[CP2K:2462] cannot restart with constraint/restraint
Teodoro Laino
teodor... at gmail.com
Thu Dec 10 08:54:41 UTC 2009
It is not a matter of using a specific keyword. It is a matter of
understanding what you are doing.
If you specify INTERMOLECULAR the topology will still be built: you may
not get that error but the problem is still there.
I see in your coord section you specify a molname for only few atoms:
why? and why not for all?
do you wish to have a connectivity built or not?
do you want to specify a restraint for intermolecular or intramolecular ?
in short words: what do you want to do?
Teo
Liu wrote:
>
> 1) is ruled out. the restraint was there, so the geometry didnot explode.
>
> 2).INTERMOLECULER
> Maybe I should have used this keyword ?
> So no connectivity was needed any longer .
>
> Am I right ?
>
> Liu
>
> 2009/12/10 Liu <xiand... at gmail.com <mailto:xiand... at gmail.com>>
>
> Hi Teo,
>
> the input is as follows,
>
>
> &FORCE_EVAL
> METHOD Quickstep
>
> &DFT
> POTENTIAL_FILE_NAME GTH_POTENTIALS
> BASIS_SET_FILE_NAME GTH_BASIS_SETS
> CHARGE 2
> &MGRID
> CUTOFF 320
> &END MGRID
> &QS
> EPS_DEFAULT 1.0E-12
> &END QS
> &SCF
> &OT T
> MINIMIZER DIIS
> &END OT
> EPS_SCF 1.0E-6
>
> SCF_GUESS RESTART
> MAX_SCF 110
> &END SCF
> &XC
> &XC_FUNCTIONAL BLYP
> &END XC_FUNCTIONAL
> &END XC
> &END DFT
> &SUBSYS
> &CELL
> ABC 10.50 10.50 10.50
> ALPHA_BETA_GAMMA 90.0000 90.0000 90.0000
> &END CELL
>
> &COLVAR
> &DISTANCE
> ATOMS 13 1
> &END DISTANCE
> &END COLVAR
> &COLVAR
> &ANGLE
> ATOMS 13 1 14
> &END ANGLE
> &END COLVAR
> &COLVAR
> &ANGLE
> ATOMS 13 1 19
> &END ANGLE
> &END COLVAR
> &COORD
> O 4.945624262365 5.235220805899 8.003244927409 mol
> O 4.007891695360 3.552175895176 5.977360545441 mol
> O 2.285433270467 5.417764639023 6.897323134184 mol
> O 5.936765184537 5.829000559392 5.593775858772 mol
> O 4.183440185942 7.470635689797 6.674994934445 mol
> O 3.439793446681 5.742570923209 4.488746955268 mol
> H 1.793348652560 4.673685333363 6.448632172866 mol
> H 1.975552174635 5.586491381857 7.823579691797 mol
> H 6.341196051434 6.210453911837 4.735768436262 mol
> H 6.691670293500 5.986498079468 6.262057248960 mol
> H 3.355172624465 7.888242164427 6.980928704617 mol
> H 4.800145134415 8.144564641311 6.279932035506 mol
> H1 5.024438896426 4.333073695541 8.420372999423 mol
> H 5.417966958607 5.879810696856 8.656369353769 mol
> H 4.044612590192 5.703785764108 3.692496314811 mol
> H 2.635152794031 6.238242225502 4.179846355098 mol
> H 4.789074411431 2.978145753930 6.248397019420 mol
> H 3.308516986446 3.025660313636 5.420256518302 mol
> Al 4.199165250044 5.577278113875 6.261316460312
> mol
> O 1.929962666627 2.386347797671 4.459074121571
> O 1.952979070957 0.358546555482 9.269519490418
> O 0.026958456120 2.197269503272 8.735038598236
> O -1.362279675283 6.955540825025 1.744054996031
> O -2.899500082333 1.789177922013 2.425421734762
> O -2.274297024247 5.797133615346 7.045592606844
> O 1.445305003994 7.051219378572 3.715192156899
> O 0.940001451447 4.990446887363 9.698689854397
> O 0.031348798328 11.381839465447 1.904616048439
> O -3.581560970691 9.411668100190 12.775652442937
> O -1.647961298578 9.922630983793 8.321980647542
> O 0.106325557834 -1.237262561258 0.213551451909
> O 4.599334494386 0.610540436556 2.704211560407
> O 6.110865497086 2.836144155293 9.037244996699
> O 8.444963101791 12.757951977677 5.545652221781
> O 4.717343810939 5.987976596723 1.780097066543
> O 6.784715588065 6.889213503169 3.276373325092
> O 0.383247580198 14.072985902428 6.230493216461
> O 3.234318655214 3.857825154773 0.818868910110
> O 1.963164530700 8.951099554455 7.068571426781
> O 6.144029555568 6.796223574397 9.580179213359
> O 8.048882212076 9.883185225311 4.810587174940
> O 2.473675663501 10.303668237070 4.613284200787
> O 3.999780862821 1.198425534797 0.139239985704
> O 5.918103249911 1.825332131822 6.347934161668
> O 5.870936669144 -0.907093857702 6.224645660032
> O 8.497631912579 3.194191743002 -0.218198563998
