCF
>> &XC
>> &XC_FUNCTIONAL PBE
>> &END XC_FUNCTIONAL
>> &VDW_POTENTIAL
>> DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>> &PAIR_POTENTIAL
>> TYPE DFTD3
>> PARAMETER_FILE_NAME dftd3.dat
>> REFERENCE_FUNCTIONAL PBE
>> &END PAIR_POTENTIAL
>> &END VDW_POTENTIAL
>> &END XC
>> &END DFT
>> &SUBSYS
>> &CELL
>> ABC 9.84650676 11.3670307 42.6
>> PERIODIC XYZ
>> &END CELL
>> &TOPOLOGY
>> COORD_FILE_NAME equil.pdb
>> COORDINATE pdb
>> CONN_FILE_FORMAT psf
>> CONN_FILE_NAME solvation_mod_mass.psf
>> PARA_RES .FALSE.
>> &END TOPOLOGY
>> &KIND LIXI
>> ELEMENT Li
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q3
>> &END KIND
>> &KIND COXI
>> ELEMENT Co
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q17
>> &END KIND
>> &KIND OXI1
>> ELEMENT O
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q6
>> &END KIND
>> &KIND OXI2
>> ELEMENT O
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q6
>> &END KIND
>> &KIND OXH1
>> ELEMENT O
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q6
>> &END KIND
>> &KIND OXH2
>> ELEMENT O
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q6
>> &END KIND
>> &KIND OXT1
>> ELEMENT O
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q6
>> &END KIND
>> &KIND OXT2
>> ELEMENT O
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q6
>> &END KIND
>> &KIND HTX
>> ELEMENT H
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q1
>> MASS 2.016
>> &END KIND
>> &KIND OT
>> ELEMENT O
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q6
>> &END KIND
>> &KIND HT
>> ELEMENT H
>> MASS 2.016
>> BASIS_SET DZVP-MOLOPT-SR-GTH
>> POTENTIAL GTH-PBE-q1
>> &END KIND
>> &END SUBSYS
>> &END FORCE_EVAL
>> &MOTION
>> &MD
>> ENSEMBLE NVT_ADIABATIC !NVT
>> TIMESTEP 0.5
>> STEPS 10000
>> &ADIABATIC_DYNAMICS
>> TEMP_FAST 1200
>> TEMP_SLOW 300
>> &THERMOSTAT_FAST
>> REGION NONE !DEFINED
>> &DEFINE_REGION
>> LIST 4
>> &END DEFINE_REGION
>> &NOSE
>> LENGTH 3
>> YOSHIDA 3
>> TIMECON 100
>> MTS 2
>> &END NOSE
>> &END THERMOSTAT_FAST
>> &THERMOSTAT_SLOW
>> REGION GLOBAL !DEFINED
>> &NOSE
>> LENGTH 3
>> YOSHIDA 3
>> TIMECON 100
>> MTS 2
>> &END NOSE
>> ! &DEFINE_REGION
>> ! LIST 1..3
>> ! LIST 5..531
>> ! &END DEFINE_REGION
>> &END THERMOSTAT_SLOW
>> &END ADIABATIC_DYNAMICS
>> ! TEMPERATURE 300
>> ! &THERMOSTAT
>> ! &NOSE
>> ! LENGTH 3
>> ! YOSHIDA 3
>> ! TIMECON 100
>> ! MTS 2
>> ! &END NOSE
>> ! &END THERMOSTAT
>> &PRINT
>> &ENERGY
>> &EACH
>> MD 1
>> &END
>> &END ENERGY
>> &COEFFICIENTS
>> &EACH
>> MD 1
>> &END
>> &END COEFFICIENTS
>> &TEMP_KIND
>> &EACH
>> MD 1
>> &END
>> &END TEMP_KIND
>> &PROGRAM_RUN_INFO
>> &EACH
>> MD 10
>> &END
>> &END PROGRAM_RUN_INFO
>> &END PRINT
>> &END MD
>> &PRINT
>> &VELOCITIES OFF
>> &END VELOCITIES
>> &FORCES OFF
>> &END FORCES
>> &RESTART_HISTORY OFF
>> &END RESTART_HISTORY
>> &RESTART
>> &EACH
>> MD 2
>> &END
>> &END RESTART
>> &TRAJECTORY
>> &EACH
>> MD 2
>> &END EACH
>> FORMAT DCD
>> &END
>> &END PRINT
>> &END MOTION
>>
>> &GLOBAL
>> PROJECT lco_md
>> RUN_TYPE MD
>> PRINT_LEVEL LOW
>> &END GLOBAL
>>
>> &EXT_RESTART
>> RESTART_FILE_NAME lco_md-1.restart
>> RESTART_DEFAULT F
>> RESTART_POS T
>> RESTART_VEL T
>> RESTART_CELL T
>> RESTART_CORE_POS T
>> RESTART_CORE_VELOCITY T
>> &END EXT_RESTART
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20210224/fef9eab2/attachment.htm>
More information about the CP2K-user
mailing list