> O 10.562268276538 4.605445613458 2.706189110743
> O 9.937102032317 8.200210165838 6.102555829864
> O 8.599241385563 5.812668445953 9.929894326533
> O 2.711405118216 8.000171931520 11.614265439006
> O 6.448641165374 9.853545022641 10.091854412172
> H 2.094505467531 1.370769732124 4.450185540604
> H 1.766899467254 2.576096119515 3.490475988652
> H 1.282647036726 -0.136316253288 9.811359473370
> H 2.655785237669 0.719499451687 9.879362070408
> H -0.608993486319 2.410722591791 9.424195138941
> H 0.567781798217 1.367820187953 8.901435796804
> H -0.746695201051 7.579922756681 1.272004746797
> H -0.756268349803 6.209154398982 2.121980920129
> H -2.895078695179 0.880540905683 2.018484814746
> H -3.812114079147 1.945095390040 2.723542853332
> H -1.450477955480 5.414594613020 6.547688311675
> H -2.100265303911 5.762411444564 7.988207299506
> H 0.856199581228 7.443072324347 4.447509731648
> H 1.683787441702 7.732202944333 3.062648462236
> H 0.914577100384 3.982820700161 9.483944679985
> H -0.013545868383 5.297204143626 9.652724302908
> H 0.842855940551 11.867508142867 1.624433490893
> H -0.554679549011 12.094267611684 2.329428790545
> H -3.648772260742 9.475561082667 11.749156370492
> H -3.946707998081 8.505718208125 13.033750646306
> H -1.349673886536 10.831974112009 7.968158045454
> H -1.467941976087 9.098874977651 7.662349937164
> H -0.157891145685 -0.548152766129 0.913773510052
> H -0.486176442427 -1.036451242486 -0.545737942048
> H 5.285066261429 -0.057476231123 2.694625810112
> H 4.079966836623 0.551927307125 3.573612525248
> H 6.015753238192 2.297712230229 8.175869506495
> H 5.470262328903 2.382741162434 9.713210640781
> H 9.282217259184 13.252061003334 5.800368726315
> H 8.310801713089 13.069470210375 4.633682212258
> H 4.392983089723 5.075736957232 1.274546475430
> H 3.981000248919 6.671489138137 1.565186021664
> H 7.666107418592 6.715687507639 2.810668805098
> H 6.049329065526 6.466893192597 2.736263305956
> H 0.792787273346 13.490990322042 5.543123131905
> H 0.418620204652 13.482889458348 7.083779005514
> H 2.540452439292 4.509285556271 0.546998335709
> H 3.399993082999 3.414505470904 -0.002840227708
> H 1.032218251313 8.673654190202 7.041983379026
> H 2.094522687566 9.533513585930 7.911335251137
> H 5.836279591854 6.578895551319 10.522628960955
> H 7.128416505935 6.551955664875 9.651665340638
> H 8.334130619874 10.823573762782 5.138777207840
> H 7.835191538334 10.053541130268 3.845182999807
> H 2.002893030136 9.680973570920 4.067457026619
> H 2.302316195807 10.008164610561 5.548627414794
> H 4.271980573949 1.089340786239 1.114383694195
> H 4.742087428870 0.658613977652 -0.337748849214
> H 5.834805046820 0.889378508637 6.043605489317
> H 6.885651604423 2.000027177721 6.057665925746
> H 6.514304273259 -0.920000002808 6.971136480943
> H 6.480216340233 -0.978037422098 5.424181543392
> H 7.718541069821 3.011662500946 -0.863906539993
> H 8.130716210257 2.931264814758 0.649970337419
> H 11.396873489626 5.053367889582 2.899398079628
> H 10.639341197546 4.446886981342 1.681298091029
> H 9.275748751503 8.741134402620 5.594644857244
> H 9.508184542015 7.278563165823 6.211855784019
> H 8.456691240675 4.796394786938 10.089977970213
> H 8.591160601702 6.196940377323 10.904893066768
> H 1.850384315640 7.951775925152 11.140192575907
> H 2.859191674027 8.984887322643 11.845765015442
> H 6.092174319778 8.925042319655 9.772217739704
> H 7.222986151208 9.962961083214 9.512548867753
> &END COORD
> &KIND H
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q1
> &END KIND
> &KIND H1
> BASIS_SET NONE
> POTENTIAL GTH-BLYP-q1
> GHOST
> &END KIND
> &KIND O
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q6
> &END KIND
> &KIND Al
> BASIS_SET DZVP-GTH
> POTENTIAL GTH-BLYP-q3
> &END KIND
>
> &END SUBSYS
> &END FORCE_EVAL
> &GLOBAL
>
> PROJECT A
> RUN_TYPE MD
> PRINT_LEVEL MEDIUM
> &PRINT
> &EACH
>
> &END EACH
> &END PRINT
> &END GLOBAL
> &MOTION
>
> &CONSTRAINT
> &COLLECTIVE
> TARGET 1.89
> MOLECULE 1
> COLVAR 1
> &RESTRAINT
> k 0.1
> &END RESTRAINT
> &END COLLECTIVE
> &COLLECTIVE
> TARGET 1.869
> MOLECULE 1
> COLVAR 2
> &RESTRAINT
> k 0.1
> &END RESTRAINT
> &END COLLECTIVE
> &COLLECTIVE
> TARGET 2.1457
> MOLECULE 1
> COLVAR 3
> &RESTRAINT
> k 0.1
> &END RESTRAINT
> &END COLLECTIVE
> &END CONSTRAINT
> &MD
> ENSEMBLE NVT
> STEPS 50000
> TIMESTEP 0.5
> TEMPERATURE 330.0
>
> &THERMOSTAT
> &NOSE
> LENGTH 3
> YOSHIDA 3
> TIMECON 1000.0
> MTS 2
> &END NOSE
> &END THERMOSTAT
> &END MD
>
> &PRINT
> &TRAJECTORY
> &EACH
> MD 20
> &END EACH
> &END TRAJECTORY
> &END PRINT
>
> &END MOTION
>
>
> could you please give some further comment on this ?
>
> Thanks for your help
>
> Liu
>
> 2009/12/10 Teodoro Laino <teodor... at gmail.com
> <mailto:teodor... at gmail.com>>
>
> Basically this issue has many different sources. The two most
> important:
>
> -) The first problem is that you should seriously think if you
> want
> help: in this case next time I would recommend to send the
> entire input
> file and not just pieces of it.
>
> -) The second problem is that CP2K has not a manual: it is
> difficult to
> learn but we do provide (for extremely motivated people) quite
> a big
> number of working input files, which cover most of its
> functionalities.
> It would be ideal that before mixing keywords and subsections
> you would
> train yourself trying first to understand (on your own) what
> is the
> logic of the code.
>
> Having said that, based on the minimal amount of information
> you sent
> us, I can try to guess:
>
> 1) probably you ask cp2k to build the topology. At the
> beginning the
> geometry is reasonable and cp2k is able to build a correct
> connectivity.
> When you restart (connectivity is not restartable!) cp2k
> builds a new
> connectivity and very probably your input
> file is so well tuned that the system just explodes -> new
> connectivity
> is a mess -> the intramolecular constraint cannot be applied (your
> restratins is intramolecular!!)
>
> 2) with the restraint setup below (the only piece you have
> sent) you are
> specifying the same restraint for all molecular types 1. if
> you want to
> apply just 1 restraint (between two atoms not belonging to the
> same
> molecule) there is a keyword to be specified:
> http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE.html#desc_INTERMOLECULAR
>
> 3) if you really want to have the same restraint appled to all
> molecular
> types 1 then I would recommend you to have a topology file.
> This will
> guarantee that even if you are trying to simulate the "big
> bang" the
> specification of molecular connectivity will not depend on how
> far are
> the atoms.
>
> 4) if you don't need the connectivity (because your goal is to
> model
> some explosion [for example..]) then just disable the
> generation of the
> connectivity.
>
> Since the possible sources are many (because mainly we cannot
> understand
> what you really want to do!) I would suggest you : take your
> time, think
> what you want to do with cp2k and your present run.
>
> Teo
>
>
> Liu wrote:
> > Hi all,
> >
> > I used the following COLVAR and CONSTRAINT to do a MD run
> and it goes
> > well.
> >
> > &COLVAR
> > &DISTANCE
> > ATOMS 13 1
> > &END DISTANCE
> > &END COLVAR
> >
> > &CONSTRAINT
> > &COLLECTIVE
> > TARGET 1.89
> > MOLECULE 1
> > COLVAR 1
> > &RESTRAINT
> > k 0.1
> > &END RESTRAINT
> > &END COLLECTIVE
> >
> > &END CONSTRAINT
> >
> > When I added this:
> > &EXT_RESTART
> > RESTART_FILE_NAME A-1.restart
> > RESTART_DEFAULT TRUE
> > &END EXT_RESTART
> >
> > the error happened:
> >
> > | Error in constraints setup!
> > | A constraint has been defined for a molecule type
> > | but the atoms specified in the constraint and the a |
> > Error in constraints setup!
> > | A constraint has been defined for a molecule type
> > | but the atoms specified in the constraint and the atoms
> > defined for
> > | the molecule DO NOT match!
> >
> > Any suggestion is appreciated !
> >
> > cheers,
> > Liu
> >
> > --
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